SYMBOL INDEX (2098 symbols across 106 files)

FILE: .agents/skills/regression-testing/compare_sample_pair.py
  function gcloud_cat (line 29) | def gcloud_cat(gcs_uri):
  function gcloud_cp (line 40) | def gcloud_cp(gcs_uri, local_path):
  function parse_tsv (line 50) | def parse_tsv(content):
  function parse_fasta (line 80) | def parse_fasta(content):
  function run_mafft_pair (line 101) | def run_mafft_pair(old_seq, new_seq, work_dir, pair_id='0'):
  function align_and_analyze_fastas (line 123) | def align_and_analyze_fastas(old_fasta_path, new_fasta_path, work_dir):
  function analyze_alignment_seqs (line 210) | def analyze_alignment_seqs(old_seq_str, new_seq_str):
  function analyze_alignment (line 346) | def analyze_alignment(aligned_fasta_path):
  function compare_assembly (line 355) | def compare_assembly(assembly_id, old_row, new_row, work_dir):
  function main (line 442) | def main():

FILE: .agents/skills/regression-testing/discover_pairs.py
  function gcloud_ls (line 25) | def gcloud_ls(path):
  function find_tsv_in_call_dir (line 41) | def find_tsv_in_call_dir(call_dir_uri):
  function discover_submission_tsvs (line 73) | def discover_submission_tsvs(bucket, submission_id):
  function main (line 103) | def main():

FILE: .agents/skills/regression-testing/generate_report.py
  function get_deps (line 16) | def get_deps():
  function load_results (line 24) | def load_results(results_dir):
  function build_comparison_table (line 36) | def build_comparison_table(results, workspace_name):
  function build_sample_summary (line 90) | def build_sample_summary(results):
  function generate_plots (line 106) | def generate_plots(df, plot_dir):
  function generate_markdown_report (line 267) | def generate_markdown_report(df, sample_df, workspace_name, report_dir, ...
  function main (line 407) | def main():

FILE: docker/scripts/calc_mem.py
  function available_cpu_count (line 34) | def available_cpu_count():
  function mem_from_proc_meminfo (line 93) | def mem_from_proc_meminfo():
  function mem_from_cgroups (line 104) | def mem_from_cgroups():
  function mem_from_psutil (line 124) | def mem_from_psutil(metric_name="total"):

FILE: docs/conf.py
  function _git_version (line 44) | def _git_version():

FILE: src/viral_ngs/assemble/freebayes.py
  class FreeBayesTool (line 23) | class FreeBayesTool(Tool):
    method __init__ (line 25) | def __init__(self):
    method call (line 29) | def call(self, inBam, refFasta, outVcf, options=None):

FILE: src/viral_ngs/assemble/gap2seq.py
  class Gap2SeqTool (line 28) | class Gap2SeqTool(viral_ngs.core.Tool):
    method __init__ (line 31) | def __init__(self, install_methods=None):
    method version (line 36) | def version(self):
    method execute (line 39) | def execute(self, args):    # pylint: disable=W0221
    method _run_gap2seq (line 44) | def _run_gap2seq(self, reads, scaffolds, filled, *args, **kwargs):
    method gapfill (line 59) | def gapfill(self, in_scaffold, in_bam, out_scaffold, solid_kmer_thresh...

FILE: src/viral_ngs/assemble/mafft.py
  class MafftTool (line 23) | class MafftTool(viral_ngs.core.Tool):
    method __init__ (line 25) | def __init__(self, install_methods=None):
    method version (line 30) | def version(self):
    method _get_tool_version (line 35) | def _get_tool_version(self):
    method __seqIdsAreAllUnique (line 38) | def __seqIdsAreAllUnique(self, filePath, inputFormat="fasta"):
    method execute (line 53) | def execute(

FILE: src/viral_ngs/assemble/mummer.py
  class MummerTool (line 22) | class MummerTool(viral_ngs.core.Tool):
    method __init__ (line 24) | def __init__(self, install_methods=None):
    method version (line 29) | def version(self):
    method _get_tool_version (line 34) | def _get_tool_version(self):
    method executable_path (line 37) | def executable_path(self):
    method execute (line 44) | def execute(self, refFasta, qryFastas):
    method nucmer (line 50) | def nucmer(self, refFasta, qryFasta, outDelta, extend=None, breaklen=N...
    method promer (line 75) | def promer(self, refFasta, qryFasta, outDelta, extend=None, breaklen=N...
    method delta_filter (line 100) | def delta_filter(self, inDelta, outDelta):
    method show_tiling (line 107) | def show_tiling(self, inDelta, outTiling, outFasta=None,
    method trim_contigs (line 136) | def trim_contigs(self, refFasta, contigsFasta, outFasta,
    method scaffold_contigs (line 182) | def scaffold_contigs(self, refFasta, contigsFasta, outFasta,
    method scaffold_contigs_custom (line 210) | def scaffold_contigs_custom(self, refFasta, contigsFasta, outFasta,
    method align_one_to_one (line 341) | def align_one_to_one(self, refFasta, otherFasta, outFasta):
  function contig_chooser (line 378) | def contig_chooser(alt_seqs, ref_len, coords_debug=""):
  class AmbiguousAlignmentException (line 454) | class AmbiguousAlignmentException(Exception):
  class AlignsReader (line 457) | class AlignsReader(object):
    method __init__ (line 460) | def __init__(self, aligns_file, ref_fasta=None):
    method _load_align (line 469) | def _load_align(self):
    method _load_fastas (line 525) | def _load_fastas(self):
    method get_alignments (line 529) | def get_alignments(self):
    method get_intervals (line 533) | def get_intervals(self):
    method _dummy_row (line 554) | def _dummy_row(self, start, stop, filler='N'):
    method get_ref_seq (line 559) | def get_ref_seq(self, start, stop):
    method retrieve_alts_by_ref (line 566) | def retrieve_alts_by_ref(self, start, stop, aln_start=None, aln_stop=N...
    method _aln_to_alt_seq (line 597) | def _aln_to_alt_seq(self, aln, start, stop):

FILE: src/viral_ngs/assemble/muscle.py
  class MuscleTool (line 22) | class MuscleTool(viral_ngs.core.Tool):
    method __init__ (line 24) | def __init__(self, install_methods=None):
    method version (line 29) | def version(self):
    method _get_tool_version (line 34) | def _get_tool_version(self):
    method execute (line 38) | def execute(

FILE: src/viral_ngs/assemble/rasusa.py
  class RasusaTool (line 19) | class RasusaTool(Tool):
    method __init__ (line 21) | def __init__(self):
    method downsample_bam (line 25) | def downsample_bam(self, inBam, outBam, coverage, seed=None):

FILE: src/viral_ngs/assemble/skani.py
  class UndirectedGraph (line 31) | class UndirectedGraph:
    method __init__ (line 34) | def __init__(self):
    method add_node (line 37) | def add_node(self, node):
    method add_edge (line 40) | def add_edge(self, node1, node2):
    method _dfs (line 44) | def _dfs(self, node, visited):
    method get_clusters (line 53) | def get_clusters(self):
  class SkaniTool (line 62) | class SkaniTool(viral_ngs.core.Tool):
    method __init__ (line 64) | def __init__(self, install_methods=None):
    method version (line 69) | def version(self):
    method _get_tool_version (line 74) | def _get_tool_version(self):
    method _is_fasta_basically_empty (line 77) | def _is_fasta_basically_empty(self, inFasta, min_length=500):
    method _sort_skani_table_by_product (line 87) | def _sort_skani_table_by_product(self, in_tsv, out_tsv):
    method execute (line 106) | def execute(self, subcommand, args, outfile, threads=None):
    method triangle (line 120) | def triangle(self, ref_fastas, outfile_ani, other_args = (), threads=N...
    method dist (line 125) | def dist(self, query_fasta, ref_fastas, outfile, other_args = (), thre...
    method find_reference_clusters (line 136) | def find_reference_clusters(self, ref_fastas,
    method find_closest_reference (line 159) | def find_closest_reference(self, contigs_fasta, ref_fastas, out_file,

FILE: src/viral_ngs/assemble/spades.py
  class SpadesTool (line 26) | class SpadesTool(viral_ngs.core.Tool):
    method __init__ (line 29) | def __init__(self, install_methods=None):
    method version (line 34) | def version(self):
    method _get_tool_version (line 39) | def _get_tool_version(self):
    method execute (line 42) | def execute(self, args):    # pylint: disable=W0221
    method assemble (line 47) | def assemble(self, reads_fwd, reads_bwd, contigs_out, reads_unpaired=N...

FILE: src/viral_ngs/assemble/vcf.py
  function make_intervals (line 17) | def make_intervals(i, n, fasta, chr_prefix='', verbose=False):
  function sliding_windows (line 58) | def sliding_windows(fasta, width, offset, chr_prefix=''):
  class GenomePosition (line 74) | class GenomePosition(object):
    method __init__ (line 80) | def __init__(self, seqDb):
    method get_gpos (line 92) | def get_gpos(self, c, p):
    method get_chr_pos (line 98) | def get_chr_pos(self, gpos):
  function parse_contig_header (line 109) | def parse_contig_header(line):
  function get_chrlens (line 127) | def get_chrlens(inFile):
  function calc_maf (line 162) | def calc_maf(genos, ancestral=None, ploidy=1):
  class TabixReader (line 200) | class TabixReader(pysam.TabixFile):
    method __init__ (line 209) | def __init__(self, inFile, parser=pysam.asTuple()):
    method __enter__ (line 225) | def __enter__(self):
    method __exit__ (line 228) | def __exit__(self, exc_type, exc_val, exc_tb):
    method chroms (line 236) | def chroms(self):
    method get (line 239) | def get(self, chrom=None, start=None, stop=None, region=None):
  function get_pos_from_vcf_record (line 245) | def get_pos_from_vcf_record(vcfrec):
  function bytes_to_string (line 250) | def bytes_to_string(o):
  class VcfReader (line 256) | class VcfReader(TabixReader):
    method __init__ (line 264) | def __init__(self, inFile, ploidy=1, parser=pysam.asVCF()):
    method samples (line 285) | def samples(self):
    method chrlens (line 288) | def chrlens(self):
    method get_positions (line 291) | def get_positions(self, c=None, start=None, stop=None, region=None):
    method get_range (line 296) | def get_range(self, c=None, start=None, stop=None, region=None, as_str...
    method get_snp_genos (line 328) | def get_snp_genos(self, c, p, as_strings=True):
    method getFullSequences (line 337) | def getFullSequences(self, c, start, stop, samples,
  function replaceAlleles (line 397) | def replaceAlleles(sample, seq, vcf_records):

FILE: src/viral_ngs/assemble/wgsim.py
  class WgsimTool (line 25) | class WgsimTool(viral_ngs.core.Tool):
    method __init__ (line 27) | def __init__(self, install_methods=None):
    method version (line 32) | def version(self):
    method _get_tool_version (line 37) | def _get_tool_version(self):
    method slice_fasta (line 56) | def slice_fasta(self, in_fasta, out_fasta, seq_id=None, start=None, en...
    method coverage_to_read_pairs (line 94) | def coverage_to_read_pairs(self, coverage, sequence_length, read_length):
    method fastqs_to_bam (line 110) | def fastqs_to_bam(self, in_fastq1, in_fastq2, out_bam, sample_name='sa...
    method execute (line 133) | def execute(self, in_fasta, out_fastq1, out_fastq2,

FILE: src/viral_ngs/assembly.py
  class DenovoAssemblyError (line 55) | class DenovoAssemblyError(RuntimeError):
    method __init__ (line 60) | def __init__(self, reason):
  function assemble_spades (line 64) | def assemble_spades(
  function parser_assemble_spades (line 108) | def parser_assemble_spades(parser=argparse.ArgumentParser()):
  function gapfill_gap2seq (line 137) | def gapfill_gap2seq(in_scaffold, in_bam, out_scaffold, threads=None, mem...
  function parser_gapfill_gap2seq (line 151) | def parser_gapfill_gap2seq(parser=argparse.ArgumentParser(description='C...
  function cluster_references_ani (line 171) | def cluster_references_ani(inRefs, outClusters, m=15, s=50, c=10, min_af...
  function parser_cluster_references_ani (line 180) | def parser_cluster_references_ani(parser=argparse.ArgumentParser(descrip...
  function skani_contigs_to_refs (line 194) | def skani_contigs_to_refs(inContigs, inRefs, out_skani_dist, out_skani_d...
  function parser_skani_contigs_to_refs (line 222) | def parser_skani_contigs_to_refs(parser=argparse.ArgumentParser(descript...
  function _order_and_orient_orig (line 241) | def _order_and_orient_orig(inFasta, inReference, outFasta,
  function _call_order_and_orient_orig (line 282) | def _call_order_and_orient_orig(inReference, outFasta, outAlternateConti...
  function order_and_orient (line 285) | def order_and_orient(inFasta, inReference, outFasta,
  function parser_order_and_orient (line 360) | def parser_order_and_orient(parser=argparse.ArgumentParser()):
  class IncompleteAssemblyError (line 472) | class IncompleteAssemblyError(Exception):
    method __init__ (line 473) | def __init__(self, actual_n, expected_n):
  class PoorAssemblyError (line 479) | class PoorAssemblyError(Exception):
    method __init__ (line 480) | def __init__(self, chr_idx, seq_len, non_n_count, min_length, segment_...
  function impute_from_reference (line 488) | def impute_from_reference(
  function parser_impute_from_reference (line 614) | def parser_impute_from_reference(parser=argparse.ArgumentParser()):
  function refine_assembly (line 663) | def refine_assembly(
  function parser_refine_assembly (line 801) | def parser_refine_assembly(parser=argparse.ArgumentParser()):
  function normalize_coverage (line 892) | def normalize_coverage(inBam, outBam, max_coverage, seed=None, threads=N...
  function parser_normalize_coverage (line 907) | def parser_normalize_coverage(parser=argparse.ArgumentParser()):
  function parser_filter_short_seqs (line 925) | def parser_filter_short_seqs(parser=argparse.ArgumentParser()):
  function main_filter_short_seqs (line 941) | def main_filter_short_seqs(args):
  function parser_modify_contig (line 959) | def parser_modify_contig(parser=argparse.ArgumentParser()):
  function main_modify_contig (line 1040) | def main_modify_contig(args):
  class ContigModifier (line 1092) | class ContigModifier(object):
    method __init__ (line 1098) | def __init__(self, ref, consensus):
    method get_stripped_consensus (line 1105) | def get_stripped_consensus(self):
    method call_reference_ns (line 1108) | def call_reference_ns(self):
    method call_reference_ambiguous (line 1114) | def call_reference_ambiguous(self):
    method trim_ends (line 1121) | def trim_ends(self):
    method replace_end_gaps (line 1131) | def replace_end_gaps(self):
    method replace_5ends (line 1140) | def replace_5ends(self, replace_length):
    method replace_3ends (line 1154) | def replace_3ends(self, replace_length):
    method remove_end_ns (line 1165) | def remove_end_ns(self):
  class MutableSequence (line 1178) | class MutableSequence(object):
    method __init__ (line 1180) | def __init__(self, name, start, stop, init_seq=None):
    method modify (line 1194) | def modify(self, p, new_base):
    method replace (line 1200) | def replace(self, start, stop, new_seq):
    method __change__ (line 1205) | def __change__(self, start, stop, new_seq):
    method replay_deletions (line 1224) | def replay_deletions(self):
    method emit (line 1228) | def emit(self):
  function alleles_to_ambiguity (line 1232) | def alleles_to_ambiguity(allelelist):
  function vcfrow_parse_and_call_snps (line 1246) | def vcfrow_parse_and_call_snps(vcfrow, samples, min_dp=0, major_cutoff=0...
  function vcf_to_seqs (line 1302) | def vcf_to_seqs(vcfIter, chrlens, samples, min_dp=0, major_cutoff=0.5, m...
  function parser_vcf_to_fasta (line 1348) | def parser_vcf_to_fasta(parser=argparse.ArgumentParser()):
  function main_vcf_to_fasta (line 1401) | def main_vcf_to_fasta(args):
  function parser_trim_fasta (line 1449) | def parser_trim_fasta(parser=argparse.ArgumentParser()):
  function trim_fasta (line 1457) | def trim_fasta(inFasta, outFasta):
  function deambig_base (line 1473) | def deambig_base(base):
  function deambig_fasta (line 1479) | def deambig_fasta(inFasta, outFasta):
  function parser_deambig_fasta (line 1492) | def parser_deambig_fasta(parser=argparse.ArgumentParser()):
  function vcf_dpdiff (line 1503) | def vcf_dpdiff(vcfs):
  function parser_dpdiff (line 1521) | def parser_dpdiff(parser=argparse.ArgumentParser()):
  function dpdiff (line 1529) | def dpdiff(inVcfs, outFile):
  function alignment_summary (line 1546) | def alignment_summary(inFastaFileOne, inFastaFileTwo, outfileName=None, ...
  function parser_alignment_summary (line 1653) | def parser_alignment_summary(parser=argparse.ArgumentParser()):
  function simulate_illumina_reads (line 1664) | def simulate_illumina_reads(
  function parser_simulate_illumina_reads (line 1798) | def parser_simulate_illumina_reads(parser=argparse.ArgumentParser()):
  function full_parser (line 1823) | def full_parser():
  function main (line 1827) | def main():

FILE: src/viral_ngs/broad_utils.py
  function get_json_from_picard (line 25) | def get_json_from_picard(picardDir):
  function get_run_date (line 35) | def get_run_date(jsonfile):
  function get_bustard_dir (line 40) | def get_bustard_dir(jsonfile):
  function parser_get_bustard_dir (line 46) | def parser_get_bustard_dir(parser=argparse.ArgumentParser()):
  function main_get_bustard_dir (line 51) | def main_get_bustard_dir(args):
  function parser_get_run_date (line 58) | def parser_get_run_date(parser=argparse.ArgumentParser()):
  function main_get_run_date (line 63) | def main_get_run_date(args):
  function iterate_wells (line 74) | def iterate_wells(runfile):
  function get_all_samples (line 80) | def get_all_samples(runfile):
  function get_all_libraries (line 84) | def get_all_libraries(runfile):
  function get_run_id (line 89) | def get_run_id(well):
  function get_all_runs (line 98) | def get_all_runs(runfile):
  function parser_get_all_names (line 103) | def parser_get_all_names(parser=argparse.ArgumentParser()):
  function main_get_all_names (line 109) | def main_get_all_names(args):
  function full_parser (line 124) | def full_parser():
  function main (line 128) | def main():

FILE: src/viral_ngs/classify/blast.py
  class BlastTools (line 27) | class BlastTools(core.Tool):
    method __init__ (line 31) | def __init__(self, install_methods=None):
    method execute (line 42) | def execute(self, *args):
  class BlastnTool (line 48) | class BlastnTool(BlastTools):
    method get_hits_pipe (line 52) | def get_hits_pipe(self, inPipe, db, threads=None, task=None, outfmt='6...
    method get_hits_bam (line 106) | def get_hits_bam(self, inBam, db, threads=None):
    method get_hits_fasta (line 112) | def get_hits_fasta(self, inFasta, db, threads=None, task=None, outfmt=...
  class MakeblastdbTool (line 119) | class MakeblastdbTool(BlastTools):
    method build_database (line 123) | def build_database(self, fasta_files, database_prefix_path):

