ks2) throws IOException {\n if (ref == 0L) return null;\n if (ks1 == null) throw new IllegalArgumentException(\"ks1 is null\");\n if (ks2 == null) throw new IllegalArgumentException(\"ks2 is null\");\n return align(\n ks1.toArray(new ShortRead[ks1.size()]),\n ks2.toArray(new ShortRead[ks2.size()])\n );\n }\n\n public String[] align(final ShortRead ks1[], final ShortRead ks2[]) throws IOException {\n if (ref == 0L) return null;\n if (ks1 == null) throw new IllegalArgumentException(\"ks1 is null\");\n if (ks2 == null) throw new IllegalArgumentException(\"ks2 is null\");\n if (ks1.length != ks2.length) throw new IllegalArgumentException(\"ks1.length!=ks2.length\");\n if (ks1.length == 0) return null;\n return align2(this.bwaIndex, ks1, ks2);\n }\n\n\n @Override\n protected void finalize() {\n dispose();\n }\n\n public native void dispose();\n\n private static native long mem_opt_init();\n\n /**\n * Verbosity (from http://bio-bwa.sourceforge.net/bwa.shtml#3)\n * A value 0 for disabling all the output to stderr;\n * 1 for outputting errors only;\n * 2 for warnings and errors;\n * 3 for all normal messages;\n * 4 or higher for debugging. When this option takes value 4, the output is not SAM.\n * \n * If this method is not called, the default level is 3.\n */\n public native void set_verbosity(int verbosity);\n\n private native void update_score_parameters(int B, int Oi, int Od, int Ei, int Ed, int L5, int L3);\n\n private native AlnRgn[] align(BwaIndex bwaIndex, byte bases[]) throws IOException;\n\n private native String[] align2(BwaIndex bwaIndex, final ShortRead ks1[], final ShortRead ks2[]) throws IOException;\n}\n"
},
{
"path": "src/main/java/com/github/lindenb/jbwa/jni/KSeq.java",
"content": "/*\n\n Apache License\n Version 2.0, January 2004\n http://www.apache.org/licenses/\n\n TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n\n 1. Definitions.\n\n \"License\" shall mean the terms and conditions for use, reproduction,\n and distribution as defined by Sections 1 through 9 of this document.\n\n \"Licensor\" shall mean the copyright owner or entity authorized by\n the copyright owner that is granting the License.\n\n \"Legal Entity\" shall mean the union of the acting entity and all\n other entities that control, are controlled by, or are under common\n control with that entity. For the purposes of this definition,\n \"control\" means (i) the power, direct or indirect, to cause the\n direction or management of such entity, whether by contract or\n otherwise, or (ii) ownership of fifty percent (50%) or more of the\n outstanding shares, or (iii) beneficial ownership of such entity.\n\n \"You\" (or \"Your\") shall mean an individual or Legal Entity\n exercising permissions granted by this License.\n\n \"Source\" form shall mean the preferred form for making modifications,\n including but not limited to software source code, documentation\n source, and configuration files.\n\n \"Object\" form shall mean any form resulting from mechanical\n transformation or translation of a Source form, including but\n not limited to compiled object code, generated documentation,\n and conversions to other media types.\n\n \"Work\" shall mean the work of authorship, whether in Source or\n Object form, made available under the License, as indicated by a\n copyright notice that is included in or attached to the work\n (an example is provided in the Appendix below).\n\n \"Derivative Works\" shall mean any work, whether in Source or Object\n form, that is based on (or derived from) the Work and for which the\n editorial revisions, annotations, elaborations, or other modifications\n represent, as a whole, an original work of authorship. For the purposes\n of this License, Derivative Works shall not include works that remain\n separable from, or merely link (or bind by name) to the interfaces of,\n the Work and Derivative Works thereof.\n\n \"Contribution\" shall mean any work of authorship, including\n the original version of the Work and any modifications or additions\n to that Work or Derivative Works thereof, that is intentionally\n submitted to Licensor for inclusion in the Work by the copyright owner\n or by an individual or Legal Entity authorized to submit on behalf of\n the copyright owner. For the purposes of this definition, \"submitted\"\n means any form of electronic, verbal, or written communication sent\n to the Licensor or its representatives, including but not limited to\n communication on electronic mailing lists, source code control systems,\n and issue tracking systems that are managed by, or on behalf of, the\n Licensor for the purpose of discussing and improving the Work, but\n excluding communication that is conspicuously marked or otherwise\n designated in writing by the copyright owner as \"Not a Contribution.\"\n\n \"Contributor\" shall mean Licensor and any individual or Legal Entity\n on behalf of whom a Contribution has been received by Licensor and\n subsequently incorporated within the Work.\n\n 2. Grant of Copyright License. Subject to the terms and conditions of\n this License, each Contributor hereby grants to You a perpetual,\n worldwide, non-exclusive, no-charge, royalty-free, irrevocable\n copyright license to reproduce, prepare Derivative Works of,\n publicly display, publicly perform, sublicense, and distribute the\n Work and such Derivative Works in Source or Object form.\n\n 3. Grant of Patent License. Subject to the terms and conditions of\n this License, each Contributor hereby grants to You a perpetual,\n worldwide, non-exclusive, no-charge, royalty-free, irrevocable\n (except as stated in this section) patent license to make, have made,\n use, offer to sell, sell, import, and otherwise transfer the Work,\n where such license applies only to those patent claims licensable\n by such Contributor that are necessarily infringed by their\n Contribution(s) alone or by combination of their Contribution(s)\n with the Work to which such Contribution(s) was submitted. If You\n institute patent litigation against any entity (including a\n cross-claim or counterclaim in a lawsuit) alleging that the Work\n or a Contribution incorporated within the Work constitutes direct\n or contributory patent infringement, then any patent licenses\n granted to You under this License for that Work shall terminate\n as of the date such litigation is filed.\n\n 4. Redistribution. You may reproduce and distribute copies of the\n Work or Derivative Works thereof in any medium, with or without\n modifications, and in Source or Object form, provided that You\n meet the following conditions:\n\n (a) You must give any other recipients of the Work or\n Derivative Works a copy of this License; and\n\n (b) You must cause any modified files to carry prominent notices\n stating that You changed the files; and\n\n (c) You must retain, in the Source form of any Derivative Works\n that You distribute, all copyright, patent, trademark, and\n attribution notices from the Source form of the Work,\n excluding those notices that do not pertain to any part of\n the Derivative Works; and\n\n (d) If the Work includes a \"NOTICE\" text file as part of its\n distribution, then any Derivative Works that You distribute must\n include a readable copy of the attribution notices contained\n within such NOTICE file, excluding those notices that do not\n pertain to any part of the Derivative Works, in at least one\n of the following places: within a NOTICE text file distributed\n as part of the Derivative Works; within the Source form or\n documentation, if provided along with the Derivative Works; or,\n within a display generated by the Derivative Works, if and\n wherever such third-party notices normally appear. The contents\n of the NOTICE file are for informational purposes only and\n do not modify the License. You may add Your own attribution\n notices within Derivative Works that You distribute, alongside\n or as an addendum to the NOTICE text from the Work, provided\n that such additional attribution notices cannot be construed\n as modifying the License.\n\n You may add Your own copyright statement to Your modifications and\n may provide additional or different license terms and conditions\n for use, reproduction, or distribution of Your modifications, or\n for any such Derivative Works as a whole, provided Your use,\n reproduction, and distribution of the Work otherwise complies with\n the conditions stated in this License.\n\n 5. Submission of Contributions. Unless You explicitly state otherwise,\n any Contribution intentionally submitted for inclusion in the Work\n by You to the Licensor shall be under the terms and conditions of\n this License, without any additional terms or conditions.\n Notwithstanding the above, nothing herein shall supersede or modify\n the terms of any separate license agreement you may have executed\n with Licensor regarding such Contributions.\n\n 6. Trademarks. This License does not grant permission to use the trade\n names, trademarks, service marks, or product names of the Licensor,\n except as required for reasonable and customary use in describing the\n origin of the Work and reproducing the content of the NOTICE file.\n\n 7. Disclaimer of Warranty. Unless required by applicable law or\n agreed to in writing, Licensor provides the Work (and each\n Contributor provides its Contributions) on an \"AS IS\" BASIS,\n WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or\n implied, including, without limitation, any warranties or conditions\n of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A\n PARTICULAR PURPOSE. You are solely responsible for determining the\n appropriateness of using or redistributing the Work and assume any\n risks associated with Your exercise of permissions under this License.\n\n 8. Limitation of Liability. In no event and under no legal theory,\n whether in tort (including negligence), contract, or otherwise,\n unless required by applicable law (such as deliberate and grossly\n negligent acts) or agreed to in writing, shall any Contributor be\n liable to You for damages, including any direct, indirect, special,\n incidental, or consequential damages of any character arising as a\n result of this License or out of the use or inability to use the\n Work (including but not limited to damages for loss of goodwill,\n work stoppage, computer failure or malfunction, or any and all\n other commercial damages or losses), even if such Contributor\n has been advised of the possibility of such damages.\n\n 9. Accepting Warranty or Additional Liability. While redistributing\n the Work or Derivative Works thereof, You may choose to offer,\n and charge a fee for, acceptance of support, warranty, indemnity,\n or other liability obligations and/or rights consistent with this\n License. However, in accepting such obligations, You may act only\n on Your own behalf and on Your sole responsibility, not on behalf\n of any other Contributor, and only if You agree to indemnify,\n defend, and hold each Contributor harmless for any liability\n incurred by, or claims asserted against, such Contributor by reason\n of your accepting any such warranty or additional liability.\n\n END OF TERMS AND CONDITIONS\n\n APPENDIX: How to apply the Apache License to your work.\n\n To apply the Apache License to your work, attach the following\n boilerplate notice, with the fields enclosed by brackets \"[]\"\n replaced with your own identifying information. (Don't include\n the brackets!) The text should be enclosed in the appropriate\n comment syntax for the file format. We also recommend that a\n file or class name and description of purpose be included on the\n same \"printed page\" as the copyright notice for easier\n identification within third-party archives.\n\n Copyright 2016 Pierre Lindenbaum\n\n Licensed under the Apache License, Version 2.0 (the \"License\");\n you may not use this file except in compliance with the License.\n You may obtain a copy of the License at\n\n http://www.apache.org/licenses/LICENSE-2.0\n\n Unless required by applicable law or agreed to in writing, software\n distributed under the License is distributed on an \"AS IS\" BASIS,\n WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n See the License for the specific language governing permissions and\n limitations under the License.\n\n\n*/\npackage com.github.lindenb.jbwa.jni;\n\nimport java.io.File;\nimport java.io.IOException;\n\npublic class KSeq {\n protected long ref = 0L;\n\n public KSeq(File f) throws IOException {\n this.ref = KSeq.init(f == null ? \"-\" : f.toString());\n }\n\n public KSeq() throws IOException {\n this(null);\n }\n\n public native ShortRead next() throws IOException;\n\n @Override\n protected void finalize() {\n dispose();\n }\n\n public native void dispose();\n\n private static native long init(String file);\n}\n"
},
{
"path": "src/main/java/com/github/lindenb/jbwa/jni/ShortRead.java",
"content": "/*\n\n Apache License\n Version 2.0, January 2004\n http://www.apache.org/licenses/\n\n TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n\n 1. Definitions.\n\n \"License\" shall mean the terms and conditions for use, reproduction,\n and distribution as defined by Sections 1 through 9 of this document.\n\n \"Licensor\" shall mean the copyright owner or entity authorized by\n the copyright owner that is granting the License.\n\n \"Legal Entity\" shall mean the union of the acting entity and all\n other entities that control, are controlled by, or are under common\n control with that entity. For the purposes of this definition,\n \"control\" means (i) the power, direct or indirect, to cause the\n direction or management of such entity, whether by contract or\n otherwise, or (ii) ownership of fifty percent (50%) or more of the\n outstanding shares, or (iii) beneficial ownership of such entity.\n\n \"You\" (or \"Your\") shall mean an individual or Legal Entity\n exercising permissions granted by this License.\n\n \"Source\" form shall mean the preferred form for making modifications,\n including but not limited to software source code, documentation\n source, and configuration files.\n\n \"Object\" form shall mean any form resulting from mechanical\n transformation or translation of a Source form, including but\n not limited to compiled object code, generated documentation,\n and conversions to other media types.\n\n \"Work\" shall mean the work of authorship, whether in Source or\n Object form, made available under the License, as indicated by a\n copyright notice that is included in or attached to the work\n (an example is provided in the Appendix below).\n\n \"Derivative Works\" shall mean any work, whether in Source or Object\n form, that is based on (or derived from) the Work and for which the\n editorial revisions, annotations, elaborations, or other modifications\n represent, as a whole, an original work of authorship. For the purposes\n of this License, Derivative Works shall not include works that remain\n separable from, or merely link (or bind by name) to the interfaces of,\n the Work and Derivative Works thereof.\n\n \"Contribution\" shall mean any work of authorship, including\n the original version of the Work and any modifications or additions\n to that Work or Derivative Works thereof, that is intentionally\n submitted to Licensor for inclusion in the Work by the copyright owner\n or by an individual or Legal Entity authorized to submit on behalf of\n the copyright owner. For the purposes of this definition, \"submitted\"\n means any form of electronic, verbal, or written communication sent\n to the Licensor or its representatives, including but not limited to\n communication on electronic mailing lists, source code control systems,\n and issue tracking systems that are managed by, or on behalf of, the\n Licensor for the purpose of discussing and improving the Work, but\n excluding communication that is conspicuously marked or otherwise\n designated in writing by the copyright owner as \"Not a Contribution.\"\n\n \"Contributor\" shall mean Licensor and any individual or Legal Entity\n on behalf of whom a Contribution has been received by Licensor and\n subsequently incorporated within the Work.\n\n 2. Grant of Copyright License. Subject to the terms and conditions of\n this License, each Contributor hereby grants to You a perpetual,\n worldwide, non-exclusive, no-charge, royalty-free, irrevocable\n copyright license to reproduce, prepare Derivative Works of,\n publicly display, publicly perform, sublicense, and distribute the\n Work and such Derivative Works in Source or Object form.\n\n 3. Grant of Patent License. Subject to the terms and conditions of\n this License, each Contributor hereby grants to You a perpetual,\n worldwide, non-exclusive, no-charge, royalty-free, irrevocable\n (except as stated in this section) patent license to make, have made,\n use, offer to sell, sell, import, and otherwise transfer the Work,\n where such license applies only to those patent claims licensable\n by such Contributor that are necessarily infringed by their\n Contribution(s) alone or by combination of their Contribution(s)\n with the Work to which such Contribution(s) was submitted. If You\n institute patent litigation against any entity (including a\n cross-claim or counterclaim in a lawsuit) alleging that the Work\n or a Contribution incorporated within the Work constitutes direct\n or contributory patent infringement, then any patent licenses\n granted to You under this License for that Work shall terminate\n as of the date such litigation is filed.\n\n 4. Redistribution. You may reproduce and distribute copies of the\n Work or Derivative Works thereof in any medium, with or without\n modifications, and in Source or Object form, provided that You\n meet the following conditions:\n\n (a) You must give any other recipients of the Work or\n Derivative Works a copy of this License; and\n\n (b) You must cause any modified files to carry prominent notices\n stating that You changed the files; and\n\n (c) You must retain, in the Source form of any Derivative Works\n that You distribute, all copyright, patent, trademark, and\n attribution notices from the Source form of the Work,\n excluding those notices that do not pertain to any part of\n the Derivative Works; and\n\n (d) If the Work includes a \"NOTICE\" text file as part of its\n distribution, then any Derivative Works that You distribute must\n include a readable copy of the attribution notices contained\n within such NOTICE file, excluding those notices that do not\n pertain to any part of the Derivative Works, in at least one\n of the following places: within a NOTICE text file distributed\n as part of the Derivative Works; within the Source form or\n documentation, if provided along with the Derivative Works; or,\n within a display generated by the Derivative Works, if and\n wherever such third-party notices normally appear. The contents\n of the NOTICE file are for informational purposes only and\n do not modify the License. You may add Your own attribution\n notices within Derivative Works that You distribute, alongside\n or as an addendum to the NOTICE text from the Work, provided\n that such additional attribution notices cannot be construed\n as modifying the License.\n\n You may add Your own copyright statement to Your modifications and\n may provide additional or different license terms and conditions\n for use, reproduction, or distribution of Your modifications, or\n for any such Derivative Works as a whole, provided Your use,\n reproduction, and distribution of the Work otherwise complies with\n the conditions stated in this License.\n\n 5. Submission of Contributions. Unless You explicitly state otherwise,\n any Contribution intentionally submitted for inclusion in the Work\n by You to the Licensor shall be under the terms and conditions of\n this License, without any additional terms or conditions.\n Notwithstanding the above, nothing herein shall supersede or modify\n the terms of any separate license agreement you may have executed\n with Licensor regarding such Contributions.\n\n 6. Trademarks. This License does not grant permission to use the trade\n names, trademarks, service marks, or product names of the Licensor,\n except as required for reasonable and customary use in describing the\n origin of the Work and reproducing the content of the NOTICE file.\n\n 7. Disclaimer of Warranty. Unless required by applicable law or\n agreed to in writing, Licensor provides the Work (and each\n Contributor provides its Contributions) on an \"AS IS\" BASIS,\n WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or\n implied, including, without limitation, any warranties or conditions\n of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A\n PARTICULAR PURPOSE. You are solely responsible for determining the\n appropriateness of using or redistributing the Work and assume any\n risks associated with Your exercise of permissions under this License.\n\n 8. Limitation of Liability. In no event and under no legal theory,\n whether in tort (including negligence), contract, or otherwise,\n unless required by applicable law (such as deliberate and grossly\n negligent acts) or agreed to in writing, shall any Contributor be\n liable to You for damages, including any direct, indirect, special,\n incidental, or consequential damages of any character arising as a\n result of this License or out of the use or inability to use the\n Work (including but not limited to damages for loss of goodwill,\n work stoppage, computer failure or malfunction, or any and all\n other commercial damages or losses), even if such Contributor\n has been advised of the possibility of such damages.\n\n 9. Accepting Warranty or Additional Liability. While redistributing\n the Work or Derivative Works thereof, You may choose to offer,\n and charge a fee for, acceptance of support, warranty, indemnity,\n or other liability obligations and/or rights consistent with this\n License. However, in accepting such obligations, You may act only\n on Your own behalf and on Your sole responsibility, not on behalf\n of any other Contributor, and only if You agree to indemnify,\n defend, and hold each Contributor harmless for any liability\n incurred by, or claims asserted against, such Contributor by reason\n of your accepting any such warranty or additional liability.\n\n END OF TERMS AND CONDITIONS\n\n APPENDIX: How to apply the Apache License to your work.\n\n To apply the Apache License to your work, attach the following\n boilerplate notice, with the fields enclosed by brackets \"[]\"\n replaced with your own identifying information. (Don't include\n the brackets!) The text should be enclosed in the appropriate\n comment syntax for the file format. We also recommend that a\n file or class name and description of purpose be included on the\n same \"printed page\" as the copyright notice for easier\n identification within third-party archives.