SYMBOL INDEX (197 symbols across 11 files) FILE: libBigWig/bigWig.h type CURLcode (line 68) | typedef int CURLcode; type CURL (line 69) | typedef void CURL; type bwStatsType (line 103) | enum bwStatsType { type bwZoomHdr_t (line 122) | typedef struct { type bigWigHdr_t (line 135) | typedef struct { type chromList_t (line 160) | typedef struct { type bwLL (line 168) | typedef struct bwLL bwLL; type bwLL (line 169) | struct bwLL { type bwZoomBuffer_t (line 173) | typedef struct bwZoomBuffer_t bwZoomBuffer_t; type bwZoomBuffer_t (line 174) | struct bwZoomBuffer_t { //each individual entry takes 32 bytes type bwWriteBuffer_t (line 185) | typedef struct { type bigWigFile_t (line 210) | typedef struct { type bwOverlappingIntervals_t (line 223) | typedef struct { type bbOverlappingEntries_t (line 234) | typedef struct { type bwOverlapIterator_t (line 246) | typedef struct { type bwStatsType (line 462) | enum bwStatsType type bwStatsType (line 476) | enum bwStatsType FILE: libBigWig/bigWigIO.h type CURLcode (line 10) | typedef int CURLcode; type CURL (line 11) | typedef void CURL; type bigWigFile_type_enum (line 28) | enum bigWigFile_type_enum { type URL_t (line 38) | typedef struct { FILE: libBigWig/bwRead.c function bwTell (line 11) | long bwTell(bigWigFile_t *fp) { function bwSetPos (line 19) | int bwSetPos(bigWigFile_t *fp, size_t pos) { function bwRead (line 26) | size_t bwRead(void *data, size_t sz, size_t nmemb, bigWigFile_t *fp) { function bwInit (line 38) | int bwInit(size_t defaultBufSize) { function bwCleanup (line 52) | void bwCleanup() { function bwZoomHdr_t (line 58) | static bwZoomHdr_t *bwReadZoomHdrs(bigWigFile_t *bw) { function bwHdrDestroy (line 109) | static void bwHdrDestroy(bigWigHdr_t *hdr) { function bwHdrRead (line 124) | static void bwHdrRead(bigWigFile_t *bw) { function destroyChromList (line 171) | static void destroyChromList(chromList_t *cl) { function readChromLeaf (line 184) | static uint64_t readChromLeaf(bigWigFile_t *bw, chromList_t *cl, uint32_... function readChromNonLeaf (line 209) | static uint64_t readChromNonLeaf(bigWigFile_t *bw, chromList_t *cl, uint... function readChromBlock (line 227) | static uint64_t readChromBlock(bigWigFile_t *bw, chromList_t *cl, uint32... function chromList_t (line 240) | static chromList_t *bwReadChromList(bigWigFile_t *bw) { function bwDestroyWriteBuffer (line 280) | static void bwDestroyWriteBuffer(bwWriteBuffer_t *wb) { function bwClose (line 289) | void bwClose(bigWigFile_t *fp) { function bwIsBigWig (line 302) | int bwIsBigWig(const char *fname, CURLcode (*callBack) (CURL*)) { function bbIsBigBed (line 332) | int bbIsBigBed(const char *fname, CURLcode (*callBack) (CURL*)) { function bigWigFile_t (line 345) | bigWigFile_t *bwOpen(const char *fname, CURLcode (*callBack) (CURL*), co... function bigWigFile_t (line 397) | bigWigFile_t *bbOpen(const char *fname, CURLcode (*callBack) (CURL*)) { FILE: libBigWig/bwStats.c function determineZoomLevel (line 11) | static int32_t determineZoomLevel(const bigWigFile_t *fp, int basesPerBi... type val_t (line 29) | struct val_t { type vals_t (line 35) | struct vals_t { function destroyVals_t (line 41) | void destroyVals_t(struct vals_t *v) { function getScalar (line 50) | double getScalar(uint32_t i_start, uint32_t i_end, uint32_t b_start, uin... type vals_t (line 63) | struct vals_t type vals_t (line 68) | struct vals_t type val_t (line 69) | struct val_t type vals_t (line 79) | struct vals_t type val_t (line 82) | struct val_t type val_t (line 112) | struct val_t type val_t (line 115) | struct val_t function blockMean (line 139) | static double blockMean(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint... function intMean (line 168) | static double intMean(bwOverlappingIntervals_t* ints, uint32_t start, ui... function blockDev (line 187) | static double blockDev(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint3... function intDev (line 223) | static double intDev(bwOverlappingIntervals_t* ints, uint32_t start, uin... function blockMax (line 246) | static double blockMax(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint3... function intMax (line 276) | static double intMax(bwOverlappingIntervals_t* ints) { function blockMin (line 290) | static double blockMin(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint3... function intMin (line 318) | static double intMin(bwOverlappingIntervals_t* ints) { function blockCoverage (line 333) | static double blockCoverage(bigWigFile_t *fp, bwOverlapBlock_t *blocks, ... function intCoverage (line 359) | static double intCoverage(bwOverlappingIntervals_t* ints, uint32_t start... function blockSum (line 376) | static double blockSum(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint3... function intSum (line 405) | static double intSum(bwOverlappingIntervals_t* ints, uint32_t start, uin... type bwStatsType (line 423) | enum bwStatsType type bwStatsType (line 485) | enum bwStatsType type bwStatsType (line 530) | enum bwStatsType FILE: libBigWig/bwValues.c function roundup (line 9) | static uint32_t roundup(uint32_t v) { function bwRTree_t (line 21) | static bwRTree_t *readRTreeIdx(bigWigFile_t *fp, uint64_t offset) { function bwRTreeNode_t (line 64) | static bwRTreeNode_t *bwGetRTreeNode(bigWigFile_t *fp, uint64_t offset) { function destroyBWOverlapBlock (line 124) | void destroyBWOverlapBlock(bwOverlapBlock_t *b) { function bwOverlapBlock_t (line 132) | static bwOverlapBlock_t *overlapsLeaf(bwRTreeNode_t *node, uint32_t tid,... function bwOverlapBlock_t (line 194) | static bwOverlapBlock_t *mergeOverlapBlocks(bwOverlapBlock_t *b1, bwOver... function bwOverlapBlock_t (line 226) | static bwOverlapBlock_t *overlapsNonLeaf(bigWigFile_t *fp, bwRTreeNode_t... function bwOverlapBlock_t (line 275) | bwOverlapBlock_t *walkRTreeNodes(bigWigFile_t *bw, bwRTreeNode_t *root, ... function bwGetTid (line 282) | uint32_t bwGetTid(const bigWigFile_t *fp, const char *chrom) { function bwOverlapBlock_t (line 291) | static bwOverlapBlock_t *bwGetOverlappingBlocks(bigWigFile_t *fp, const ... function bwFillDataHdr (line 313) | void bwFillDataHdr(bwDataHeader_t *hdr, void *b) { function bwDestroyOverlappingIntervals (line 323) | void bwDestroyOverlappingIntervals(bwOverlappingIntervals_t *o) { function bbDestroyOverlappingEntries (line 331) | void bbDestroyOverlappingEntries(bbOverlappingEntries_t *o) { function bwOverlappingIntervals_t (line 346) | static bwOverlappingIntervals_t *pushIntervals(bwOverlappingIntervals_t ... function bbOverlappingEntries_t (line 366) | static bbOverlappingEntries_t *pushBBIntervals(bbOverlappingEntries_t *o... function