FILE: src/viral_ngs/classify/bmtagger.py
  class BmtaggerTools (line 16) | class BmtaggerTools(core.Tool):
    method __init__ (line 31) | def __init__(self, install_methods=None):
    method execute (line 38) | def execute(self, *args):
    method silent_execute (line 43) | def silent_execute(self, *args):
  class BmtaggerShTool (line 50) | class BmtaggerShTool(BmtaggerTools):
  class BmfilterTool (line 55) | class BmfilterTool(BmtaggerTools):
  class BmtoolTool (line 60) | class BmtoolTool(BmtaggerTools):
    method build_database (line 64) | def build_database(self, fasta_files, bitmask_file_path, max_ambig=0, ...
  class ExtractFullseqTool (line 95) | class ExtractFullseqTool(BmtaggerTools):
  class SrprismTool (line 100) | class SrprismTool(BmtaggerTools):
    method build_database (line 104) | def build_database(self, fasta_files, database_prefix_path):

FILE: src/viral_ngs/classify/kb.py
  class kb (line 25) | class kb(core.Tool):
    method __init__ (line 28) | def __init__(self, install_methods=None):
    method version (line 34) | def version(self):
    method libexec (line 38) | def libexec(self):
    method execute (line 44) | def execute(self, command,output, args=None, options=None):
    method build (line 100) | def build(self, ref_fasta, index, workflow='standard', kmer_len=31,  p...
    method classify (line 123) | def classify(self, in_bam, index_file, out_dir, t2g_file, k=31, parity...
    method extract (line 229) | def extract(self, in_bam, index_file, target_ids, out_dir, t2g_file, p...
    method _extract_h5ad_from_tarball_to_tmpdir (line 309) | def _extract_h5ad_from_tarball_to_tmpdir(self, count_tar, tmp_dir):
    method _add_sample_metadata_to_h5ad (line 331) | def _add_sample_metadata_to_h5ad(self, h5ad_or_tarball, sample_name=No...
    method merge_h5ads (line 389) | def merge_h5ads(self, in_count_tars, out_h5ad, tmp_dir_parent=None):
    method parse_h5ad_counts (line 433) | def parse_h5ad_counts(self, h5ad_file):
    method extract_hit_ids_from_h5ad (line 454) | def extract_hit_ids_from_h5ad(self, h5ad_file, threshold=1):

FILE: src/viral_ngs/classify/kma.py
  class KMA (line 19) | class KMA(core.Tool):
    method __init__ (line 21) | def __init__(self, install_methods=None):
    method version (line 27) | def version(self):
    method libexec (line 41) | def libexec(self):
    method execute (line 46) | def execute(self, command, args=None, options=None):
    method build (line 70) | def build(self, ref_fasta, db_prefix, num_threads=None):
    method classify (line 87) | def classify(self, in_bam, db, out_prefix, num_threads=None):

FILE: src/viral_ngs/classify/kmc.py
  class KmcTool (line 36) | class KmcTool(core.Tool):
    method __init__ (line 39) | def __init__(self, install_methods=None):
    method version (line 45) | def version(self):
    method _kmer_db_name (line 48) | def _kmer_db_name(self, kmer_db):
    method is_kmer_db (line 53) | def is_kmer_db(self, kmer_db):
    method _get_file_format_opt (line 58) | def _get_file_format_opt(self, fname):
    method build_kmer_db (line 70) | def build_kmer_db(self, seq_files, kmer_db, kmer_size=DEFAULT_KMER_SIZ...
    method execute (line 129) | def execute(self, args, threads=None, return_output=False):  # pylint:...
    method dump_kmer_counts (line 144) | def dump_kmer_counts(self, kmer_db, out_kmers, min_occs=1, max_occs=mi...
    method read_kmer_counts (line 152) | def read_kmer_counts(self, kmer_counts_txt):
    method get_kmer_counts (line 161) | def get_kmer_counts(self, kmer_db, **kwargs):
    method get_kmer_db_info (line 168) | def get_kmer_db_info(self, kmer_db):
    method filter_reads (line 188) | def filter_reads(self, kmer_db, in_reads, out_reads, db_min_occs=1, db...
    method kmers_binary_op (line 285) | def kmers_binary_op(self, op, kmer_db1, kmer_db2, kmer_db_out,
    method set_kmer_counts (line 298) | def set_kmer_counts(self, kmer_db_in, value, kmer_db_out, threads=None):

FILE: src/viral_ngs/classify/kraken2.py
  class Kraken2 (line 24) | class Kraken2(core.Tool):
    method __init__ (line 26) | def __init__(self, install_methods=None):
    method version (line 32) | def version(self):
    method libexec (line 36) | def libexec(self):
    method build (line 41) | def build(self, db, standard_libraries=(), custom_libraries=(), taxdum...
    method inspect (line 121) | def inspect(self, db, output, num_threads=None):
    method execute (line 128) | def execute(self, command, db, output, args=None, options=None):
    method pipeline (line 153) | def pipeline(self, db, in_bams, out_reports=None, out_reads=None,
    method classify (line 165) | def classify(self, in_bam, db, out_reads=None, out_report=None,

FILE: src/viral_ngs/classify/krona.py
  class Krona (line 10) | class Krona(core.Tool):
    method __init__ (line 11) | def __init__(self, install_methods=None):
    method opt (line 17) | def opt(self):
    method import_taxonomy (line 25) | def import_taxonomy(self,
    method create_db (line 60) | def create_db(self, db_dir):
    method build_db (line 72) | def build_db(self, db_dir, taxdump_tar_gz=None, get_accessions=False):

FILE: src/viral_ngs/classify/last.py
  class LastTools (line 20) | class LastTools(core.Tool):
    method __init__ (line 26) | def __init__(self, install_methods=None):
  class Lastal (line 33) | class Lastal(LastTools):
    method get_hits (line 37) | def get_hits(self, inBam, db,
  class Lastdb (line 85) | class Lastdb(LastTools):
    method is_indexed (line 89) | def is_indexed(self, db_prefix):
    method build_database (line 93) | def build_database(self, fasta_files, database_prefix_path=None): # py...
    method execute (line 123) | def execute(self, inputFasta, outputDirectory, outputFilePrefix):    #...

FILE: src/viral_ngs/classify/taxonomy.py
  class TaxIdError (line 21) | class TaxIdError(ValueError):
  function maybe_compressed (line 25) | def maybe_compressed(fn):
  function blast_records (line 44) | def blast_records(f):
  function paired_query_id (line 61) | def paired_query_id(record):
  function blast_m8_taxids (line 72) | def blast_m8_taxids(record):
  function extract_tax_id (line 76) | def extract_tax_id(sam1):
  function coverage_lca (line 85) | def coverage_lca(query_ids, parents, lca_percent=100):
  function parents_to_children (line 125) | def parents_to_children(parents):
  function rank_code (line 140) | def rank_code(rank):
  class TaxonomyDb (line 164) | class TaxonomyDb(object):
    method __init__ (line 172) | def __init__(
    method load_gi_single_dmp (line 218) | def load_gi_single_dmp(self, dmp_path):
    method load_names (line 231) | def load_names(self, names_db, scientific_only=True):
    method load_nodes (line 249) | def load_nodes(self, nodes_db):
    method get_ordered_ancestors (line 263) | def get_ordered_ancestors(self, taxid):
    method process_blast_hits (line 270) | def process_blast_hits(self, hits, top_percent):
    method process_sam_hits (line 296) | def process_sam_hits(self, sam_hits, top_percent):
    method translate_gi_to_tax_id (line 316) | def translate_gi_to_tax_id(self, record):
    method sam_lca (line 324) | def sam_lca(self, sam_file, output=None, top_percent=10, unique_only=T...
    method sam_lca_report (line 367) | def sam_lca_report(self, bam_aligned, outReport, outReads=None, unique...
    method blast_lca (line 378) | def blast_lca(self,
    method kraken_dfs (line 412) | def kraken_dfs(self, lines, taxa_hits, total_hits, taxid, level):
    method kraken_dfs_report (line 424) | def kraken_dfs_report(self, taxa_hits):

FILE: src/viral_ngs/core/__init__.py
  function iter_leaf_subclasses (line 28) | def iter_leaf_subclasses(a_class):
  function all_tool_classes (line 40) | def all_tool_classes():
  function get_tool_by_name (line 44) | def get_tool_by_name(name):
  function skip_install_test (line 50) | def skip_install_test(condition=None):
  function is_osx (line 62) | def is_osx():
  class Tool (line 66) | class Tool(object):
    method __init__ (line 70) | def __init__(self, install_methods=None):
    method is_installed (line 78) | def is_installed(self):
    method install (line 81) | def install(self):
    method get_install_methods (line 92) | def get_install_methods(self):
    method set_install_methods (line 95) | def set_install_methods(self, methods):
    method version (line 98) | def version(self):
    method _get_tool_version (line 103) | def _get_tool_version(self):
    method executable_path (line 106) | def executable_path(self):
    method execute (line 109) | def execute(self, *args):
    method install_and_get_path (line 112) | def install_and_get_path(self):
  class InstallMethod (line 119) | class InstallMethod(object):
    method __init__ (line 126) | def __init__(self):
    method is_attempted (line 129) | def is_attempted(self):
    method attempt_install (line 132) | def attempt_install(self):    # Override _attempt_install, not this.
    method _attempt_install (line 136) | def _attempt_install(self):
    method is_installed (line 139) | def is_installed(self):
    method executable_path (line 142) | def executable_path(self):
  class PrexistingUnixCommand (line 146) | class PrexistingUnixCommand(InstallMethod):
    method __init__ (line 152) | def __init__(self, path, verifycmd=None, verifycode=0, require_executa...
    method _attempt_install (line 160) | def _attempt_install(self):
    method is_installed (line 169) | def is_installed(self):
    method executable_path (line 174) | def executable_path(self):

FILE: src/viral_ngs/core/bbmap.py
  class BBMapTool (line 19) | class BBMapTool(Tool):
    method __init__ (line 22) | def __init__(self, install_methods=None):
    method _get_tool_version (line 27) | def _get_tool_version(self):
    method execute (line 30) | def execute(self, tool, **kwargs):  # pylint: disable=arguments-differ
    method align (line 39) | def align(self, inBam, refFasta, outBam, min_qual=0, nodisk=True, JVMm...
    method bbnorm (line 65) | def bbnorm(self, inFastq, outFastq, tmpdir=None, target=None, k=None,

FILE: src/viral_ngs/core/bwa.py
  class Bwa (line 25) | class Bwa(Tool):
    method __init__ (line 27) | def __init__(self, install_methods=None):
    method execute (line 32) | def execute(self, command, args, stdout=None, stdin=None, background=F...
    method index (line 44) | def index(self, inFasta, output=None, algorithm=None):
    method align_mem_bam (line 56) | def align_mem_bam(self, inBam, refDb, outBam, options=None,
    method align_mem_one_rg (line 128) | def align_mem_one_rg(self, inBam, refDb, outBam, rgid=None, options=None,
    method mem (line 206) | def mem(self, inReads, refDb, outAlign, options=None, min_score_to_fil...
    method filter_sam_on_alignment_score (line 240) | def filter_sam_on_alignment_score(self, in_sam, out_sam, min_score_to_...

FILE: src/viral_ngs/core/cdhit.py
  class CdHit (line 18) | class CdHit(Tool):
    method __init__ (line 28) | def __init__(self, install_methods=None):
    method execute (line 33) | def execute(self, command, input_fn, output_fn, options=None, option_s...

FILE: src/viral_ngs/core/cmd.py
  class color (line 29) | class color(object):
  function setup_logger (line 43) | def setup_logger(log_level):
  function script_name (line 52) | def script_name():
  function common_args (line 56) | def common_args(parser, arglist=(('tmp_dir', None), ('loglevel', None))):
  function main_command (line 97) | def main_command(mainfunc):
  function attach_main (line 112) | def attach_main(parser, cmd_main, split_args=False):
  class _HelpAction (line 121) | class _HelpAction(argparse._HelpAction):
    method __call__ (line 123) | def __call__(self, parser, namespace, values, option_string=None):
  class storeMultiArgsOrFallBackToConst (line 156) | class storeMultiArgsOrFallBackToConst(argparse.Action):
    method __call__ (line 180) | def __call__(self, parser, namespace, values, option_string=None):
  function make_parser (line 189) | def make_parser(commands, description):
  function main_argparse (line 220) | def main_argparse(commands, description):
  function find_tmp_dir (line 264) | def find_tmp_dir():
  class BadInputError (line 285) | class BadInputError(RuntimeError):
    method __init__ (line 289) | def __init__(self, reason):
  function check_input (line 292) | def check_input(condition, error_msg):
  function parse_cmd (line 297) | def parse_cmd(module, cmd, args):
  function run_cmd (line 307) | def run_cmd(module, cmd, args):

FILE: src/viral_ngs/core/errors.py
  class QCError (line 3) | class QCError(RuntimeError):
    method __init__ (line 6) | def __init__(self, reason):
  class InvalidBamHeaderError (line 9) | class InvalidBamHeaderError(ValueError):

FILE: src/viral_ngs/core/fastqc.py
  class FastQC (line 21) | class FastQC(Tool):
    method __init__ (line 23) | def __init__(self, install_methods=None):
    method _get_tool_version (line 28) | def _get_tool_version(self):
    method execute (line 31) | def execute(self, inBam, out_html, out_zip=None, threads=None):    # p...

FILE: src/viral_ngs/core/file.py
  class StringNotFoundException (line 57) | class StringNotFoundException(Exception):
  function get_project_path (line 62) | def get_project_path():
  function get_build_path (line 96) | def get_build_path():
  function get_test_path (line 101) | def get_test_path():
  function get_test_input_path (line 106) | def get_test_input_path(testClassInstance=None):
  function check_paths (line 115) | def check_paths(read=(), write=(), read_and_write=()):
  function mkstempfname (line 137) | def mkstempfname(suffix='', prefix='tmp', directory=None, text=False):
  function tempfname (line 149) | def tempfname(*args, **kwargs):
  function tempfnames (line 162) | def tempfnames(suffixes, *args, **kwargs):
  function tmp_dir (line 176) | def tmp_dir(*args, **kwargs):
  function pushd_popd (line 199) | def pushd_popd(target_dir):
  function keep_tmp (line 208) | def keep_tmp():
  function set_tmp_dir (line 214) | def set_tmp_dir(name):
  function destroy_tmp_dir (line 228) | def destroy_tmp_dir(tempdir=None):
  function extract_tarball (line 237) | def extract_tarball(tarfile, out_dir=None, threads=None, compression='au...
  function fifo (line 320) | def fifo(num_pipes=1, names=None, name=None):
  function mkdir_p (line 343) | def mkdir_p(dirpath):
  function touch_p (line 355) | def touch_p(path, times=None):
  function zstd_open (line 362) | def zstd_open(fname, mode='r', **kwargs):
  function open_or_gzopen (line 384) | def open_or_gzopen(fname, mode='r', **kwargs):
  function read_tabfile_dict (line 409) | def read_tabfile_dict(inFile, header_prefix="#", skip_prefix=None, rowco...
  function read_tabfile (line 440) | def read_tabfile(inFile):
  function readFlatFileHeader (line 450) | def readFlatFileHeader(filename, headerPrefix='#', delim='\t'):
  class FlatFileParser (line 458) | class FlatFileParser(object):
    method __init__ (line 462) | def __init__(self, lineIter=None, name=None, outType='dict',
    method __enter__ (line 477) | def __enter__(self):
    method __exit__ (line 480) | def __exit__(self, exc_type, exc_val, exc_tb):
    method __iter__ (line 483) | def __iter__(self):
    method parse (line 490) | def parse(self, row):
    method parseHeader (line 516) | def parseHeader(self, row):
    method parseRow (line 522) | def parseRow(self, row):
  function fastaMaker (line 534) | def fastaMaker(seqs, linewidth=60):
  function makeFastaFile (line 549) | def makeFastaFile(seqs, outFasta):
  function bam_is_sorted (line 557) | def bam_is_sorted(bam_file_path):
  function concat (line 566) | def concat(inputFilePaths, outputFilePath, append=False):
  function download_file (line 580) | def download_file(uriToGet, dest, destFileName=None):
  function webfile_readlines (line 605) | def webfile_readlines(uriToGet):
  function replace_in_file (line 613) | def replace_in_file(filename, original, new):
  function cat (line 627) | def cat(output_file, input_files):
  function temp_catted_files (line 636) | def temp_catted_files(input_files, suffix=None, prefix=None):
  function _get_pathconf (line 645) | def _get_pathconf(file_system_path, param_suffix, default):
  function max_file_name_length (line 656) | def max_file_name_length(file_system_path):
  function max_path_length (line 660) | def max_path_length(file_system_path):
  function sanitize_id_for_sam_rname (line 664) | def sanitize_id_for_sam_rname(string_in):
  function write_fasta_with_sanitized_ids (line 683) | def write_fasta_with_sanitized_ids(fasta_in, out_filepath):
  function fastas_with_sanitized_ids (line 696) | def fastas_with_sanitized_ids(input_fasta_paths, use_tmp=False):
  class TranspositionError (line 728) | class TranspositionError(Exception):
    method __init___ (line 729) | def __init___(self, *args, **kwargs):
  function transposeChromosomeFiles (line 732) | def transposeChromosomeFiles(inputFilenamesList, sampleRelationFile=None...
  function string_to_file_name (line 783) | def string_to_file_name(string_value, file_system_path=None, length_marg...
  function grep_count (line 848) | def grep_count(file_path, to_match, additional_flags=None, fixed_mode=Tr...
  function count_occurrences_in_tsv (line 879) | def count_occurrences_in_tsv(filePath,
  function count_occurrences_in_tsv_sqlite_backed (line 892) | def count_occurrences_in_tsv_sqlite_backed(db_file_path,
  function count_str_in_file (line 907) | def count_str_in_file(in_file, query_str, starts_with=False):
  function fasta_length (line 923) | def fasta_length(fasta_path):
  function count_fastq_reads (line 929) | def count_fastq_reads(inFastq):
  function line_count (line 941) | def line_count(infname):
  function touch (line 948) | def touch(fname, times=None):
  function make_empty (line 952) | def make_empty(fname):
  function dump_file (line 957) | def dump_file(fname, value):
  function slurp_file (line 962) | def slurp_file(fname, maxSizeMb=50):
  function is_broken_link (line 973) | def is_broken_link(filename):
  function find_broken_symlinks (line 984) | def find_broken_symlinks(rootdir, followlinks=False):
  function uncompressed_file_type (line 1008) | def uncompressed_file_type(fname):
  function repack_tarballs (line 1015) | def repack_tarballs(out_compressed_tarball,
  class DBConnection (line 1140) | class DBConnection:
    method __init__ (line 1141) | def __init__(self, db_file=None):
    method start (line 1158) | def start(self):
    method __enter__ (line 1160) | def __enter__(self):
    method __exit__ (line 1162) | def __exit__(self, exc_type, exc_val, exc_tb):
    method close (line 1165) | def close(self):
  class CountDB (line 1176) | class CountDB(DBConnection):
    method __init__ (line 1182) | def __init__(self, db_file=None):
    method start (line 1185) | def start(self):
    method get_count_for_ID (line 1191) | def get_count_for_ID(self, idval):
    method get_count_for_multiple_IDs (line 1196) | def get_count_for_multiple_IDs(self, idvals):
    method set_count_for_ID (line 1201) | def set_count_for_ID(self, idval, count):
    method set_count_for_multiple_IDs (line 1206) | def set_count_for_multiple_IDs(self, idvals, count):
    method increment_count_for_multiple_IDs (line 1212) | def increment_count_for_multiple_IDs(self, idvals, increment_val=1):
    method add_counts_from_other_db (line 1222) | def add_counts_from_other_db(self, other_db):
    method increment_count_for_ID (line 1240) | def increment_count_for_ID(self, idval, increment_val=1):
    method decrement_count_for_multiple_IDs (line 1243) | def decrement_count_for_multiple_IDs(self, idvals, decrement_val=-1):
    method decrement_count_for_ID (line 1246) | def decrement_count_for_ID(self, idval, decrement_val=-1):
    method get_counts_descending (line 1249) | def get_counts_descending(self):
    method get_num_IDS (line 1254) | def get_num_IDS(self):