\n\n Copyright 2016 Pierre Lindenbaum\n\n Licensed under the Apache License, Version 2.0 (the \"License\");\n you may not use this file except in compliance with the License.\n You may obtain a copy of the License at\n\n http://www.apache.org/licenses/LICENSE-2.0\n\n Unless required by applicable law or agreed to in writing, software\n distributed under the License is distributed on an \"AS IS\" BASIS,\n WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n See the License for the specific language governing permissions and\n limitations under the License.\n\n\n*/\npackage com.github.lindenb.jbwa.jni;\n\npublic class ShortRead {\n private String name;\n private byte[] seq;\n private byte[] qual;\n\n public ShortRead(String name, byte[] seq, byte[] qual) {\n this.name = name;\n this.seq = seq;\n this.qual = qual;\n }\n\n public String getName() {\n return this.name;\n }\n\n public byte[] getBases() {\n return this.seq;\n }\n\n public byte[] getQualities() {\n return this.qual;\n }\n\n @Override\n public String toString() {\n return \"@\" + name + \"\\n\" + new String(this.seq) + \"\\n+\\n\" + new String(qual);\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/ApplyBQSRAdaptor.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.adapters;\n\nimport htsjdk.samtools.SAMRecord;\nimport htsjdk.samtools.SAMSequenceDictionary;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.reference.RefContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.sam.GATKSAMRecord;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.sam.SamContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.RODContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.RODNames;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLocParser;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.reports.GATKReport;\nimport org.ncic.bioinfo.sparkseq.algorithms.walker.printreads.PrintReads;\nimport org.ncic.bioinfo.sparkseq.data.basic.BasicSamRecord;\nimport org.ncic.bioinfo.sparkseq.data.common.RefContigInfo;\nimport org.ncic.bioinfo.sparkseq.data.partition.FastaPartition;\nimport org.ncic.bioinfo.sparkseq.data.partition.SamRecordPartition;\nimport org.ncic.bioinfo.sparkseq.data.partition.VcfRecordPartition;\nimport org.ncic.bioinfo.sparkseq.transfer.GATKReportTransfer;\nimport org.ncic.bioinfo.sparkseq.transfer.SAMRecord2BasicTransfer;\nimport org.ncic.bioinfo.sparkseq.transfer.SAMSequenceDictTransfer;\nimport scala.collection.JavaConversions;\n\nimport java.util.ArrayList;\nimport java.util.List;\n\n/**\n * Author: wbc\n */\npublic class ApplyBQSRAdaptor {\n\n public static List applyBQSR(RefContigInfo refContigInfo,\n SamRecordPartition samRecordPartition,\n FastaPartition refPartition,\n List rodPartitions,\n List bqsrTableLines) {\n SAMSequenceDictionary samSequenceDictionary = SAMSequenceDictTransfer.transfer(refContigInfo);\n GenomeLocParser parser = new GenomeLocParser(samSequenceDictionary);\n\n SamContentProvider samContentProvider = new SamContentProvider(samRecordPartition);\n RefContentProvider refContentProvider = new RefContentProvider(samSequenceDictionary, refPartition);\n\n List rodContentProviders = new java.util.ArrayList<>();\n rodPartitions.forEach(\n rodPartition -> rodContentProviders.add(\n new RODContentProvider(RODNames.KNOWN_ALLELES + rodPartition.key(), rodPartition, parser))\n );\n\n GATKReport bqsrTable = GATKReportTransfer.lines2Report(bqsrTableLines);\n\n // 使用bqsr进行read transform\n PrintReads printReads = new PrintReads(parser, refContentProvider,\n samContentProvider, rodContentProviders, bqsrTable);\n\n printReads.run();\n\n // 将结果sam record转化为base sam record\n List samRecords = printReads.getResultRecords();\n List basicSamRecords = new ArrayList<>();\n SAMRecord2BasicTransfer transfer = new SAMRecord2BasicTransfer();\n samRecords.forEach(record -> {\n basicSamRecords.add(transfer.transfer(record));\n });\n\n return basicSamRecords;\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/BQSRTableGather.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.adapters;\n\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.reports.GATKReport;\nimport org.ncic.bioinfo.sparkseq.algorithms.walker.printreads.RecalibrationReport;\nimport org.ncic.bioinfo.sparkseq.exceptions.GATKException;\nimport org.ncic.bioinfo.sparkseq.exceptions.PipelineException;\nimport org.ncic.bioinfo.sparkseq.transfer.GATKReportTransfer;\nimport scala.collection.JavaConversions;\n\nimport java.util.ArrayList;\nimport java.util.List;\nimport java.util.concurrent.ExecutorService;\nimport java.util.concurrent.Executors;\nimport java.util.concurrent.ForkJoinPool;\nimport java.util.concurrent.Future;\nimport java.util.concurrent.LinkedBlockingQueue;\nimport java.util.concurrent.RecursiveTask;\nimport java.util.concurrent.TimeUnit;\n\n/**\n * Author: wbc\n */\npublic class BQSRTableGather {\n\n public static List gatherBQSRTables(List> reportLinesGroup) {\n\n if (reportLinesGroup.size() == 0) {\n throw new PipelineException(\"No bqsr tables to merge\");\n }\n\n final RecalibrationReport finalReport = new RecalibrationReport(\n GATKReportTransfer.lines2Report(reportLinesGroup.get(0)));\n\n int count = reportLinesGroup.size();\n for (int i = 1; i < count; i++) {\n List reportLines = reportLinesGroup.get(i);\n GATKReport gatkReport = GATKReportTransfer.lines2Report(reportLines);\n if (gatkReport.getTable(\"RecalTable0\").getNumRows() != 0) {\n finalReport.combine(new RecalibrationReport(gatkReport));\n }\n }\n\n finalReport.calculateQuantizedQualities();\n GATKReport gatkReport = finalReport.createGATKReport();\n return GATKReportTransfer.report2Lines(gatkReport);\n }\n\n public static List gatherBQSRTablesInParallel(final List> rawReportLinesGroup, int threadCount, int tableCount) {\n ExecutorService pool = Executors.newFixedThreadPool(threadCount);\n\n int tableSize = (rawReportLinesGroup.size() < tableCount) ? rawReportLinesGroup.size() : tableCount;\n List> reportLinesGroup = rawReportLinesGroup.subList(0, tableSize);\n\n RecalibrationReport[] reports = new RecalibrationReport[reportLinesGroup.size()];\n\n for (int i = 0; i < reportLinesGroup.size(); i++) {\n final int reportId = i;\n pool.execute(new Runnable() {\n @Override\n public void run() {\n List lines = reportLinesGroup.get(reportId);\n GATKReport gatkReport = GATKReportTransfer.lines2Report(lines);\n reports[reportId] = new RecalibrationReport(gatkReport);\n }\n });\n }\n\n pool.shutdown();\n\n try {\n while (!pool.awaitTermination(1, TimeUnit.SECONDS)) ;\n } catch (InterruptedException e) {\n e.printStackTrace();\n }\n\n RecalibrationReport finalReport = reports[0];\n for (int i = 1; i < reports.length; i++) {\n if (reports[i].getRecalibrationTables().getTable(0).getDimensions()[0] != 0) {\n finalReport.combine(reports[i]);\n }\n }\n finalReport.calculateQuantizedQualities();\n GATKReport gatkReport = finalReport.createGATKReport();\n return GATKReportTransfer.report2Lines(gatkReport);\n\n /*ForkJoinPool forkJoinPool = new ForkJoinPool();\n Future futureResult = forkJoinPool.submit(new ForkJoinMergeTask(reports, 0, reports.length - 1));\n\n try {\n RecalibrationReport finalReport = futureResult.get();\n finalReport.calculateQuantizedQualities();\n GATKReport gatkReport = finalReport.createGATKReport();\n return GATKReportTransfer.report2Lines(gatkReport);\n } catch (Exception e) {\n throw new GATKException(\"Error when combine BQSR report:\" + e.getMessage());\n }*/\n }\n\n /**\n * 暂时弃用，因为结果会不一致\n */\n private static class ForkJoinMergeTask extends RecursiveTask {\n private int start;\n private int stop;\n RecalibrationReport[] reports;\n\n public ForkJoinMergeTask(RecalibrationReport[] reports, int start, int end) {\n this.reports = reports;\n this.start = start;\n this.stop = end;\n }\n\n public RecalibrationReport compute() {\n if (start == stop) {\n return reports[start];\n } else if (start == stop - 1) {\n reports[start].combine(reports[stop]);\n return reports[start];\n } else {\n int middle = (start + stop) / 2;\n ForkJoinMergeTask leftTask = new ForkJoinMergeTask(reports, start, middle);\n ForkJoinMergeTask rightTask = new ForkJoinMergeTask(reports, middle + 1, stop);\n leftTask.fork();\n rightTask.fork();\n RecalibrationReport leftRes = leftTask.join();\n RecalibrationReport rightRes = rightTask.join();\n leftRes.combine(rightRes);\n return leftRes;\n }\n }\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/BaseRecalibratorAdapter.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.adapters;\n\nimport htsjdk.samtools.SAMSequenceDictionary;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.reference.RefContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.sam.SamContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.RODContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.RODNames;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLocParser;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.reports.GATKReport;\nimport org.ncic.bioinfo.sparkseq.algorithms.walker.baserecalibrator.BaseRecalibrator;\nimport org.ncic.bioinfo.sparkseq.data.common.RefContigInfo;\nimport org.ncic.bioinfo.sparkseq.data.partition.FastaPartition;\nimport org.ncic.bioinfo.sparkseq.data.partition.SamRecordPartition;\nimport org.ncic.bioinfo.sparkseq.data.partition.VcfRecordPartition;\nimport org.ncic.bioinfo.sparkseq.transfer.GATKReportTransfer;\nimport org.ncic.bioinfo.sparkseq.transfer.SAMSequenceDictTransfer;\nimport scala.collection.JavaConversions;\n\nimport java.util.List;\n\n/**\n * Author: wbc\n */\npublic class BaseRecalibratorAdapter {\n\n public static List getRecalTableLines(RefContigInfo refContigInfo,\n SamRecordPartition samRecordPartition,\n FastaPartition refPartition,\n List rodPartitions) {\n SAMSequenceDictionary samSequenceDictionary = SAMSequenceDictTransfer.transfer(refContigInfo);\n GenomeLocParser parser = new GenomeLocParser(samSequenceDictionary);\n\n SamContentProvider samContentProvider = new SamContentProvider(samRecordPartition);\n RefContentProvider refContentProvider = new RefContentProvider(samSequenceDictionary, refPartition);\n\n List rodContentProviders = new java.util.ArrayList<>();\n rodPartitions.forEach(\n rodPartition -> rodContentProviders.add(\n new RODContentProvider(RODNames.KNOWN_ALLELES + rodPartition.key(), rodPartition, parser))\n );\n\n // 生成recal table\n BaseRecalibrator baseRecalibrator = new BaseRecalibrator(\n parser, refContentProvider, samContentProvider, rodContentProviders);\n baseRecalibrator.run();\n\n GATKReport bqsrTable = baseRecalibrator.getReport();\n\n return GATKReportTransfer.report2Lines(bqsrTable);\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/BwaMemAdapter.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.adapters;\n\nimport com.github.lindenb.jbwa.jni.BwaIndex;\nimport com.github.lindenb.jbwa.jni.BwaMem;\nimport com.github.lindenb.jbwa.jni.ShortRead;\nimport org.apache.commons.lang3.StringUtils;\nimport org.ncic.bioinfo.sparkseq.data.basic.BasicSamRecord;\nimport org.ncic.bioinfo.sparkseq.data.basic.FastqPairRecord;\nimport org.ncic.bioinfo.sparkseq.data.common.ReadGroupInfo;\nimport org.ncic.bioinfo.sparkseq.data.common.RefContigInfo;\nimport org.ncic.bioinfo.sparkseq.exceptions.PipelineException;\nimport org.ncic.bioinfo.sparkseq.transfer.FastqRecord2ShortReadTransfer;\nimport scala.collection.JavaConversions;\n\nimport java.io.File;\nimport java.io.IOException;\nimport java.util.ArrayList;\nimport java.util.List;\n\n/**\n * 该类用单例模式控制了每一个进程只加载一份index\n * \n * Author: wbc\n */\npublic class BwaMemAdapter {\n\n private static volatile BwaIndex bwaIndexInstance = null;\n\n private static BwaIndex getBwaIndexInstance(String bwaJNILibPath, String referencePath) throws IOException {\n if (bwaIndexInstance == null) {\n synchronized (BwaMemAdapter.class) {\n if (bwaIndexInstance == null) {\n System.load(bwaJNILibPath);\n bwaIndexInstance = new BwaIndex(new File(referencePath));\n }\n }\n }\n return bwaIndexInstance;\n }\n\n\n public static List pairAlign(String bwaJNILibPath,\n String referencePath,\n ReadGroupInfo readGroupInfo,\n RefContigInfo refContigInfo,\n List fastqPairRecords) {\n\n List results = new ArrayList<>();\n BwaIndex bwaIndex = null;\n try {\n bwaIndex = getBwaIndexInstance(bwaJNILibPath, referencePath);\n } catch (IOException e) {\n e.printStackTrace();\n throw new PipelineException(\"Error when load index in JNI bwa\");\n }\n\n int chunkSize = 1000;\n List reads1 = new ArrayList<>(chunkSize);\n List reads2 = new ArrayList<>(chunkSize);\n\n for(FastqPairRecord pairRecord : fastqPairRecords) {\n if(reads1.size() == chunkSize) {\n alignAndAddIntoResult(bwaIndex, results, readGroupInfo, refContigInfo, reads1, reads2);\n reads1.clear();\n reads2.clear();\n }\n\n reads1.add(FastqRecord2ShortReadTransfer.transferRead1(pairRecord));\n reads2.add(FastqRecord2ShortReadTransfer.transferRead2(pairRecord));\n }\n if(reads1.size() > 0) {\n alignAndAddIntoResult(bwaIndex, results, readGroupInfo, refContigInfo, reads1, reads2);\n }\n return results;\n }\n\n private static void alignAndAddIntoResult(BwaIndex bwaIndex, List results,\n ReadGroupInfo readGroupInfo, RefContigInfo refContigInfo,\n List reads1, List reads2){\n try {\n BwaMem mem = new BwaMem(bwaIndex);\n String[] rawResults = mem.align(reads1, reads2);\n String rgInfo = \"RG:Z:\" + readGroupInfo.id();\n String rgInfoWithTab = \"\\t\" + rgInfo;\n for (String rawResult : rawResults) {\n // 这个库有时候会一次出现多条，中间以\\n间隔\n String[] rawReads = StringUtils.split(rawResult, '\\n');\n for (String rawRead : rawReads) {\n String finalReadString = null;\n if (rawRead.endsWith(\"\\t\")) {\n finalReadString = rawRead + rgInfo;\n } else {\n finalReadString = rawRead + rgInfoWithTab;\n }\n results.add(BasicSamRecord.apply(finalReadString, refContigInfo, false));\n }\n }\n } catch (IOException e) {\n e.printStackTrace();\n throw new PipelineException(\"Error when call JNI bwa\");\n }\n }\n\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/HaplotypeCallerAdapter.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.adapters;\n\nimport htsjdk.samtools.SAMFileHeader;\nimport htsjdk.samtools.SAMReadGroupRecord;\nimport htsjdk.samtools.SAMSequenceDictionary;\nimport htsjdk.variant.variantcontext.VariantContext;\nimport htsjdk.variant.vcf.VCFCodec;\nimport htsjdk.variant.vcf.VCFHeader;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.reference.RefContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.sam.SamContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.RODContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.RODNames;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.VCFHeaderLineIterable;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.header.StandardWGSVCFHeader;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLocParser;\nimport org.ncic.bioinfo.sparkseq.algorithms.walker.SerializableActiveRegionMapData;\nimport org.ncic.bioinfo.sparkseq.algorithms.walker.genotypegvcfs.GenotypeGVCFs;\nimport org.ncic.bioinfo.sparkseq.algorithms.walker.haplotypecaller.ActiveRegionFinder;\nimport org.ncic.bioinfo.sparkseq.algorithms.walker.haplotypecaller.ActiveRegionMapData;\nimport org.ncic.bioinfo.sparkseq.algorithms.walker.haplotypecaller.HaplotypeCaller;\nimport org.ncic.bioinfo.sparkseq.algorithms.walker.haplotypecaller.SampleList;\nimport org.ncic.bioinfo.sparkseq.data.basic.VcfRecord;\nimport org.ncic.bioinfo.sparkseq.data.common.ReadGroupInfo;\nimport org.ncic.bioinfo.sparkseq.data.common.RefContigInfo;\nimport org.ncic.bioinfo.sparkseq.data.common.SamHeaderInfo;\nimport org.ncic.bioinfo.sparkseq.data.common.VcfHeaderInfo;\nimport org.ncic.bioinfo.sparkseq.data.partition.FastaPartition;\nimport org.ncic.bioinfo.sparkseq.data.partition.SamRecordPartition;\nimport org.ncic.bioinfo.sparkseq.data.partition.VcfRecordPartition;\nimport org.ncic.bioinfo.sparkseq.transfer.*;\nimport scala.collection.JavaConversions;\n\nimport java.util.ArrayList;\nimport java.util.List;\n\n/**\n * Author: wbc\n */\npublic class HaplotypeCallerAdapter {\n\n public static List getActiveRegions(RefContigInfo refContigInfo,\n SamRecordPartition samRecordPartition,\n FastaPartition refPartition,\n List rodPartitions,\n boolean useGVCF) {\n\n SAMSequenceDictionary samSequenceDictionary = SAMSequenceDictTransfer.transfer(refContigInfo);\n GenomeLocParser parser = new GenomeLocParser(samSequenceDictionary);\n\n SamContentProvider samContentProvider = new SamContentProvider(samRecordPartition);\n RefContentProvider refContentProvider = new RefContentProvider(samSequenceDictionary, refPartition);\n\n List rodContentProviders = new java.util.ArrayList<>();\n rodPartitions.forEach(\n rodPartition -> rodContentProviders.add(\n new RODContentProvider(rodPartition.key(), rodPartition, parser))\n );\n\n // 先找出active region的信息\n ActiveRegionFinder activeRegionFinder = new ActiveRegionFinder(\n parser, refContentProvider, samContentProvider, rodContentProviders, useGVCF);\n activeRegionFinder.run();\n List activeRegionMapDatas = activeRegionFinder.getResultActiveRegions();\n\n SAMRecord2BasicTransfer samTransfer = new SAMRecord2BasicTransfer();\n VCFHeader header = StandardWGSVCFHeader.getHeader();\n VC2VcfRecordTransfer vcfTransfer = new VC2VcfRecordTransfer(header, refContigInfo);\n\n List serializableActiveRegionMapDataList = new ArrayList<>(activeRegionMapDatas.size());\n for (ActiveRegionMapData mapData : activeRegionMapDatas) {\n serializableActiveRegionMapDataList.add(new SerializableActiveRegionMapData(mapData, samTransfer, vcfTransfer));\n }\n\n return serializableActiveRegionMapDataList;\n }\n\n public static class StaticData {\n public HaplotypeCaller haplotypeCaller = null;\n public GenomeLocParser genomeLocParser = null;\n public Basic2SAMRecordTransfer basic2SAMRecordTransfer = null;\n public VCFHeader vcfFileHeader = null;\n public VCFCodec codec = null;\n }\n\n public static StaticData getStaticDataInstance(RefContigInfo refContigInfo,\n boolean useGVCF,\n SamHeaderInfo samHeaderInfo,\n VcfHeaderInfo vcfHeaderInfo) {\n StaticData data = new StaticData();\n SAMSequenceDictionary samSequenceDictionary = SAMSequenceDictTransfer.transfer(refContigInfo);\n data.genomeLocParser = new GenomeLocParser(samSequenceDictionary);\n samHeaderInfo.addReadGroupInfo(ReadGroupInfo.apply(\"rg1\", \"sample1\"));\n SAMFileHeader header = SAMHeaderTransfer.transfer(samHeaderInfo);\n List readGroupInfos = header.getReadGroups();\n List samples = new ArrayList<>();\n for (SAMReadGroupRecord readGroup : readGroupInfos) {\n samples.add(readGroup.getSample());\n }\n data.haplotypeCaller = new HaplotypeCaller(data.genomeLocParser, samples, useGVCF);\n data.basic2SAMRecordTransfer = new Basic2SAMRecordTransfer(header);\n\n VCFCodec codec = new VCFCodec();\n VCFHeaderLineIterable headerLineIterable = new VCFHeaderLineIterable(vcfHeaderInfo);\n data.vcfFileHeader = (VCFHeader) codec.readActualHeader(headerLineIterable);\n data.codec = codec;\n return data;\n }\n\n public static List callVariants(RefContigInfo refContigInfo,\n scala.collection.immutable.List serializableActiveRegionMapDataList,\n boolean useGVCF,\n SamHeaderInfo samHeaderInfo,\n VcfHeaderInfo vcfHeaderInfo) {\n return callVariants(refContigInfo, CollectionConverter.asJavaList(serializableActiveRegionMapDataList),\n useGVCF, samHeaderInfo, vcfHeaderInfo);\n }\n\n public static List callVariants(RefContigInfo refContigInfo,\n List serializableActiveRegionMapDataList,\n boolean useGVCF,\n SamHeaderInfo samHeaderInfo,\n VcfHeaderInfo vcfHeaderInfo) {\n StaticData staticData = getStaticDataInstance(refContigInfo, false, samHeaderInfo, vcfHeaderInfo);\n GenomeLocParser parser = staticData.genomeLocParser;\n HaplotypeCaller haplotypeCaller = staticData.haplotypeCaller;\n Basic2SAMRecordTransfer basic2SAMRecordTransfer = staticData.basic2SAMRecordTransfer;\n VCFHeader vcfFileHeader = staticData.vcfFileHeader;\n VCFCodec codec = staticData.codec;\n\n List variantContexts = new ArrayList<>();\n\n for(SerializableActiveRegionMapData mapData: serializableActiveRegionMapDataList) {\n ActiveRegionMapData activeRegionMapData = mapData.toActiveRegionMapData(\n parser, basic2SAMRecordTransfer, vcfFileHeader, codec);\n variantContexts.addAll(haplotypeCaller.map(activeRegionMapData));\n }\n\n // 如果使用了gvcf，则需要加一个genotypeGVCFs\n List finalResult = variantContexts;\n\n VCFHeader header = StandardWGSVCFHeader.getHeader();\n VC2VcfRecordTransfer transfer = new VC2VcfRecordTransfer(header, refContigInfo);\n List vcfRecords = new ArrayList<>(finalResult.size());\n finalResult.forEach(vc -> vcfRecords.add(transfer.transfer(vc)));\n return vcfRecords;\n }\n\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/IndelRealignAdapter.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.adapters;\n\nimport htsjdk.samtools.SAMRecord;\nimport htsjdk.samtools.SAMSequenceDictionary;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.reference.RefContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.sam.SamContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.RODContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.RODNames;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLoc;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLocParser;\nimport org.ncic.bioinfo.sparkseq.algorithms.walker.indelrealigner.IndelRealigner;\nimport org.ncic.bioinfo.sparkseq.algorithms.walker.realignertargetcreator.RealignerTargetCreator;\nimport org.ncic.bioinfo.sparkseq.data.basic.BasicSamRecord;\nimport org.ncic.bioinfo.sparkseq.data.common.RefContigInfo;\nimport org.ncic.bioinfo.sparkseq.data.common.SamHeaderInfo;\nimport org.ncic.bioinfo.sparkseq.data.partition.FastaPartition;\nimport org.ncic.bioinfo.sparkseq.data.partition.SamRecordPartition;\nimport org.ncic.bioinfo.sparkseq.data.partition.VcfRecordPartition;\nimport org.ncic.bioinfo.sparkseq.transfer.SAMRecord2BasicTransfer;\nimport org.ncic.bioinfo.sparkseq.transfer.SAMSequenceDictTransfer;\nimport scala.collection.JavaConversions;\n\nimport java.util.ArrayList;\nimport java.util.List;\n\n/**\n * Author: wbc\n */\npublic class IndelRealignAdapter {\n\n public static List realign(RefContigInfo refContigInfo,\n SamRecordPartition samRecordPartition,\n FastaPartition refPartition,\n List rodPartitions) {\n // 数据准备\n SAMSequenceDictionary samSequenceDictionary = SAMSequenceDictTransfer.transfer(refContigInfo);\n GenomeLocParser parser = new GenomeLocParser(samSequenceDictionary);\n\n SamContentProvider samContentProvider = new SamContentProvider(samRecordPartition);\n RefContentProvider refContentProvider = new RefContentProvider(samSequenceDictionary, refPartition);\n\n List rodContentProviders = new java.util.ArrayList<>();\n rodPartitions.forEach(\n rodPartition -> rodContentProviders.add(\n new RODContentProvider(RODNames.KNOWN_ALLELES + rodPartition.key(), rodPartition, parser))\n );\n\n // 找target interval\n RealignerTargetCreator realignerTargetCreator = new RealignerTargetCreator(\n parser, refContentProvider, samContentProvider, rodContentProviders);\n realignerTargetCreator.run();\n\n List targetIntervals = realignerTargetCreator.getTargetIntervals();\n\n // realign reads\n IndelRealigner indelRealigner = new IndelRealigner(\n parser, refContentProvider, samContentProvider, rodContentProviders, targetIntervals);\n indelRealigner.run();\n\n // 将结果sam record转化为base sam record\n List samRecords = indelRealigner.getResultSam();\n List basicSamRecords = new ArrayList<>();\n SAMRecord2BasicTransfer transfer = new SAMRecord2BasicTransfer();\n samRecords.forEach(record -> {\n basicSamRecords.add(transfer.transfer(record));\n });\n return basicSamRecords;\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/MutectAdapter.