bwOverlappingIntervals_t (line 390) | bwOverlappingIntervals_t *bwGetOverlappingIntervalsCore(bigWigFile_t *fp... function bbOverlappingEntries_t (line 486) | bbOverlappingEntries_t *bbGetOverlappingEntriesCore(bigWigFile_t *fp, bw... function bwOverlappingIntervals_t (line 561) | bwOverlappingIntervals_t *bwGetOverlappingIntervals(bigWigFile_t *fp, co... function bbOverlappingEntries_t (line 573) | bbOverlappingEntries_t *bbGetOverlappingEntries(bigWigFile_t *fp, const ... function bwOverlapIterator_t (line 585) | bwOverlapIterator_t *bwOverlappingIntervalsIterator(bigWigFile_t *fp, co... function bwOverlapIterator_t (line 613) | bwOverlapIterator_t *bbOverlappingEntriesIterator(bigWigFile_t *fp, cons... function bwIteratorDestroy (line 641) | void bwIteratorDestroy(bwOverlapIterator_t *iter) { function bwOverlapIterator_t (line 650) | bwOverlapIterator_t *bwIteratorNext(bwOverlapIterator_t *iter) { function bwOverlappingIntervals_t (line 711) | bwOverlappingIntervals_t *bwGetValues(bigWigFile_t *fp, const char *chro... function bwDestroyIndexNode (line 761) | void bwDestroyIndexNode(bwRTreeNode_t *node) { function bwDestroyIndex (line 782) | void bwDestroyIndex(bwRTree_t *idx) { function bwRTree_t (line 789) | bwRTree_t *bwReadIndex(bigWigFile_t *fp, uint64_t offset) { FILE: libBigWig/bwValues.h type bwRTreeNode_t (line 20) | typedef struct bwRTreeNode_t { type bwRTree_t (line 39) | typedef struct { type bwOverlapBlock_t (line 56) | typedef struct { type bwDataHeader_t (line 67) | typedef struct { FILE: libBigWig/bwWrite.c type val_t (line 10) | struct val_t { function chromList_t (line 22) | chromList_t *bwCreateChromList(const char* const* chroms, const uint32_t... function bwCreateHdr (line 56) | int bwCreateHdr(bigWigFile_t *fp, int32_t maxZooms) { function writeAtPos (line 85) | static int writeAtPos(void *ptr, size_t sz, size_t nmemb, size_t pos, FI... function writeChromList (line 94) | static int writeChromList(FILE *fp, chromList_t *cl) { function bwWriteHdr (line 187) | int bwWriteHdr(bigWigFile_t *bw) { function insertIndexNode (line 230) | static int insertIndexNode(bigWigFile_t *fp, bwRTreeNode_t *leaf) { function appendIndexNodeEntry (line 246) | static int appendIndexNodeEntry(bigWigFile_t *fp, uint32_t tid0, uint32_... function addIndexEntry (line 262) | static int addIndexEntry(bigWigFile_t *fp, uint32_t tid0, uint32_t tid1,... function flushBuffer (line 312) | static int flushBuffer(bigWigFile_t *fp) { function updateStats (line 362) | static void updateStats(bigWigFile_t *fp, uint32_t span, float val) { function bwAddIntervals (line 374) | int bwAddIntervals(bigWigFile_t *fp, const char* const* chrom, const uin... function bwAppendIntervals (line 434) | int bwAppendIntervals(bigWigFile_t *fp, const uint32_t *start, const uin... function bwAddIntervalSpans (line 462) | int bwAddIntervalSpans(bigWigFile_t *fp, const char *chrom, const uint32... function bwAppendIntervalSpans (line 495) | int bwAppendIntervalSpans(bigWigFile_t *fp, const uint32_t *start, const... function bwAddIntervalSpanSteps (line 520) | int bwAddIntervalSpanSteps(bigWigFile_t *fp, const char *chrom, uint32_t... function bwAppendIntervalSpanSteps (line 552) | int bwAppendIntervalSpanSteps(bigWigFile_t *fp, const float *values, uin... function writeSummary (line 576) | int