FILE: src/viral_ngs/core/illumina_indices.py
  function memoize (line 22) | def memoize(obj):
  class IlluminaIndexReference (line 33) | class IlluminaIndexReference(object):
    method __init__ (line 35) | def __init__(self, kit=None, instrument=None):
    method neighbors (line 2315) | def neighbors(cls, seq, distance=1):
    method reverse_complement (line 2333) | def reverse_complement(seq):
    method _barcodes_meta_all (line 2342) | def _barcodes_meta_all(self):
    method kits (line 2355) | def kits(cls):
    method instruments (line 2359) | def instruments(self):
    method index_for_seq (line 2369) | def index_for_seq(self, seq, kit=None, instrument=None):
    method seq_for_index (line 2385) | def seq_for_index(self, index, kit=None, instrument=None):
    method guess_index (line 2402) | def guess_index(self, seq, distance=1, kit=None, instrument=None):
  class UncertainSamplesheetError (line 2416) | class UncertainSamplesheetError(Exception):
  class IlluminaBarcodeHelper (line 2419) | class IlluminaBarcodeHelper(object):
    method __init__ (line 2421) | def __init__(self, barcode_counts, picard_metrics, sample_name, rows_l...
    method outlier_barcodes (line 2456) | def outlier_barcodes(self, outlier_threshold=0.775, expected_assigned_...
    method mean (line 2530) | def mean(cls, nums):
    method stddevp (line 2534) | def stddevp(cls, nums):
    method median (line 2541) | def median(cls, nums):
    method guess_barcodes_for_sample (line 2555) | def guess_barcodes_for_sample(self, sample_name):
    method find_uncertain_barcodes (line 2660) | def find_uncertain_barcodes(self, sample_names=None, outlier_threshold...
    method write_guessed_barcodes (line 2721) | def write_guessed_barcodes(self, out_tsv, guessed_barcodes):

FILE: src/viral_ngs/core/illumina_utils.py
  class IlluminaDirectory (line 29) | class IlluminaDirectory(object):
    method __init__ (line 32) | def __init__(self, uri):
    method __enter__ (line 39) | def __enter__(self):
    method __exit__ (line 43) | def __exit__(self, exc_type, exc_val, exc_tb):
    method load (line 47) | def load(self):
    method _fix_path (line 58) | def _fix_path(self):
    method _extract_tarball (line 84) | def _extract_tarball(self, tarfile):
    method close (line 89) | def close(self):
    method get_RunInfo (line 94) | def get_RunInfo(self):
    method get_SampleSheet (line 101) | def get_SampleSheet(self, only_lane=None, append_run_id=None, **kwargs):
    method get_intensities_dir (line 113) | def get_intensities_dir(self):
    method get_BCLdir (line 116) | def get_BCLdir(self):
  class RunInfo (line 125) | class RunInfo(object):
    method __init__ (line 130) | def __init__(self, xml_fname):
    method get_fname (line 134) | def get_fname(self):
    method get_run_id (line 137) | def get_run_id(self):
    method get_flowcell_raw (line 140) | def get_flowcell_raw(self):
    method get_flowcell (line 143) | def get_flowcell(self):
    method _get_rundate_obj (line 159) | def _get_rundate_obj(self):
    method get_rundate_american (line 182) | def get_rundate_american(self):
    method get_rundate_iso (line 185) | def get_rundate_iso(self):
    method get_machine (line 188) | def get_machine(self):
    method get_read_structure (line 191) | def get_read_structure(self):
    method num_reads (line 201) | def num_reads(self):
    method get_lane_count (line 208) | def get_lane_count(self):
    method get_surface_count (line 212) | def get_surface_count(self):
    method get_swath_count (line 216) | def get_swath_count(self):
    method get_tile_count (line 220) | def get_tile_count(self):
    method get_section_count (line 224) | def get_section_count(self):
    method tile_count (line 228) | def tile_count(self):
    method machine_model_from_tile_count (line 240) | def machine_model_from_tile_count(self):
    method get_flowcell_chemistry (line 300) | def get_flowcell_chemistry(self):
    method get_flowcell_lane_count (line 304) | def get_flowcell_lane_count(self):
    method get_machine_model (line 311) | def get_machine_model(self):
    method get_machines_for_flowcell_id (line 316) | def get_machines_for_flowcell_id(cls, fcid):
    method infer_sequencer_model (line 325) | def infer_sequencer_model(self):
  class SampleSheetError (line 479) | class SampleSheetError(Exception):
    method __init__ (line 480) | def __init__(self, message, fname):
  class SampleSheet (line 486) | class SampleSheet(object):
    method __init__ (line 491) | def __init__(
    method _detect_and_load_sheet (line 531) | def _detect_and_load_sheet(self, infile):
    method can_be_collapsed (line 675) | def can_be_collapsed(self) -> bool:
    method collapse_sample_index_duplicates (line 685) | def collapse_sample_index_duplicates(self, output_tsv=None, overwrite_...
    method inner_demux_mapper (line 768) | def inner_demux_mapper(self):
    method make_barcodes_file (line 825) | def make_barcodes_file(self, outFile):
    method write_tsv (line 842) | def write_tsv(self, outFile, force=False):
    method rev_comp_barcode_values (line 852) | def rev_comp_barcode_values(self, barcode_columns_to_revcomp=None, inp...
    method make_params_file (line 884) | def make_params_file(self, bamDir, outFile):
    method get_fname (line 909) | def get_fname(self):
    method get_rows (line 912) | def get_rows(self):
    method print_rows (line 915) | def print_rows(self, row_indices=None):
    method num_indexes (line 926) | def num_indexes(self):
    method num_samples (line 931) | def num_samples(self):
    method fetch_by_index (line 934) | def fetch_by_index(self, idx):

FILE: src/viral_ngs/core/minimap2.py
  class Minimap2 (line 25) | class Minimap2(Tool):
    method __init__ (line 27) | def __init__(self, install_methods=None):
    method _get_tool_version (line 33) | def _get_tool_version(self):
    method execute (line 36) | def execute(self, args, stdout=None, stdin=None, background=False):   ...
    method align_bam (line 48) | def align_bam(self, inBam, refDb, outBam, options=None,
    method align_one_rg (line 104) | def align_one_rg(self, inBam, refDb, outBam, rgid=None, preset=None, o...
    method align_cmd (line 203) | def align_cmd(self, inReads, refDb, outAlign, options=None, threads=No...
    method scaffold (line 226) | def scaffold(self, contigs_fasta, ref_fasta, outAlign, divergence=20, ...
    method idxstats (line 252) | def idxstats(self, inReads, refDb, outIdxstats, outReadlist=None, thre...

FILE: src/viral_ngs/core/misc.py
  function unambig_count (line 37) | def unambig_count(seq):
  function timer (line 42) | def timer(prefix):
  function memoize (line 50) | def memoize(obj):
  function unique (line 62) | def unique(items):
  function collapse_dup_strs_to_str_or_md5 (line 70) | def collapse_dup_strs_to_str_or_md5(values,
  function md5_digest (line 123) | def md5_digest(in_str, last_n_chr=8):
  function reverse_complement (line 127) | def reverse_complement(seq):
  function histogram (line 135) | def histogram(items):
  function freqs (line 144) | def freqs(items, zero_checks=None):
  function intervals (line 170) | def intervals(i, n, l):
  function pairwise (line 187) | def pairwise(iterable):
  function batch_iterator (line 195) | def batch_iterator(iterator, batch_size):
  function list_contains (line 214) | def list_contains(sublist, list_):
  function run_and_print (line 223) | def run_and_print(args, stdout=None, stderr=subprocess.STDOUT,
  function run_and_save (line 307) | def run_and_save(args, stdout=None, stdin=None,
  class FeatureSorter (line 333) | class FeatureSorter(object):
    method __init__ (line 337) | def __init__(self, collection=None):
    method add (line 346) | def add(self, c, start, stop, strand='+', other=None):
    method _cleanup (line 360) | def _cleanup(self):
    method get_seqids (line 366) | def get_seqids(self):
    method get_features (line 369) | def get_features(self, c=None, left=0, right=float('inf')):
    method get_intervals (line 386) | def get_intervals(self, c=None):
  function available_cpu_count (line 403) | def available_cpu_count():
  function sanitize_thread_count (line 459) | def sanitize_thread_count(threads=None, tool_max_cores_value=available_c...
  function which (line 492) | def which(application_binary_name):
  function is_nonstr_iterable (line 506) | def is_nonstr_iterable(x, str_types=str):
  function make_seq (line 510) | def make_seq(x, str_types=str):
  function load_yaml_or_json (line 517) | def load_yaml_or_json(fname):
  function load_config (line 525) | def load_config(cfg, include_directive='include', std_includes=(), param...
  function as_type (line 630) | def as_type(val, types):
  function subdict (line 641) | def subdict(d, keys):
  function chk (line 647) | def chk(condition, message='Check failed', exc=RuntimeError):
  function wraps (line 652) | def wraps(f):
  function unwrap (line 658) | def unwrap(f):
  function convert_size_str (line 662) | def convert_size_str(input_size_str, output_unit="m", round_number=True):
  class ReadIdStore (line 690) | class ReadIdStore:
    method __init__ (line 698) | def __init__(self, db_path):
    method add_from_fastq (line 720) | def add_from_fastq(self, fastq_path):
    method add_from_readlist (line 766) | def add_from_readlist(self, readlist_path):
    method __len__ (line 777) | def __len__(self):
    method __iter__ (line 782) | def __iter__(self):
    method __contains__ (line 788) | def __contains__(self, read_id):
    method contains_batch (line 796) | def contains_batch(self, read_ids, batch_size=10000):
    method add (line 828) | def add(self, read_id):
    method extend (line 845) | def extend(self, read_ids):
    method __delitem__ (line 882) | def __delitem__(self, read_id):
    method discard (line 900) | def discard(self, read_id):
    method write_to_file (line 913) | def write_to_file(self, out_path, max_reads=None):
    method shrink_to_subsample (line 941) | def shrink_to_subsample(self, n):
    method filter_bam_by_ids (line 971) | def filter_bam_by_ids(self, inBam, outBam, include=True):
    method close (line 1072) | def close(self):
    method __enter__ (line 1076) | def __enter__(self):
    method __exit__ (line 1079) | def __exit__(self, exc_type, exc_val, exc_tb):
  class CoordMapperError (line 1086) | class CoordMapperError(Exception):
    method __init___ (line 1087) | def __init___(self, *args, **kwargs):
  class CoordMapper (line 1091) | class CoordMapper(collections.abc.MutableMapping):
    method __init__ (line 1106) | def __init__(self, alignerTool=None):
    method __getitem__ (line 1130) | def __getitem__(self, key):
    method __setitem__ (line 1133) | def __setitem__(self, key, value):
    method __delitem__ (line 1136) | def __delitem__(self, key):
    method __len__ (line 1139) | def __len__(self):
    method __iter__ (line 1142) | def __iter__(self):
    method __contains__ (line 1146) | def __contains__(self, key):
    method keys (line 1152) | def keys(self):
    method mapAtoB (line 1155) | def mapAtoB(self, fromChrom, fromPos=None, side=0):
    method mapBtoA (line 1169) | def mapBtoA(self, fromChrom, fromPos=None, side=0):
    method mapChr (line 1183) | def mapChr(self, fromChrom, toChrom, fromPos=None, side=0):
    method load_alignments (line 1206) | def load_alignments(self, aligned_files, a_idx=None, b_idx=None):
    method align_and_load_sequences (line 1260) | def align_and_load_sequences(self, unaligned_fasta_files, aligner=None):
  class CoordMapper2Seqs (line 1281) | class CoordMapper2Seqs(object):
    method __init__ (line 1308) | def __init__(self, seq0, seq1):
    method __call__ (line 1336) | def __call__(self, fromPos, fromWhich):

FILE: src/viral_ngs/core/mvicuna.py
  class MvicunaTool (line 17) | class MvicunaTool(Tool):
    method __init__ (line 19) | def __init__(self, install_methods=None):
    method rmdup (line 24) | def rmdup(self, inPair, outPair, outUnpaired=None):
    method rmdup_single (line 60) | def rmdup_single(self, inFastq, outFastq):

FILE: src/viral_ngs/core/novoalign.py
  class NovoalignTool (line 27) | class NovoalignTool(Tool):
    method __init__ (line 29) | def __init__(self, path=None, license_path=None):
    method _get_tool_version (line 60) | def _get_tool_version(self):
    method _fasta_to_idx_name (line 63) | def _fasta_to_idx_name(self, fasta):
    method execute (line 68) | def execute(self, inBam, refFasta, outBam, options=None, min_qual=0, J...
    method align_one_rg_bam (line 120) | def align_one_rg_bam(self, inBam, refFasta, outBam, rgid=None, rgs=Non...
    method index_fasta (line 194) | def index_fasta(self, refFasta, k=None, s=None):

FILE: src/viral_ngs/core/picard.py
  class PicardTools (line 25) | class PicardTools(Tool):
    method is_installed (line 29) | def is_installed(self):
    method __init__ (line 32) | def __init__(self, install_methods=None):
    method _get_tool_version (line 37) | def _get_tool_version(self):
    method execute (line 40) | def execute(self, command, picardOptions=None, JVMmemory=None, backgro...
    method dict_to_picard_opts (line 59) | def dict_to_picard_opts(options):
  class RevertSamTool (line 63) | class RevertSamTool(PicardTools):
    method execute (line 66) | def execute(self, inBam, outBam, picardOptions=None, JVMmemory=None, b...
  class CheckIlluminaDirectoryTool (line 75) | class CheckIlluminaDirectoryTool(PicardTools):
    method execute (line 78) | def execute(self,
  class MarkDuplicatesTool (line 123) | class MarkDuplicatesTool(PicardTools):
    method execute (line 126) | def execute(
  class SplitSamByLibraryTool (line 139) | class SplitSamByLibraryTool(PicardTools):
    method execute (line 142) | def execute(
  class SamToFastqTool (line 155) | class SamToFastqTool(PicardTools):
    method execute (line 159) | def execute(self, inBam, outFastq1, outFastq2=None, outFastq0=None,
    method execute_tmp (line 192) | def execute_tmp(self, inBam, sfx='', includeUnpaired=False, **kwargs):
    method per_read_group (line 206) | def per_read_group(self, inBam, outDir, picardOptions=None, JVMmemory=...
  class FastqToSamTool (line 217) | class FastqToSamTool(PicardTools):
    method isFastqEmpty (line 222) | def isFastqEmpty(fastq_file):
    method execute (line 252) | def execute(
  class SortSamTool (line 322) | class SortSamTool(PicardTools):
    method execute (line 327) | def execute(
  class DownsampleSamTool (line 339) | class DownsampleSamTool(PicardTools):
    method execute (line 346) | def execute(self,
    method downsample_to_approx_count (line 386) | def downsample_to_approx_count(
  class MergeSamFilesTool (line 414) | class MergeSamFilesTool(PicardTools):
    method execute (line 417) | def execute(self, inBams, outBam, picardOptions=None, JVMmemory=None, ...
  class ReplaceSamHeaderTool (line 427) | class ReplaceSamHeaderTool(PicardTools):
    method execute (line 430) | def execute(self, inBam, headerBam, outBam, picardOptions=None, JVMmem...
  class FilterSamReadsTool (line 438) | class FilterSamReadsTool(PicardTools):
    method execute (line 450) | def execute(self, inBam, exclude, readList, outBam, picardOptions=None...
  class CreateSequenceDictionaryTool (line 485) | class CreateSequenceDictionaryTool(PicardTools):
    method execute (line 489) | def execute(
  class BuildBamIndexTool (line 512) | class BuildBamIndexTool(PicardTools):
    method execute (line 516) | def execute(self, inBam, picardOptions=None, JVMmemory=None):    # pyl...
  class CollectIlluminaLaneMetricsTool (line 522) | class CollectIlluminaLaneMetricsTool(PicardTools):
    method execute (line 530) | def execute(
  class ExtractIlluminaBarcodesTool (line 555) | class ExtractIlluminaBarcodesTool(PicardTools):
    method execute (line 570) | def execute(
  class AddCommentsToBamTool (line 602) | class AddCommentsToBamTool(PicardTools):
    method execute (line 607) | def execute(self,
  class IlluminaBasecallsToSamTool (line 637) | class IlluminaBasecallsToSamTool(PicardTools):
    method execute (line 660) | def execute(self,
    method execute_single_sample (line 691) | def execute_single_sample(self,

FILE: src/viral_ngs/core/prinseq.py
  class PrinseqTool (line 15) | class PrinseqTool(Tool):
    method __init__ (line 17) | def __init__(self, install_methods=None):
    method _get_tool_version (line 22) | def _get_tool_version(self):
    method rmdup_fastq_single (line 25) | def rmdup_fastq_single(self, inFastq, outFastq):
    method rmdup_fastq_paired (line 45) | def rmdup_fastq_paired(self, inFastq1, inFastq2, outFastq1, outFastq2,...