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.adapters;\n\nimport htsjdk.samtools.SAMSequenceDictionary;\nimport htsjdk.variant.variantcontext.VariantContext;\nimport htsjdk.variant.vcf.VCFHeader;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.reference.RefContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.sam.SamContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.RODContentProvider;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.header.StandardWGSVCFHeader;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLoc;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLocParser;\nimport org.ncic.bioinfo.sparkseq.algorithms.walker.mutect.Mutect;\nimport org.ncic.bioinfo.sparkseq.data.basic.VcfRecord;\nimport org.ncic.bioinfo.sparkseq.data.common.Locus;\nimport org.ncic.bioinfo.sparkseq.data.common.RefContigInfo;\nimport org.ncic.bioinfo.sparkseq.data.partition.FastaPartition;\nimport org.ncic.bioinfo.sparkseq.data.partition.SamRecordPartition;\nimport org.ncic.bioinfo.sparkseq.data.partition.VcfRecordPartition;\nimport org.ncic.bioinfo.sparkseq.transfer.SAMSequenceDictTransfer;\nimport org.ncic.bioinfo.sparkseq.transfer.VC2VcfRecordTransfer;\nimport scala.collection.JavaConversions;\n\nimport java.util.ArrayList;\nimport java.util.List;\n\n/**\n * Author: wbc\n */\npublic class MutectAdapter {\n public static List callVariants(RefContigInfo refContigInfo,\n SamRecordPartition tumorSamRecordPartition,\n SamRecordPartition normalSamRecordPartition,\n FastaPartition refPartition,\n List rodPartitions,\n List intervals) {\n SAMSequenceDictionary samSequenceDictionary = SAMSequenceDictTransfer.transfer(refContigInfo);\n GenomeLocParser parser = new GenomeLocParser(samSequenceDictionary);\n\n SamContentProvider tumorSamContentProvider = new SamContentProvider(tumorSamRecordPartition);\n SamContentProvider normalSamContentProvider = new SamContentProvider(normalSamRecordPartition);\n RefContentProvider refContentProvider = new RefContentProvider(samSequenceDictionary, refPartition);\n\n List rodContentProviders = new java.util.ArrayList<>();\n rodPartitions.forEach(\n rodPartition -> rodContentProviders.add(\n new RODContentProvider(rodPartition.key(), rodPartition, parser))\n );\n\n List intervalLocus = new ArrayList<>();\n GenomeLoc traverseLocus = refContentProvider.getLocus();\n intervals.forEach(\n locus -> {\n GenomeLoc interval = new GenomeLoc(locus.contigName(), locus.contigId(), locus.start(), locus.stop());\n if (interval.overlapsP(traverseLocus)) {\n intervalLocus.add(interval);\n }\n }\n );\n\n Mutect mutect = new Mutect(parser, refContentProvider,\n tumorSamContentProvider, normalSamContentProvider, rodContentProviders, intervalLocus);\n\n List finalResult = mutect.getResultVCFRecords();\n\n VCFHeader header = StandardWGSVCFHeader.getHeader();\n VC2VcfRecordTransfer transfer = new VC2VcfRecordTransfer(header, refContigInfo);\n List vcfRecords = new ArrayList<>(finalResult.size());\n finalResult.forEach(vc -> vcfRecords.add(transfer.transfer(vc)));\n return vcfRecords;\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/CountSet.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.basic;\n\nimport java.lang.reflect.Array;\nimport java.util.Arrays;\nimport java.util.Collection;\nimport java.util.Iterator;\nimport java.util.NoSuchElementException;\nimport java.util.Set;\n\n/**\n * Author: wbc\n */\npublic class CountSet implements Cloneable, Set {\n\n /**\n * The size of the set.\n */\n private int size;\n\n /**\n * Holds the element of the set within the subrange [0 .. size - 1] in ascending order.\n */\n private int[] elements;\n\n /**\n * Creates a copy of an existing int-set.\n * @param template the intset to copy values from.\n */\n public CountSet(final CountSet template) {\n elements = template.elements.clone();\n size = template.size;\n }\n\n /**\n * Creates a new set indicating the expected maximum number of elements it will contain.\n * @param initialCapacity the desired initial capacity of the set.\n * @throws IllegalArgumentException if initialCapacity is negative.\n */\n public CountSet(int initialCapacity) {\n if (initialCapacity < 0)\n throw new IllegalArgumentException();\n elements = new int[initialCapacity];\n size = 0;\n }\n\n /**\n * Set the set contents to a single integer value.\n * @param value the integer value to set the set to.\n */\n public void setTo(int value) {\n ensureCapacity(1);\n size = 1;\n elements[0] = value;\n }\n\n /**\n * Set the content of this set to a collection of integers.\n * @param values the new values to be included in the set.\n * @throws NullPointerException if value is null.\n */\n public void setTo(int ... values) {\n ensureCapacity(values.length);\n size = values.length;\n System.arraycopy(values, 0, elements, 0, size);\n Arrays.sort(elements,0,size);\n }\n\n /**\n * Increase (or decrease) all elements in the set by a number.\n * @param delta the number of add (or substract if negative) to all elements.\n *\n * @return true if the set changed as a result of this invocation, false otherwise.\n */\n public boolean incAll(final int delta) {\n if (size == 0 || delta == 0)\n return false;\n for (int i = 0; i < size; i++)\n elements[i] += delta;\n return true;\n }\n\n /**\n * Returns the smallest integer value in the set.\n *\n * @throws NoSuchElementException if the set is empty (thus there is no minimum).\n * @return the smallest integer value in the set.\n */\n public int min() {\n if (size == 0)\n throw new NoSuchElementException(\"cannot have a min from an empty set\");\n return elements[0];\n }\n\n /**\n * Returns the largest integer value in the set.\n *\n * @throws NoSuchElementException if the set is empty (thus there is no maximum).\n * @return the largest integer value in the set.\n */\n public int max() {\n if (size == 0)\n throw new NoSuchElementException(\"cannot have a max from an empty set\");\n return elements[size - 1];\n }\n\n /**\n * Adds a range of integer values to the collection.\n *\n * This method avoid the need to explicity indicate all values in that range. Notice that the range is fully inclusive.\n * You can indicate a decrease range (fromValue > toValue).\n *\n * @param fromValue the first value to add in the set (inclusive).\n * @param toValue the last value to add to the set (inclusive).\n * @return true if the set changed as a result of this invocation, false otherwise.\n */\n public boolean addRange(final int fromValue, final int toValue) {\n final int lowEnd;\n final int highEnd;\n\n if (fromValue <= toValue) {\n lowEnd = fromValue; highEnd = toValue;\n } else {\n highEnd = fromValue; lowEnd = toValue;\n }\n\n //TODO to be optimized to add missing sub-ranges in one go:\n boolean result = false;\n for (int i = lowEnd; i <= highEnd; i++)\n result = add(i) | result;\n return result;\n }\n\n /**\n * Add an integer value to the set.\n * @param value to add to the set.\n * @return true if the set changed as a result of this invocation, false otherwise.\n */\n public boolean add(final int value) {\n int pos = Arrays.binarySearch(elements,0,size,value);\n if (pos >= 0) return false;\n int insertPos = - pos - 1;\n ensureCapacity(size + 1);\n System.arraycopy(elements, insertPos, elements, insertPos + 1, size - insertPos);\n elements[insertPos] = value;\n size++;\n return true;\n }\n\n /**\n * Add a arbitrary number of integers to the set.\n *\n * @param values integer to add to the set.\n * @return true if the set changed as a result of this invocation, false otherwise.\n */\n public boolean addAll(final int ... values) {\n ensureCapacity(size + values.length);\n boolean result = false;\n for (final int v : values)\n result = add(v) | result;\n return result;\n }\n\n @Override\n public boolean addAll(final Collection numbers) {\n ensureCapacity(size + numbers.size());\n boolean result = false;\n for (final Number n : numbers)\n result = add(n.intValue()) | result;\n return result;\n }\n\n /**\n * Add all values within a range in an integer array.\n *\n * @param source array where the values to add are found.\n * @param fromIndex first position from source to add (inclusive).\n * @param toIndex index after the last position in source to add (thus exclusive).\n * @throws NullPointerException if source is null.\n * @throws NegativeArraySizeException if fromIndex or toIndex are negative.\n * @throws ArrayIndexOutOfBoundsException if fromIndex or toIndex are beyond bounds\n * allowed [0 .. source.length].\n * @return true if the set changed as a result of this invocation, false otherwise.\n */\n public boolean addAll(final int[] source, final int fromIndex, final int toIndex) {\n ensureCapacity(size + source.length);\n boolean result = false;\n for (int i = fromIndex; i < toIndex; i++)\n result = add(source[i]) | result;\n return result;\n }\n\n\n /**\n * Add all elements present in a int-set.\n *\n * @param other the other inset.\n *\n * @throws NullPointerException if other is null.\n * @return true if this set changed due to this operation, false otherwise.\n */\n public boolean addAll(final CountSet other) {\n return addAll(other.elements,0,other.size);\n }\n\n /**\n * Checks whether a integer value is included in the set.\n * @param value the value to check.\n * @return true if value is inside the set, false otherwise.\n */\n public boolean contains(final int value) {\n return Arrays.binarySearch(elements, 0, size, value) >= 0;\n }\n\n /**\n * Make sure that this int-set has capacity to handle a number of elements.\n * \n * If the set has already that or greater capacity nothing would be changed.\n *\n * @param capacity the requested capacity.\n */\n private void ensureCapacity(final int capacity) {\n if (elements.length >= capacity) return;\n int newLength = Math.max(elements.length << 1, capacity);\n elements = Arrays.copyOf(elements,newLength);\n }\n\n\n @Override\n public int size() {\n return size;\n }\n\n @Override\n public boolean isEmpty() {\n return size() == 0;\n }\n\n @Override\n public boolean contains(final Object o) {\n if (o instanceof Integer) {\n final int i = (Integer)o;\n return contains(i);\n } else\n return false; //To change body of implemented methods use File | Settings | File Templates.\n }\n\n\n @Override\n public Iterator iterator() {\n return new MyIterator();\n }\n\n @Override\n public Object[] toArray() {\n final Integer[] result = new Integer[size];\n for (int i = 0; i < size; i++)\n result[i] = elements[i];\n return result;\n }\n\n @Override\n @SuppressWarnings(\"unchecked\")\n public T[] toArray(final T[] a) {\n if (a == null)\n throw new NullPointerException();\n\n @SuppressWarnings(\"unchecked\")\n final Class componentClass = (Class) a.getClass().getComponentType();\n if (!componentClass.isAssignableFrom(Integer.class))\n throw new ArrayStoreException();\n\n @SuppressWarnings(\"unchecked\")\n final T[] dest = (a.length < size) ? (T[]) Array.newInstance(componentClass, size) : a;\n\n for (int i = 0; i < size; i++)\n dest[i] = (T) (Integer) elements[i];\n return dest;\n }\n\n /**\n * Copies the content of the set into an integer array. The result can be freely modified by the invoker.\n * @return never null but a zero-length array if the set is empty.\n */\n public int[] toIntArray() {\n return Arrays.copyOfRange(elements,0,size);\n }\n\n /**\n * Copy the content of the set into an array.\n * @param dest the destination array.\n * @param offset where to store the first element of the set.\n * @throws NullPointerException if dest is null.\n * @throws ArrayIndexOutOfBoundsException if offset is out of range of there is not enough\n * space after offset in the destination array to hold all values in the set.\n */\n public void copyTo(final int[] dest, int offset) {\n if (dest == null)\n throw new NullPointerException();\n if (dest.length < (size + offset))\n throw new ArrayIndexOutOfBoundsException(\"destination is to short\");\n System.arraycopy(elements,0,dest,offset,size);\n }\n\n /**\n * Copy the content of the set into an array.\n * @param dest the destination array.\n * @throws NullPointerException if dest is null.\n * @throws ArrayIndexOutOfBoundsException if there is not enough\n * space after offset in the destination array to hold all values in the set.\n */\n public void copyTo(final int[] dest) {\n copyTo(dest,0);\n }\n\n\n @Override\n public boolean add(final Integer integer) {\n return add((int) integer);\n }\n\n @Override\n public boolean remove(final Object o) {\n return o instanceof Integer && remove((int)o);\n }\n\n /**\n * Removes a single integer value for the set.\n * @param i the value to remove.\n * @return true if the set has changed as a result of this invocation, false otherwise.\n */\n public boolean remove(final int i) {\n final int pos = Arrays.binarySearch(elements,0,size,i);\n if (pos < 0)\n return false;\n else {\n removeIndex(pos);\n return true;\n }\n }\n\n @Override\n public boolean containsAll(final Collection c) {\n for (final Object o : c)\n if (!contains(o))\n return false;\n return true;\n }\n\n\n @Override\n public boolean retainAll(final Collection c) {\n if (size == 0)\n return false;\n @SuppressWarnings(\"all\")\n final CountSet retainIndices = new CountSet(c.size() + 2);\n retainIndices.add(-1);\n retainIndices.add(size);\n for (final Object o : c) {\n if (!(o instanceof Integer))\n continue;\n final int pos = Arrays.binarySearch(elements,0,size,(int) o);\n if (pos < 0)\n continue;\n retainIndices.add(pos);\n }\n if (retainIndices.size == 2) {\n size = 0;\n return true;\n } else if (retainIndices.size == size + 2) {\n return false;\n } else {\n for (int idx = retainIndices.size - 1; idx > 0; idx--) {\n final int toIdx = retainIndices.elements[idx];\n final int fromIdx = retainIndices.elements[idx - 1] + 1;\n removeIndices(toIdx,fromIdx);\n }\n return true;\n }\n }\n\n /**\n * Removes the values found in a range of indexes in {@link #elements}.\n * @param fromIdx first index to remove (inclusive).\n * @param toIdx right after last index to remove (exclusive).\n */\n private void removeIndices(final int fromIdx, final int toIdx) {\n System.arraycopy(elements,toIdx,elements,fromIdx,size - toIdx);\n size -= toIdx - fromIdx;\n }\n\n @Override\n public boolean removeAll(final Collection c) {\n boolean result = false;\n for (final Object o : c)\n result = remove(o) | result;\n return result;\n }\n\n private void removeIndex(int idx) {\n System.arraycopy(elements,idx+1,elements,idx,size - idx - 1);\n }\n\n @Override\n public void clear() {\n size = 0;\n }\n\n /**\n * Returns a copy of this set which can be changed without modifying the original one.\n * @return never {@code null}.\n */\n @SuppressWarnings(\"all\")\n public CountSet clone() {\n return new CountSet(this);\n }\n\n @Override\n public String toString() {\n final StringBuilder sb = new StringBuilder(2 + size() * 10);\n sb.append('{');\n for (int i = 0; i < size; i++)\n sb.append(elements[i]).append(',');\n sb.replace(sb.length()-1,sb.length(),\"}\");\n return sb.toString();\n\n }\n\n\n /**\n * Custom iterator class for {@link CountSet IntSets}\n */\n private class MyIterator implements Iterator {\n /** What position I am in. */\n private int next = 0;\n\n @Override\n public boolean hasNext() {\n return next < size;\n }\n\n @Override\n public Integer next() {\n if (next >= size)\n throw new NoSuchElementException();\n return elements[next];\n }\n\n @Override\n public void remove() {\n if (next == 0)\n throw new IllegalStateException();\n if (next >= size)\n throw new NoSuchElementException();\n removeIndex(next - 1);\n }\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/DefaultHashMap.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.basic;\n\nimport java.util.HashMap;\n\n/**\n * Author: wbc\n */\npublic class DefaultHashMap extends HashMap {\n\n public void setDefaultValue(V defaultValue) {\n this.defaultValue = defaultValue;\n }\n protected V defaultValue;\n public DefaultHashMap(V defaultValue) {\n this.defaultValue = defaultValue;\n }\n @Override\n public V get(Object k) {\n V v = super.get(k);\n return ((v == null) && !this.containsKey(k)) ? this.defaultValue : v;\n }\n\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/IndexedSet.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.basic;\n\nimport it.unimi.dsi.fastutil.objects.Object2IntMap;\nimport it.unimi.dsi.fastutil.objects.Object2IntOpenHashMap;\n\nimport java.util.AbstractSet;\nimport java.util.ArrayList;\nimport java.util.Collection;\nimport java.util.Collections;\nimport java.util.Iterator;\nimport java.util.List;\nimport java.util.ListIterator;\nimport java.util.Set;\n\n/**\n * Set set where each element can be reference by a unique integer index that runs from\n * 0 to the size of the set - 1.\n *\n * @author Valentin Ruano-Rubio <valentin@broadinstitute.org>\n */\npublic class IndexedSet extends AbstractSet implements Set {\n\n /**\n * Elements stored in an array-list by their index.\n */\n private final ArrayList elements;\n\n /**\n * A unmodifiable view to the element list. Initially {@code null} it is thread-unsafe lazy instantiated\n * when requested first time through {@link #asList}. Therefore typically it is shared by invoking code but\n * there could be some extra copies (rare though) in multi-thread runs.\n */\n private transient List unmodifiableElementsListView;\n\n /**\n * Quick element to index lookup map.\n * \n * Uses a primitive int value map for efficiency sake.\n *
\n */\n private final Object2IntMap indexByElement;\n\n /**\n * Creates an empty indexed set indicating the expected number of elements.\n *\n * @param initialCapacity the initial number of elements.\n */\n public IndexedSet(final int initialCapacity) {\n elements = new ArrayList<>(initialCapacity);\n indexByElement = new Object2IntOpenHashMap<>(initialCapacity);\n }\n\n /**\n * Creates a new sample list from a existing collection of elements.\n *\n * \n * Elements will be indexed as they appear in the input array. Repeats will be ignored.\n *
\n *\n * @param values the original sample list.\n *\n * @throws IllegalArgumentException\n * if {@code values} array is {@code null} itself, or it contains {@code null}.\n */\n @SuppressWarnings(\"unchecked\")\n public IndexedSet(final Collection values) {\n if (values == null)\n throw new IllegalArgumentException(\"input values cannot be null\");\n\n final int initialCapacity = values.size();\n elements = new ArrayList<>(initialCapacity);\n indexByElement = new Object2IntOpenHashMap<>(initialCapacity);\n int nextIndex = 0;\n for (final E value : values) {\n if (value == null)\n throw new IllegalArgumentException(\"null element not allowed: index == \" + nextIndex);\n if (indexByElement.containsKey(value))\n continue;\n indexByElement.put(value, nextIndex++);\n elements.add(value);\n }\n }\n\n /**\n * Creates a new sample list from a existing array of elements.\n *\n * \n * Elements will be indexed as they appear in the collection. Repeats will be ignored.\n *
\n *\n * @param values the original sample list.\n *\n * @throws IllegalArgumentException\n * if {@code values} collection is {@code null} itself, or it contains {@code null}.\n */\n @SuppressWarnings(\"unchecked\")\n public IndexedSet(final E ... values) {\n if (values == null)\n throw new IllegalArgumentException(\"input values cannot be null\");\n\n final int initialCapacity = values.length;\n elements = new ArrayList<>(initialCapacity);\n indexByElement = new Object2IntOpenHashMap<>(initialCapacity);\n int nextIndex = 0;\n for (final E value : values) {\n if (value == null)\n throw new IllegalArgumentException(\"null element not allowed: index == \" + nextIndex);\n if (indexByElement.containsKey(value))\n continue;\n indexByElement.put(value, nextIndex++);\n elements.add(value);\n }\n }\n\n /**\n * Returns a list view of the elements in the set.\n *\n * \n * Elements are sorted by their index within the set.\n *
\n *\n * \n * This view changes as the indexed set changes but it cannot be used to update its contents.\n * In such case a {@link UnsupportedOperationException} exception will be thrown if the calling\n * code tries to tho just that.\n *
\n *\n * @return never {@code null}.\n */\n public List asList() {\n if (unmodifiableElementsListView == null)\n unmodifiableElementsListView = Collections.unmodifiableList(elements);\n return unmodifiableElementsListView;\n }\n\n /**\n * Throws an exception if an index is out of bounds.\n *\n * \n * An element index is valid iff is within [0,{@link #size()}).\n *
\n *\n * @param index the query index.\n *\n * @throws IllegalArgumentException {@code index} is out of bounds.\n */\n protected void checkIndex(final int index) {\n if (index < 0)\n throw new IllegalArgumentException(\"the index cannot be negative: \" + index);\n if (index >= size())\n throw new IllegalArgumentException(\"the index is equal or larger than the list length: \" + index + \" >= \" + size());\n }\n\n @Override\n public Iterator iterator() {\n return asList().iterator();\n }\n\n /**\n * Returns number of elements in the set.\n * @return never {@code null}.\n */\n @Override\n public int size() {\n return elements.size();\n }\n\n /**\n *\n * @param o\n * @return {@code true} iff {@code o} is in\n */\n @Override\n @SuppressWarnings(\"all\")\n public boolean contains(final Object o) {\n return o != null && indexByElement.containsKey(o);\n }\n\n /**\n * Adds a new element to the set.\n *\n * \n * If the element was already in th set nothing will happen and the method will return {@code false}. However,\n * if the element is new to this set, it will assigned the next index available (equal to the size before addition).\n * The method will return {@code true} in this case.\n *