writeSummary(bigWigFile_t *fp) { function bwRTreeNode_t (line 585) | static bwRTreeNode_t *makeEmptyNode(uint32_t blockSize) { function bwRTreeNode_t (line 616) | static bwRTreeNode_t *addLeaves(bwLL **ll, uint64_t *sz, uint64_t toProc... function writeIndexTreeNode (line 657) | int writeIndexTreeNode(FILE *fp, bwRTreeNode_t *n, uint8_t *wrote, int l... function writeIndexOffsets (line 694) | int writeIndexOffsets(FILE *fp, bwRTreeNode_t *n, uint64_t offset) { function writeIndexTree (line 706) | int writeIndexTree(bigWigFile_t *fp) { function writeIndex (line 731) | int writeIndex(bigWigFile_t *fp) { function makeZoomLevels (line 808) | int makeZoomLevels(bigWigFile_t *fp) { function nextPos (line 884) | void nextPos(bigWigFile_t *fp, uint32_t size, uint32_t *pos, uint32_t de... function overlapsInterval (line 905) | uint32_t overlapsInterval(uint32_t tid0, uint32_t start0, uint32_t end0,... function updateInterval (line 919) | uint32_t updateInterval(bigWigFile_t *fp, bwZoomBuffer_t *buffer, double... function addIntervalValue (line 984) | int addIntervalValue(bigWigFile_t *fp, uint64_t *nEntries, double *sum, ... function constructZoomLevels (line 1021) | int constructZoomLevels(bigWigFile_t *fp) { function writeZoomLevels (line 1066) | int writeZoomLevels(bigWigFile_t *fp) { function bwFinalize (line 1229) | int bwFinalize(bigWigFile_t *fp) { FILE: libBigWig/io.c function getContentLength (line 15) | uint64_t getContentLength(const URL_t *URL) { function CURLcode (line 25) | CURLcode urlFetchData(URL_t *URL, unsigned long bufSize) { function url_fread (line 47) | size_t url_fread(void *obuf, size_t obufSize, URL_t *URL) { function urlRead (line 89) | size_t urlRead(URL_t *URL, void *buf, size_t bufSize) { function bwFillBuffer (line 101) | size_t bwFillBuffer(const void *inBuf, size_t l, size_t nmemb, void *pUR... function CURLcode (line 120) | CURLcode urlSeek(URL_t *URL, size_t pos) { function URL_t (line 161) | URL_t *urlOpen(const char *fname, CURLcode (*callBack)(CURL*), const cha... function urlClose (line 286) | void urlClose(URL_t *URL) { FILE: pyBigWig.c function getNumpyU32 (line 15) | uint32_t getNumpyU32(PyArrayObject *obj, Py_ssize_t i) { function getNumpyL (line 83) | long getNumpyL(PyObject *obj) { function getNumpyF (line 130) | float getNumpyF(PyArrayObject *obj, Py_ssize_t i) { function hasEntries (line 199) | int hasEntries(bigWigFile_t *bw) { function PyObject (line 205) | PyObject* pyBwEnter(pyBigWigFile_t*self, PyObject *args) { function PyObject (line 218) | PyObject* pyBwOpen(PyObject *self, PyObject *pyFname) { function pyBwDealloc (line 259) | static void pyBwDealloc(pyBigWigFile_t *self) { function PyObject (line 264) | static PyObject *pyBwClose(pyBigWigFile_t *self, PyObject *args) { function PyObject (line 272) | static PyObject *pyBwGetHeader(pyBigWigFile_t *self, PyObject *args) { function PyObject (line 318) | static PyObject *pyBwGetChroms(pyBigWigFile_t *self, PyObject *args) { function char2enum (line 364) | enum bwStatsType char2enum(char *s) { function PyObject (line 652) | static PyObject *pyBwGetIntervals(pyBigWigFile_t *self, PyObject *args, ... function PyString_Check (line 765) | int PyString_Check(PyObject *obj) { function isNumeric (line 779) | int isNumeric(PyObject *obj) { function Numeric2Uint (line 790) | uint32_t