FILE: src/viral_ngs/core/priorities.py
  function compactify_sequences (line 16) | def compactify_sequences(sparse_matrix, sequence_names):
  function sequence_to_int_array (line 30) | def sequence_to_int_array(s, fill_value=110, fill_gaps=True):
  function calculate_snp_matrix (line 39) | def calculate_snp_matrix(fastafile, consensus=None, zipped=False, fill_v...
  function calculate_distance_matrix (line 101) | def calculate_distance_matrix(sparse_matrix_A, sparse_matrix_B, consensus):

FILE: src/viral_ngs/core/sambamba.py
  class SambambaTool (line 27) | class SambambaTool(Tool):
    method __init__ (line 30) | def __init__(self, install_methods=None):
    method _get_tool_version (line 37) | def _get_tool_version(self):
    method execute (line 57) | def execute(self, command, args, stdout=None, stderr=None):
    method sort (line 73) | def sort(self, inBam, outBam, sort_order='coordinate', threads=None):
    method index (line 104) | def index(self, inBam, threads=None):
    method merge (line 128) | def merge(self, inBams, outBam, threads=None):
    method flagstat (line 148) | def flagstat(self, inBam, threads=None):
    method _parse_flagstat (line 171) | def _parse_flagstat(self, output):
    method markdup (line 230) | def markdup(self, inBam, outBam, remove_duplicates=False, threads=None,

FILE: src/viral_ngs/core/samtools.py
  class SamtoolsTool (line 38) | class SamtoolsTool(Tool):
    method __init__ (line 40) | def __init__(self, install_methods=None):
    method _get_tool_version (line 45) | def _get_tool_version(self):
    method execute (line 48) | def execute(self, command, args, stdout=None, stderr=None, background=...
    method view (line 68) | def view(self, args, inFile, outFile, regions=None, threads=None, back...
    method bam2fq (line 79) | def bam2fq(self, inBam, outFq1, outFq2=None):
    method bam2fq_pipe (line 85) | def bam2fq_pipe(self, inBam, threads=None):
    method bam2fa (line 94) | def bam2fa(self, inBam, outFa1, outFa2=None, outFa0=None, append_mate_...
    method bam2fa_pipe (line 107) | def bam2fa_pipe(self, inBam):
    method bam2fq_tmp (line 114) | def bam2fq_tmp(self, inBam):
    method bam2fa_tmp (line 120) | def bam2fa_tmp(self, inBam):
    method import_fastq (line 125) | def import_fastq(self, inFastq1, inFastq2, outBam,
    method _is_fastq_empty (line 188) | def _is_fastq_empty(self, fastq_file):
    method _create_empty_bam_with_header (line 209) | def _create_empty_bam_with_header(self, outBam, sample_name, library_n...
    method sort (line 253) | def sort(self, inFile, outFile, args=None, threads=None):
    method merge (line 265) | def merge(self, inFiles, outFile, options=None):
    method index (line 274) | def index(self, inBam, threads=None):
    method faidx (line 283) | def faidx(self, inFasta, overwrite=False):
    method depth (line 297) | def depth(self, inBam, outFile, options=None):
    method idxstats (line 303) | def idxstats(self, inBam, statsFile, threads=None):
    method reheader (line 311) | def reheader(self, inBam, headerFile, outBam):
    method dumpHeader (line 314) | def dumpHeader(self, inBam, outHeader):
    method removeDoublyMappedReads (line 323) | def removeDoublyMappedReads(self, inBam, outBam):
    method filter_to_proper_primary_mapped_reads (line 328) | def filter_to_proper_primary_mapped_reads(self, inBam, outBam, require...
    method filterByCigarString (line 380) | def filterByCigarString(self, inBam, outBam,
    method downsample (line 411) | def downsample(self, inBam, outBam, probability):
    method downsample_to_approx_count (line 421) | def downsample_to_approx_count(self, inBam, outBam, read_count):
    method getHeader (line 432) | def getHeader(self, inBam):
    method getReadGroups (line 441) | def getReadGroups(self, inBam):
    method count (line 453) | def count(self, inBam, opts=None, regions=None):
    method mpileup (line 464) | def mpileup(self, inBam, outPileup, opts=None):
    method isEmpty (line 469) | def isEmpty(self, inBam):

FILE: src/viral_ngs/core/splitcode.py
  class SplitCodeTool (line 22) | class SplitCodeTool(Tool):
    method __init__ (line 24) | def __init__(self, install_methods=None):
    method _get_tool_version (line 29) | def _get_tool_version(self):
    method execute (line 32) | def execute(    self,
    method check_installation (line 104) | def check_installation(self):
    method run_splitcode (line 109) | def run_splitcode(self, **kwargs):
  function create_splitcode_lookup_table (line 134) | def create_splitcode_lookup_table(sample_sheet_or_dataframe, csv_out, un...
  function plot_read_counts (line 533) | def plot_read_counts(df_csv_path, outDir):
  function plot_sorted_curve (line 607) | def plot_sorted_curve(df_csv_path, out_dir, unmatched_name, out_basename...
  function run_splitcode_on_pool (line 697) | def run_splitcode_on_pool(  pool_id,
  function generate_splitcode_config_and_keep_files (line 799) | def generate_splitcode_config_and_keep_files(
  function convert_splitcode_demux_metrics_to_picard_style (line 952) | def convert_splitcode_demux_metrics_to_picard_style(

FILE: src/viral_ngs/core/stats.py
  function product (line 9) | def product(iterable):
  function chi2_contingency (line 16) | def chi2_contingency(contingencyTable, correction=True):
  function fisher_exact (line 64) | def fisher_exact(contingencyTable):
  function log_choose (line 132) | def log_choose(n, k):
  function gammainc_halfint (line 139) | def gammainc_halfint(s, x):
  function pchisq (line 174) | def pchisq(x, k):

FILE: src/viral_ngs/core/trimmomatic.py
  class TrimmomaticTool (line 15) | class TrimmomaticTool(Tool):
    method __init__ (line 17) | def __init__(self, install_methods=None):
    method _get_tool_version (line 22) | def _get_tool_version(self):
    method execute (line 25) | def execute(self,

FILE: src/viral_ngs/core/version.py
  function get_project_path (line 21) | def get_project_path(include_derived_modules=True):
  function call_git_describe (line 63) | def call_git_describe():
  function release_file (line 80) | def release_file():
  function read_release_version (line 84) | def read_release_version():
  function write_release_version (line 93) | def write_release_version(version):
  function approx_version_number (line 98) | def approx_version_number():
  function get_version (line 143) | def get_version():

FILE: src/viral_ngs/file_utils.py
  function merge_tarballs (line 24) | def merge_tarballs(out_tarball, in_tarballs, threads=None, extract_to_di...
  function parser_merge_tarballs (line 30) | def parser_merge_tarballs(parser=argparse.ArgumentParser()):
  function parser_rename_fasta_sequences (line 60) | def parser_rename_fasta_sequences(parser=argparse.ArgumentParser()):
  function main_rename_fasta_sequences (line 75) | def main_rename_fasta_sequences(args):
  class Adder_Table_Map (line 103) | class Adder_Table_Map:
    method __init__ (line 104) | def __init__(self, tab_file):
    method _make_key_str (line 119) | def _make_key_str(self, row):
    method extra_headers (line 122) | def extra_headers(self):
    method modify_row (line 124) | def modify_row(self, row):
  class Adder_Source_Lab_Subset (line 132) | class Adder_Source_Lab_Subset:
    method __init__ (line 133) | def __init__(self, restrict_string):
    method extra_headers (line 136) | def extra_headers(self):
    method modify_row (line 138) | def modify_row(self, row):
  function parser_tsv_derived_cols (line 144) | def parser_tsv_derived_cols(parser=argparse.ArgumentParser()):
  function tsv_derived_cols (line 152) | def tsv_derived_cols(in_tsv, out_tsv, table_map=None, lab_highlight_loc=...
  function parser_tsv_join (line 178) | def parser_tsv_join(parser=argparse.ArgumentParser()):
  function tsv_join (line 185) | def tsv_join(in_tsvs, out_tsv, join_id=None):
  function full_parser (line 235) | def full_parser():
  function main (line 239) | def main():

FILE: src/viral_ngs/illumina.py
  function parse_illumina_fastq_filename (line 49) | def parse_illumina_fastq_filename(filename):
  function normalize_barcode (line 141) | def normalize_barcode(barcode):
  function barcode_n_fraction (line 190) | def barcode_n_fraction(barcode):
  function barcode_matches_with_n (line 204) | def barcode_matches_with_n(observed, expected):
  function barcode_matches_fuzzy (line 245) | def barcode_matches_fuzzy(observed, expected, max_mismatches=1):
  function match_barcodes_with_orientation (line 285) | def match_barcodes_with_orientation(target_bc1, target_bc2, sample_rows,
  function build_run_info_json (line 465) | def build_run_info_json(
  function illumina_metadata (line 549) | def illumina_metadata(
  function parser_illumina_metadata (line 692) | def parser_illumina_metadata(parser=argparse.ArgumentParser()):
  function run_picard_fastq_to_sam_for_splitcode_demux (line 753) | def run_picard_fastq_to_sam_for_splitcode_demux(
  function _parse_barcode_from_header (line 824) | def _parse_barcode_from_header(header_line):
  function consensus_barcode_from_fastq (line 854) | def consensus_barcode_from_fastq(fastq_path, num_reads=10):
  function splitcode_demux_fastqs (line 944) | def splitcode_demux_fastqs(
  function parser_splitcode_demux_fastqs (line 1684) | def parser_splitcode_demux_fastqs(parser=argparse.ArgumentParser()):
  function parser_illumina_demux (line 1777) | def parser_illumina_demux(parser=argparse.ArgumentParser()):
  function main_illumina_demux (line 1921) | def main_illumina_demux(args):
  function parser_flowcell_metadata (line 2225) | def parser_flowcell_metadata(parser=argparse.ArgumentParser()):
  function main_flowcell_metadata (line 2261) | def main_flowcell_metadata(args):
  function parser_lane_metrics (line 2301) | def parser_lane_metrics(parser=argparse.ArgumentParser()):
  function main_lane_metrics (line 2327) | def main_lane_metrics(args):
  function parser_common_barcodes (line 2369) | def parser_common_barcodes(parser=argparse.ArgumentParser()):
  function main_common_barcodes (line 2445) | def main_common_barcodes(args):
  function count_and_sort_barcodes (line 2525) | def count_and_sort_barcodes(
  function parser_guess_barcodes (line 2658) | def parser_guess_barcodes(parser=argparse.ArgumentParser()):
  function main_guess_barcodes (line 2731) | def main_guess_barcodes(
  function miseq_fastq_to_bam (line 2789) | def miseq_fastq_to_bam(
  function parser_miseq_fastq_to_bam (line 2885) | def parser_miseq_fastq_to_bam(parser=argparse.ArgumentParser()):
  function extract_fc_metadata (line 2920) | def extract_fc_metadata(flowcell, outRunInfo, outSampleSheet):
  function parser_extract_fc_metadata (line 2929) | def parser_extract_fc_metadata(parser=argparse.ArgumentParser()):
  function write_barcode_metrics_for_pools (line 2948) | def write_barcode_metrics_for_pools(input_csv_path,
  function run_picard_fastq_to_ubam (line 3053) | def run_picard_fastq_to_ubam(fq1,
  function splitcode_demux (line 3076) | def splitcode_demux(
  function main_splitcode_demux (line 3587) | def main_splitcode_demux(args):
  function parser_splitcode_demux (line 3619) | def parser_splitcode_demux(parser=None):
  function add_constant_column_to_metrics (line 3799) | def add_constant_column_to_metrics(
  function merge_demux_metrics (line 3872) | def merge_demux_metrics(
  function parser_merge_demux_metrics (line 3991) | def parser_merge_demux_metrics(parser=argparse.ArgumentParser()):
  function full_parser (line 4018) | def full_parser():
  function main (line 4022) | def main():

FILE: src/viral_ngs/interhost.py
  function parser_snpEff (line 33) | def parser_snpEff(parser=argparse.ArgumentParser()):
  function parser_general_mafft (line 54) | def parser_general_mafft(parser=argparse.ArgumentParser()):
  function parser_align_mafft (line 94) | def parser_align_mafft(parser):
  function main_align_mafft (line 104) | def main_align_mafft(args):
  function parser_multichr_mafft (line 131) | def parser_multichr_mafft(parser):
  function multichr_mafft (line 155) | def multichr_mafft(args):
  function call_snps_3 (line 203) | def call_snps_3(inFasta, outVcf, REF="KJ660346.2"):
  function find_ref (line 212) | def find_ref(a, ref):
  function vcf_header (line 219) | def vcf_header(a):
  function make_vcf (line 229) | def make_vcf(a, ref_idx, chrom):
  function full_parser (line 252) | def full_parser():
  function main (line 256) | def main():

FILE: src/viral_ngs/intrahost.py
  class AlleleFieldParser (line 40) | class AlleleFieldParser(object):
    method __init__ (line 48) | def __init__(self, field=None, allele=None, fcount=None, rcount=None, ...
    method __repr__ (line 64) | def __repr__(self):
    method allele (line 69) | def allele(self):
    method total (line 77) | def total(self):
    method strand_counts (line 80) | def strand_counts(self):
    method allele_and_strand_counts (line 84) | def allele_and_strand_counts(self):
    method lib_counts (line 87) | def lib_counts(self):
    method lib_bias_pval (line 94) | def lib_bias_pval(self):
  function vphaser_one_sample (line 104) | def vphaser_one_sample(inBam, inConsFasta, outTab, vphaserNumThreads=None,
  function filter_strand_bias (line 155) | def filter_strand_bias(isnvs, minReadsEach=None, maxBias=None):
  function compute_library_bias (line 181) | def compute_library_bias(isnvs, inBam, inConsFasta):
  function parse_alleles_string (line 264) | def parse_alleles_string(allelesStr):
  function get_mpileup_allele_counts (line 298) | def get_mpileup_allele_counts(inBam, chrom, pos, inConsFasta, samtools=N...
  function parser_vphaser_one_sample (line 344) | def parser_vphaser_one_sample(parser=argparse.ArgumentParser()):
  function parser_vphaser (line 372) | def parser_vphaser(parser=argparse.ArgumentParser()):
  function vphaser_main (line 381) | def vphaser_main(inBam, outTab, numThreads=None):
  function tabfile_values_rename (line 396) | def tabfile_values_rename(inFile, mapFile, outFile, col=0):
  function parser_tabfile_rename (line 417) | def parser_tabfile_rename(parser=argparse.ArgumentParser()):
  function count_iter_items (line 439) | def count_iter_items(iterable):
  function strip_accession_version (line 449) | def strip_accession_version(acc):
  function merge_to_vcf (line 463) | def merge_to_vcf(
  function parser_merge_to_vcf (line 902) | def parser_merge_to_vcf(parser=argparse.ArgumentParser()):
  function compute_Fws (line 954) | def compute_Fws(vcfrow):
  function add_Fws_vcf (line 978) | def add_Fws_vcf(inVcf, outVcf):
  function parser_Fws (line 999) | def parser_Fws(parser=argparse.ArgumentParser()):
  function parse_eff (line 1012) | def parse_eff(eff_field):
  class SnpEffException (line 1033) | class SnpEffException(Exception):
  function parse_ann (line 1037) | def parse_ann(ann_field, alleles, transcript_blacklist=None):
  function iSNV_table (line 1084) | def iSNV_table(vcf_iter):
  function parser_iSNV_table (line 1128) | def parser_iSNV_table(parser=argparse.ArgumentParser()):
  function main_iSNV_table (line 1136) | def main_iSNV_table(args):
  function iSNP_per_patient (line 1156) | def iSNP_per_patient(table, agg_fun=median):
  function parser_iSNP_per_patient (line 1172) | def parser_iSNP_per_patient(parser=argparse.ArgumentParser()):
  function main_iSNP_per_patient (line 1180) | def main_iSNP_per_patient(args):
  function sampleIDMatch (line 1198) | def sampleIDMatch(inputString):
  function full_parser (line 1212) | def full_parser():
  function main (line 1216) | def main():

FILE: src/viral_ngs/kmer_utils.py
  function build_kmer_db (line 27) | def build_kmer_db(seq_files, kmer_db, kmer_size=kmc.DEFAULT_KMER_SIZE, m...
  function parser_build_kmer_db (line 33) | def parser_build_kmer_db(parser=argparse.ArgumentParser()):
  function dump_kmer_counts (line 59) | def dump_kmer_counts(kmer_db, out_kmers, min_occs=1, max_occs=misc.MAX_I...
  function parser_dump_kmer_counts (line 63) | def parser_dump_kmer_counts(parser=argparse.ArgumentParser()):
  function filter_reads (line 80) | def filter_reads(kmer_db, in_reads, out_reads, db_min_occs=1, db_max_occ...
  function parser_filter_reads (line 118) | def parser_filter_reads(parser=argparse.ArgumentParser()):
  function kmers_binary_op (line 148) | def kmers_binary_op(op, kmer_db1, kmer_db2, kmer_db_out,
  function parser_kmers_binary_op (line 155) | def parser_kmers_binary_op(parser=argparse.ArgumentParser()):
  function kmers_set_counts (line 176) | def kmers_set_counts(kmer_db_in, value, kmer_db_out, threads=None):
  function parser_kmers_set_counts (line 181) | def parser_kmers_set_counts(parser=argparse.ArgumentParser()):
  function full_parser (line 194) | def full_parser():
  function main (line 199) | def main():

FILE: src/viral_ngs/metagenomics.py
  function tree_level_lookup (line 55) | def tree_level_lookup(parents, node, level_cache):
  function push_up_tree_hits (line 77) | def push_up_tree_hits(parents, hits, min_support_percent=None, min_suppo...
  function file_lines (line 125) | def file_lines(filename):
  function collect_children (line 132) | def collect_children(children, original_taxids):
  function collect_parents (line 142) | def collect_parents(parents, taxids):
  function parser_subset_taxonomy (line 154) | def parser_subset_taxonomy(parser=argparse.ArgumentParser()):
  function subset_taxonomy (line 204) | def subset_taxonomy(taxDb, outputDb, whitelistTaxids=None, whitelistTaxi...
  function parser_filter_taxids_to_focal_hits (line 304) | def parser_filter_taxids_to_focal_hits(parser=argparse.ArgumentParser()):
  function filter_taxids_to_focal_hits (line 314) | def filter_taxids_to_focal_hits(taxids_tsv, focal_report_tsv, taxdb_dir,...
  function taxa_hits_from_tsv (line 344) | def taxa_hits_from_tsv(f, taxid_column=2):
  function parser_kraken2 (line 353) | def parser_kraken2(parser=argparse.ArgumentParser()):
  function main_kraken2 (line 370) | def main_kraken2(db, inBams, outReports=None, outReads=None, min_base_qu...
  function parser_kb (line 383) | def parser_kb(parser=argparse.ArgumentParser()):
  function kb_python (line 407) | def kb_python(in_bam, index=None, t2g=None, kmer_len=31, parity='single'...
  function parser_kma (line 441) | def parser_kma(parser=argparse.ArgumentParser()):
  function main_kma (line 450) | def main_kma(db, inBams, outPrefixes=None, threads=None):
  function parser_kma_build (line 459) | def parser_kma_build(parser=argparse.ArgumentParser()):
  function main_kma_build (line 467) | def main_kma_build(ref_fasta, db_prefix, threads=None):
  function parser_krona (line 474) | def parser_krona(parser=argparse.ArgumentParser()):
  function main_krona (line 489) | def main_krona(inReports, db, outHtml, queryColumn=None, taxidColumn=Non...
  function parser_metagenomic_report_merge (line 541) | def parser_metagenomic_report_merge(parser=argparse.ArgumentParser()):
  function metagenomic_report_merge (line 555) | def metagenomic_report_merge(metagenomic_reports, out_krona_input):
  function parser_filter_bam_to_taxa (line 569) | def parser_filter_bam_to_taxa(parser=argparse.ArgumentParser()):
  function filter_bam_to_taxa (line 586) | def filter_bam_to_taxa(in_bam, read_IDs_to_tax_IDs, out_bam,
  function parser_kraken_taxlevel_summary (line 673) | def parser_kraken_taxlevel_summary(parser=argparse.ArgumentParser()):
  function taxlevel_summary (line 689) | def taxlevel_summary(summary_files_in, json_out, csv_out, tax_headings, ...
  function parser_kraken_taxlevel_plurality (line 944) | def parser_kraken_taxlevel_plurality(parser=argparse.ArgumentParser()):
  function taxlevel_plurality (line 953) | def taxlevel_plurality(summary_file, tax_heading, out_report, min_reads):
  function parser_kb_extract (line 1051) | def parser_kb_extract(parser=argparse.ArgumentParser()):
  function kb_extract (line 1071) | def kb_extract(in_bam, index, t2g, targets, protein=False, out_dir=None,...
  function parser_kb_top_taxa (line 1109) | def parser_kb_top_taxa(parser=argparse.ArgumentParser()):
  function kb_top_taxa (line 1118) | def kb_top_taxa(counts_tar, out_report, id_to_tax_map=None, target_taxon...
  function parser_kb_merge_h5ads (line 1249) | def parser_kb_merge_h5ads(parser=argparse.ArgumentParser()):
  function kb_merge_h5ads (line 1255) | def kb_merge_h5ads(in_count_tars, out_h5ad, tmp_dir=None):
  function parser_krona_build (line 1276) | def parser_krona_build(parser=argparse.ArgumentParser()):
  function krona_build (line 1283) | def krona_build(db, taxdump_tar_gz=None, get_accessions=False):
  function parser_kraken2_build (line 1292) | def parser_kraken2_build(parser=argparse.ArgumentParser()):
  function kraken2_build (line 1312) | def kraken2_build(db,
  function parser_kb_build (line 1341) | def parser_kb_build(parser=argparse.ArgumentParser()):
  function kb_build (line 1351) | def kb_build(ref_fasta, index, workflow='standard', kmer_len=31, protein...
  function full_parser (line 1373) | def full_parser():
  function main (line 1377) | def main():