\n *\n * @param o the object to add.\n *\n * @throw IllegalArgumentException if {@code o} is {@code null}.\n *\n * @return {@code true} iff the set was modified by this operation.\n */\n @Override\n public boolean add(final E o) {\n if (o == null)\n throw new IllegalArgumentException(\"the input argument cannot be null\");\n if (contains(o))\n return false;\n final int nextIndex = size();\n elements.add(o);\n indexByElement.put(o, nextIndex);\n return true;\n }\n\n /**\n * Removes an element from the set.\n *\n * \n * If the element was not present in the set, nothing happens and the method return false. However,\n * if the element is new to this set, it will be assigned the next index available (equal to the size\n * before addition).\n * The method will return {@code true} in this case.\n *
\n *\n * @param o the object to add.\n *\n * @throw IllegalArgumentException if {@code o} is {@code null}.\n *\n * @return {@code true} iff the set was modified by this operation.\n */ @Override\n public boolean remove(final Object o) {\n final int index = indexByElement.removeInt(o);\n if (index == -1)\n return false;\n elements.remove(index);\n indexByElement.remove(o);\n final ListIterator it = elements.listIterator(index);\n int nextIndex = index;\n while (it.hasNext())\n indexByElement.put(it.next(),nextIndex++);\n return true;\n }\n\n /**\n * Removes all elements in the set.\n */\n @Override\n public void clear() {\n elements.clear();\n indexByElement.clear();\n }\n\n /**\n * Compares this with another indexed set.\n * @param o the other object to compare to.\n * @return {@code false} unless {@code o} is a indexed-set that contains the same elements in the same order.\n */\n @Override\n public boolean equals(final Object o) {\n if (o == this)\n return true;\n if (o == null)\n return false;\n if (!(o instanceof IndexedSet))\n return false;\n\n final IndexedSet other = (IndexedSet)o;\n\n return equals(other);\n }\n\n /**\n * Compare to another indexed set.\n *\n * @param other the target indexed set.\n *\n * @throws java.lang.IllegalArgumentException if {@code other} is {@code null}.\n *\n * @return {@code true} iff {@other} is not {@code null}, and contains exactly the same elements\n * (as compared using {@link Object#equals} a this set with matching indices.\n */\n public boolean equals(final IndexedSet other) {\n if (other == null)\n throw new IllegalArgumentException(\"other cannot be null\");\n final ArrayList otherElements = other.elements;\n\n final int elementCount = elements.size();\n if (otherElements.size() != elementCount)\n return false;\n for (int i = 0; i < elementCount; i++)\n if (!elements.get(i).equals(otherElements.get(i)))\n return false;\n return true;\n }\n\n @Override\n public int hashCode() {\n int result = 1;\n\n for (final E element : elements)\n result = 31 * result + (element == null ? 0 : element.hashCode());\n return result;\n }\n\n /**\n * Returns the element given its index within the set.\n * @param index the target element's index.\n *\n * @throws IllegalArgumentException if {@code index} is not valid; in [0,{@link #size()}).\n *\n * @return never {@code null}; as null is not a valid element.\n */\n public E get(final int index) {\n checkIndex(index);\n return elements.get(index);\n }\n\n /**\n * Returns the index of an object.\n * @param o the object of interest.\n *\n * @throws IllegalArgumentException if {@code o} is {@code null}.\n *\n * @return {@code -1} if such an object is not an element of this set, otherwise is index in the set thus a\n * values within [0,{@link #size()}).\n */\n public int indexOf(final E o) {\n if (o == null)\n throw new IllegalArgumentException(\"the query object cannot be null\");\n return indexByElement.containsKey(o) ? indexByElement.getInt(o) : -1;\n }\n\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/IntMaxHeap.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.basic;\n\nimport java.util.Arrays;\n\n/**\n * Author: wbc\n */\npublic class IntMaxHeap {\n\n private int size;\n\n private int[] values;\n\n /**\n * Creates a new empty heap indicating its initial capacity.\n * @param initialCapacity number of elements you expect to have at most in the heap.\n *\n * @throws IllegalArgumentException if {@code initialCapacity} is negative.\n */\n public IntMaxHeap(final int initialCapacity) {\n if (initialCapacity < 0)\n throw new IllegalArgumentException();\n // We force it to have at least length 1 so that the capacity expansion works when adding;\n // it doubles current length and twice 0 = 0.\n values = new int[initialCapacity == 0 ? 1 : initialCapacity];\n }\n\n /**\n * Adds a new element to the heap.\n *\n * The heap with grow if it runs out of capacity to hold the new element
\n *\n * @param v the new element.\n */\n public void add(final int v) {\n // Double capacity if overflow:\n ensureCapacity(size + 1);\n addWithoutCheckingCapacity(v);\n }\n\n /**\n * Implements the heap addition floating up the value.\n * @param v the value to add.\n */\n private void addWithoutCheckingCapacity(final int v) {\n int p;\n values[p = size++] = v;\n\n // Float up the recently added element:\n while (p > 0) {\n final int q = (p - 1) >> 1; // parent index.\n final int u = values[q]; // parent value.\n\n //Finish check and update:\n if (u >= v)\n break;\n values[p] = u;\n values[q] = v;\n p = q;\n }\n }\n\n /**\n * Add several integers into the heap.\n * @param v values to add.\n */\n public void add(final int ... v) {\n if (v == null)\n throw new IllegalArgumentException(\"the input array cannot be null\");\n ensureCapacity(v.length + size);\n for (int i : v)\n addWithoutCheckingCapacity(i);\n }\n\n private void ensureCapacity(final int newSize) {\n if (newSize > values.length)\n values = Arrays.copyOf(values,Math.max(newSize,10 + values.length << 1));\n }\n\n /**\n * Returns the current minimum element.\n *\n * @throws IllegalStateException if the heap is empty.\n *\n * @return the minimum element in the heap.\n */\n public int peek() {\n if (size == 0)\n throw new IllegalStateException(\"the heap is empty\");\n return values[0];\n }\n\n /**\n * Returns the minimum element of the heap and removes it.\n *\n * @throws IllegalStateException if the heap is empty.\n *\n * @return the minimum element in the heap before removing it.\n */\n public int remove() {\n if (size == 0)\n throw new IllegalArgumentException(\"the heap is empty\");\n final int result = values[0];\n removeUpdate();\n return result;\n }\n\n /**\n * Updates the heap after a removal, sinking the last element from the top-down.\n */\n private void removeUpdate() {\n // if the remove make the heap to be empty there is nothing to do.\n if (--size == 0)\n return;\n\n final int v = values[size]; // the last value.\n\n int p;\n values[p = 0] = v;\n\n // limit := first index in the heap that does not have any descendants within the heap.\n final int limit = (size >> 1);\n\n // Sorry! for the big loop but doesn't seem to be any other *practical* option that would reduce its size.\n while (p < limit) {\n\n // Initialize variables:\n final int r = (p + 1) << 1; // left descendant index.\n final int l = r - 1; // right descendant index (no guarantee to be in the heap).\n int u = v; // will contain min(v,values[l],values[r]).\n int q = p; // wilL contain argmin_x(values[x], x in {p,l,r}).\n\n // Check left descendant:\n int lv = values[l]; // left descendant value.\n if (lv > u) { // is the left descendant'v value more than v.\n u = lv;\n q = l;\n }\n\n // Check right descendant:\n if (r < size) { // make sure that r is within the heap.\n int rv = values[r];\n if (rv > u) { // is the right descendant's value less than v or left's\n u = rv;\n q = r;\n }\n }\n\n // Finish check and update:\n if (p == q) // q == p if neither left or right descendants are less than v.\n break;\n\n values[p] = u;\n values[q] = v;\n p = q;\n }\n }\n\n /**\n * Checks whether the heap is empty.\n *\n * @return {@code true} iff the heap is empty.\n */\n public boolean isEmpty() {\n return size == 0;\n }\n\n /**\n * Returns the current size of the heap.\n *\n * @return 0 or greater.\n */\n public int size() {\n return size;\n }\n\n /**\n * Removes all elements from the heap.\n */\n public void clear() {\n size = 0;\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/NestedIntegerArray.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.basic;\n\nimport org.apache.log4j.Logger;\nimport org.ncic.bioinfo.sparkseq.exceptions.ReviewedGATKException;\n\nimport java.util.ArrayList;\nimport java.util.Arrays;\nimport java.util.List;\n\n/**\n * Author: wbc\n */\npublic class NestedIntegerArray {\n\n private static Logger logger = Logger.getLogger(NestedIntegerArray.class);\n\n protected final Object[] data;\n\n protected final int numDimensions;\n protected final int[] dimensions;\n\n // Preallocate the first two dimensions to limit contention during tree traversals in put()\n private static final int NUM_DIMENSIONS_TO_PREALLOCATE = 2;\n\n public NestedIntegerArray(final int... dimensions) {\n numDimensions = dimensions.length;\n if ( numDimensions == 0 )\n throw new ReviewedGATKException(\"There must be at least one dimension to an NestedIntegerArray\");\n this.dimensions = dimensions.clone();\n\n int dimensionsToPreallocate = Math.min(dimensions.length, NUM_DIMENSIONS_TO_PREALLOCATE);\n\n if ( logger.isDebugEnabled() ) logger.debug(String.format(\"Creating NestedIntegerArray with dimensions %s\", Arrays.toString(dimensions)));\n if ( logger.isDebugEnabled() ) logger.debug(String.format(\"Pre-allocating first %d dimensions\", dimensionsToPreallocate));\n\n data = new Object[dimensions[0]];\n preallocateArray(data, 0, dimensionsToPreallocate);\n\n if ( logger.isDebugEnabled() ) logger.debug(String.format(\"Done pre-allocating first %d dimensions\", dimensionsToPreallocate));\n }\n\n /**\n * @return the dimensions of this nested integer array. DO NOT MODIFY\n */\n public int[] getDimensions() {\n return dimensions;\n }\n\n /**\n * Recursively allocate the first dimensionsToPreallocate dimensions of the tree\n *\n * Pre-allocating the first few dimensions helps limit contention during tree traversals in put()\n *\n * @param subarray current node in the tree\n * @param dimension current level in the tree\n * @param dimensionsToPreallocate preallocate only this many dimensions (starting from the first)\n */\n private void preallocateArray( Object[] subarray, int dimension, int dimensionsToPreallocate ) {\n if ( dimension >= dimensionsToPreallocate - 1 ) {\n return;\n }\n\n for ( int i = 0; i < subarray.length; i++ ) {\n subarray[i] = new Object[dimensions[dimension + 1]];\n preallocateArray((Object[])subarray[i], dimension + 1, dimensionsToPreallocate);\n }\n }\n\n public T get(final int... keys) {\n final int numNestedDimensions = numDimensions - 1;\n Object[] myData = data;\n\n for( int i = 0; i < numNestedDimensions; i++ ) {\n if ( keys[i] >= dimensions[i] )\n return null;\n\n myData = (Object[])myData[keys[i]];\n if ( myData == null )\n return null;\n }\n\n return (T)myData[keys[numNestedDimensions]];\n }\n\n /**\n * Insert a value at the position specified by the given keys.\n *\n * This method is thread-safe, however the caller MUST check the\n * return value to see if the put succeeded. This method RETURNS FALSE if\n * the value could not be inserted because there already was a value present\n * at the specified location. In this case the caller should do a get() to get\n * the already-existing value and (potentially) update it.\n *\n * @param value value to insert\n * @param keys keys specifying the location of the value in the tree\n * @return true if the value was inserted, false if it could not be inserted because there was already\n * a value at the specified position\n */\n public boolean put(final T value, final int... keys) { // WARNING! value comes before the keys!\n if ( keys.length != numDimensions )\n throw new ReviewedGATKException(\"Exactly \" + numDimensions + \" keys should be passed to this NestedIntegerArray but \" + keys.length + \" were provided\");\n\n final int numNestedDimensions = numDimensions - 1;\n Object[] myData = data;\n for ( int i = 0; i < numNestedDimensions; i++ ) {\n if ( keys[i] >= dimensions[i] )\n throw new ReviewedGATKException(\"Key \" + keys[i] + \" is too large for dimension \" + i + \" (max is \" + (dimensions[i]-1) + \")\");\n\n // If we're at or beyond the last dimension that was pre-allocated, we need to do a synchronized\n // check to see if the next branch exists, and if it doesn't, create it\n if ( i >= NUM_DIMENSIONS_TO_PREALLOCATE - 1 ) {\n synchronized ( myData ) {\n if ( myData[keys[i]] == null ) {\n myData[keys[i]] = new Object[dimensions[i + 1]];\n }\n }\n }\n\n myData = (Object[])myData[keys[i]];\n }\n\n synchronized ( myData ) { // lock the bottom row while we examine and (potentially) update it\n\n // Insert the new value only if there still isn't any existing value in this position\n if ( myData[keys[numNestedDimensions]] == null ) {\n myData[keys[numNestedDimensions]] = value;\n }\n else {\n // Already have a value for this leaf (perhaps another thread came along and inserted one\n // while we traversed the tree), so return false to notify the caller that we didn't put\n // the item\n return false;\n }\n }\n\n return true;\n }\n\n public List getAllValues() {\n final List result = new ArrayList();\n fillAllValues(data, result);\n return result;\n }\n\n private void fillAllValues(final Object[] array, final List result) {\n for ( Object value : array ) {\n if ( value == null )\n continue;\n if ( value instanceof Object[] )\n fillAllValues((Object[])value, result);\n else\n result.add((T)value);\n }\n }\n\n public static class Leaf {\n public final int[] keys;\n public final T value;\n\n public Leaf(final int[] keys, final T value) {\n this.keys = keys;\n this.value = value;\n }\n }\n\n public List> getAllLeaves() {\n final List> result = new ArrayList>();\n fillAllLeaves(data, new int[0], result);\n return result;\n }\n\n private void fillAllLeaves(final Object[] array, final int[] path, final List> result) {\n for ( int key = 0; key < array.length; key++ ) {\n final Object value = array[key];\n if ( value == null )\n continue;\n final int[] newPath = appendToPath(path, key);\n if ( value instanceof Object[] ) {\n fillAllLeaves((Object[]) value, newPath, result);\n } else {\n result.add(new Leaf(newPath, (T)value));\n }\n }\n }\n\n private int[] appendToPath(final int[] path, final int newKey) {\n final int[] newPath = new int[path.length + 1];\n for ( int i = 0; i < path.length; i++ )\n newPath[i] = path[i];\n newPath[path.length] = newKey;\n return newPath;\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/Pair.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.basic;\n\n/**\n * Author: wbc\n */\npublic class Pair {\n // declare public, STL-style for easier and more efficient access:\n public X first;\n public Y second;\n\n public Pair(X x, Y y) { first = x; second = y; }\n\n public void set(X x, Y y) { first = x; second = y; }\n\n /** Java-style getter; note that we currently allow direct access to\n the member field.\n */\n public X getFirst() { return first; }\n\n /** Java-style getter; note that we currently allow direct access to\n the member field.\n */\n public Y getSecond() { return second; }\n\n /**\n * Calculate whether this pair object is equal to another object.\n * @param o The other object (hopefully a pair).\n * @return True if the two are equal; false otherwise.\n */\n @Override\n public boolean equals( Object o ) {\n if( o == null )\n return false;\n if( !(o instanceof Pair) )\n return false;\n\n Pair other = (Pair)o;\n\n // Check to see whether one is null but not the other.\n if( this.first == null && other.first != null ) return false;\n if( this.second == null && other.second != null ) return false;\n\n // Check to see whether the values are equal.\n // If the param of equals is null, it should by contract return false.\n if( this.first != null && !this.first.equals(other.first) ) return false;\n if( this.second != null && !this.second.equals(other.second) ) return false;\n\n return true;\n }\n\n /**\n * Basic hashcode function. Assume hashcodes of first and second are\n * randomly distributed and return the XOR of the two.\n * @return Randomly distributed hashcode of the pair.\n */\n @Override\n public int hashCode() {\n if( second == null && first == null )\n return 0;\n if( second == null )\n return first.hashCode();\n if( first == null )\n return second.hashCode();\n return first.hashCode() ^ second.hashCode();\n }\n\n public String toString() {\n return first+\",\"+second;\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/Permutation.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.basic;\n\nimport java.util.List;\n\n/**\n * Represent a permutation of a ordered set or list of elements.\n *\n * @author Valentin Ruano-Rubio <valentin@broadinstitute.org>\n */\npublic interface Permutation {\n\n /**\n * Checks whether this permutation is a partial one of the original list.\n *\n * \n * A partial permutation is one in that no all original elements take part of.\n *
\n *\n * @return {@code true} iff this is a partial permutation.\n */\n public boolean isPartial();\n\n /**\n * Checks whether this is a trivial permutation where the resulting element list is the same as original.\n *\n * @return {@code true} iff the resulting element list is the same as the original.\n */\n public boolean isNonPermuted();\n\n /**\n * Given an index on the original list, returns the position of tha element in the resulting list.\n *\n * @param fromIndex the query original element index.\n *\n * @throws IllegalArgumentException if {@code fromIndex} is not a valid index within the original list.\n *\n * @return -1 if that element is not part of the result (partial) permutation, otherwise some number between\n * 0 and {@link #toSize()} - 1.\n */\n public int toIndex(final int fromIndex);\n\n /**\n * Given an index on the resulting list, it gives you the index of that element on the original list.\n * @param toIndex the query resulting list index.\n *\n * @throws IllegalArgumentException if {@code toIndex} is not a valid index, i.e. in [0,{@link #toSize()}-1).\n *\n * @return a value between 0 and {@link #fromSize()} - 1.\n */\n public int fromIndex(final int toIndex);\n\n /**\n * Length of the original element list.\n *\n * @return 0 or greater.\n */\n public int fromSize();\n\n /**\n * Length of the resulting element list.\n *\n * @return 0 or greater.\n */\n public int toSize();\n\n /**\n * Returns an unmodifiable view to the original element list.\n * @return never {@code null}.\n */\n public List fromList();\n\n /**\n * Returns an unmodifiable view to the original element list.\n *\n * @return never {@code null}.\n */\n public List toList();\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/PrimitivePair.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.basic;\n\n/**\n * Author: wbc\n */\npublic class PrimitivePair {\n\n /** Pair of two integers */\n public static class Int {\n // declare public, STL-style for easier and more efficient access:\n public int first;\n public int second;\n\n public Int(int x, int y) { first = x; second = y; }\n public Int() { first = second = 0; }\n\n public void set(int x, int y) { first = x; second = y; }\n\n /** Java-style getter; note that we currently allow direct access to\n the member field.\n */\n public int getFirst() { return first; }\n\n /** Java-style getter; note that we currently allow direct access to\n the member field.\n */\n public int getSecond() { return second; }\n\n /** Increments the elements of this pair by the\n * corresponding elements of the pair p and returns this\n * pair (modified). This method does not allocate a new pair, but changes\n * in place the values stored in the object the method is invoked from. The\n * method is unsafe: if p is null, a runtime exception will be thrown.\n * @param p\n * @return\n */\n public PrimitivePair.Int add(PrimitivePair.Int p) {\n first += p.first;\n second += p.second;\n return this;\n }\n\n /** Decrements the elements of this pair by the\n * corresponding elements of the pair p and returns this\n * pair (modified). This method does not allocate a new pair, but changes\n * in place the values stored in the object the method is invoked from. The\n * method is unsafe: if p is null, a runtime exception will be thrown.\n * @param p\n * @return\n */\n public PrimitivePair.Int subtract(PrimitivePair.Int p) {\n first -= p.first;\n second -= p.second;\n return this;\n }\n\n /** Copies values from the argument p into the corresponding\n * elements of this pair and returns this pair (modified).\n * @param p\n * @return\n */\n public PrimitivePair.Int assignFrom(PrimitivePair.Int p ) {\n first = p.first;\n second = p.second;\n return this;\n }\n\n\n }\n\n public static class Long {\n // declare public, STL-style for easier and more efficient access:\n public long first;\n public long second;\n\n public Long(long x, long y) { first = x; second = y; }\n public Long() { first = second = 0; }\n\n public void set(long x, long y) { first = x; second = y; }\n\n /** Java-style getter; note that we currently allow direct access to\n the member field.\n */\n public long getFirst() { return first; }\n\n /** Java-style getter; note that we currently allow direct access to\n the member field.\n */\n public long getSecond() { return second; }\n\n /** Increments the elements of this pair by the\n * corresponding elements of the pair p and returns this\n * pair (modified). This method does not allocate a new pair, but changes\n * in place the values stored in the object the method is invoked from. The\n * method is unsafe: if p is null, a runtime exception will be thrown.\n * @param p\n * @return\n */\n public PrimitivePair.Long add(PrimitivePair.Int p) {\n first += p.first;\n second += p.second;\n return this;\n }\n\n /** Increments the elements of this pair by the\n * corresponding elements of the pair p and returns this\n * pair (modified). This method does not allocate a new pair, but changes\n * in place the values stored in the object the method is invoked from. The\n * method is unsafe: if p is null, a runtime exception will be thrown.\n * @param p\n * @return\n */\n public PrimitivePair.Long add(PrimitivePair.Long p) {\n first += p.first;\n second += p.second;\n return this;\n }\n\n /** Decrements the elements of this pair by the\n * corresponding elements of the pair p and returns this\n * pair (modified). This method does not allocate a new pair, but changes\n * in place the values stored in the object the method is invoked from. The\n * method is unsafe: if p is null, a runtime exception will be thrown.