Numeric2Uint(PyObject *obj) { function PyObject (line 807) | PyObject *pyBwAddHeader(pyBigWigFile_t *self, PyObject *args, PyObject *... function isType0 (line 923) | int isType0(PyObject *chroms, PyObject *starts, PyObject *ends, PyObject... function isType1 (line 1020) | int isType1(PyObject *chroms, PyObject *starts, PyObject *values, PyObje... function isType2 (line 1072) | int isType2(PyObject *chroms, PyObject *starts, PyObject *values, PyObje... function getType (line 1097) | int getType(PyObject *chroms, PyObject *starts, PyObject *ends, PyObject... function else (line 1157) | else if(desiredType == 1) { function else (line 1175) | else if(desiredType == 2) { function PyAddIntervals (line 1197) | int PyAddIntervals(pyBigWigFile_t *self, PyObject *chroms, PyObject *sta... function PyAppendIntervals (line 1275) | int PyAppendIntervals(pyBigWigFile_t *self, PyObject *starts, PyObject *... function PyAddIntervalSpans (line 1335) | int PyAddIntervalSpans(pyBigWigFile_t *self, PyObject *chroms, PyObject ... function PyAppendIntervalSpans (line 1400) | int PyAppendIntervalSpans(pyBigWigFile_t *self, PyObject *starts, PyObje... function PyAddIntervalSpanSteps (line 1458) | int PyAddIntervalSpanSteps(pyBigWigFile_t *self, PyObject *chroms, PyObj... function PyAppendIntervalSpanSteps (line 1507) | int PyAppendIntervalSpanSteps(pyBigWigFile_t *self, PyObject *values) { function else (line 1612) | else if(type == 1) { function else (line 1652) | else if(type == 2) { function PyObject (line 1675) | PyObject *pyBwAddEntries(pyBigWigFile_t *self, PyObject *args, PyObject ... function PyObject (line 1746) | static PyObject *pyBBGetEntries(pyBigWigFile_t *self, PyObject *args, Py... function PyObject (line 1854) | static PyObject *pyBBGetSQL(pyBigWigFile_t *self, PyObject *args) { function PyObject (line 1881) | static PyObject *pyIsBigWig(pyBigWigFile_t *self, PyObject *args) { function PyObject (line 1892) | static PyObject *pyIsBigBed(pyBigWigFile_t *self, PyObject *args) { function PyMODINIT_FUNC (line 1918) | PyMODINIT_FUNC initpyBigWig(void) { FILE: pyBigWig.h type pyBigWigFile_t (line 7) | typedef struct { type pyBigWigmodule_state (line 391) | struct pyBigWigmodule_state { FILE: pyBigWigTest/test.py class TestRemote (line 8) | class TestRemote(): method doOpen (line 11) | def doOpen(self): method doOpenWith (line 16) | def doOpenWith(self): method doChroms (line 20) | def doChroms(self, bw): method doHeader (line 25) | def doHeader(self, bw): method doStats (line 28) | def doStats(self, bw): method doValues (line 35) | def doValues(self, bw): method doIntervals (line 40) | def doIntervals(self, bw): method doSum (line 45) | def doSum(self, bw): method doWrite (line 48) | def doWrite(self, bw): method doWrite2 (line 85) | def doWrite2(self): method doWriteEmpty (line 144) | def doWriteEmpty(self): method doWriteNumpy (line 167) | def doWriteNumpy(self): method testAll (line 193) | def testAll(self): class TestLocal (line 209) | class TestLocal(): method testFoo (line 210) | def testFoo(self): class TestBigBed (line 215) | class TestBigBed(): method testBigBed (line 216) | def testBigBed(self): class TestNumpy (line 247) | class TestNumpy(): method testNumpy (line 248) | def testNumpy(self): method testNumpyValues (line 312) | def testNumpyValues(self):