FILE: src/viral_ngs/ncbi.py
  function fasta_chrlens (line 29) | def fasta_chrlens(fasta):
  function tbl_transfer_common (line 36) | def tbl_transfer_common(cmap, ref_tbl, out_tbl, alt_chrlens, oob_clip=Fa...
  function tbl_transfer (line 141) | def tbl_transfer(ref_fasta, ref_tbl, alt_fasta, out_tbl, oob_clip=False,...
  function parser_tbl_transfer (line 152) | def parser_tbl_transfer(parser=argparse.ArgumentParser()):
  function tbl_transfer_multichr (line 182) | def tbl_transfer_multichr(ref_fastas, ref_tbls, alt_fasta, out_dir, oob_...
  function parser_tbl_transfer_multichr (line 209) | def parser_tbl_transfer_multichr(parser=argparse.ArgumentParser()):
  function tbl_transfer_prealigned (line 241) | def tbl_transfer_prealigned(inputFasta, refFasta, refAnnotTblFiles, outp...
  function parser_tbl_transfer_prealigned (line 321) | def parser_tbl_transfer_prealigned(parser=argparse.ArgumentParser()):
  function fetch_fastas (line 356) | def fetch_fastas(accession_IDs, destinationDir, emailAddress, forceOverw...
  function fetch_feature_tables (line 374) | def fetch_feature_tables(accession_IDs, destinationDir, emailAddress, fo...
  function fetch_genbank_records (line 392) | def fetch_genbank_records(accession_IDs, destinationDir, emailAddress, f...
  function parser_fetch_reference_common (line 410) | def parser_fetch_reference_common(parser=argparse.ArgumentParser()):
  function parser_fetch_fastas (line 451) | def parser_fetch_fastas(parser):
  function parser_fetch_feature_tables (line 462) | def parser_fetch_feature_tables(parser):
  function parser_fetch_genbank_records (line 473) | def parser_fetch_genbank_records(parser):
  function biosample_to_genbank (line 484) | def biosample_to_genbank(attributes, num_segments, taxid, out_genbank_sm...
  function parser_biosample_to_genbank (line 566) | def parser_biosample_to_genbank(parser=argparse.ArgumentParser()):
  function fasta2fsa (line 594) | def fasta2fsa(infname, outdir, biosample=None):
  function multi_smt_table (line 615) | def multi_smt_table(in_table, out_cmt):
  function make_structured_comment_file (line 628) | def make_structured_comment_file(cmt_fname, name=None, seq_tech=None, co...
  function prep_genbank_files (line 651) | def prep_genbank_files(templateFile, fasta_files, annotDir,
  function parser_prep_genbank_files (line 727) | def parser_prep_genbank_files(parser=argparse.ArgumentParser()):
  function prep_sra_table (line 756) | def prep_sra_table(lib_fname, biosampleFile, md5_fname, outFile):
  function parser_prep_sra_table (line 795) | def parser_prep_sra_table(parser=argparse.ArgumentParser()):
  function full_parser (line 815) | def full_parser():
  function main (line 819) | def main():

FILE: src/viral_ngs/phylo/feature_table.py
  class SeqPosition (line 8) | class SeqPosition(object):
    method __init__ (line 9) | def __init__(self, position, location_operator=None, allow_fuzzy=True):
    method __str__ (line 14) | def __str__(self):
    method __int__ (line 20) | def __int__(self):
    method is_fuzzy (line 23) | def is_fuzzy(self):
    method __eq__ (line 26) | def __eq__(self, other):
    method __ne__ (line 29) | def __ne__(self, other):
    method __lt__ (line 32) | def __lt__(self, other):
    method __le__ (line 35) | def __le__(self, other):
    method __gt__ (line 38) | def __gt__(self, other):
    method __ge__ (line 41) | def __ge__(self, other):
  class SeqQualifier (line 44) | class SeqQualifier(object):
    method __init__ (line 45) | def __init__(self, qualifier_key, qualifier_value):
    method __str__ (line 49) | def __str__(self):
  class SeqLocation (line 55) | class SeqLocation(object):
    method __init__ (line 56) | def __init__(self, start_pos, end_pos, feature_type=None):
    method __str__ (line 61) | def __str__(self):
    method __eq__ (line 69) | def __eq__(self, other):
    method __ne__ (line 72) | def __ne__(self, other):
    method __lt__ (line 75) | def __lt__(self, other):
    method __le__ (line 78) | def __le__(self, other):
    method __gt__ (line 81) | def __gt__(self, other):
    method __ge__ (line 84) | def __ge__(self, other):
  class SeqFeature (line 87) | class SeqFeature(object):
    method __init__ (line 88) | def __init__(self, locations=None, feature_type=None):
    method add_location (line 93) | def add_location(self, location):
    method add_location (line 96) | def add_location(self, start, location_operator_start, end, location_o...
    method sort (line 101) | def sort(self):
    method add_qualifier (line 105) | def add_qualifier(self, qualifier_key, qualifier_value, *args, **kwargs):
    method add_note (line 108) | def add_note(self, note_text):
    method lines (line 112) | def lines(self):
  class AttrDict (line 127) | class AttrDict(dict):
    method __init__ (line 136) | def __init__(self, *args, **kwargs):
  class FeatureTable (line 140) | class FeatureTable(object):
    method __init__ (line 144) | def __init__(self, filepath=None, valid_feature_types=None):
    method _parse_line (line 160) | def _parse_line(self, line):
    method features (line 171) | def features(self):
    method default_feature_types (line 175) | def default_feature_types(self):
    method add_feature (line 179) | def add_feature(self, feature):
    method read_feature_table (line 182) | def read_feature_table(self, filepath, map_function=None, allow_fuzzy=...
    method _is_valid_location (line 233) | def _is_valid_location(self, location):
    method remap_locations (line 247) | def remap_locations(self, map_function=None):
    method lines (line 327) | def lines(self, exclude_patterns=None):

FILE: src/viral_ngs/phylo/genbank.py
  function parse_accession_str (line 15) | def parse_accession_str(chr_ref):
  function get_feature_table_id (line 25) | def get_feature_table_id(featureTableFile):
  function _seq_chunks (line 46) | def _seq_chunks(seq, n):
  function _fetch_from_nuccore (line 52) | def _fetch_from_nuccore(accessionList, destinationDir, emailAddress,
  function fetch_fastas_from_genbank (line 176) | def fetch_fastas_from_genbank(
  function fetch_feature_tables_from_genbank (line 193) | def fetch_feature_tables_from_genbank(
  function fetch_full_records_from_genbank (line 210) | def fetch_full_records_from_genbank(

FILE: src/viral_ngs/phylo/mafft.py
  class MafftTool (line 23) | class MafftTool(core.Tool):
    method __init__ (line 25) | def __init__(self, install_methods=None):
    method version (line 30) | def version(self):
    method _get_tool_version (line 35) | def _get_tool_version(self):
    method __seqIdsAreAllUnique (line 38) | def __seqIdsAreAllUnique(self, filePath, inputFormat="fasta"):
    method execute (line 53) | def execute(

FILE: src/viral_ngs/phylo/mummer.py
  class MummerTool (line 22) | class MummerTool(core.Tool):
    method __init__ (line 24) | def __init__(self, install_methods=None):
    method version (line 29) | def version(self):
    method _get_tool_version (line 34) | def _get_tool_version(self):
    method executable_path (line 37) | def executable_path(self):
    method execute (line 44) | def execute(self, refFasta, qryFastas):
    method nucmer (line 50) | def nucmer(self, refFasta, qryFasta, outDelta, extend=None, breaklen=N...
    method promer (line 75) | def promer(self, refFasta, qryFasta, outDelta, extend=None, breaklen=N...
    method delta_filter (line 100) | def delta_filter(self, inDelta, outDelta):
    method show_tiling (line 107) | def show_tiling(self, inDelta, outTiling, outFasta=None,
    method trim_contigs (line 136) | def trim_contigs(self, refFasta, contigsFasta, outFasta,
    method scaffold_contigs (line 182) | def scaffold_contigs(self, refFasta, contigsFasta, outFasta,
    method scaffold_contigs_custom (line 210) | def scaffold_contigs_custom(self, refFasta, contigsFasta, outFasta,
    method align_one_to_one (line 341) | def align_one_to_one(self, refFasta, otherFasta, outFasta):
  function contig_chooser (line 378) | def contig_chooser(alt_seqs, ref_len, coords_debug=""):
  class AmbiguousAlignmentException (line 454) | class AmbiguousAlignmentException(Exception):
  class AlignsReader (line 457) | class AlignsReader(object):
    method __init__ (line 460) | def __init__(self, aligns_file, ref_fasta=None):
    method _load_align (line 469) | def _load_align(self):
    method _load_fastas (line 525) | def _load_fastas(self):
    method get_alignments (line 529) | def get_alignments(self):
    method get_intervals (line 533) | def get_intervals(self):
    method _dummy_row (line 554) | def _dummy_row(self, start, stop, filler='N'):
    method get_ref_seq (line 559) | def get_ref_seq(self, start, stop):
    method retrieve_alts_by_ref (line 566) | def retrieve_alts_by_ref(self, start, stop, aln_start=None, aln_stop=N...
    method _aln_to_alt_seq (line 597) | def _aln_to_alt_seq(self, aln, start, stop):

FILE: src/viral_ngs/phylo/muscle.py
  class MuscleTool (line 22) | class MuscleTool(core.Tool):
    method __init__ (line 24) | def __init__(self, install_methods=None):
    method version (line 29) | def version(self):
    method _get_tool_version (line 34) | def _get_tool_version(self):
    method execute (line 38) | def execute(

FILE: src/viral_ngs/phylo/snpeff.py
  class SnpEff (line 29) | class SnpEff(core.Tool):
    method __init__ (line 31) | def __init__(self, install_methods=None, extra_genomes=None):
    method version (line 39) | def version(self):
    method execute (line 42) | def execute(self, command, args, JVMmemory=None, stdin=None, stdout=No...
    method has_genome (line 60) | def has_genome(self, genome):
    method download_db (line 67) | def download_db(self, dbname, verbose=False):
    method create_db (line 75) | def create_db(self, accessions, emailAddress=None, JVMmemory=None):
    method available_databases (line 135) | def available_databases(self):
    method annotate_vcf (line 159) | def annotate_vcf(self, inVcf, genomes, outVcf, emailAddress=None, JVMm...
  function get_data_dir (line 220) | def get_data_dir(config_file):
  function add_genomes_to_snpeff_config_file (line 230) | def add_genomes_to_snpeff_config_file(config_file, new_genomes):

FILE: src/viral_ngs/phylo/vcf.py
  function make_intervals (line 18) | def make_intervals(i, n, fasta, chr_prefix='', verbose=False):
  function sliding_windows (line 59) | def sliding_windows(fasta, width, offset, chr_prefix=''):
  class GenomePosition (line 75) | class GenomePosition(object):
    method __init__ (line 81) | def __init__(self, seqDb):
    method get_gpos (line 93) | def get_gpos(self, c, p):
    method get_chr_pos (line 99) | def get_chr_pos(self, gpos):
  function get_chrlens (line 110) | def get_chrlens(inFile):
  function calc_maf (line 145) | def calc_maf(genos, ancestral=None, ploidy=1):
  class TabixReader (line 183) | class TabixReader(pysam.TabixFile):
    method __init__ (line 192) | def __init__(self, inFile, parser=pysam.asTuple()):
    method __enter__ (line 208) | def __enter__(self):
    method __exit__ (line 211) | def __exit__(self, exc_type, exc_val, exc_tb):
    method chroms (line 219) | def chroms(self):
    method get (line 222) | def get(self, chrom=None, start=None, stop=None, region=None):
  function get_pos_from_vcf_record (line 228) | def get_pos_from_vcf_record(vcfrec):
  function bytes_to_string (line 233) | def bytes_to_string(o):
  class VcfReader (line 239) | class VcfReader(TabixReader):
    method __init__ (line 247) | def __init__(self, inFile, ploidy=1, parser=pysam.asVCF()):
    method samples (line 268) | def samples(self):
    method chrlens (line 271) | def chrlens(self):
    method get_positions (line 274) | def get_positions(self, c=None, start=None, stop=None, region=None):
    method get_range (line 279) | def get_range(self, c=None, start=None, stop=None, region=None, as_str...
    method get_snp_genos (line 311) | def get_snp_genos(self, c, p, as_strings=True):
    method getFullSequences (line 320) | def getFullSequences(self, c, start, stop, samples,
  function replaceAlleles (line 380) | def replaceAlleles(sample, seq, vcf_records):

FILE: src/viral_ngs/phylo/vphaser2.py
  class Vphaser2Tool (line 19) | class Vphaser2Tool(core.Tool):
    method __init__ (line 21) | def __init__(self, install_methods=None):
    method execute (line 26) | def execute(self, inBam, outDir, numThreads=None):    # pylint: disabl...
    method iterate (line 51) | def iterate(self, inBam, numThreads=None):

FILE: src/viral_ngs/read_utils.py
  function parser_index_fasta_samtools (line 51) | def parser_index_fasta_samtools(parser=argparse.ArgumentParser()):
  function main_index_fasta_samtools (line 58) | def main_index_fasta_samtools(args):
  function parser_index_fasta_picard (line 71) | def parser_index_fasta_picard(parser=argparse.ArgumentParser()):
  function main_index_fasta_picard (line 89) | def main_index_fasta_picard(args):
  function parser_mkdup_picard (line 106) | def parser_mkdup_picard(parser=argparse.ArgumentParser()):
  function main_mkdup_picard (line 133) | def main_mkdup_picard(args):
  function parser_revert_sam_common (line 152) | def parser_revert_sam_common(parser=argparse.ArgumentParser()):
  function parser_revert_bam_picard (line 183) | def parser_revert_bam_picard(parser=argparse.ArgumentParser()):
  function main_revert_bam_picard (line 203) | def main_revert_bam_picard(inBam, outBam, clear_tags=False, tags_to_clea...
  function revert_bam_if_aligned (line 220) | def revert_bam_if_aligned(inBam, revert_bam=None, clear_tags=True, tags_...
  function parser_picard (line 267) | def parser_picard(parser=argparse.ArgumentParser()):
  function main_picard (line 284) | def main_picard(args):
  function parser_sort_bam (line 297) | def parser_sort_bam(parser=argparse.ArgumentParser()):
  function main_sort_bam (line 336) | def main_sort_bam(args):
  function parser_downsample_bams (line 356) | def parser_downsample_bams(parser=argparse.ArgumentParser()):
  function main_downsample_bams (line 381) | def main_downsample_bams(in_bams, out_path, specified_read_count=None, d...
  function parser_merge_bams (line 477) | def parser_merge_bams(parser=argparse.ArgumentParser()):
  function main_merge_bams (line 496) | def main_merge_bams(args):
  function parser_filter_bam (line 510) | def parser_filter_bam(parser=argparse.ArgumentParser()):
  function main_filter_bam (line 528) | def main_filter_bam(args):
  function fastq_to_bam (line 547) | def fastq_to_bam(
  function parser_fastq_to_bam (line 607) | def parser_fastq_to_bam(parser=argparse.ArgumentParser()):
  function join_paired_fastq (line 642) | def join_paired_fastq(
  function parser_join_paired_fastq (line 656) | def parser_join_paired_fastq(parser=argparse.ArgumentParser()):
  function split_bam (line 675) | def split_bam(inBam, outBams):
  function parser_split_bam (line 724) | def parser_split_bam(parser=argparse.ArgumentParser()):
  function parser_reheader_bam (line 739) | def parser_reheader_bam(parser=argparse.ArgumentParser()):
  function main_reheader_bam (line 748) | def main_reheader_bam(args):
  function parser_reheader_bams (line 776) | def parser_reheader_bams(parser=argparse.ArgumentParser()):
  function main_reheader_bams (line 783) | def main_reheader_bams(args):
  function mvicuna_fastqs_to_readlist (line 820) | def mvicuna_fastqs_to_readlist(inFastq1, inFastq2, readList):
  function rmdup_cdhit_bam (line 848) | def rmdup_cdhit_bam(inBam, outBam, max_mismatches=None, jvm_memory=None):
  function parser_rmdup_cdhit_bam (line 897) | def parser_rmdup_cdhit_bam(parser=argparse.ArgumentParser()):
  function _merge_fastqs_and_mvicuna (line 913) | def _merge_fastqs_and_mvicuna(lb, files):
  function rmdup_mvicuna_bam (line 943) | def rmdup_mvicuna_bam(inBam, outBam, threads=None):
  function parser_rmdup_mvicuna_bam (line 991) | def parser_rmdup_mvicuna_bam(parser=argparse.ArgumentParser()):
  function rmdup_bbnorm_bam (line 1002) | def rmdup_bbnorm_bam(inBam, outBam,
  function parser_rmdup_bbnorm_bam (line 1077) | def parser_rmdup_bbnorm_bam(parser=argparse.ArgumentParser()):
  function parser_rmdup_prinseq_fastq (line 1126) | def parser_rmdup_prinseq_fastq(parser=argparse.ArgumentParser()):
  function main_rmdup_prinseq_fastq (line 1144) | def main_rmdup_prinseq_fastq(args):
  function filter_bam_mapped_only (line 1156) | def filter_bam_mapped_only(inBam, outBam):
  function parser_filter_bam_mapped_only (line 1166) | def parser_filter_bam_mapped_only(parser=argparse.ArgumentParser()):
  function parser_novoalign (line 1179) | def parser_novoalign(parser=argparse.ArgumentParser()):
  function main_novoalign (line 1201) | def main_novoalign(args):
  function parser_novoindex (line 1217) | def parser_novoindex(parser=argparse.ArgumentParser()):
  function main_novoindex (line 1229) | def main_novoindex(args):
  function align_and_fix (line 1239) | def align_and_fix(
  function parser_align_and_fix (line 1352) | def parser_align_and_fix(parser=argparse.ArgumentParser()):
  function filter_bam_to_proper_primary_mapped_reads (line 1407) | def filter_bam_to_proper_primary_mapped_reads(inBam, outBam, doNotRequir...
  function parser_filter_bam_to_proper_primary_mapped_reads (line 1430) | def parser_filter_bam_to_proper_primary_mapped_reads(parser=argparse.Arg...
  function minimap2_idxstats (line 1456) | def minimap2_idxstats(inBam, refFasta, outStats, outReadlist=None, threa...
  function parser_minimap2_idxstats (line 1474) | def parser_minimap2_idxstats(parser=argparse.ArgumentParser()):
  function bwamem_idxstats (line 1487) | def bwamem_idxstats(inBam, refFasta, outBam=None, outStats=None,
  function parser_bwamem_idxstats (line 1530) | def parser_bwamem_idxstats(parser=argparse.ArgumentParser()):
  function parser_extract_tarball (line 1584) | def parser_extract_tarball(parser=argparse.ArgumentParser()):
  function main_extract_tarball (line 1597) | def main_extract_tarball(*args, **kwargs):
  function fasta_read_names (line 1607) | def fasta_read_names(in_fasta, out_read_names):
  function read_names (line 1621) | def read_names(in_reads, out_read_names, threads=None):
  function parser_read_names (line 1630) | def parser_read_names(parser=argparse.ArgumentParser()):
  function trim_rmdup_subsamp_reads (line 1645) | def trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=100000, trim...
  function parser_trim_rmdup_subsamp (line 1829) | def parser_trim_rmdup_subsamp(parser=argparse.ArgumentParser()):
  function full_parser (line 1855) | def full_parser():
  function main (line 1859) | def main():