\n * @param p\n * @return\n */\n public PrimitivePair.Long subtract(PrimitivePair.Int p) {\n first -= p.first;\n second -= p.second;\n return this;\n }\n\n /** Decrements the elements of this pair by the\n * corresponding elements of the pair p and returns this\n * pair (modified). This method does not allocate a new pair, but changes\n * in place the values stored in the object the method is invoked from. The\n * method is unsafe: if p is null, a runtime exception will be thrown.\n * @param p\n * @return\n */\n public PrimitivePair.Long subtract(PrimitivePair.Long p) {\n first -= p.first;\n second -= p.second;\n return this;\n }\n\n /** Copies values from the argument p into the corresponding\n * elements of this pair and returns this pair (modified).\n * @param p\n * @return\n */\n public PrimitivePair.Long assignFrom(PrimitivePair.Long p ) {\n first = p.first;\n second = p.second;\n return this;\n }\n\n /** Copies values from the argument p into the corresponding\n * elements of this pair and returns this pair (modified).\n * @param p\n * @return\n */\n public PrimitivePair.Long assignFrom(PrimitivePair.Int p ) {\n first = p.first;\n second = p.second;\n return this;\n }\n\n }\n\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/reference/RefContentProvider.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.reference;\n\nimport htsjdk.samtools.SAMSequenceDictionary;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLoc;\nimport org.ncic.bioinfo.sparkseq.data.partition.FastaPartition;\n\n/**\n * 提供reference上的base信息，封装FastaPartition\n * \n * Author: wbc\n */\npublic class RefContentProvider {\n\n /**\n * 一个contig上的字符组\n */\n private final byte[] content;\n\n /**\n * contig的Id\n */\n private final int contigId;\n\n /**\n * contig的name\n */\n private final String contigName;\n\n /**\n * safe overalp只用于取reference的数据\n */\n private final int safeOverlappedStartCoordinate;\n private final int safeOverlappedEndCoordinate;\n\n private final int overlappedStartCoordinate;\n private final int overlappedEndCoordinate;\n\n private final int originStartCoordinate;\n private final int originEndCoordinate;\n\n private final SAMSequenceDictionary samSequenceDictionary;\n\n public RefContentProvider(SAMSequenceDictionary samSequenceDictionary,\n FastaPartition fastaPartition) {\n contigId = fastaPartition.contigId();\n contigName = fastaPartition.contigName();\n String rawContent = fastaPartition.content();\n int contentLen = rawContent.length();\n content = new byte[contentLen];\n\n // 对于ref中不是AGCTN的base，全部换成N\n for (int i = 0; i < contentLen; i++) {\n byte base = (byte) rawContent.charAt(i);\n if (base == 'A' || base == 'G' || base == 'C' || base == 'T') {\n content[i] = base;\n } else {\n content[i] = 'N';\n }\n }\n\n safeOverlappedStartCoordinate = fastaPartition.safeOverlappedStart();\n safeOverlappedEndCoordinate = fastaPartition.safeOverlappedEnd();\n\n overlappedStartCoordinate = fastaPartition.overlappedStart();\n overlappedEndCoordinate = fastaPartition.overlappedEnd();\n\n originStartCoordinate = fastaPartition.originStart();\n originEndCoordinate = fastaPartition.originEnd();\n\n this.samSequenceDictionary = samSequenceDictionary;\n }\n\n /**\n * 获取partition负责的interval，是overlapped\n *\n * @return\n */\n public GenomeLoc getLocus() {\n return new GenomeLoc(contigName, contigId, overlappedStartCoordinate, overlappedEndCoordinate);\n }\n\n /**\n * 在截取时会判断是否超出长度，所以返回的长度可能小于locus的长度\n *\n * @param locus\n * @return\n */\n public ReferenceContext getReferenceContext(GenomeLoc locus) {\n int start = locus.getStart() - safeOverlappedStartCoordinate;\n if (start < 0) {\n start = 0;\n }\n int end = locus.getStop() - safeOverlappedStartCoordinate;\n if (end >= content.length) {\n end = content.length - 1;\n }\n if(end-start+1 <=0) {\n int a = 0;\n }\n byte[] basesCache = new byte[end - start + 1];\n int idx = 0;\n for (int i = start; i <= end; i++) {\n basesCache[idx] = content[i];\n idx++;\n }\n\n GenomeLoc newLocus = new GenomeLoc(locus.getContig(), locus.getContigIndex(),\n start + safeOverlappedStartCoordinate, end + safeOverlappedStartCoordinate);\n return new ReferenceContext(newLocus, contigId, basesCache);\n }\n\n public ReferenceContext getReferenceContext(GenomeLoc locus, int overlapLength) {\n GenomeLoc newLocus = new GenomeLoc(locus.getContig(), locus.getContigIndex(),\n locus.getStart() - overlapLength, locus.getStop() + overlapLength);\n return getReferenceContext(newLocus);\n }\n\n public SAMSequenceDictionary getSamSequenceDictionary() {\n return samSequenceDictionary;\n }\n\n public int getOriginStartCoordinate() {\n return originStartCoordinate;\n }\n\n public int getOriginEndCoordinate() {\n return originEndCoordinate;\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/reference/RefMetaDataTracker.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.reference;\n\nimport htsjdk.tribble.Feature;\nimport org.apache.log4j.Logger;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLoc;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.GATKFeature;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.RODRecordList;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.RODRecordListImpl;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.vcf.RodBinding;\nimport org.ncic.bioinfo.sparkseq.exceptions.UserException;\n\nimport java.util.ArrayList;\nimport java.util.Arrays;\nimport java.util.Collection;\nimport java.util.Collections;\nimport java.util.HashMap;\nimport java.util.List;\nimport java.util.Map;\n\n/**\n * Author: wbc\n */\npublic class RefMetaDataTracker {\n private final static RODRecordList EMPTY_ROD_RECORD_LIST = new RODRecordListImpl(\"EMPTY\");\n\n final Map bindings;\n final protected static Logger logger = Logger.getLogger(RefMetaDataTracker.class);\n public final static RefMetaDataTracker EMPTY_TRACKER = new RefMetaDataTracker();\n\n /**\n * Create an tracker with no bindings\n */\n public RefMetaDataTracker() {\n bindings = Collections.emptyMap();\n }\n\n public RefMetaDataTracker(final Collection allBindings) {\n // set up the bindings\n if (allBindings.isEmpty())\n bindings = Collections.emptyMap();\n else {\n final Map tmap = new HashMap(allBindings.size());\n for (RODRecordList rod : allBindings) {\n if (rod != null && !rod.isEmpty())\n tmap.put(canonicalName(rod.getName()), rod);\n }\n\n // ensure that no one modifies the bindings itself\n bindings = Collections.unmodifiableMap(tmap);\n }\n }\n\n\n // ------------------------------------------------------------------------------------------\n //\n //\n // Generic accessors\n //\n //\n // ------------------------------------------------------------------------------------------\n\n /**\n * Gets all of the Tribble features spanning this locus, returning them as a list of specific\n * type T extending Feature. This function looks across all tracks to find the Features, so\n * if you have two tracks A and B each containing 1 Feature, then getValues will return\n * a list containing both features.\n * \n * Note that this function assumes that all of the bound features are instances of or\n * subclasses of T. A ClassCastException will occur if this isn't the case. If you want\n * to get all Features without any danger of such an exception use the root Tribble\n * interface Feature.\n *\n * @param type The type of the underlying objects bound here\n * @param as above\n * @return A freshly allocated list of all of the bindings, or an empty list if none are bound.\n */\n public List getValues(final Class type) {\n return addValues(bindings.keySet(), type, new ArrayList(), null, false, false);\n }\n\n /**\n * Provides the same functionality as @link #getValues(Class) but will only include\n * Features that start as the GenomeLoc provide onlyAtThisLoc.\n *\n * @param type The type of the underlying objects bound here\n * @param onlyAtThisLoc\n * @param as above\n * @return A freshly allocated list of all of the bindings, or an empty list if none are bound.\n */\n public List getValues(final Class type, final GenomeLoc onlyAtThisLoc) {\n return addValues(bindings.keySet(), type, new ArrayList(), onlyAtThisLoc, true, false);\n }\n\n /**\n * Uses the same logic as @link #getValues(Class) but arbitrary select one of the resulting\n * elements of the list to return. That is, if there would be two elements in the result of\n *\n * @param type The type of the underlying objects bound here\n * @param as above\n * @return A random single element the RODs bound here, or null if none are bound.\n * @link #getValues(Class), one of these two is selected, and which one it will be isn't\n * specified. Consequently, this method is only really safe if (1) you absolutely know\n * that only one binding will meet the constraints of @link #getValues(Class) or (2)\n * you truly don't care which of the multiple bindings available you are going to examine.\n * \n * If there are no bindings here, getFirstValue() return null\n */\n public T getFirstValue(final Class type) {\n return safeGetFirst(getValues(type));\n }\n\n /**\n * Uses the same logic as @link #getValue(Class,GenomeLoc) to determine the list\n * of eligible Features and @link #getFirstValue(Class) to select a single\n * element from the interval list.\n *\n * @param type The type of the underlying objects bound here\n * @param as above\n * @param onlyAtThisLoc only Features starting at this site are considered\n * @return A random single element the RODs bound here starting at onlyAtThisLoc, or null if none are bound.\n */\n public T getFirstValue(final Class type, final GenomeLoc onlyAtThisLoc) {\n return safeGetFirst(getValues(type, onlyAtThisLoc));\n }\n\n /**\n * Same logic as @link #getFirstValue(RodBinding, boolean) but prioritizes records from prioritizeThisLoc if available\n *\n * @param rodBindings Only Features coming from the tracks associated with one of rodBindings are fetched\n * @param The Tribble Feature type of the rodBinding, and consequently the type of the resulting list of Features\n * @param prioritizeThisLoc only Features starting at this site are considered\n * @return A freshly allocated list of all of the bindings, or an empty list if none are bound.\n */\n public List getPrioritizedValue(final Collection> rodBindings, final GenomeLoc prioritizeThisLoc) {\n final List results = new ArrayList<>();\n\n for (final RodBinding rodBinding : rodBindings) {\n\n // if there's a value at the prioritized location, take it\n T value = getFirstValue(rodBinding, prioritizeThisLoc);\n\n // otherwise, grab any one\n if (value == null)\n value = getFirstValue(rodBinding);\n\n // add if not null\n if (value != null)\n results.add(value);\n }\n\n return results;\n }\n\n /**\n * Gets all of the Tribble features bound to RodBinding spanning this locus, returning them as\n * a list of specific type T extending Feature.\n * \n * Note that this function assumes that all of the bound features are instances of or\n * subclasses of T. A ClassCastException will occur if this isn't the case.\n *\n * @param rodBinding Only Features coming from the track associated with this rodBinding are fetched\n * @param The Tribble Feature type of the rodBinding, and consequently the type of the resulting list of Features\n * @return A freshly allocated list of all of the bindings, or an empty list if none are bound.\n */\n public List getValues(final RodBinding rodBinding) {\n return addValues(rodBinding.getName(), rodBinding.getType(), new ArrayList(1), getTrackDataByName(rodBinding), null, false, false);\n }\n\n /**\n * Gets all of the Tribble features bound to any RodBinding in rodBindings,\n * spanning this locus, returning them as a list of specific type T extending Feature.\n * \n * Note that this function assumes that all of the bound features are instances of or\n * subclasses of T. A ClassCastException will occur if this isn't the case.\n *\n * @param rodBindings Only Features coming from the tracks associated with one of rodBindings are fetched\n * @param The Tribble Feature type of the rodBinding, and consequently the type of the resulting list of Features\n * @return A freshly allocated list of all of the bindings, or an empty list if none are bound.\n */\n public List getValues(final Collection> rodBindings) {\n List results = new ArrayList(1);\n for (RodBinding rodBinding : rodBindings)\n results.addAll(getValues(rodBinding));\n return results;\n }\n\n public List getValues(String name) {\n List results = new ArrayList(1);\n RODRecordList recordList = bindings.get(name);\n if (recordList != null) {\n for (GATKFeature feature : recordList)\n results.add((T) feature);\n }\n return results;\n }\n\n public List getAllValues() {\n List results = new ArrayList(1);\n for (RODRecordList recordList : bindings.values()) {\n if (recordList != null) {\n for (GATKFeature feature : recordList)\n results.add((T) feature);\n }\n }\n return results;\n }\n\n /**\n * The same logic as @link #getValues(RodBinding) but enforces that each Feature start at onlyAtThisLoc\n *\n * @param rodBinding Only Features coming from the track associated with this rodBinding are fetched\n * @param The Tribble Feature type of the rodBinding, and consequently the type of the resulting list of Features\n * @param onlyAtThisLoc only Features starting at this site are considered\n * @return A freshly allocated list of all of the bindings, or an empty list if none are bound.\n */\n public List getValues(final RodBinding rodBinding, final GenomeLoc onlyAtThisLoc) {\n return addValues(rodBinding.getName(), rodBinding.getType(), new ArrayList(1), getTrackDataByName(rodBinding), onlyAtThisLoc, true, false);\n }\n\n /**\n * The same logic as @link #getValues(List) but enforces that each Feature start at onlyAtThisLoc\n *\n * @param rodBindings Only Features coming from the tracks associated with one of rodBindings are fetched\n * @param The Tribble Feature type of the rodBinding, and consequently the type of the resulting list of Features\n * @param onlyAtThisLoc only Features starting at this site are considered\n * @return A freshly allocated list of all of the bindings, or an empty list if none are bound.\n */\n public List getValues(final Collection> rodBindings, final GenomeLoc onlyAtThisLoc) {\n List results = new ArrayList(1);\n for (RodBinding rodBinding : rodBindings)\n results.addAll(getValues(rodBinding, onlyAtThisLoc));\n return results;\n }\n\n /**\n * Uses the same logic as @getValues(RodBinding) to determine the list\n * of eligible Features and select a single element from the resulting set\n * of eligible features.\n *\n * @param rodBinding Only Features coming from the track associated with this rodBinding are fetched\n * @param as above\n * @return A random single element the eligible Features found, or null if none are bound.\n */\n public T getFirstValue(final RodBinding rodBinding) {\n return safeGetFirst(addValues(rodBinding.getName(), rodBinding.getType(), null, getTrackDataByName(rodBinding), null, false, true));\n }\n\n /**\n * Uses the same logic as @getValues(RodBinding, GenomeLoc) to determine the list\n * of eligible Features and select a single element from the resulting set\n * of eligible features.\n *\n * @param rodBinding Only Features coming from the track associated with this rodBinding are fetched\n * @param as above\n * @param onlyAtThisLoc only Features starting at this site are considered\n * @return A random single element the eligible Features found, or null if none are bound.\n */\n public T getFirstValue(final RodBinding rodBinding, final GenomeLoc onlyAtThisLoc) {\n return safeGetFirst(addValues(rodBinding.getName(), rodBinding.getType(), null, getTrackDataByName(rodBinding), onlyAtThisLoc, true, true));\n }\n\n /**\n * Uses the same logic as @getValues(List) to determine the list\n * of eligible Features and select a single element from the resulting set\n * of eligible features.\n *\n * @param rodBindings Only Features coming from the tracks associated with these rodBindings are fetched\n * @param as above\n * @return A random single element the eligible Features found, or null if none are bound.\n */\n public T getFirstValue(final Collection> rodBindings) {\n for (RodBinding rodBinding : rodBindings) {\n T val = getFirstValue(rodBinding);\n if (val != null)\n return val;\n }\n return null;\n }\n\n /**\n * Uses the same logic as @getValues(RodBinding,GenomeLoc) to determine the list\n * of eligible Features and select a single element from the resulting set\n * of eligible features.\n *\n * @param rodBindings Only Features coming from the tracks associated with these rodBindings are fetched\n * @param as above\n * @param onlyAtThisLoc only Features starting at this site are considered\n * @return A random single element the eligible Features found, or null if none are bound.\n */\n public T getFirstValue(final Collection> rodBindings, final GenomeLoc onlyAtThisLoc) {\n for (RodBinding rodBinding : rodBindings) {\n T val = getFirstValue(rodBinding, onlyAtThisLoc);\n if (val != null)\n return val;\n }\n return null;\n }\n\n /**\n * Is there a binding at this site to a ROD/track with the specified name?\n *\n * @param rodBinding the rod binding we want to know about\n * @return true if any Features are bound in this tracker to rodBinding\n */\n public boolean hasValues(final RodBinding rodBinding) {\n return bindings.containsKey(canonicalName(rodBinding.getName()));\n }\n\n /**\n * Get all of the RMD tracks at the current site. Each track is returned as a single compound\n * object (RODRecordList) that may contain multiple RMD records associated with the current site.\n *\n * @return List of all tracks\n */\n public List getBoundRodTracks() {\n return new ArrayList(bindings.values());\n }\n\n /**\n * The number of tracks with at least one value bound here\n *\n * @return the number of tracks with at least one bound Feature\n */\n public int getNTracksWithBoundFeatures() {\n return bindings.size();\n }\n\n // ------------------------------------------------------------------------------------------\n // Protected accessors using strings for unit testing\n // ------------------------------------------------------------------------------------------\n\n protected boolean hasValues(final String name) {\n return bindings.containsKey(canonicalName(name));\n }\n\n protected List getValues(final Class type, final String name) {\n return addValues(name, type, new ArrayList(), getTrackDataByName(name), null, false, false);\n }\n\n protected List getValues(final Class type, final String name, final GenomeLoc onlyAtThisLoc) {\n return addValues(name, type, new ArrayList(), getTrackDataByName(name), onlyAtThisLoc, true, false);\n }\n\n protected T getFirstValue(final Class type, final String name) {\n return safeGetFirst(getValues(type, name));\n }\n\n protected T getFirstValue(final Class type, final String name, final GenomeLoc onlyAtThisLoc) {\n return safeGetFirst(getValues(type, name, onlyAtThisLoc));\n }\n\n // ------------------------------------------------------------------------------------------\n //\n //\n // Private utility functions\n //\n //\n // ------------------------------------------------------------------------------------------\n\n /**\n * Helper function for getFirst() operations that takes a list of and\n * returns the first element, or null if no such element exists.\n *\n * @param l\n * @param \n * @return\n */\n private T safeGetFirst(final List l) {\n return l.isEmpty() ? null : l.get(0);\n }\n\n private List addValues(final Collection names,\n final Class type,\n List values,\n final GenomeLoc curLocation,\n final boolean requireStartHere,\n final boolean takeFirstOnly) {\n for (String name : names) {\n RODRecordList rodList = getTrackDataByName(name); // require that the name is an exact match\n values = addValues(name, type, values, rodList, curLocation, requireStartHere, takeFirstOnly);\n if (takeFirstOnly && !values.isEmpty())\n break;\n }\n\n return values;\n }\n\n\n private List addValues(final String name,\n final Class type,\n List values,\n final RODRecordList rodList,\n final GenomeLoc curLocation,\n final boolean requireStartHere,\n final boolean takeFirstOnly) {\n for (GATKFeature rec : rodList) {\n if (!requireStartHere || rec.getLocation().getStart() == curLocation.getStart()) { // ok, we are going to keep this thing\n Object obj = rec.getUnderlyingObject();\n if (!(type.isAssignableFrom(obj.getClass())))\n throw new UserException.CommandLineException(\"Unable to cast track named \" + name + \" to type of \" + type.toString()\n + \" it's of type \" + obj.getClass());\n\n T objT = (T) obj;\n if (takeFirstOnly) {\n if (values == null)\n values = Arrays.asList(objT);\n else\n values.add(objT);\n\n break;\n } else {\n if (values == null)\n values = new ArrayList();\n values.add(objT);\n }\n }\n }\n\n return values == null ? Collections.emptyList() : values;\n }\n\n /**\n * Finds the reference metadata track named 'name' and returns all ROD records from that track associated\n * with the current site as a RODRecordList List object. If no data track with specified name is available,\n * returns defaultValue wrapped as RODRecordList object. NOTE: if defaultValue is null, it will be wrapped up\n * with track name set to 'name' and location set to null; otherwise the wrapper object will have name and\n * location set to defaultValue.getID() and defaultValue.getLocation(), respectively (use caution,\n * defaultValue.getLocation() may be not equal to what RODRecordList's location would be expected to be otherwise:\n * for instance, on locus traversal, location is usually expected to be a single base we are currently looking at,\n * regardless of the presence of \"extended\" RODs overlapping with that location).\n *\n * @param name track name\n * @return track data for the given rod\n */\n private RODRecordList getTrackDataByName(final String name) {\n final String luName = canonicalName(name);\n RODRecordList l = bindings.get(luName);\n return l == null ? EMPTY_ROD_RECORD_LIST : l;\n }\n\n private RODRecordList getTrackDataByName(final RodBinding binding) {\n return getTrackDataByName(binding.getName());\n }\n\n /**\n * Returns the canonical name of the rod name (lowercases it)\n *\n * @param name the name of the rod\n * @return canonical name of the rod\n */\n private String canonicalName(final String name) {\n // todo -- remove me after switch to RodBinding syntax\n return name.toLowerCase();\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/reference/ReferenceContext.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.reference;\n\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLoc;\n\n/**\n * Author: wbc\n */\npublic class ReferenceContext {\n\n final int contigId;\n final private GenomeLoc locus;\n final private byte[] bases;\n\n /**\n * The window of reference information around the current locus.