FILE: src/viral_ngs/reports.py
  function get_assembly_stats (line 35) | def get_assembly_stats(sample,
  function genome_coverage_stats_only (line 131) | def genome_coverage_stats_only(mapped_bam, chr_name=None, cov_thresholds...
  function assembly_stats (line 144) | def assembly_stats(samples, outFile, cov_thresholds, assembly_dir, assem...
  function parser_assembly_stats (line 164) | def parser_assembly_stats(parser=argparse.ArgumentParser()):
  function _get_samples_from_bam (line 195) | def _get_samples_from_bam(bam):
  function _get_chrs_from_bam (line 198) | def _get_chrs_from_bam(bam):
  function parser_coverage_only (line 202) | def parser_coverage_only(parser=argparse.ArgumentParser()):
  function coverage_only (line 213) | def coverage_only(mapped_bams, out_report, cov_thresholds=(1, 5, 20, 100)):
  function consolidate_fastqc (line 244) | def consolidate_fastqc(inDirs, outFile):
  function parser_consolidate_fastqc (line 266) | def parser_consolidate_fastqc(parser=argparse.ArgumentParser()):
  function get_bam_info (line 277) | def get_bam_info(bamstats_dir):
  function get_lib_info (line 290) | def get_lib_info(runfile):
  function get_earliest_date (line 306) | def get_earliest_date(inDir):
  function consolidate_spike_count (line 312) | def consolidate_spike_count(in_dir, out_file):
  function parser_consolidate_spike_count (line 328) | def parser_consolidate_spike_count(parser=argparse.ArgumentParser()):
  function aggregate_spike_count (line 339) | def aggregate_spike_count(in_dir, out_file):
  function parser_aggregate_spike_count (line 371) | def parser_aggregate_spike_count(parser=argparse.ArgumentParser()):
  function aggregate_alignment_counts (line 380) | def aggregate_alignment_counts(in_reports, out_file):
  function parser_aggregate_alignment_counts (line 408) | def parser_aggregate_alignment_counts(parser=argparse.ArgumentParser()):
  function parser_plot_coverage_common (line 420) | def parser_plot_coverage_common(parser=argparse.ArgumentParser()):    # ...
  function plot_coverage (line 543) | def plot_coverage(
  function parser_plot_coverage (line 758) | def parser_plot_coverage(parser=argparse.ArgumentParser()):
  function align_and_plot_coverage (line 774) | def align_and_plot_coverage(
  function parser_align_and_plot_coverage (line 890) | def parser_align_and_plot_coverage(parser=argparse.ArgumentParser()):
  function parser_fastqc (line 952) | def parser_fastqc(parser=argparse.ArgumentParser()):
  function full_parser (line 964) | def full_parser():
  function main (line 968) | def main():

FILE: src/viral_ngs/taxon_filter.py
  function parser_deplete (line 58) | def parser_deplete(parser=argparse.ArgumentParser()):
  function main_deplete (line 106) | def main_deplete(args):
  function filter_lastal_bam (line 179) | def filter_lastal_bam(
  function parser_filter_lastal_bam (line 226) | def parser_filter_lastal_bam(parser=argparse.ArgumentParser()):
  function deplete_bmtagger_bam (line 291) | def deplete_bmtagger_bam(inBam, db, outBam, srprism_memory=7168):
  function parser_deplete_bam_bmtagger (line 340) | def parser_deplete_bam_bmtagger(parser=argparse.ArgumentParser()):
  function main_deplete_bam_bmtagger (line 356) | def main_deplete_bam_bmtagger(args):
  function multi_db_deplete_bam (line 377) | def multi_db_deplete_bam(inBam, refDbs, deplete_method, outBam, **kwargs):
  function _run_blastn_chunk (line 413) | def _run_blastn_chunk(db, input_fasta, out_hits, blast_threads, task=Non...
  function blastn_chunked_fasta (line 428) | def blastn_chunked_fasta(fasta, db, out_hits, chunkSize=1000000, threads...
  function deplete_blastn_bam (line 518) | def deplete_blastn_bam(inBam, db, outBam, threads=None, chunkSize=1000000):
  function chunk_blast_hits (line 545) | def chunk_blast_hits(inFasta, db, blast_hits_output, threads=None, chunk...
  function parser_chunk_blast_hits (line 564) | def parser_chunk_blast_hits(parser=argparse.ArgumentParser()):
  function parser_deplete_blastn_bam (line 578) | def parser_deplete_blastn_bam(parser=argparse.ArgumentParser()):
  function main_deplete_blastn_bam (line 590) | def main_deplete_blastn_bam(args):
  function extract_build_or_use_database (line 607) | def extract_build_or_use_database(db, db_build_command, db_extension_to_...
  function deplete_bwa_bam (line 647) | def deplete_bwa_bam(inBam, db, outBam, threads=None, clear_tags=True, ta...
  function parser_deplete_bwa_bam (line 675) | def parser_deplete_bwa_bam(parser=argparse.ArgumentParser()):
  function main_deplete_bwa_bam (line 690) | def main_deplete_bwa_bam(args):
  function deplete_minimap2_bam (line 710) | def deplete_minimap2_bam(inBam, db, outBam, threads=None):
  function parser_deplete_minimap2_bam (line 736) | def parser_deplete_minimap2_bam(parser=argparse.ArgumentParser()):
  function main_deplete_minimap2_bam (line 746) | def main_deplete_minimap2_bam(args):
  function lastal_build_db (line 771) | def lastal_build_db(inputFasta, outputDirectory, outputFilePrefix):
  function parser_lastal_build_db (line 783) | def parser_lastal_build_db(parser=argparse.ArgumentParser()):
  function merge_compressed_files (line 801) | def merge_compressed_files(inFiles, outFile, sep=''):
  function bwa_build_db (line 821) | def bwa_build_db(inputFasta, outputDirectory, outputFilePrefix):
  function parser_bwa_build_db (line 848) | def parser_bwa_build_db(parser=argparse.ArgumentParser()):
  function blastn_build_db (line 868) | def blastn_build_db(inputFasta, outputDirectory, outputFilePrefix):
  function parser_blastn_build_db (line 892) | def parser_blastn_build_db(parser=argparse.ArgumentParser()):
  function bmtagger_build_db (line 911) | def bmtagger_build_db(inputFasta, outputDirectory, outputFilePrefix, wor...
  function parser_bmtagger_build_db (line 941) | def parser_bmtagger_build_db(parser=argparse.ArgumentParser()):
  function full_parser (line 967) | def full_parser():
  function main (line 971) | def main():

FILE: tests/__init__.py
  function assert_equal_contents (line 38) | def assert_equal_contents(testCase, filename1, filename2):
  function assert_equal_bam_reads (line 43) | def assert_equal_bam_reads(testCase, bam_filename1, bam_filename2):
  function assert_md5_equal_to_line_in_file (line 92) | def assert_md5_equal_to_line_in_file(testCase, filename, checksum_file, ...
  class TestCaseWithTmp (line 114) | class TestCaseWithTmp(unittest.TestCase):
    method assertEqualContents (line 117) | def assertEqualContents(self, f1, f2):
    method assertEqualFasta (line 120) | def assertEqualFasta(self, f1, f2):
    method assertEqualFastaSeqs (line 126) | def assertEqualFastaSeqs(self, f1, f2):
    method input (line 132) | def input(self, fname):
    method inputs (line 136) | def inputs(self, *fnames):
    method assertEqualSamHeaders (line 140) | def assertEqualSamHeaders(self, tested_samfile, expected_samfile, othe...
  function assert_valid_feature_table (line 190) | def assert_valid_feature_table(testCase, tbl_file, fasta_file, temp_dir):
  function assert_none_executable (line 211) | def assert_none_executable():

FILE: tests/conftest.py
  function timer (line 19) | def timer():
  function pytest_addoption (line 25) | def pytest_addoption(parser):
  function pytest_configure (line 40) | def pytest_configure(config):
  function pytest_collection_modifyitems (line 49) | def pytest_collection_modifyitems(config, items):
  function _tmpdir_aux (line 67) | def _tmpdir_aux(base_dir, scope, name):
  function tmpdir_session (line 74) | def tmpdir_session(request, tmpdir_factory):
  function tmpdir_module (line 81) | def tmpdir_module(request, tmpdir_session):
  function tmpdir_class (line 87) | def tmpdir_class(request, tmpdir_module):
  function tmpdir_function (line 94) | def tmpdir_function(request, tmpdir_class, monkeypatch):
  function monkeypatch_function_result (line 103) | def monkeypatch_function_result(monkeypatch):
  class FixtureReporter (line 146) | class FixtureReporter:
    method __init__ (line 148) | def __init__(self, config):
    method pytest_fixture_setup (line 156) | def pytest_fixture_setup(self, fixturedef, request):
    method pytest_terminal_summary (line 167) | def pytest_terminal_summary(self, terminalreporter, exitstatus):

FILE: tests/unit/assemble/test_assembly.py
  function makeFasta (line 31) | def makeFasta(seqs, outFasta):
  class TestCommandHelp (line 37) | class TestCommandHelp(unittest.TestCase):
    method test_help_parser_for_each_command (line 39) | def test_help_parser_for_each_command(self):
  class TestRefineAssemble (line 45) | class TestRefineAssemble(TestCaseWithTmp):
    method _align_with_minimap2 (line 48) | def _align_with_minimap2(self, refFasta, inBam):
    method test_empty_input_bam_assembly (line 57) | def test_empty_input_bam_assembly(self):
    method test_aligned_empty_input_bam_assembly (line 74) | def test_aligned_empty_input_bam_assembly(self):
    method test_empty_input_fasta_assembly (line 97) | def test_empty_input_fasta_assembly(self):
    method test_empty_input_succeed (line 111) | def test_empty_input_succeed(self):
  class TestNormalizeCoverage (line 126) | class TestNormalizeCoverage(TestCaseWithTmp):
    method test_help_parser (line 129) | def test_help_parser(self):
    method test_normalize_coverage_on_aligned_bam (line 135) | def test_normalize_coverage_on_aligned_bam(self):
  class TestAssembleSpades (line 159) | class TestAssembleSpades(TestCaseWithTmp):
    method test_assembly (line 162) | def test_assembly(self):
    method test_assembly_with_previously_assembled_contigs (line 174) | def test_assembly_with_previously_assembled_contigs(self):
    method test_empty_input_succeed (line 188) | def test_empty_input_succeed(self):
    method test_always_succeed (line 196) | def test_always_succeed(self):
  class TestAmbiguityBases (line 206) | class TestAmbiguityBases(unittest.TestCase):
    method test_non_failure (line 208) | def test_non_failure(self):
  class TestUndirectedGraph (line 220) | class TestUndirectedGraph(unittest.TestCase):
    method test_simple (line 221) | def test_simple(self):
    method test_disconnected (line 229) | def test_disconnected(self):
    method test_both (line 236) | def test_both(self):
  class TestOrderAndOrient (line 251) | class TestOrderAndOrient(TestCaseWithTmp):
    method test_varicella_big (line 254) | def test_varicella_big(self):
    method test_lassa_multisegment (line 266) | def test_lassa_multisegment(self):
    method test_lassa_multisegment_refsel (line 277) | def test_lassa_multisegment_refsel(self):
    method test_influenza_multisegment (line 291) | def test_influenza_multisegment(self):
    method test_ebov_palindrome (line 302) | def test_ebov_palindrome(self):
    method test_ebov_palindrome_refsel (line 315) | def test_ebov_palindrome_refsel(self):
    method test_hiv_wraparound (line 326) | def test_hiv_wraparound(self):
    method test_alternate_contigs (line 339) | def test_alternate_contigs(self):
    method test_lassa_protein (line 355) | def test_lassa_protein(self):
    method test_multi_overlap (line 367) | def test_multi_overlap(self):
    method test_ambig_align (line 379) | def test_ambig_align(self):
    method test_ambig_align_ebov (line 396) | def test_ambig_align_ebov(self):
    method test_obscure_mummer3_bug (line 413) | def test_obscure_mummer3_bug(self):
    method test_not_all_segments_fail (line 426) | def test_not_all_segments_fail(self):
    method test_not_all_segments_succeed (line 436) | def test_not_all_segments_succeed(self):
    method test_empty_output_succeed (line 446) | def test_empty_output_succeed(self):
  class TestGap2Seq (line 459) | class TestGap2Seq(TestCaseWithTmp):
    method test_gapfill (line 462) | def test_gapfill(self):
    method test_empty_fasta_input (line 473) | def test_empty_fasta_input(self):
  class TestImputeFromReference (line 483) | class TestImputeFromReference(TestCaseWithTmp):
    method test_varicella_big_muscle (line 487) | def test_varicella_big_muscle(self):
    method test_varicella_big_mummer (line 504) | def test_varicella_big_mummer(self):
    method test_small_muscle (line 522) | def test_small_muscle(self):
    method test_small_mafft (line 539) | def test_small_mafft(self):
    method test_small_mummer (line 556) | def test_small_mummer(self):
    method test_empty_fasta_input (line 573) | def test_empty_fasta_input(self):
  class TestSkaniReferenceSelection (line 588) | class TestSkaniReferenceSelection(TestCaseWithTmp):
    method test_skani_contigs_to_refs (line 591) | def test_skani_contigs_to_refs(self):
    method test_skani_no_big_contigs (line 618) | def test_skani_no_big_contigs(self):
    method test_skani_no_matches (line 639) | def test_skani_no_matches(self):
    method test_output_sorted_by_product (line 660) | def test_output_sorted_by_product(self):
    method test_sort_skani_table_empty_file (line 682) | def test_sort_skani_table_empty_file(self):
    method test_sort_skani_table_header_only (line 699) | def test_sort_skani_table_header_only(self):
  class TestMutableSequence (line 721) | class TestMutableSequence(unittest.TestCase):
    method test_bad_coords (line 724) | def test_bad_coords(self):
    method test_good_coords (line 730) | def test_good_coords(self):
    method test_modify_one (line 738) | def test_modify_one(self):
    method test_modify_blank (line 756) | def test_modify_blank(self):
    method test_modify_insertions (line 762) | def test_modify_insertions(self):
    method test_modify_deletions (line 771) | def test_modify_deletions(self):
    method test_modify_deletions_simple (line 787) | def test_modify_deletions_simple(self):
    method test_modify_deletions_remember (line 792) | def test_modify_deletions_remember(self):
  class TestManualSnpCaller (line 802) | class TestManualSnpCaller(unittest.TestCase):
    method test_missing_dp (line 805) | def test_missing_dp(self):
    method test_dp_inaccurate (line 811) | def test_dp_inaccurate(self):
    method test_invariant_sites (line 823) | def test_invariant_sites(self):
    method test_het_edgecases (line 841) | def test_het_edgecases(self):
    method test_indels (line 872) | def test_indels(self):
    method test_vcf_to_seqs_indels1 (line 887) | def test_vcf_to_seqs_indels1(self):
    method test_vcf_to_seqs_indels2 (line 896) | def test_vcf_to_seqs_indels2(self):
  class TestDeambigAndTrimFasta (line 909) | class TestDeambigAndTrimFasta(TestCaseWithTmp):
    method run_method (line 912) | def run_method(self, inseqs, parser_fun):
    method test_trim_fasta (line 920) | def test_trim_fasta(self):
    method test_deambig_fasta (line 931) | def test_deambig_fasta(self):
  class TestContigChooser (line 948) | class TestContigChooser(unittest.TestCase):
    method test_no_seqs (line 951) | def test_no_seqs(self):
    method test_one_seq (line 956) | def test_one_seq(self):
    method test_most_popular_seq (line 961) | def test_most_popular_seq(self):
    method test_most_popular_seq_len (line 969) | def test_most_popular_seq_len(self):
    method test_same_as_ref_len (line 985) | def test_same_as_ref_len(self):
  class TestWgsimTool (line 991) | class TestWgsimTool(TestCaseWithTmp):
    method test_slice_fasta_whole_sequence (line 994) | def test_slice_fasta_whole_sequence(self):
    method test_slice_fasta_with_coordinates (line 1013) | def test_slice_fasta_with_coordinates(self):
    method test_slice_fasta_no_params (line 1031) | def test_slice_fasta_no_params(self):
    method test_coverage_to_read_pairs (line 1050) | def test_coverage_to_read_pairs(self):
  class TestSimulateIlluminaReads (line 1075) | class TestSimulateIlluminaReads(TestCaseWithTmp):
    method setUp (line 1078) | def setUp(self):
    method count_bam_reads (line 1086) | def count_bam_reads(self, bam_file):
    method expected_read_count (line 1094) | def expected_read_count(self, coverage, seq_length, read_length=150):
    method test_simulate_uniform_coverage (line 1102) | def test_simulate_uniform_coverage(self):
    method test_simulate_per_sequence_coverage (line 1131) | def test_simulate_per_sequence_coverage(self):
    method test_simulate_bed_coverage (line 1164) | def test_simulate_bed_coverage(self):
  function _find_script (line 1204) | def _find_script(script_name):
  class TestFastaTrimTerminalAmbigs (line 1217) | class TestFastaTrimTerminalAmbigs(TestCaseWithTmp):
    method test_script_runs_successfully (line 1220) | def test_script_runs_successfully(self):
    method test_script_with_3rules_option (line 1247) | def test_script_with_3rules_option(self):

FILE: tests/unit/assemble/test_assembly_integration.py
  function _align_with_minimap2 (line 23) | def _align_with_minimap2(refFasta, inBam):
  class TestRefineAssembly (line 33) | class TestRefineAssembly(TestCaseWithTmp):
    method test_ebov_refine1 (line 34) | def test_ebov_refine1(self):
    method test_ebov_refine2 (line 52) | def test_ebov_refine2(self):
  class TestOrderOrientAndImputeFromReference (line 71) | class TestOrderOrientAndImputeFromReference(TestCaseWithTmp):
    method setUp (line 73) | def setUp(self):
    method tearDown (line 85) | def tearDown(self):
    method test_impute_from_oriented_muscle (line 89) | def test_impute_from_oriented_muscle(self):
    method test_impute_from_oriented_mafft (line 92) | def test_impute_from_oriented_mafft(self):
    method test_impute_from_oriented_mummer (line 95) | def test_impute_from_oriented_mummer(self):
    method influenza_impute (line 99) | def influenza_impute(self, aligner):

FILE: tests/unit/assemble/test_util_vcf.py
  class StubGenome (line 22) | class StubGenome:
    method __init__ (line 28) | def __init__(self, chromlist):
    method chrlens (line 33) | def chrlens(self):
  class TestGenomePosition (line 37) | class TestGenomePosition(unittest.TestCase):
    method test_fail_OOB_get_gpos (line 40) | def test_fail_OOB_get_gpos(self):
    method test_fail_OOB_get_chr_pos (line 48) | def test_fail_OOB_get_chr_pos(self):
    method test_fail_non_int_pos (line 55) | def test_fail_non_int_pos(self):
    method test_spotcheck_edges (line 63) | def test_spotcheck_edges(self):
    method test_equality_1chrGenome (line 72) | def test_equality_1chrGenome(self):
    method test_equality_3chrGenome (line 80) | def test_equality_3chrGenome(self):
    method test_gpos_inbounds (line 96) | def test_gpos_inbounds(self):
    method test_chr_pos_inbounds (line 107) | def test_chr_pos_inbounds(self):
    method test_unique_gpos (line 119) | def test_unique_gpos(self):
    method test_unique_chr_pos (line 130) | def test_unique_chr_pos(self):
  class TestVcfContigHeaderParsing (line 141) | class TestVcfContigHeaderParsing(unittest.TestCase):
    method test_simple_contig_header (line 144) | def test_simple_contig_header(self):
    method test_contig_header_with_assembly (line 149) | def test_contig_header_with_assembly(self):
    method test_contig_header_with_multiple_extra_attrs (line 154) | def test_contig_header_with_multiple_extra_attrs(self):
    method test_multiple_contigs_mixed_formats (line 159) | def test_multiple_contigs_mixed_formats(self):
    method test_contig_header_without_length_raises (line 168) | def test_contig_header_without_length_raises(self):
    method test_invalid_header_raises (line 172) | def test_invalid_header_raises(self):
  class TestVcfReaderPositions (line 177) | class TestVcfReaderPositions(unittest.TestCase):
    method setUp (line 180) | def setUp(self):
    method test_sample_names (line 188) | def test_sample_names(self):
    method test_get_one_base (line 195) | def test_get_one_base(self):
    method test_get_positions_edges (line 204) | def test_get_positions_edges(self):
    method test_get_range_edges (line 210) | def test_get_range_edges(self):

FILE: tests/unit/classify/fixtures.py
  function krona (line 10) | def krona():
  function db_type (line 17) | def db_type(request):
  function krona_db (line 22) | def krona_db(request, tmpdir_module, krona, db_type):
  function taxonomy_db (line 37) | def taxonomy_db(request, tmpdir_module, db_type):

FILE: tests/unit/classify/test_integration_kb.py
  function kb_inputs (line 20) | def kb_inputs():
  function kb_bam (line 33) | def kb_bam(tmp_path_factory, kb_inputs):
  function kb_count_result (line 45) | def kb_count_result(tmp_path_factory, kb_inputs, kb_bam):
  function kb_extract_result (line 71) | def kb_extract_result(tmp_path_factory, kb_inputs, kb_bam):
  function kb_ref_result (line 92) | def kb_ref_result(tmp_path_factory, kb_inputs):
  function _run_metagenomics (line 111) | def _run_metagenomics(parser_fn, argv, cwd=None):
  function test_kb_help_reports_usage (line 124) | def test_kb_help_reports_usage():
  function test_kb_count_produces_h5ad (line 132) | def test_kb_count_produces_h5ad(kb_count_result):
  function test_kb_extract_yields_expected_reads (line 138) | def test_kb_extract_yields_expected_reads(kb_extract_result):
  function test_kb_ref_builds_index (line 142) | def test_kb_ref_builds_index(kb_ref_result):

FILE: tests/unit/classify/test_integration_kraken2.py
  function is_gz_file (line 22) | def is_gz_file(filepath):
  function input_bam (line 32) | def input_bam(db_type):
  function kraken2_tool (line 37) | def kraken2_tool():
  function db_type (line 44) | def db_type(request):
  function kraken2_db (line 49) | def kraken2_db(request, tmpdir_module, kraken2_tool, db_type):
  function test_kraken2 (line 65) | def test_kraken2(kraken2_db, input_bam):
  function test_kraken2_krona (line 94) | def test_kraken2_krona(kraken2_db, krona_db, input_bam):
  function test_kraken2_on_empty (line 121) | def test_kraken2_on_empty(kraken2_db, input_bam):

FILE: tests/unit/classify/test_integration_taxon_filter.py
  class TestDepleteHuman (line 22) | class TestDepleteHuman(TestCaseWithTmp):
    method setUp (line 32) | def setUp(self):
    method test_deplete_human (line 45) | def test_deplete_human(self):
    method test_deplete_human_aligned_input (line 76) | def test_deplete_human_aligned_input(self):
    method test_deplete_empty (line 106) | def test_deplete_empty(self):

FILE: tests/unit/classify/test_kmer_utils.py
  class TestCommandHelp (line 29) | class TestCommandHelp(unittest.TestCase):
    method test_help_parser_for_each_command (line 31) | def test_help_parser_for_each_command(self):
  function _seq_as_str (line 40) | def _seq_as_str(s):  # pylint: disable=invalid-name
  function _yield_seq_recs (line 48) | def _yield_seq_recs(seq_file):
  function _list_seq_recs (line 59) | def _list_seq_recs(seq_file):
  function _yield_seqs_as_strs (line 64) | def _yield_seqs_as_strs(seqs):
  function _list_seqs_as_strs (line 75) | def _list_seqs_as_strs(seqs):
  function _getargs (line 80) | def _getargs(args, valid_args):
  function _strip_mate_num (line 85) | def _strip_mate_num(rec_id):
  class KmcPy (line 92) | class KmcPy(object):
    method _revcomp (line 100) | def _revcomp(self, kmer):
    method _canonicalize (line 105) | def _canonicalize(self, kmer):
    method _compute_kmers_iter (line 109) | def _compute_kmers_iter(self, seq_strs, kmer_size, single_strand, **ig...
    method _compute_kmers (line 131) | def _compute_kmers(self, *args, **kw):
    method compute_kmer_counts (line 139) | def compute_kmer_counts(self, seq_files, kmer_size, min_occs, max_occs,
    method _filter_kmer_counts (line 149) | def _filter_kmer_counts(self, counts, min_occs=None, max_occs=None, co...
    method filter_reads (line 158) | def filter_reads(self, db_kmer_counts, in_reads, kmer_size, single_str...
    method binary_op (line 216) | def binary_op(self, op, kmer_counts_1, kmer_counts_2, result_counter_c...
  function _inp (line 237) | def _inp(fname):
  function _stringify (line 241) | def _stringify(arg):
  function _do_build_kmer_db (line 245) | def _do_build_kmer_db(t_dir, val_cache, seq_files, kmer_db_opts):
  function dict_module (line 294) | def dict_module():
  function kmer_db_fixture (line 298) | def kmer_db_fixture(request, tmpdir_module, dict_module):
  function kmer_db_fixture2 (line 302) | def kmer_db_fixture2(request, tmpdir_module, dict_module):
  function test_build_kmer_db (line 307) | def test_build_kmer_db(kmer_db_fixture):
  function _test_build_kmer_db (line 310) | def _test_build_kmer_db(kmer_db_fixture):
  function test_build_kmer_db_combo (line 346) | def test_build_kmer_db_combo(kmer_db_fixture):
  function _test_filter_reads (line 352) | def _test_filter_reads(kmer_db_fixture, reads_file, filter_opts, tmpdir_...
  function test_filter_with_empty_db (line 392) | def test_filter_with_empty_db(kmer_db_fixture, reads_file, filter_opts, ...
  function test_filter_reads (line 401) | def test_filter_reads(kmer_db_fixture, reads_file, filter_opts, tmpdir_f...
  function test_kmer_set_counts (line 407) | def test_kmer_set_counts(kmer_db_fixture, tmpdir_function, set_to_val):
  function test_kmers_binary_op (line 417) | def test_kmers_binary_op(kmer_db_fixture, kmer_db_fixture2, op, tmpdir_f...

FILE: tests/unit/classify/test_metagenomics.py
  class TestCommandHelp (line 29) | class TestCommandHelp(unittest.TestCase):
    method test_help_parser_for_each_command (line 31) | def test_help_parser_for_each_command(self):
  class TestKronaCalls (line 37) | class TestKronaCalls(TestCaseWithTmp):
    method setUp (line 39) | def setUp(self):
    method test_krona_import_taxonomy (line 48) | def test_krona_import_taxonomy(self):
  function taxa_db_simple (line 58) | def taxa_db_simple():
  function taxa_db (line 66) | def taxa_db(parents, names, ranks):
  function parents (line 75) | def parents():
  function names (line 90) | def names():
  function ranks (line 108) | def ranks():
  function simple_m8 (line 125) | def simple_m8():
  function test_tree_level_lookup (line 131) | def test_tree_level_lookup(parents):
  function test_push_up_tree_hits (line 141) | def test_push_up_tree_hits(parents):
  function test_parents_to_children (line 160) | def test_parents_to_children(parents):
  function test_rank_code (line 165) | def test_rank_code():
  function test_blast_records (line 172) | def test_blast_records(simple_m8):
  function test_blast_lca (line 182) | def test_blast_lca(taxa_db_simple, simple_m8):
  function test_paired_query_id (line 201) | def test_paired_query_id():
  function test_translate_gi_to_tax_id (line 224) | def test_translate_gi_to_tax_id(taxa_db_simple):
  function test_ancestor_lookup (line 234) | def test_ancestor_lookup(taxa_db_simple):
  function test_kraken_dfs_report (line 238) | def test_kraken_dfs_report(taxa_db):
  function test_coverage_lca (line 255) | def test_coverage_lca(taxa_db):
  function test_krakenuniq (line 263) | def test_krakenuniq():
  class TestBamFilter (line 276) | class TestBamFilter(TestCaseWithTmp):
    method test_bam_filter_simple (line 277) | def test_bam_filter_simple(self):
    method test_bam_filter_by_tax_id (line 298) | def test_bam_filter_by_tax_id(self):

FILE: tests/unit/classify/test_taxon_filter.py
  class TestCommandHelp (line 34) | class TestCommandHelp(unittest.TestCase):
    method test_help_parser_for_each_command (line 36) | def test_help_parser_for_each_command(self):
  class TestFilterLastal (line 43) | class TestFilterLastal(TestCaseWithTmp):
    method setUp (line 45) | def setUp(self):
    method test_filter_lastal_bam_polio (line 54) | def test_filter_lastal_bam_polio(self):
    method test_lastal_empty_input (line 63) | def test_lastal_empty_input(self):
    method test_lastal_empty_output (line 73) | def test_lastal_empty_output(self):
    method test_lastal_unbuilt_db (line 84) | def test_lastal_unbuilt_db(self):
  class TestBmtagger (line 97) | class TestBmtagger(TestCaseWithTmp):
    method setUp (line 105) | def setUp(self):
    method test_deplete_bmtagger_bam (line 112) | def test_deplete_bmtagger_bam(self):
    method test_deplete_bmtagger_fasta_db (line 122) | def test_deplete_bmtagger_fasta_db(self):
    method test_deplete_bmtagger_tar_db (line 132) | def test_deplete_bmtagger_tar_db(self):
    method test_bmtagger_empty_input (line 145) | def test_bmtagger_empty_input(self):
    method test_bmtagger_empty_output (line 153) | def test_bmtagger_empty_output(self):
  class TestBlastnDbBuild (line 163) | class TestBlastnDbBuild(TestCaseWithTmp):
    method test_blastn_db_build (line 165) | def test_blastn_db_build(self):
    method test_blastn_db_build_gz (line 193) | def test_blastn_db_build_gz(self):
  class TestBmtaggerDbBuild (line 238) | class TestBmtaggerDbBuild(TestCaseWithTmp):
    method test_bmtagger_db_build (line 240) | def test_bmtagger_db_build(self):
    method test_bmtagger_db_build_gz (line 277) | def test_bmtagger_db_build_gz(self):
  class TestLastalDbBuild (line 312) | class TestLastalDbBuild(TestCaseWithTmp):
    method test_lastal_db_build (line 314) | def test_lastal_db_build(self):
  class TestDepleteBlastnBam (line 346) | class TestDepleteBlastnBam(TestCaseWithTmp):
    method setUp (line 355) | def setUp(self):
    method test_deplete_blastn_bam (line 381) | def test_deplete_blastn_bam(self):
    method test_deplete_blastn_bam_chunked (line 402) | def test_deplete_blastn_bam_chunked(self):
    method test_blastn_empty_input (line 423) | def test_blastn_empty_input(self):
    method test_blastn_empty_output (line 434) | def test_blastn_empty_output(self):
  class TestDepleteMinimap2Bam (line 446) | class TestDepleteMinimap2Bam(TestCaseWithTmp):
    method setUp (line 452) | def setUp(self):
    method test_deplete_minimap2_bam (line 459) | def test_deplete_minimap2_bam(self):
    method test_minimap2_empty_input (line 470) | def test_minimap2_empty_input(self):
    method test_minimap2_empty_output (line 482) | def test_minimap2_empty_output(self):
  class TestDepletePipeline (line 495) | class TestDepletePipeline(TestCaseWithTmp):
    method setUp (line 500) | def setUp(self):
    method test_deplete_pipeline_with_minimap (line 506) | def test_deplete_pipeline_with_minimap(self):
    method test_deplete_pipeline_empty_minimap_dbs (line 531) | def test_deplete_pipeline_empty_minimap_dbs(self):

FILE: tests/unit/classify/test_taxonomy.py
  function test_taxonomy_subset_zaire (line 8) | def test_taxonomy_subset_zaire(request, tmpdir_factory):

FILE: tests/unit/classify/test_tools_kb_python.py
  function kb_tool (line 13) | def kb_tool():
  function kb_inputs (line 19) | def kb_inputs():
  function test_build_invokes_kb_ref_with_expected_arguments (line 32) | def test_build_invokes_kb_ref_with_expected_arguments(kb_tool, kb_inputs):
  function test_classify_runs_kb_count_single_end_from_bam (line 51) | def test_classify_runs_kb_count_single_end_from_bam(kb_tool, kb_inputs):
  function test_classify_runs_kb_count_with_fastq_input (line 100) | def test_classify_runs_kb_count_with_fastq_input(kb_tool, kb_inputs):
  function test_classify_returns_early_when_bam_is_empty (line 125) | def test_classify_returns_early_when_bam_is_empty(kb_tool, kb_inputs):

FILE: tests/unit/classify/test_tools_kma.py
  function kma_tool (line 13) | def kma_tool():
  function kma_inputs (line 19) | def kma_inputs():
  function test_build_invokes_kma_index_with_expected_arguments (line 29) | def test_build_invokes_kma_index_with_expected_arguments(kma_tool, kma_i...
  function test_classify_single_end_from_bam (line 41) | def test_classify_single_end_from_bam(kma_tool, kma_inputs):
  function test_classify_paired_end_from_bam (line 84) | def test_classify_paired_end_from_bam(kma_tool, kma_inputs):
  function test_classify_returns_early_when_bam_is_empty (line 127) | def test_classify_returns_early_when_bam_is_empty(kma_tool, kma_inputs):

FILE: tests/unit/classify/test_tools_krona.py
  class TestToolKrona (line 13) | class TestToolKrona(TestCaseWithTmp):
    method setUp (line 15) | def setUp(self):
    method test_import_taxonomy (line 26) | def test_import_taxonomy(self):
    method test_create_db (line 51) | def test_create_db(self):

FILE: tests/unit/core/test_conftest.py
  function test_monkeypatch_function_result (line 13) | def test_monkeypatch_function_result(monkeypatch_function_result):

FILE: tests/unit/core/test_file_utils.py
  class TestCommandHelp (line 16) | class TestCommandHelp(unittest.TestCase):
    method test_help_parser_for_each_command (line 17) | def test_help_parser_for_each_command(self):
  class TestTarballMerger (line 22) | class TestTarballMerger(TestCaseWithTmp):
    method setUp (line 23) | def setUp(self):
    method test_simple_merge (line 30) | def test_simple_merge(self):
  class TestTsvJoin (line 41) | class TestTsvJoin(TestCaseWithTmp):
    method test_join (line 43) | def test_join(self):