\n */\n final private GenomeLoc window;\n\n public ReferenceContext(GenomeLoc locus, int contigId, byte[] bases) {\n this.locus = locus;\n this.window = locus;\n this.contigId = contigId;\n this.bases = bases;\n }\n\n public ReferenceContext(GenomeLoc locus, GenomeLoc window, int contigId, byte[] bases) {\n this.locus = locus;\n this.window = window;\n this.contigId = contigId;\n this.bases = bases;\n }\n\n /**\n * Contig id of this reference\n *\n * @return contig id\n */\n public int getContigId() {\n return contigId;\n }\n\n /**\n * The locus currently being examined.\n *\n * @return The current locus.\n */\n public GenomeLoc getLocus() {\n return locus;\n }\n\n public GenomeLoc getWindow() {\n return window;\n }\n\n /**\n * Get the base at the given locus.\n *\n * @return The base at the given locus from the reference.\n */\n public byte getBase() {\n return bases[0];\n }\n\n /**\n * All the bases in the window currently being examined.\n *\n * @return All bases available. If the window is of size [0,0], the array will\n * contain only the base at the given locus.\n */\n public byte[] getBases() {\n return bases;\n }\n\n public byte[] getForwardBases() {\n final byte[] bases = getBases();\n final int mid = locus.getStart() - window.getStart();\n // todo -- warning of performance problem, especially if this is called over and over\n return new String(bases).substring(mid).getBytes();\n }\n\n}\n\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/AlignmentContext.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.sam;\n\nimport org.ncic.bioinfo.sparkseq.exceptions.ReviewedGATKException;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLoc;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.HasGenomeLocation;\n\n/**\n * Useful class for forwarding on locusContext data from this iterator\n * Author: wbc\n */\npublic class AlignmentContext implements HasGenomeLocation {\n protected GenomeLoc loc = null;\n protected ReadBackedPileup basePileup = null;\n protected boolean hasPileupBeenDownsampled;\n\n /**\n * The number of bases we've skipped over in the reference since the last map invocation.\n * Only filled in by RodTraversals right now. By default, nothing is being skipped, so skippedBases == 0.\n */\n private long skippedBases = 0;\n\n public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup) {\n this(loc, basePileup, 0, false);\n }\n\n public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup, long skippedBases, boolean hasPileupBeenDownsampled) {\n if (loc == null)\n throw new ReviewedGATKException(\"BUG: GenomeLoc in Alignment context is null\");\n if (basePileup == null)\n throw new ReviewedGATKException(\"BUG: ReadBackedPileup in Alignment context is null\");\n if (skippedBases < 0)\n throw new ReviewedGATKException(\"BUG: skippedBases is -1 in Alignment context\");\n\n this.loc = loc;\n this.basePileup = basePileup;\n this.skippedBases = skippedBases;\n this.hasPileupBeenDownsampled = hasPileupBeenDownsampled;\n }\n\n /**\n * Returns base pileup over the current genomic location. May return null if this context keeps only\n * extended event (indel) pileup.\n *\n * @return\n */\n public ReadBackedPileup getBasePileup() {\n return basePileup;\n }\n\n /**\n * Returns true if any reads have been filtered out of the pileup due to excess DoC.\n *\n * @return True if reads have been filtered out. False otherwise.\n */\n public boolean hasPileupBeenDownsampled() {\n return hasPileupBeenDownsampled;\n }\n\n /**\n * How many reads cover this locus?\n *\n * @return\n */\n public int size() {\n return basePileup.getNumberOfElements();\n }\n\n public String getContig() {\n return getLocation().getContig();\n }\n\n public long getPosition() {\n return getLocation().getStart();\n }\n\n public GenomeLoc getLocation() {\n return loc;\n }\n\n}"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/AlignmentStateMachine.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.sam;\n\nimport htsjdk.samtools.Cigar;\nimport htsjdk.samtools.CigarElement;\nimport htsjdk.samtools.CigarOperator;\nimport org.ncic.bioinfo.sparkseq.exceptions.UserException;\n\n/**\n * Steps a single read along its alignment to the genome\n *\n * The logical model for generating extended events is as follows: the \"record state\"\n * implements the traversal along the reference; thus stepForwardOnGenome() returns\n * on every and only on actual reference bases. This can be a (mis)match or a deletion\n * (in the latter case, we still return on every individual reference base the deletion spans).\n *\n * User: depristo\n * Date: 1/5/13\n * Time: 1:08 PM\n */\npublic class AlignmentStateMachine {\n /**\n * Our read\n */\n private final GATKSAMRecord read;\n private final Cigar cigar;\n private final int nCigarElements;\n private int currentCigarElementOffset = -1;\n\n /**\n * how far are we offset from the start of the read bases?\n */\n private int readOffset;\n\n /**\n * how far are we offset from the alignment start on the genome?\n */\n private int genomeOffset;\n\n /**\n * Our cigar element\n */\n private CigarElement currentElement;\n\n /**\n * how far are we into our cigarElement?\n */\n private int offsetIntoCurrentCigarElement;\n\n public AlignmentStateMachine(final GATKSAMRecord read) {\n this.read = read;\n this.cigar = read.getCigar();\n this.nCigarElements = cigar.numCigarElements();\n initializeAsLeftEdge();\n }\n\n /**\n * Initialize the state variables to put this machine one bp before the\n * start of the alignment, so that a call to stepForwardOnGenome() will advance\n * us to the first proper location\n */\n private void initializeAsLeftEdge() {\n readOffset = offsetIntoCurrentCigarElement = genomeOffset = -1;\n currentElement = null;\n }\n\n /**\n * Get the read we are aligning to the genome\n * @return a non-null GATKSAMRecord\n */\n public GATKSAMRecord getRead() {\n return read;\n }\n\n /**\n * Get the reference index of the underlying read\n *\n * @return the reference index of the read\n */\n public int getReferenceIndex() {\n return getRead().getReferenceIndex();\n }\n\n /**\n * Is this the left edge state? I.e., one that is before or after the current read?\n * @return true if this state is an edge state, false otherwise\n */\n public boolean isLeftEdge() {\n return readOffset == -1;\n }\n\n /**\n * Are we on the right edge? I.e., is the current state off the right of the alignment?\n * @return true if off the right edge, false if otherwise\n */\n public boolean isRightEdge() {\n return readOffset == read.getReadLength();\n }\n\n /**\n * What is our current offset in the read's bases that aligns us with the reference genome?\n *\n * @return the current read offset position. If an edge will be == -1\n */\n public int getReadOffset() {\n return readOffset;\n }\n\n\n /**\n * Get the cigar element we're currently aligning with.\n *\n * For example, if the cigar string is 2M2D2M and we're in the second step of the\n * first 2M, then this function returns the element 2M. After calling stepForwardOnGenome\n * this function would return 2D.\n *\n * @return the cigar element, or null if we're the left edge\n */\n public CigarElement getCurrentCigarElement() {\n return currentElement;\n }\n\n /**\n * Get the offset of the current cigar element among all cigar elements in the read\n *\n * Suppose our read's cigar is 1M2D3M, and we're at the first 1M. This would\n * return 0. Stepping forward puts us in the 2D, so our offset is 1. Another\n * step forward would result in a 1 again (we're in the second position of the 2D).\n * Finally, one more step forward brings us to 2 (for the 3M element)\n *\n * @return the offset of the current cigar element in the reads's cigar. Will return -1 for\n * when the state is on the left edge, and be == the number of cigar elements in the\n * read when we're past the last position on the genome\n */\n public int getCurrentCigarElementOffset() {\n return currentCigarElementOffset;\n }\n\n /**\n * Get the offset of the current state into the current cigar element\n *\n * That is, suppose we have a read with cigar 2M3D4M, and we're right at\n * the second M position. offsetIntoCurrentCigarElement would be 1, as\n * it's two elements into the 2M cigar. Now stepping forward we'd be\n * in cigar element 3D, and our offsetIntoCurrentCigarElement would be 0.\n *\n * @return the offset (from 0) of the current state in the current cigar element.\n * Will be 0 on the right edge, and -1 on the left.\n */\n public int getOffsetIntoCurrentCigarElement() {\n return offsetIntoCurrentCigarElement;\n }\n\n /**\n * Convenience accessor of the CigarOperator of the current cigar element\n *\n * Robust to the case where we're on the edge, and currentElement is null, in which\n * case this function returns null as well\n *\n * @return null if this is an edge state\n */\n public CigarOperator getCigarOperator() {\n return currentElement == null ? null : currentElement.getOperator();\n }\n\n @Override\n public String toString() {\n return String.format(\"%s ro=%d go=%d cec=%d %s\", read.getReadName(), readOffset, genomeOffset, offsetIntoCurrentCigarElement, currentElement);\n }\n\n // -----------------------------------------------------------------------------------------------\n //\n // Code for setting up prev / next states\n //\n // -----------------------------------------------------------------------------------------------\n\n /**\n * Step the state machine forward one unit\n *\n * Takes the current state of this machine, and advances the state until the next on-genome\n * cigar element (M, X, =, D) is encountered, at which point this function returns with the\n * cigar operator of the current element.\n *\n * Assumes that the AlignmentStateMachine is in the left edge state at the start, so that\n * stepForwardOnGenome() can be called to move the machine to the first alignment position. That\n * is, the normal use of this code is:\n *\n * AlignmentStateMachine machine = new AlignmentStateMachine(read)\n * machine.stepForwardOnGenome()\n * // now the machine is at the first position on the genome\n *\n * When stepForwardOnGenome() advances off the right edge of the read, the state machine is\n * left in a state such that isRightEdge() returns true and returns null, indicating the\n * the machine cannot advance further. The machine may explode, though this is not contracted,\n * if stepForwardOnGenome() is called after a previous call returned null.\n *\n * @return the operator of the cigar element that machine stopped at, null if we advanced off the end of the read\n */\n public CigarOperator stepForwardOnGenome() {\n // loop until we either find a cigar element step that moves us one base on the genome, or we run\n // out of cigar elements\n while ( true ) {\n // we enter this method with readOffset = index of the last processed base on the read\n // (-1 if we did not process a single base yet); this can be last matching base,\n // or last base of an insertion\n if (currentElement == null || (offsetIntoCurrentCigarElement + 1) >= currentElement.getLength()) {\n currentCigarElementOffset++;\n if (currentCigarElementOffset < nCigarElements) {\n currentElement = cigar.getCigarElement(currentCigarElementOffset);\n offsetIntoCurrentCigarElement = -1;\n // next line: guards against cigar elements of length 0; when new cigar element is retrieved,\n // we reenter in order to re-check offsetIntoCurrentCigarElement against currentElement's length\n continue;\n } else {\n if (currentElement != null && currentElement.getOperator() == CigarOperator.D)\n throw new UserException(read + \"read ends with deletion. Cigar: \" + read.getCigarString() + \". Although the SAM spec technically permits such reads, this is often indicative of malformed files. If you are sure you want to use this file, re-run your analysis with the extra option: -rf BadCigar\");\n\n // we're done, so set the offset of the cigar to 0 for cleanliness, as well as the current element\n offsetIntoCurrentCigarElement = 0;\n readOffset = read.getReadLength();\n currentElement = null;\n\n // Reads that contain indels model the genomeOffset as the following base in the reference. Because\n // we fall into this else block only when indels end the read, increment genomeOffset such that the\n // current offset of this read is the next ref base after the end of the indel. This position will\n // model a point on the reference somewhere after the end of the read.\n genomeOffset++; // extended events need that. Logically, it's legal to advance the genomic offset here:\n\n // we do step forward on the ref, and by returning null we also indicate that we are past the read end.\n return null;\n }\n }\n\n offsetIntoCurrentCigarElement++;\n boolean done = false;\n switch (currentElement.getOperator()) {\n case H: // ignore hard clips\n case P: // ignore pads\n offsetIntoCurrentCigarElement = currentElement.getLength();\n break;\n case I: // insertion w.r.t. the reference\n case S: // soft clip\n offsetIntoCurrentCigarElement = currentElement.getLength();\n readOffset += currentElement.getLength();\n break;\n case D: // deletion w.r.t. the reference\n if (readOffset < 0) // we don't want reads starting with deletion, this is a malformed cigar string\n throw new UserException(read + \"read starts with deletion. Cigar: \" + read.getCigarString() + \". Although the SAM spec technically permits such reads, this is often indicative of malformed files. If you are sure you want to use this file, re-run your analysis with the extra option: -rf BadCigar\");\n // should be the same as N case\n genomeOffset++;\n done = true;\n break;\n case N: // reference skip (looks and gets processed just like a \"deletion\", just different logical meaning)\n genomeOffset++;\n done = true;\n break;\n case M:\n case EQ:\n case X:\n readOffset++;\n genomeOffset++;\n done = true;\n break;\n default:\n throw new IllegalStateException(\"Case statement didn't deal with cigar op: \" + currentElement.getOperator());\n }\n\n if ( done )\n return currentElement.getOperator();\n }\n }\n\n /**\n * Create a new PileupElement based on the current state of this element\n *\n * Must not be a left or right edge\n *\n * @return a pileup element\n */\n public final PileupElement makePileupElement() {\n if ( isLeftEdge() || isRightEdge() )\n throw new IllegalStateException(\"Cannot make a pileup element from an edge alignment state\");\n return new PileupElement(read,\n getReadOffset(),\n getCurrentCigarElement(),\n getCurrentCigarElementOffset(),\n getOffsetIntoCurrentCigarElement());\n }\n}\n\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/GATKSAMReadGroupRecord.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.sam;\n\nimport htsjdk.samtools.SAMReadGroupRecord;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.NGSPlatform;\n\n/**\n * Author: wbc\n */\npublic class GATKSAMReadGroupRecord extends SAMReadGroupRecord {\n // the SAMReadGroupRecord data we're caching\n private String mSample = null;\n private String mPlatform = null;\n private NGSPlatform mNGSPlatform = null;\n\n // because some values can be null, we don't want to duplicate effort\n private boolean retrievedSample = false;\n private boolean retrievedPlatform = false;\n private boolean retrievedNGSPlatform = false;\n\n public GATKSAMReadGroupRecord(final String id) {\n super(id);\n }\n\n public GATKSAMReadGroupRecord(SAMReadGroupRecord record) {\n super(record.getReadGroupId(), record);\n }\n\n /**\n * Get the NGSPlatform enum telling us the platform of this read group\n * \n * This function call is caching, so subsequent calls to it are free, while\n * the first time it's called there's a bit of work to resolve the enum\n *\n * @return an NGSPlatform enum value\n */\n public NGSPlatform getNGSPlatform() {\n if (!retrievedNGSPlatform) {\n mNGSPlatform = NGSPlatform.fromReadGroupPL(getPlatform());\n retrievedNGSPlatform = true;\n }\n\n return mNGSPlatform;\n }\n\n @Override\n public String toString() {\n return \"GATKSAMReadGroupRecord @RG:\" + getReadGroupId();\n }\n\n ///////////////////////////////////////////////////////////////////////////////\n // *** The following methods are overloaded to cache the appropriate data ***//\n ///////////////////////////////////////////////////////////////////////////////\n\n @Override\n public String getSample() {\n if (!retrievedSample) {\n mSample = super.getSample();\n retrievedSample = true;\n }\n return mSample;\n }\n\n @Override\n public void setSample(String s) {\n super.setSample(s);\n mSample = s;\n retrievedSample = true;\n }\n\n @Override\n public String getPlatform() {\n if (!retrievedPlatform) {\n mPlatform = super.getPlatform();\n retrievedPlatform = true;\n }\n return mPlatform;\n }\n\n @Override\n public void setPlatform(String s) {\n super.setPlatform(s);\n mPlatform = s;\n retrievedPlatform = true;\n retrievedNGSPlatform = false; // recalculate the NGSPlatform\n }\n\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/GATKSAMRecord.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.sam;\n\nimport htsjdk.samtools.CigarElement;\nimport htsjdk.samtools.CigarOperator;\nimport htsjdk.samtools.SAMFileHeader;\nimport htsjdk.samtools.SAMReadGroupRecord;\nimport htsjdk.samtools.SAMRecord;\nimport htsjdk.samtools.SAMUtils;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.ReadUtils;\nimport org.ncic.bioinfo.sparkseq.exceptions.ReviewedGATKException;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.EventType;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.NGSPlatform;\n\nimport java.util.Arrays;\nimport java.util.HashMap;\nimport java.util.List;\nimport java.util.Map;\n\n/**\n * Author: wbc\n */\npublic class GATKSAMRecord extends SAMRecord implements Cloneable{\n\n // Base Quality Score Recalibrator specific attribute tags\n public static final String BQSR_BASE_INSERTION_QUALITIES = \"BI\"; // base qualities for insertions\n public static final String BQSR_BASE_DELETION_QUALITIES = \"BD\"; // base qualities for deletions\n\n /**\n * The default quality score for an insertion or deletion, if\n * none are provided for this read.\n */\n public static final byte DEFAULT_INSERTION_DELETION_QUAL = (byte)45;\n\n // the SAMRecord data we're caching\n private String mReadString = null;\n private GATKSAMReadGroupRecord mReadGroup = null;\n private final static int UNINITIALIZED = -1;\n private int softStart = UNINITIALIZED;\n private int softEnd = UNINITIALIZED;\n private Integer adapterBoundary = null;\n\n private boolean isStrandlessRead = false;\n\n // because some values can be null, we don't want to duplicate effort\n private boolean retrievedReadGroup = false;\n\n // These temporary attributes were added here to make life easier for\n // certain algorithms by providing a way to label or attach arbitrary data to\n // individual GATKSAMRecords.\n // These attributes exist in memory only, and are never written to disk.\n private Map temporaryAttributes;\n\n // from old BamRecord\n private short mReadNameLength;\n private int mCigarLength;\n private int mReadLength;\n private byte[] mRestOfBinaryData = null;\n\n /**\n * HACK TO CREATE GATKSAMRECORD WITH ONLY A HEADER FOR TESTING PURPOSES ONLY\n * @param header\n */\n public GATKSAMRecord(final SAMFileHeader header) {\n this(new SAMRecord(header));\n }\n\n /**\n * HACK TO CREATE GATKSAMRECORD BASED ONLY A SAMRECORD FOR TESTING PURPOSES ONLY\n * @param read\n */\n public GATKSAMRecord(final SAMRecord read) {\n super(read.getHeader());\n setReferenceIndex(read.getReferenceIndex());\n setAlignmentStart(read.getAlignmentStart());\n mReadNameLength = (short)read.getReadNameLength();\n setMappingQuality(read.getMappingQuality());\n mCigarLength = read.getCigarLength();\n setFlags(read.getFlags());\n mReadLength = read.getReadLength();\n setMateReferenceIndex(read.getMateReferenceIndex());\n setMateAlignmentStart(read.getMateAlignmentStart());\n setInferredInsertSize(read.getInferredInsertSize());\n mRestOfBinaryData = null;\n\n super.setReadName(read.getReadName());\n super.setCigarString(read.getCigarString());\n super.setReadBases(read.getReadBases());\n super.setBaseQualities(read.getBaseQualities());\n\n SAMReadGroupRecord samRG = read.getReadGroup();\n clearAttributes();\n if (samRG != null) {\n GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);\n setReadGroup(rg);\n }\n List attributes = read.getAttributes();\n for(SAMTagAndValue tagAndValue : attributes) {\n setAttribute(tagAndValue.tag, tagAndValue.value);\n }\n }\n\n public GATKSAMRecord(final SAMFileHeader header,\n final int referenceSequenceIndex,\n final int alignmentStart,\n final short readNameLength,\n final short mappingQuality,\n final int indexingBin, //暂时没法用到，因为访问权限问题。不写也没啥关系\n final int cigarLen,\n final int flags,\n final int readLen,\n final int mateReferenceSequenceIndex,\n final int mateAlignmentStart,\n final int insertSize,\n final byte[] variableLengthBlock) {\n\n super(header);\n setReferenceIndex(referenceSequenceIndex);\n setAlignmentStart(alignmentStart);\n mReadNameLength = readNameLength;\n setMappingQuality(mappingQuality);\n mCigarLength = cigarLen;\n setFlags(flags);\n mReadLength = readLen;\n setMateReferenceIndex(mateReferenceSequenceIndex);\n setMateAlignmentStart(mateAlignmentStart);\n setInferredInsertSize(insertSize);\n mRestOfBinaryData = variableLengthBlock;\n\n super.setReadName(null);\n super.setCigarString(null);\n super.setReadBases(null);\n super.setBaseQualities(null);\n }\n\n\n ///////////////////////////////////////////////////////////////////////////////\n // *** support for reads without meaningful strand information ***//\n ///////////////////////////////////////////////////////////////////////////////\n\n /**\n * Does this read have a meaningful strandedness value?\n *\n * Some advanced types of reads, such as reads coming from merged fragments,\n * don't have meaningful strandedness values, as they are composites of multiple\n * other reads. Strandless reads need to be handled specially by code that cares about\n * stranded information, such as FS.\n *\n * @return true if this read doesn't have meaningful strand information\n */\n public boolean isStrandless() {\n return isStrandlessRead;\n }\n\n /**\n * Set the strandless state of this read to isStrandless\n * @param isStrandless true if this read doesn't have a meaningful strandedness value\n */\n public void setIsStrandless(final boolean isStrandless) {\n this.isStrandlessRead = isStrandless;\n }\n\n @Override\n public boolean getReadNegativeStrandFlag() {\n return ! isStrandless() && super.getReadNegativeStrandFlag();\n }\n\n @Override\n public void setReadNegativeStrandFlag(final boolean flag) {\n if ( isStrandless() )\n throw new IllegalStateException(\"Cannot set the strand of a strandless read\");\n super.setReadNegativeStrandFlag(flag);\n }\n\n\n ///////////////////////////////////////////////////////////////////////////////\n // *** The following methods are overloaded to cache the appropriate data ***//\n ///////////////////////////////////////////////////////////////////////////////\n\n @Override\n public String getReadString() {\n if ( mReadString == null )\n mReadString = super.getReadString();\n return mReadString;\n }\n\n @Override\n public void setReadString(String s) {\n super.setReadString(s);\n mReadString = s;\n }\n\n /**\n * Get the GATKSAMReadGroupRecord of this read\n * @return a non-null GATKSAMReadGroupRecord\n */\n @Override\n public GATKSAMReadGroupRecord getReadGroup() {\n if ( ! retrievedReadGroup ) {\n final SAMReadGroupRecord rg = super.getReadGroup();\n\n // three cases: rg may be null (no rg, rg may already be a GATKSAMReadGroupRecord, or it may be\n // a regular SAMReadGroupRecord in which case we have to make it a GATKSAMReadGroupRecord\n if ( rg == null )\n mReadGroup = null;\n else if ( rg instanceof GATKSAMReadGroupRecord )\n mReadGroup = (GATKSAMReadGroupRecord)rg;\n else\n mReadGroup = new GATKSAMReadGroupRecord(rg);\n\n retrievedReadGroup = true;\n }\n return mReadGroup;\n }\n\n public void setReadGroup( final GATKSAMReadGroupRecord readGroup ) {\n mReadGroup = readGroup;\n retrievedReadGroup = true;\n setAttribute(\"RG\", mReadGroup.getId()); // todo -- this should be standardized, but we don't have access to SAMTagUtils!\n }\n\n\n @Override\n public int hashCode() {\n return super.hashCode();\n }\n\n @Override\n public boolean equals(Object o) {\n if (this == o) return true;\n\n if (!(o instanceof GATKSAMRecord)) return false;\n\n // note that we do not consider the GATKSAMRecord internal state at all\n return super.equals(o);\n }\n\n /**\n * Setters and Accessors for base insertion and base deletion quality scores\n */\n public void setBaseQualities( final byte[] quals, final EventType errorModel ) {\n switch( errorModel ) {\n case BASE_SUBSTITUTION:\n setBaseQualities(quals);\n break;\n case BASE_INSERTION:\n setAttribute( GATKSAMRecord.BQSR_BASE_INSERTION_QUALITIES, quals == null ? null : SAMUtils.phredToFastq(quals) );\n break;\n case BASE_DELETION:\n setAttribute( GATKSAMRecord.BQSR_BASE_DELETION_QUALITIES, quals == null ? null : SAMUtils.phredToFastq(quals) );\n break;\n default:\n throw new ReviewedGATKException(\"Unrecognized Base Recalibration type: \" + errorModel );\n }\n }\n\n public byte[] getBaseQualities( final EventType errorModel ) {\n switch( errorModel ) {\n case BASE_SUBSTITUTION:\n return getBaseQualities();\n case BASE_INSERTION:\n return getBaseInsertionQualities();\n case BASE_DELETION:\n return getBaseDeletionQualities();\n default:\n throw new ReviewedGATKException(\"Unrecognized Base Recalibration type: \" + errorModel );\n }\n }\n\n /**\n * @return whether or not this read has base insertion or deletion qualities (one of the two is sufficient to return true)\n */\n public boolean hasBaseIndelQualities() {\n return getAttribute( BQSR_BASE_INSERTION_QUALITIES ) != null || getAttribute( BQSR_BASE_DELETION_QUALITIES ) != null;\n }\n\n /**\n * @return the base deletion quality or null if read doesn't have one\n */\n public byte[] getExistingBaseInsertionQualities() {\n return SAMUtils.fastqToPhred( getStringAttribute(BQSR_BASE_INSERTION_QUALITIES));\n }\n\n /**\n * @return the base deletion quality or null if read doesn't have one\n */\n public byte[] getExistingBaseDeletionQualities() {\n return SAMUtils.fastqToPhred( getStringAttribute(BQSR_BASE_DELETION_QUALITIES));\n }\n\n /**\n * Default utility to query the base insertion quality of a read. If the read doesn't have one, it creates an array of default qualities (currently Q45)\n * and assigns it to the read.\n *\n * @return the base insertion quality array\n */\n public byte[] getBaseInsertionQualities() {\n byte [] quals = getExistingBaseInsertionQualities();\n if( quals == null ) {\n quals = new byte[getBaseQualities().length];\n Arrays.fill(quals, DEFAULT_INSERTION_DELETION_QUAL); // Some day in the future when base insertion and base deletion quals exist the samtools API will\n // be updated and the original quals will be pulled here, but for now we assume the original quality is a flat Q45\n }\n return quals;\n }\n\n /**\n * Default utility to query the base deletion quality of a read. If the read doesn't have one, it creates an array of default qualities (currently Q45)\n * and assigns it to the read.\n *\n * @return the base deletion quality array\n */\n public byte[] getBaseDeletionQualities() {\n byte[] quals = getExistingBaseDeletionQualities();\n if( quals == null ) {\n quals = new byte[getBaseQualities().length];\n Arrays.fill(quals, DEFAULT_INSERTION_DELETION_QUAL); // Some day in the future when base insertion and base deletion quals exist the samtools API will\n // be updated and the original quals will be pulled here, but for now we assume the original quality is a flat Q45\n }\n return quals;\n }\n\n /**\n * Efficient caching accessor that returns the GATK NGSPlatform of this read\n * @return\n */\n public NGSPlatform getNGSPlatform() {\n return getReadGroup().getNGSPlatform();\n }\n\n ///////////////////////////////////////////////////////////////////////////////\n // *** GATKSAMRecord specific methods ***//\n ///////////////////////////////////////////////////////////////////////////////\n\n /**\n * Checks whether an attribute has been set for the given key.\n *\n * Temporary attributes provide a way to label or attach arbitrary data to\n * individual GATKSAMRecords. These attributes exist in memory only,\n * and are never written to disk.\n *\n * @param key key\n * @return True if an attribute has been set for this key.\n */\n public boolean containsTemporaryAttribute(Object key) {\n return temporaryAttributes != null && temporaryAttributes.containsKey(key);\n }\n\n /**\n * Sets the key to the given value, replacing any previous value. The previous\n * value is returned.\n *\n * Temporary attributes provide a way to label or attach arbitrary data to\n * individual GATKSAMRecords. These attributes exist in memory only,\n * and are never written to disk.\n *\n * @param key key\n * @param value value\n * @return attribute\n */\n public Object setTemporaryAttribute(Object key, Object value) {\n if(temporaryAttributes == null) {\n temporaryAttributes = new HashMap<>();\n }\n return temporaryAttributes.put(key, value);\n }\n\n /**\n * Looks up the value associated with the given key.\n *\n * Temporary attributes provide a way to label or attach arbitrary data to\n * individual GATKSAMRecords. These attributes exist in memory only,\n * and are never written to disk.\n *\n * @param key key\n * @return The value, or null.\n */\n public Object getTemporaryAttribute(Object key) {\n if(temporaryAttributes != null) {\n return temporaryAttributes.get(key);\n }\n return null;\n }\n\n /**\n * Checks whether if the read has any bases.\n *\n * Empty reads can be dangerous as it may have no cigar strings, no read names and\n * other missing attributes.\n *\n * @return true if the read has no bases\n */\n public boolean isEmpty() {\n return super.getReadBases() == null || super.getReadLength() == 0;\n }\n\n /**\n * Clears all attributes except ReadGroup of the read.\n */\n public GATKSAMRecord simplify () {\n GATKSAMReadGroupRecord rg = getReadGroup(); // save the read group information\n byte[] insQuals = (this.getAttribute(BQSR_BASE_INSERTION_QUALITIES) == null) ? null : getBaseInsertionQualities();\n byte[] delQuals = (this.getAttribute(BQSR_BASE_DELETION_QUALITIES) == null) ? null : getBaseDeletionQualities();\n this.clearAttributes(); // clear all attributes from the read\n this.setReadGroup(rg); // restore read group\n if (insQuals != null)\n this.setBaseQualities(insQuals, EventType.BASE_INSERTION); // restore base insertion if we had any\n if (delQuals != null)\n this.setBaseQualities(delQuals, EventType.BASE_DELETION); // restore base deletion if we had any\n return this;\n }\n\n /**\n * Calculates the reference coordinate for the beginning of the read taking into account soft clips but not hard clips.\n *\n * Note: getUnclippedStart() adds soft and hard clips, this function only adds soft clips.\n *\n * @return the unclipped start of the read taking soft clips (but not hard clips) into account\n */\n public int getSoftStart() {\n if ( softStart == UNINITIALIZED ) {\n softStart = getAlignmentStart();\n for (final CigarElement cig : getCigar().getCigarElements()) {\n final CigarOperator op = cig.getOperator();\n\n if (op == CigarOperator.SOFT_CLIP)\n softStart -= cig.getLength();\n else if (op != CigarOperator.HARD_CLIP)\n break;\n }\n }\n return softStart;\n }\n\n /**\n * Calculates the reference coordinate for the end of the read taking into account soft clips but not hard clips.\n *\n * Note: getUnclippedEnd() adds soft and hard clips, this function only adds soft clips.\n *\n * @return the unclipped end of the read taking soft clips (but not hard clips) into account\n */\n public int getSoftEnd() {\n if ( softEnd == UNINITIALIZED ) {\n boolean foundAlignedBase = false;\n softEnd = getAlignmentEnd();\n final List cigs = getCigar().getCigarElements();\n for (int i = cigs.size() - 1; i >= 0; --i) {\n final CigarElement cig = cigs.get(i);\n final CigarOperator op = cig.getOperator();\n\n if (op == CigarOperator.SOFT_CLIP) // assumes the soft clip that we found is at the end of the aligned read\n softEnd += cig.getLength();\n else if (op != CigarOperator.HARD_CLIP) {\n foundAlignedBase = true;\n break;\n }\n }\n if( !foundAlignedBase ) { // for example 64H14S, the soft end is actually the same as the alignment end\n softEnd = getAlignmentEnd();\n }\n }\n\n return softEnd;\n }\n\n /**\n * If the read is hard clipped, the soft start and end will change. You can set manually or just reset the cache\n * so that the next call to getSoftStart/End will recalculate it lazily.\n */\n public void resetSoftStartAndEnd() {\n softStart = -1;\n softEnd = -1;\n }\n\n /**\n * If the read is hard clipped, the soft start and end will change. You can set manually or just reset the cache\n * so that the next call to getSoftStart/End will recalculate it lazily.\n */\n public void resetSoftStartAndEnd(int softStart, int softEnd) {\n this.softStart = softStart;\n this.softEnd = softEnd;\n }\n\n /**\n * Determines the original alignment start of a previously clipped read.\n *\n * This is useful for reads that have been trimmed to a variant region and lost the information of it's original alignment end\n *\n * @return the alignment start of a read before it was clipped\n */\n public int getOriginalAlignmentStart() {\n return getUnclippedStart();\n }\n\n /**\n * Determines the original alignment end of a previously clipped read.\n *\n * This is useful for reads that have been trimmed to a variant region and lost the information of it's original alignment end\n *\n * @return the alignment end of a read before it was clipped\n */\n public int getOriginalAlignmentEnd() {\n return getUnclippedEnd();\n }\n\n /**\n * Creates an empty GATKSAMRecord with the read's header, read group and mate\n * information, but empty (not-null) fields:\n * - Cigar String\n * - Read Bases\n * - Base Qualities\n *\n * Use this method if you want to create a new empty GATKSAMRecord based on\n * another GATKSAMRecord\n *\n * @param read a read to copy the header from\n * @return a read with no bases but safe for the GATK\n */\n public static GATKSAMRecord emptyRead(GATKSAMRecord read) {\n GATKSAMRecord emptyRead = new GATKSAMRecord(read.getHeader(),\n read.getReferenceIndex(),\n 0,\n (short) 0,\n (short) 0,\n 0,\n 0,\n read.getFlags(),\n 0,\n read.getMateReferenceIndex(),\n read.getMateAlignmentStart(),\n read.getInferredInsertSize(),\n null);\n\n emptyRead.setCigarString(\"\");\n emptyRead.setReadBases(new byte[0]);\n emptyRead.setBaseQualities(new byte[0]);\n\n SAMReadGroupRecord samRG = read.getReadGroup();\n emptyRead.clearAttributes();\n if (samRG != null) {\n GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);\n emptyRead.setReadGroup(rg);\n }\n\n return emptyRead;\n }\n\n /**\n * Creates a new GATKSAMRecord with the source read's header, read group and mate\n * information, but with the following fields set to user-supplied values:\n * - Read Bases\n * - Base Qualities\n * - Base Insertion Qualities\n * - Base Deletion Qualities\n *\n * Cigar string is empty (not-null)\n *\n * Use this method if you want to create a new GATKSAMRecord based on\n * another GATKSAMRecord, but with modified bases and qualities\n *\n * @param read a read to copy the header from\n * @param readBases an array containing the new bases you wish use in place of the originals\n * @param baseQualities an array containing the new base qualities you wish use in place of the originals\n * @param baseInsertionQualities an array containing the new base insertion qaulities\n * @param baseDeletionQualities an array containing the new base deletion qualities\n * @return a read with modified bases and qualities, safe for the GATK\n */\n public static GATKSAMRecord createQualityModifiedRead(final GATKSAMRecord read,\n final byte[] readBases,\n final byte[] baseQualities,\n final byte[] baseInsertionQualities,\n final byte[] baseDeletionQualities) {\n if ( baseQualities.length != readBases.length || baseInsertionQualities.length != readBases.length || baseDeletionQualities.length != readBases.length )\n throw new IllegalArgumentException(\"Read bases and read quality arrays aren't the same size: Bases:\" + readBases.length\n + \" vs Base Q's:\" + baseQualities.length\n + \" vs Insert Q's:\" + baseInsertionQualities.length\n + \" vs Delete Q's:\" + baseDeletionQualities.length);\n\n final GATKSAMRecord processedRead = GATKSAMRecord.emptyRead(read);\n processedRead.setReadBases(readBases);\n processedRead.setBaseQualities(baseQualities, EventType.BASE_SUBSTITUTION);\n processedRead.setBaseQualities(baseInsertionQualities, EventType.BASE_INSERTION);\n processedRead.setBaseQualities(baseDeletionQualities, EventType.BASE_DELETION);\n\n return processedRead;\n }\n\n /**\n * Shallow copy of everything, except for the attribute list and the temporary attributes.\n * A new list of the attributes is created for both, but the attributes themselves are copied by reference.\n * This should be safe because callers should never modify a mutable value returned by any of the get() methods anyway.\n *\n * @return a shallow copy of the GATKSAMRecord\n */\n @Override\n public Object clone() {\n try {\n final GATKSAMRecord clone = (GATKSAMRecord) super.clone();\n if (temporaryAttributes != null) {\n clone.temporaryAttributes = new HashMap<>();\n for (Object attribute : temporaryAttributes.keySet())\n clone.setTemporaryAttribute(attribute, temporaryAttributes.get(attribute));\n }\n return clone;\n } catch (final CloneNotSupportedException e) {\n throw new RuntimeException( e );\n }\n }\n\n /**\n * A caching version of ReadUtils.getAdaptorBoundary()\n *\n * see #ReadUtils.getAdaptorBoundary(SAMRecord) for more information about the meaning of this function\n *\n * WARNING -- this function caches a value depending on the inferred insert size and alignment starts\n * and stops of this read and its mate. Changing these values in any way will invalidate the cached value.\n * However, we do not monitor those setter functions, so modifying a GATKSAMRecord in any way may\n * result in stale cached values.\n *\n * @return the result of calling ReadUtils.getAdaptorBoundary on this read\n */\n public int getAdaptorBoundary() {\n if ( adapterBoundary == null )\n adapterBoundary = ReadUtils.getAdaptorBoundary(this);\n return adapterBoundary;\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/IntervalLocusSamTraverser.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.sam;\n\nimport org.apache.commons.collections.CollectionUtils;\nimport org.ncic.bioinfo.sparkseq.algorithms.data.sam.filter.FilterUtils;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLoc;\nimport org.ncic.bioinfo.sparkseq.exceptions.GATKException;\n\nimport java.util.ArrayList;\nimport java.util.Collections;\nimport java.util.List;\nimport java.util.stream.Collectors;\n\n/**\n * Author: wbc\n */\npublic class IntervalLocusSamTraverser {\n\n private static final int OVERLAP_LEN = 100;\n private final List intervals;\n private final LocusSamTraverser locusSamTraverser;\n\n public IntervalLocusSamTraverser(SamContentProvider samContentProvider,\n GenomeLoc refLocus,\n List rawTraverseIntervals) {\n this(samContentProvider, refLocus, rawTraverseIntervals, new FilterUtils());\n }\n\n public IntervalLocusSamTraverser(SamContentProvider samContentProvider,\n GenomeLoc refLocus,\n List rawTraverseIntervals,\n FilterUtils filterUtils) {\n this.intervals = getOverlappedIntervals(refLocus, rawTraverseIntervals);\n this.locusSamTraverser = new LocusSamTraverser(samContentProvider, refLocus, filterUtils);\n rewind();\n }\n\n private List getOverlappedIntervals(GenomeLoc refLocus, List rawTraverseIntervals) {\n // 如果没有intervals，就把整个refLocus作为遍历对象\n if (CollectionUtils.isEmpty(rawTraverseIntervals)) {\n List singleGenomeLoc = new ArrayList<>(1);\n singleGenomeLoc.add(refLocus);\n return singleGenomeLoc;\n }\n\n List rawOverlappedIntervals = rawTraverseIntervals.stream()\n .filter(interval -> interval.overlapsP(refLocus))\n .map(interval -> new GenomeLoc(interval.getContig(), interval.getContigIndex(),\n (interval.getStart() - OVERLAP_LEN) < refLocus.getStart() ? refLocus.getStart() : (interval.getStart() - OVERLAP_LEN),\n (interval.getStop() + OVERLAP_LEN) > refLocus.getStop() ? refLocus.getStop() : (interval.getStop() + OVERLAP_LEN)))\n .collect(Collectors.toList());\n\n Collections.sort(rawOverlappedIntervals,\n (interval1, interval2) -> interval1.getStart() - interval2.getStart());\n\n //处理intervals粘连的情况\n List finalIntervals = new ArrayList<>();\n GenomeLoc tmpInterval = null;\n for (GenomeLoc interval : rawOverlappedIntervals) {\n if (tmpInterval == null) {\n tmpInterval = interval;\n } else {\n if (tmpInterval.overlapsP(interval)) {\n tmpInterval = new GenomeLoc(tmpInterval.getContig(), tmpInterval.getContigIndex(),\n Integer.min(tmpInterval.getStart(), interval.getStart()),\n Integer.max(tmpInterval.getStop(), interval.getStop()));\n } else {\n finalIntervals.add(tmpInterval);\n tmpInterval = interval;\n }\n }\n }\n if (tmpInterval != null) {\n finalIntervals.add(tmpInterval);\n }\n\n return finalIntervals;\n }\n\n private int curIntervalIdx = -1;\n private int curCoordinate = -1;\n\n public void rewind() {\n curIntervalIdx = 0;\n curCoordinate = intervals.get(curIntervalIdx).getStart();\n }\n\n public boolean hasNext() {\n return curIntervalIdx < intervals.size() - 1 ||\n (curIntervalIdx == intervals.size() - 1 && curCoordinate <= intervals.get(intervals.size() - 1).getStop());\n }\n\n public AlignmentContext next() {\n if (!hasNext()) {\n throw new GATKException(\"Out of bound when traverse sam content provider\");\n }\n\n locusSamTraverser.forwardToCoordinate(curCoordinate);\n AlignmentContext alignmentContext = locusSamTraverser.next();\n\n // 更新curCoordinate\n if (curCoordinate == intervals.get(curIntervalIdx).getStop()) {\n curIntervalIdx++;\n if (curIntervalIdx < intervals.size()) { // 如果有下一个interval，更新coordinate\n curCoordinate = intervals.get(curIntervalIdx).getStart();\n }\n } else {\n curCoordinate++;\n }\n\n return alignmentContext;\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/LocusSamTraverser.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.sam;\n\nimport org.ncic.bioinfo.sparkseq.algorithms.data.sam.filter.FilterUtils;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.ReadUtils;\nimport org.ncic.bioinfo.sparkseq.exceptions.GATKException;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLoc;\n\nimport java.util.ArrayList;\nimport java.util.LinkedList;\nimport java.util.List;\nimport java.util.stream.Collectors;\n\n/**\n * Author: wbc\n */\npublic class LocusSamTraverser {\n\n protected final List samList;\n protected final String contigName;\n protected final int contigId;\n protected final int startCoordinate;\n protected final int endCoordinate;\n protected final int readCount;\n\n // 遍历过程中的变量\n protected int curCoordinate = 0;\n protected LinkedList bufferList = new LinkedList<>();\n // 当前指向的samList中的下标，以及当前代表下标指向read的tracker\n protected int curIndex = 0;\n protected PileupTraker curTracker = null;\n\n public LocusSamTraverser(SamContentProvider samContentProvider, GenomeLoc traverseInterval) {\n this(samContentProvider, traverseInterval, new FilterUtils());\n }\n\n public LocusSamTraverser(SamContentProvider samContentProvider, GenomeLoc traverseInterval,\n FilterUtils filterUtils) {\n samList = samContentProvider.getGatksamRecords().stream()\n .filter(record -> filterUtils.filter(record))\n .collect(Collectors.toList());\n\n readCount = samList.size();\n contigName = traverseInterval.getContig();\n contigId = traverseInterval.getContigIndex();\n startCoordinate = traverseInterval.getStart();\n endCoordinate = traverseInterval.getStop();\n\n rewind();\n }\n\n public void rewind() {\n curCoordinate = startCoordinate;\n bufferList.clear();\n curIndex = 0;\n if (readCount > 0) {\n curTracker = new PileupTraker(samList.get(0));\n }\n }\n\n public boolean hasNext() {\n return curCoordinate <= endCoordinate;\n }\n\n public AlignmentContext next() {\n if (!hasNext()) {\n throw new GATKException(\"Out of bound when traverse sam content provider\");\n }\n\n // 删除bufferList中已经超出的头部部分。通过判断尾部是否已经越过当前coordinate来删除\n // 因为read是不等长的，所以有可能更早的read没有超出，而晚一点的更短read已经超出，\n // 所以buffer中并不是所有的read都可以生成pileup。\n while (!bufferList.isEmpty()\n && !bufferList.getFirst().isBeforeEnd(curCoordinate)) {\n bufferList.removeFirst();\n }\n\n // 加入新的read\n // 需要判断：1.read尾在coordinate之前，直接跳过\n // 2.read头在coordinate之前，read尾在coordinate之后，加入buffer\n // 3.read头在coordinate之后，break\n while (curIndex < readCount) {\n if (!curTracker.isBeforeEnd(curCoordinate)) {\n curIndex++;\n if (curIndex < readCount) {\n curTracker = new PileupTraker(samList.get(curIndex));\n }\n continue;\n }\n if (curTracker.isAfterStart(curCoordinate)) {\n // 如果遍历的位点截断了一些read，需要先做一个调整，让machine移动到当前位点\n int readStart = curTracker.stateMachine.getRead().getAlignmentStart();\n for (int i = 0; i < curCoordinate - readStart; i++) {\n curTracker.stepForwardOnGenome();\n }\n bufferList.addLast(curTracker);\n curIndex++;\n if (curIndex < readCount) {\n curTracker = new PileupTraker(samList.get(curIndex));\n }\n } else {\n break;\n }\n }\n\n //Get pileup to a arrayList\n List pileupReads = new ArrayList<>();\n bufferList.forEach(tracker -> {\n if (tracker.isBeforeEnd(curCoordinate)) {\n tracker.stepForwardOnGenome();\n\n if (!ReadUtils.isBaseInsideAdaptor(tracker.stateMachine.getRead(), curCoordinate)) {\n PileupElement element = tracker.stateMachine.makePileupElement();\n pileupReads.add(element);\n }\n }\n });\n\n GenomeLoc locus = new GenomeLoc(contigName, contigId, curCoordinate, curCoordinate);\n ReadBackedPileup readBackedPileup = new ReadBackedPileupImpl(locus, pileupReads);\n\n curCoordinate++;\n return new AlignmentContext(locus, readBackedPileup);\n }\n\n class PileupTraker {\n private int start = 0;\n private int end = 0;\n private AlignmentStateMachine stateMachine;\n\n PileupTraker(GATKSAMRecord read) {\n this.stateMachine = new AlignmentStateMachine(read);\n this.start = read.getAlignmentStart();\n this.end = read.getAlignmentEnd();\n }\n\n void stepForwardOnGenome() {\n stateMachine.stepForwardOnGenome();\n }\n\n boolean isBeforeEnd(int coordinate) {\n return (coordinate <= end);\n }\n\n boolean isAfterStart(int coordinate) {\n return (coordinate >= start);\n }\n }\n\n /**\n * 设置新的coordinate，但是不能向后倒退\n *\n * @param newCoordinate\n */\n public void forwardToCoordinate(int newCoordinate) {\n if(this.curCoordinate > newCoordinate) {\n throw new GATKException(\"Can't go back when traverse in locus mode\");\n }\n this.curCoordinate = newCoordinate;\n }\n\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/MergingPileupElementIterator.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.sam;\n\nimport htsjdk.samtools.util.PeekableIterator;\n\nimport java.util.Comparator;\nimport java.util.Iterator;\nimport java.util.PriorityQueue;\n\n/**\n * Author: wbc\n */\nclass MergingPileupElementIterator implements Iterator {\n private final PriorityQueue> perSampleIterators;\n\n public MergingPileupElementIterator(PerSamplePileupElementTracker tracker) {\n perSampleIterators = new PriorityQueue>(Math.max(1,tracker.getSamples().size()),new PileupElementIteratorComparator());\n for(final String sample: tracker.getSamples()) {\n PileupElementTracker trackerPerSample = tracker.getElements(sample);\n if(trackerPerSample.size() != 0)\n perSampleIterators.add(new PeekableIterator(trackerPerSample.iterator()));\n }\n }\n\n public boolean hasNext() {\n return !perSampleIterators.isEmpty();\n }\n\n public PE next() {\n PeekableIterator currentIterator = perSampleIterators.remove();\n PE current = currentIterator.next();\n if(currentIterator.hasNext())\n perSampleIterators.add(currentIterator);\n return current;\n }\n\n public void remove() {\n throw new UnsupportedOperationException(\"Cannot remove from a merging iterator.\");\n }\n\n /**\n * Compares two peekable iterators consisting of pileup elements.\n */\n private class PileupElementIteratorComparator implements Comparator> {\n public int compare(PeekableIterator lhs, PeekableIterator rhs) {\n return rhs.peek().getOffset() - lhs.peek().getOffset();\n }\n }\n}\n"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/PileupElement.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.sam;\n\nimport htsjdk.samtools.CigarElement;\nimport htsjdk.samtools.CigarOperator;\nimport org.ncic.bioinfo.sparkseq.algorithms.utils.BaseUtils;\n\nimport java.util.Arrays;\nimport java.util.EnumSet;\nimport java.util.LinkedList;\nimport java.util.List;\n\n/**\n * Author: wbc\n */\npublic class PileupElement implements Comparable {\n private final static LinkedList EMPTY_LINKED_LIST = new LinkedList<>();\n\n private final static EnumSet ON_GENOME_OPERATORS =\n EnumSet.of(CigarOperator.M, CigarOperator.EQ, CigarOperator.X, CigarOperator.D);\n\n public static final byte DELETION_BASE = BaseUtils.Base.D.base;\n public static final byte DELETION_QUAL = (byte) 16;\n public static final byte A_FOLLOWED_BY_INSERTION_BASE = (byte) 87;\n public static final byte C_FOLLOWED_BY_INSERTION_BASE = (byte) 88;\n public static final byte T_FOLLOWED_BY_INSERTION_BASE = (byte) 89;\n public static final byte G_FOLLOWED_BY_INSERTION_BASE = (byte) 90;\n\n protected final GATKSAMRecord read; // the read this base belongs to\n protected final int offset; // the offset in the bases array for this base\n\n private final CigarElement currentCigarElement;\n private final int currentCigarOffset;\n private final int offsetInCurrentCigar;\n\n /**\n * Create a new pileup element\n *\n * @param read a non-null read to pileup\n * @param baseOffset the offset into the read's base / qual vector aligned to this position on the genome. If the\n * current cigar element is a deletion, offset should be the offset of the last M/=/X position.\n * @param currentElement a non-null CigarElement that indicates the cigar element aligning the read to the genome\n * @param currentCigarOffset the offset of currentElement in read.getCigar().getElement(currentCigarOffset) == currentElement)\n * @param offsetInCurrentCigar how far into the currentElement are we in our alignment to the genome?\n */\n public PileupElement(final GATKSAMRecord read, final int baseOffset,\n final CigarElement currentElement, final int currentCigarOffset,\n final int offsetInCurrentCigar) {\n assert currentElement != null;\n\n this.read = read;\n this.offset = baseOffset;\n this.currentCigarElement = currentElement;\n this.currentCigarOffset = currentCigarOffset;\n this.offsetInCurrentCigar = offsetInCurrentCigar;\n\n // for performance regions these are assertions\n assert this.read != null;\n assert this.offset >= 0 && this.offset < this.read.getReadLength();\n assert this.currentCigarOffset >= 0;\n assert this.currentCigarOffset < read.getCigarLength();\n assert this.offsetInCurrentCigar >= 0;\n assert this.offsetInCurrentCigar < currentElement.getLength();\n }\n\n /**\n * Create a new PileupElement that's a copy of toCopy\n * @param toCopy the element we want to copy\n */\n public PileupElement(final PileupElement toCopy) {\n this(toCopy.read, toCopy.offset, toCopy.currentCigarElement, toCopy.currentCigarOffset, toCopy.offsetInCurrentCigar);\n }\n\n /**\n * Is this element a deletion w.r.t. the reference genome?\n *\n * @return true if this is a deletion, false otherwise\n */\n public boolean isDeletion() {\n return currentCigarElement.getOperator() == CigarOperator.D;\n }\n\n /**\n * Is the current element immediately before a deletion, but itself not a deletion?\n *\n * Suppose we are aligning a read with cigar 3M2D1M. This function is true\n * if we are in the last cigar position of the 3M, but not if we are in the 2D itself.\n *\n * @return true if the next alignment position is a deletion w.r.t. the reference genome\n */\n public boolean isBeforeDeletionStart() {\n return ! isDeletion() && atEndOfCurrentCigar() && hasOperator(getNextOnGenomeCigarElement(), CigarOperator.D);\n }\n\n /**\n * Is the current element immediately after a deletion, but itself not a deletion?\n *\n * Suppose we are aligning a read with cigar 1M2D3M. This function is true\n * if we are in the first cigar position of the 3M, but not if we are in the 2D itself or\n * in any but the first position of the 3M.\n *\n * @return true if the previous alignment position is a deletion w.r.t. the reference genome\n */\n public boolean isAfterDeletionEnd() {\n return ! isDeletion() && atStartOfCurrentCigar() && hasOperator(getPreviousOnGenomeCigarElement(), CigarOperator.D);\n }\n\n /**\n * Get the read for this pileup element\n * @return a non-null GATKSAMRecord\n */\n public GATKSAMRecord getRead() {\n return read;\n }\n\n /**\n * Get the offset of the this element into the read that aligns that read's base to this genomic position.\n *\n * If the current element is a deletion then offset is the offset of the last base containing offset.\n *\n * @return a valid offset into the read's bases\n */\n public int getOffset() {\n return offset;\n }\n\n /**\n * Get the base aligned to the genome at this location\n *\n * If the current element is a deletion returns DELETION_BASE\n *\n * @return a base encoded as a byte\n */\n public byte getBase() {\n return isDeletion() ? DELETION_BASE : read.getReadBases()[offset];\n }\n\n @Deprecated\n public int getBaseIndex() {\n return BaseUtils.simpleBaseToBaseIndex(getBase());\n }\n\n /**\n * Get the base quality score of the base at this aligned position on the genome\n * @return a phred-scaled quality score as a byte\n */\n public byte getQual() {\n return isDeletion() ? DELETION_QUAL : read.getBaseQualities()[offset];\n }\n\n /**\n * Get the Base Insertion quality at this pileup position\n * @return a phred-scaled quality score as a byte\n */\n public byte getBaseInsertionQual() {\n return isDeletion() ? DELETION_QUAL : read.getBaseInsertionQualities()[offset];\n }\n\n /**\n * Get the Base Deletion quality at this pileup position\n * @return a phred-scaled quality score as a byte\n */\n public byte getBaseDeletionQual() {\n return isDeletion() ? DELETION_QUAL : read.getBaseDeletionQualities()[offset];\n }\n\n /**\n * Get the length of an immediately following insertion or deletion event, or 0 if no such event exists\n *\n * Only returns a positive value when this pileup element is immediately before an indel. Being\n * immediately before a deletion means that this pileup element isn't an deletion, and that the\n * next genomic alignment for this read is a deletion. For the insertion case, this means\n * that an insertion cigar occurs immediately after this element, between this one and the\n * next genomic position.\n *\n * Note this function may be expensive, so multiple uses should be cached by the caller\n *\n * @return length of the event (number of inserted or deleted bases), or 0\n */\n public int getLengthOfImmediatelyFollowingIndel() {\n final CigarElement element = getNextIndelCigarElement();\n return element == null ? 0 : element.getLength();\n }\n\n /**\n * Helpful function to get the immediately following cigar element, for an insertion or deletion\n *\n * if this state precedes a deletion (i.e., next position on genome) or insertion (immediately between\n * this and the next position) returns the CigarElement corresponding to this event. Otherwise returns\n * null.\n *\n * @return a CigarElement, or null if the next alignment state ins't an insertion or deletion.\n */\n private CigarElement getNextIndelCigarElement() {\n if ( isBeforeDeletionStart() ) {\n final CigarElement element = getNextOnGenomeCigarElement();\n if ( element == null || element.getOperator() != CigarOperator.D )\n throw new IllegalStateException(\"Immediately before deletion but the next cigar element isn't a deletion \" + element);\n return element;\n } else if ( isBeforeInsertion() ) {\n final CigarElement element = getBetweenNextPosition().get(0);\n if ( element.getOperator() != CigarOperator.I )\n throw new IllegalStateException(\"Immediately before insertion but the next cigar element isn't an insertion \" + element);\n return element;\n } else {\n return null;\n }\n }\n\n /**\n * Get the bases for an insertion that immediately follows this alignment state, or null if none exists\n *\n * @see #getLengthOfImmediatelyFollowingIndel() for details on the meaning of immediately.\n *\n * If the immediately following state isn't an insertion, returns null\n *\n * @return actual sequence of inserted bases, or a null if the event is a deletion or if there is no event in the associated read.\n */\n public String getBasesOfImmediatelyFollowingInsertion() {\n final CigarElement element = getNextIndelCigarElement();\n if ( element != null && element.getOperator() == CigarOperator.I ) {\n final int getFrom = offset + 1;\n final byte[] bases = Arrays.copyOfRange(read.getReadBases(), getFrom, getFrom + element.getLength());\n return new String(bases);\n } else\n return null;\n }\n\n /**\n * Get the mapping quality of the read of this element\n * @return the mapping quality of the underlying SAM record\n */\n public int getMappingQual() {\n return read.getMappingQuality();\n }\n\n public String toString() {\n return String.format(\"%s @ %d = %c Q%d\", getRead().getReadName(), getOffset(), (char) getBase(), getQual());\n }\n\n @Override\n public int compareTo(final PileupElement pileupElement) {\n if (offset < pileupElement.offset)\n return -1;\n else if (offset > pileupElement.offset)\n return 1;\n else if (read.getAlignmentStart() < pileupElement.read.getAlignmentStart())\n return -1;\n else if (read.getAlignmentStart() > pileupElement.read.getAlignmentStart())\n return 1;\n else\n return 0;\n }\n\n // --------------------------------------------------------------------------\n //\n // Reduced read accessors\n //\n // --------------------------------------------------------------------------\n\n /**\n * Get the cigar element aligning this element to the genome\n * @return a non-null CigarElement\n */\n public CigarElement getCurrentCigarElement() {\n return currentCigarElement;\n }\n\n /**\n * Get the offset of this cigar element in the Cigar of the current read (0-based)\n *\n * Suppose the cigar is 1M2D3I4D. If we are in the 1M state this function returns\n * 0. If we are in 2D, the result is 1. If we are in the 4D, the result is 3.\n *\n * @return an offset into the read.getCigar() that brings us to the current cigar element\n */\n public int getCurrentCigarOffset() {\n return currentCigarOffset;\n }\n\n /**\n * Get the offset into the *current* cigar element for this alignment position\n *\n * We can be anywhere from offset 0 (first position) to length - 1 of the current\n * cigar element aligning us to this genomic position.\n *\n * @return a valid offset into the current cigar element\n */\n public int getOffsetInCurrentCigar() {\n return offsetInCurrentCigar;\n }\n\n /**\n * Get the cigar elements that occur before the current position but after the previous position on the genome\n *\n * For example, if we are in the 3M state of 1M2I3M state then 2I occurs before this position.\n *\n * Note that this function does not care where we are in the current cigar element. In the previous\n * example this list of elements contains the 2I state regardless of where you are in the 3M.\n *\n * Note this returns the list of all elements that occur between this and the prev site, so for\n * example we might have 5S10I2M and this function would return [5S, 10I].\n *\n * @return a non-null list of CigarElements\n */\n public LinkedList getBetweenPrevPosition() {\n return atStartOfCurrentCigar() ? getBetween(Direction.PREV) : EMPTY_LINKED_LIST;\n }\n\n /**\n * Get the cigar elements that occur after the current position but before the next position on the genome\n *\n * @see #getBetweenPrevPosition() for more details\n *\n * @return a non-null list of CigarElements\n */\n public LinkedList getBetweenNextPosition() {\n return atEndOfCurrentCigar() ? getBetween(Direction.NEXT) : EMPTY_LINKED_LIST;\n }\n\n /** for some helper functions */\n private enum Direction { PREV, NEXT }\n\n /**\n * Helper function to get cigar elements between this and either the prev or next genomic position\n *\n * @param direction PREVIOUS if we want before, NEXT if we want after\n * @return a non-null list of cigar elements between this and the neighboring position in direction\n */\n private LinkedList getBetween(final Direction direction) {\n final int increment = direction == Direction.NEXT ? 1 : -1;\n LinkedList elements = null;\n final int nCigarElements = read.getCigarLength();\n for ( int i = currentCigarOffset + increment; i >= 0 && i < nCigarElements; i += increment) {\n final CigarElement elt = read.getCigar().getCigarElement(i);\n if ( ON_GENOME_OPERATORS.contains(elt.getOperator()) )\n break;\n else {\n // optimization: don't allocate list if not necessary\n if ( elements == null )\n elements = new LinkedList();\n\n if ( increment > 0 )\n // to keep the list in the right order, if we are incrementing positively add to the end\n elements.add(elt);\n else\n // counting down => add to front\n elements.addFirst(elt);\n }\n }\n\n // optimization: elements is null because nothing got added, just return the empty list\n return elements == null ? EMPTY_LINKED_LIST : elements;\n }\n\n /**\n * Get the cigar element of the previous genomic aligned position\n *\n * For example, we might have 1M2I3M, and be sitting at the someone in the 3M. This\n * function would return 1M, as the 2I isn't on the genome. Note this function skips\n * all of the positions that would occur in the current element. So the result\n * is always 1M regardless of whether we're in the first, second, or third position of the 3M\n * cigar.\n *\n * @return a CigarElement, or null (indicating that no previous element exists)\n */\n public CigarElement getPreviousOnGenomeCigarElement() {\n return getNeighboringOnGenomeCigarElement(Direction.PREV);\n }\n\n /**\n * Get the cigar element of the next genomic aligned position\n *\n * @see #getPreviousOnGenomeCigarElement() for more details\n *\n * @return a CigarElement, or null (indicating that no next element exists)\n */\n public CigarElement getNextOnGenomeCigarElement() {\n return getNeighboringOnGenomeCigarElement(Direction.NEXT);\n }\n\n /**\n * Helper function to get the cigar element of the next or previous genomic position\n * @param direction the direction to look in\n * @return a CigarElement, or null if no such element exists\n */\n private CigarElement getNeighboringOnGenomeCigarElement(final Direction direction) {\n final int increment = direction == Direction.NEXT ? 1 : -1;\n final int nCigarElements = read.getCigarLength();\n\n for ( int i = currentCigarOffset + increment; i >= 0 && i < nCigarElements; i += increment) {\n final CigarElement elt = read.getCigar().getCigarElement(i);\n if ( ON_GENOME_OPERATORS.contains(elt.getOperator()) )\n return elt;\n }\n\n // getting here means that you didn't find anything\n return null;\n }\n\n /**\n * Does the cigar element (which may be null) have operation toMatch?\n *\n * @param maybeCigarElement a CigarElement that might be null\n * @param toMatch a CigarOperator we want to match against the one in maybeCigarElement\n * @return true if maybeCigarElement isn't null and has operator toMatch\n */\n private boolean hasOperator(final CigarElement maybeCigarElement, final CigarOperator toMatch) {\n return maybeCigarElement != null && maybeCigarElement.getOperator() == toMatch;\n }\n\n /**\n * Does an insertion occur immediately before the current position on the genome?\n *\n * @return true if yes, false if no\n */\n public boolean isAfterInsertion() { return isAfter(getBetweenPrevPosition(), CigarOperator.I); }\n\n /**\n * Does an insertion occur immediately after the current position on the genome?\n *\n * @return true if yes, false if no\n */\n public boolean isBeforeInsertion() { return isBefore(getBetweenNextPosition(), CigarOperator.I); }\n\n /**\n * Does a soft-clipping event occur immediately before the current position on the genome?\n *\n * @return true if yes, false if no\n */\n public boolean isAfterSoftClip() { return isAfter(getBetweenPrevPosition(), CigarOperator.S); }\n\n /**\n * Does a soft-clipping event occur immediately after the current position on the genome?\n *\n * @return true if yes, false if no\n */\n public boolean isBeforeSoftClip() { return isBefore(getBetweenNextPosition(), CigarOperator.S); }\n\n /**\n * Does a soft-clipping event occur immediately before or after the current position on the genome?\n *\n * @return true if yes, false if no\n */\n public boolean isNextToSoftClip() { return isAfterSoftClip() || isBeforeSoftClip(); }\n\n /**\n * Is the current position at the end of the current cigar?\n *\n * For example, if we are in element 3M, this function returns true if we are at offsetInCurrentCigar\n * of 2, but not 0 or 1.\n *\n * @return true if we're at the end of the current cigar\n */\n public boolean atEndOfCurrentCigar() {\n return offsetInCurrentCigar == currentCigarElement.getLength() - 1;\n }\n\n /**\n * Is the current position at the start of the current cigar?\n *\n * For example, if we are in element 3M, this function returns true if we are at offsetInCurrentCigar\n * of 0, but not 1 or 2.\n *\n * @return true if we're at the start of the current cigar\n */\n public boolean atStartOfCurrentCigar() {\n return offsetInCurrentCigar == 0;\n }\n\n /**\n * Is op the last element in the list of elements?\n *\n * @param elements the elements to examine\n * @param op the op we want the last element's op to equal\n * @return true if op == last(elements).op\n */\n private boolean isAfter(final LinkedList elements, final CigarOperator op) {\n return ! elements.isEmpty() && elements.peekLast().getOperator() == op;\n }\n\n /**\n * Is op the first element in the list of elements?\n *\n * @param elements the elements to examine\n * @param op the op we want the last element's op to equal\n * @return true if op == first(elements).op\n */\n private boolean isBefore(final List elements, final CigarOperator op) {\n return ! elements.isEmpty() && elements.get(0).getOperator() == op;\n }\n}"
},
{
"path": "src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/PileupElementTracker.java",
"content": "/*\n * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\npackage org.ncic.bioinfo.sparkseq.algorithms.data.sam;\n\nimport org.apache.commons.collections.iterators.IteratorChain;\n\nimport java.util.Collection;\nimport java.util.HashMap;\nimport java.util.Iterator;\nimport java.util.LinkedList;\nimport java.util.List;\nimport java.util.Map;\n\n/**\n * Author: wbc\n */\nabstract class PileupElementTracker implements Iterable {\n public abstract int size();\n\n /**\n * Iterate through the PEs here, but in any order, which may improve performance\n * if you don't care about the underlying order the reads are coming to you in.\n * @return an iteratable over all pileup elements in this tracker\n */\n public abstract Iterable unorderedIterable();\n\n /**\n * Same as @see #unorderedIterable but the actual iterator itself\n * @return\n */\n public Iterator unorderedIterator() { return unorderedIterable().iterator(); }\n\n public abstract PileupElementTracker copy();\n}\n\nclass UnifiedPileupElementTracker extends PileupElementTracker {\n private final List pileup;\n\n @Override\n public UnifiedPileupElementTracker copy() {\n UnifiedPileupElementTracker result = new UnifiedPileupElementTracker();\n for(PE element : pileup)\n result.add(element);\n return result;\n }\n\n public UnifiedPileupElementTracker() { pileup = new LinkedList(); }\n public UnifiedPileupElementTracker(List pileup) { this.pileup = pileup; }\n\n public void add(PE element) {\n pileup.add(element);\n }\n\n public PE get(int index) {\n return pileup.get(index);\n }\n\n public int size() {\n return pileup.size();\n }\n\n public Iterator iterator() { return pileup.iterator(); }\n public Iterable unorderedIterable() { return this; }\n}\n\nclass PerSamplePileupElementTracker extends PileupElementTracker {\n private final Map> pileup;\n private int size = 0;\n\n public PerSamplePileupElementTracker() {\n pileup = new HashMap>();\n }\n\n public PerSamplePileupElementTracker copy() {\n PerSamplePileupElementTracker