FILE: tests/unit/core/test_illumina.py
  class TestCommandHelp (line 23) | class TestCommandHelp(unittest.TestCase):
    method test_help_parser_for_each_command (line 25) | def test_help_parser_for_each_command(self):
  class TestSampleSheet (line 31) | class TestSampleSheet(TestCaseWithTmp):
    method test_miseq (line 33) | def test_miseq(self):
    method test_broad_platform (line 39) | def test_broad_platform(self):
    method test_walkup_submission_no_header_no_lf (line 47) | def test_walkup_submission_no_header_no_lf(self):
    method test_walkup_submission (line 53) | def test_walkup_submission(self):
    method test_walkup_submission_no_lf (line 59) | def test_walkup_submission_no_lf(self):
    method test_tabfile (line 65) | def test_tabfile(self):
    method test_dup_index_collapse_at_init (line 71) | def test_dup_index_collapse_at_init(self):
    method test_dup_index_collapse (line 81) | def test_dup_index_collapse(self):
    method test_tabfile_win_endings (line 113) | def test_tabfile_win_endings(self):
    method test_gz_tabfile_win_endings (line 119) | def test_gz_tabfile_win_endings(self):
    method test_tabfile_macos9_endings (line 125) | def test_tabfile_macos9_endings(self):
    method test_tabfile_extras (line 131) | def test_tabfile_extras(self):
    method test_tabfile_extras_win (line 137) | def test_tabfile_extras_win(self):
    method test_blank_line_in_tabular_section (line 143) | def test_blank_line_in_tabular_section(self):
    method test_picard_block (line 149) | def test_picard_block(self):
    method test_rev_comp_barcode_values (line 155) | def test_rev_comp_barcode_values(self):
    method test_rev_comp_barcode_value_barcode2_at_load (line 162) | def test_rev_comp_barcode_value_barcode2_at_load(self):
    method test_rev_comp_barcode_values_specified_at_load_two_columns (line 170) | def test_rev_comp_barcode_values_specified_at_load_two_columns(self):
    method test_rev_comp_barcode_values_specified_one_column (line 179) | def test_rev_comp_barcode_values_specified_one_column(self):
    method test_rev_comp_barcode_values_specified_two_columns (line 190) | def test_rev_comp_barcode_values_specified_two_columns(self):
    method test_rev_comp_barcode_values_undo (line 201) | def test_rev_comp_barcode_values_undo(self):
    method test_rev_comp_barcode_values_not_inplace (line 210) | def test_rev_comp_barcode_values_not_inplace(self):
  class TestRunInfo (line 220) | class TestRunInfo(TestCaseWithTmp):
    method test_miseq (line 222) | def test_miseq(self):
    method test_hiseq (line 234) | def test_hiseq(self):
    method test_novaseq (line 246) | def test_novaseq(self):
    method test_nextseq550 (line 258) | def test_nextseq550(self):
    method test_novaseq_x_plus (line 270) | def test_novaseq_x_plus(self):
    method test_nextseq_1000_2000_p1 (line 282) | def test_nextseq_1000_2000_p1(self):
    method test_novel_tile_count_but_known_fcid (line 294) | def test_novel_tile_count_but_known_fcid(self):
    method test_novel_fcid_but_known_tile_count (line 299) | def test_novel_fcid_but_known_tile_count(self):
    method test_novel_tile_count_and_fcid (line 304) | def test_novel_tile_count_and_fcid(self):
  class TestIlluminaDir (line 310) | class TestIlluminaDir(TestCaseWithTmp):
    method test_directory (line 312) | def test_directory(self):
    method test_tarball_normal (line 318) | def test_tarball_normal(self):
    method test_tarball_indented (line 327) | def test_tarball_indented(self):
    method test_tarball_sample_sheet (line 332) | def test_tarball_sample_sheet(self):
    method test_tarball_uncompressed (line 341) | def test_tarball_uncompressed(self):
    method test_tarball_deep_dir_tree (line 347) | def test_tarball_deep_dir_tree(self):
    method test_zip_archive (line 353) | def test_zip_archive(self):
    method test_tarball_run_info (line 359) | def test_tarball_run_info(self):
    method test_tarball_fail_missing_data (line 371) | def test_tarball_fail_missing_data(self):
  class TestDifficultSampleNames (line 379) | class TestDifficultSampleNames(TestCaseWithTmp):
    method test_paired_1 (line 381) | def test_paired_1(self):
    method test_inline_commas_strings (line 401) | def test_inline_commas_strings(self):
  class TestIlluminaBarcodeHelper (line 417) | class TestIlluminaBarcodeHelper(TestCaseWithTmp):
    method test_one_correction (line 418) | def test_one_correction(self):
    method test_ambiguous (line 432) | def test_ambiguous(self):
    method test_single_index_run (line 446) | def test_single_index_run(self):
    method test_single_index_i5_only_run (line 460) | def test_single_index_i5_only_run(self):
    method test_few_assigned (line 474) | def test_few_assigned(self):
  class TestMiseqToBam (line 483) | class TestMiseqToBam(TestCaseWithTmp):
    method test_paired_1 (line 485) | def test_paired_1(self):
    method test_paired_2 (line 505) | def test_paired_2(self):
    method test_paired_custom_seq_center (line 525) | def test_paired_custom_seq_center(self):
    method test_fail_missing_pair (line 545) | def test_fail_missing_pair(self):
    method test_fail_backwards_pair (line 553) | def test_fail_backwards_pair(self):
    method test_fail_mismatched_pair (line 562) | def test_fail_mismatched_pair(self):
    method test_fail_oob_index (line 571) | def test_fail_oob_index(self):
    method test_fail_bad_format (line 580) | def test_fail_bad_format(self):
  class TestSplitcodeDemuxIntegration (line 596) | class TestSplitcodeDemuxIntegration(TestCaseWithTmp):
    method setUp (line 607) | def setUp(self):
    method create_test_bam_with_inline_barcodes (line 612) | def create_test_bam_with_inline_barcodes(self, output_bam, barcode_rea...
    method create_expected_output_bam (line 660) | def create_expected_output_bam(self, output_bam, sample_name, barcode,...
    method test_splitcode_demux_basic (line 717) | def test_splitcode_demux_basic(self):
  class TestParseIlluminaFastqFilename (line 827) | class TestParseIlluminaFastqFilename(unittest.TestCase):
    method test_standard_dragen_format_r1 (line 834) | def test_standard_dragen_format_r1(self):
    method test_standard_dragen_format_r2 (line 848) | def test_standard_dragen_format_r2(self):
    method test_sample_name_with_underscores (line 857) | def test_sample_name_with_underscores(self):
    method test_different_flowcells (line 870) | def test_different_flowcells(self):
    method test_different_lane_numbers (line 883) | def test_different_lane_numbers(self):
    method test_different_sample_numbers (line 891) | def test_different_sample_numbers(self):
    method test_different_chunk_numbers (line 902) | def test_different_chunk_numbers(self):
    method test_with_full_path (line 912) | def test_with_full_path(self):
    method test_without_gz_extension (line 921) | def test_without_gz_extension(self):
    method test_simple_format_without_flowcell (line 929) | def test_simple_format_without_flowcell(self):
    method test_simple_format_r2 (line 945) | def test_simple_format_r2(self):
    method test_malformed_invalid_format (line 955) | def test_malformed_invalid_format(self):
    method test_empty_filename (line 962) | def test_empty_filename(self):
    method test_malformed_missing_read_number (line 967) | def test_malformed_missing_read_number(self):
    method test_index_reads_not_supported (line 974) | def test_index_reads_not_supported(self):
  class TestNormalizeBarcode (line 985) | class TestNormalizeBarcode(unittest.TestCase):
    method test_uppercase_conversion (line 988) | def test_uppercase_conversion(self):
    method test_whitespace_trimming (line 994) | def test_whitespace_trimming(self):
    method test_combined_normalization (line 1000) | def test_combined_normalization(self):
    method test_already_normalized (line 1005) | def test_already_normalized(self):
    method test_empty_string (line 1010) | def test_empty_string(self):
    method test_valid_characters_only (line 1015) | def test_valid_characters_only(self):
    method test_invalid_characters (line 1023) | def test_invalid_characters(self):
    method test_mixed_case_with_n (line 1038) | def test_mixed_case_with_n(self):
    method test_typical_illumina_barcodes (line 1043) | def test_typical_illumina_barcodes(self):
    method test_none_input (line 1055) | def test_none_input(self):
    method test_non_string_input (line 1060) | def test_non_string_input(self):
  class TestBarcodeOrientationAutoDetection (line 1069) | class TestBarcodeOrientationAutoDetection(unittest.TestCase):
    method test_direct_match (line 1081) | def test_direct_match(self):
    method test_barcode2_revcomp_match (line 1094) | def test_barcode2_revcomp_match(self):
    method test_no_match_returns_empty (line 1107) | def test_no_match_returns_empty(self):
    method test_single_barcode_matching (line 1119) | def test_single_barcode_matching(self):
    method test_case_insensitive_matching (line 1129) | def test_case_insensitive_matching(self):
    method test_multiple_samples_same_outer_barcodes (line 1139) | def test_multiple_samples_same_outer_barcodes(self):
    method test_barcode2_revcomp_with_multiple_samples (line 1152) | def test_barcode2_revcomp_with_multiple_samples(self):
    method test_n_wildcard_in_fastq_barcode (line 1165) | def test_n_wildcard_in_fastq_barcode(self):
    method test_n_wildcard_in_barcode2 (line 1182) | def test_n_wildcard_in_barcode2(self):
    method test_n_wildcard_with_revcomp (line 1194) | def test_n_wildcard_with_revcomp(self):
    method test_multiple_n_wildcards (line 1212) | def test_multiple_n_wildcards(self):
    method test_high_n_fraction_returns_empty (line 1223) | def test_high_n_fraction_returns_empty(self):
    method test_high_n_fraction_in_bc2_returns_empty (line 1235) | def test_high_n_fraction_in_bc2_returns_empty(self):
    method test_exactly_50_percent_n_allowed (line 1247) | def test_exactly_50_percent_n_allowed(self):
    method test_ambiguous_n_match_returns_empty (line 1267) | def test_ambiguous_n_match_returns_empty(self):
    method test_n_in_samplesheet_does_not_match_with_strict (line 1280) | def test_n_in_samplesheet_does_not_match_with_strict(self):
    method test_n_in_samplesheet_matches_with_fuzzy (line 1297) | def test_n_in_samplesheet_matches_with_fuzzy(self):
    method test_n_wildcard_no_false_positives (line 1311) | def test_n_wildcard_no_false_positives(self):
  class TestBarcodeFuzzyMatching (line 1325) | class TestBarcodeFuzzyMatching(unittest.TestCase):
    method test_exact_match_zero_mismatches (line 1328) | def test_exact_match_zero_mismatches(self):
    method test_one_mismatch_allowed (line 1333) | def test_one_mismatch_allowed(self):
    method test_two_mismatches_rejected_at_threshold_1 (line 1338) | def test_two_mismatches_rejected_at_threshold_1(self):
    method test_two_mismatches_allowed_at_threshold_2 (line 1343) | def test_two_mismatches_allowed_at_threshold_2(self):
    method test_n_not_counted_as_mismatch (line 1348) | def test_n_not_counted_as_mismatch(self):
    method test_n_plus_real_mismatch (line 1353) | def test_n_plus_real_mismatch(self):
    method test_length_mismatch (line 1359) | def test_length_mismatch(self):
    method test_zero_max_mismatches_is_strict (line 1363) | def test_zero_max_mismatches_is_strict(self):
    method test_all_n_matches_anything (line 1374) | def test_all_n_matches_anything(self):
  class TestFuzzyMatchInOrientation (line 1380) | class TestFuzzyMatchInOrientation(unittest.TestCase):
    method test_fuzzy_match_one_mismatch_bc1 (line 1383) | def test_fuzzy_match_one_mismatch_bc1(self):
    method test_fuzzy_match_one_mismatch_bc2 (line 1394) | def test_fuzzy_match_one_mismatch_bc2(self):
    method test_fuzzy_match_rejected_at_zero_tolerance (line 1404) | def test_fuzzy_match_rejected_at_zero_tolerance(self):
    method test_fuzzy_prefers_exact_over_fuzzy (line 1415) | def test_fuzzy_prefers_exact_over_fuzzy(self):
    method test_fuzzy_ambiguous_same_distance (line 1427) | def test_fuzzy_ambiguous_same_distance(self):
    method test_fuzzy_match_with_revcomp (line 1440) | def test_fuzzy_match_with_revcomp(self):
  class TestSamplesheetAuthoritativeBarcodes (line 1454) | class TestSamplesheetAuthoritativeBarcodes(unittest.TestCase):
    method test_matched_bc_contains_samplesheet_values (line 1457) | def test_matched_bc_contains_samplesheet_values(self):
    method test_matched_bc_with_n_contains_samplesheet_values (line 1468) | def test_matched_bc_with_n_contains_samplesheet_values(self):
    method test_matched_bc_with_mismatch_contains_samplesheet_values (line 1480) | def test_matched_bc_with_mismatch_contains_samplesheet_values(self):
    method test_matched_bc_with_revcomp_contains_samplesheet_values (line 1492) | def test_matched_bc_with_revcomp_contains_samplesheet_values(self):
  class TestConsensusBarcodeFromFastq (line 1507) | class TestConsensusBarcodeFromFastq(unittest.TestCase):
    method setUp (line 1510) | def setUp(self):
    method tearDown (line 1513) | def tearDown(self):
    method _write_fastq (line 1516) | def _write_fastq(self, path, reads):
    method test_identical_reads (line 1530) | def test_identical_reads(self):
    method test_consensus_resolves_single_n (line 1542) | def test_consensus_resolves_single_n(self):
    method test_consensus_majority_vote (line 1553) | def test_consensus_majority_vote(self):
    method test_consensus_all_n_stays_n (line 1565) | def test_consensus_all_n_stays_n(self):
    method test_empty_fastq_returns_none (line 1576) | def test_empty_fastq_returns_none(self):
    method test_single_barcode_no_plus (line 1585) | def test_single_barcode_no_plus(self):
    method test_single_read (line 1597) | def test_single_read(self):
    method test_consensus_resolves_mismatch (line 1608) | def test_consensus_resolves_mismatch(self):
    method test_consensus_tie_returns_n (line 1621) | def test_consensus_tie_returns_n(self):
    method test_unparseable_headers_raises (line 1634) | def test_unparseable_headers_raises(self):
  class TestParseBarcode (line 1648) | class TestParseBarcode(unittest.TestCase):
    method test_dual_index (line 1651) | def test_dual_index(self):
    method test_single_index (line 1658) | def test_single_index(self):
    method test_invalid_header (line 1665) | def test_invalid_header(self):
  class TestBuildRunInfoJson (line 1671) | class TestBuildRunInfoJson(TestCaseWithTmp):
    method test_build_with_all_parameters (line 1674) | def test_build_with_all_parameters(self):
    method test_build_with_minimal_parameters (line 1706) | def test_build_with_minimal_parameters(self):
    method test_integer_to_string_conversion (line 1731) | def test_integer_to_string_conversion(self):
    method test_consistency_with_existing_output_schema (line 1750) | def test_consistency_with_existing_output_schema(self):
    method test_none_values_handled (line 1777) | def test_none_values_handled(self):
  class TestIlluminaMetadata (line 1796) | class TestIlluminaMetadata(TestCaseWithTmp):
    method setUp (line 1811) | def setUp(self):
    method test_runinfo_xml_parsing (line 1826) | def test_runinfo_xml_parsing(self):
    method test_samplesheet_parsing (line 1841) | def test_samplesheet_parsing(self):
    method test_metadata_json_generation (line 1859) | def test_metadata_json_generation(self):
    method test_metadata_generation_with_optional_params (line 1929) | def test_metadata_generation_with_optional_params(self):
    method test_metadata_consistency_with_existing_demux (line 1954) | def test_metadata_consistency_with_existing_demux(self):
    method test_invalid_runinfo_path (line 1988) | def test_invalid_runinfo_path(self):
    method test_invalid_samplesheet_path (line 1997) | def test_invalid_samplesheet_path(self):
    method test_illumina_metadata_via_parser (line 2006) | def test_illumina_metadata_via_parser(self):
    method test_three_barcode_samplesheet (line 2052) | def test_three_barcode_samplesheet(self):
    method test_mixed_two_and_three_barcode_samplesheet (line 2125) | def test_mixed_two_and_three_barcode_samplesheet(self):
    method test_three_barcode_barcode_uniqueness (line 2191) | def test_three_barcode_barcode_uniqueness(self):
    method test_optional_lane_parameter (line 2241) | def test_optional_lane_parameter(self):
    method test_optional_lane_backwards_compatibility (line 2293) | def test_optional_lane_backwards_compatibility(self):
    method test_metadata_with_append_run_id (line 2338) | def test_metadata_with_append_run_id(self):
    method test_metadata_without_append_run_id (line 2383) | def test_metadata_without_append_run_id(self):
    method test_metadata_append_run_id_via_parser (line 2420) | def test_metadata_append_run_id_via_parser(self):
    method test_illumina_metadata_runinfo_only (line 2458) | def test_illumina_metadata_runinfo_only(self):
    method test_illumina_metadata_sample_output_requires_samplesheet (line 2493) | def test_illumina_metadata_sample_output_requires_samplesheet(self):
    method test_illumina_metadata_optional_samplesheet_via_parser (line 2520) | def test_illumina_metadata_optional_samplesheet_via_parser(self):
  class TestSplitcodeDemuxFastqs (line 2553) | class TestSplitcodeDemuxFastqs(TestCaseWithTmp):
    method setUp (line 2578) | def setUp(self):
    method test_parse_fastq_filename_from_test_data (line 2596) | def test_parse_fastq_filename_from_test_data(self):
    method test_barcode_normalization_on_samplesheet (line 2608) | def test_barcode_normalization_on_samplesheet(self):
    method test_basic_demux_workflow (line 2627) | def test_basic_demux_workflow(self):
    method test_barcode_matching_perfect_match (line 2672) | def test_barcode_matching_perfect_match(self):
    method test_unmatched_barcodes (line 2710) | def test_unmatched_barcodes(self):
    method test_empty_barcode_sample (line 2750) | def test_empty_barcode_sample(self):
    method test_output_schema_consistency (line 2792) | def test_output_schema_consistency(self):
    method test_multi_pool_samplesheet_collapsibility_check (line 2830) | def test_multi_pool_samplesheet_collapsibility_check(self):
    method test_fastq_filename_parsing (line 2894) | def test_fastq_filename_parsing(self):
    method test_two_barcode_sample_bypass_splitcode (line 2925) | def test_two_barcode_sample_bypass_splitcode(self):
    method test_splitcode_demux_fastqs_via_parser (line 2984) | def test_splitcode_demux_fastqs_via_parser(self):
    method test_i5_reverse_complement_3bc_demux (line 3020) | def test_i5_reverse_complement_3bc_demux(self):
    method test_splitcode_demux_3bc_with_n_bases_in_bc2_and_i5_rc (line 3102) | def test_splitcode_demux_3bc_with_n_bases_in_bc2_and_i5_rc(self):
    method test_no_barcode_match_produces_zero_bams (line 3193) | def test_no_barcode_match_produces_zero_bams(self):
    method test_append_run_id_3bc (line 3264) | def test_append_run_id_3bc(self):
    method test_append_run_id_2bc (line 3308) | def test_append_run_id_2bc(self):
    method test_append_run_id_requires_flowcell (line 3345) | def test_append_run_id_requires_flowcell(self):
    method test_splitcode_demux_fastqs_metadata_output (line 3369) | def test_splitcode_demux_fastqs_metadata_output(self):
    method test_splitcode_demux_fastqs_metadata_lane_from_fastq (line 3426) | def test_splitcode_demux_fastqs_metadata_lane_from_fastq(self):
    method test_splitcode_demux_fastqs_metadata_run_matches_bam (line 3462) | def test_splitcode_demux_fastqs_metadata_run_matches_bam(self):
    method test_splitcode_demux_fastqs_2bc_metadata (line 3504) | def test_splitcode_demux_fastqs_2bc_metadata(self):
  class TestMergeDemuxMetrics (line 3555) | class TestMergeDemuxMetrics(TestCaseWithTmp):
    method test_merge_demux_metrics_via_parser (line 3562) | def test_merge_demux_metrics_via_parser(self):

FILE: tests/unit/core/test_read_utils.py
  class TestCommandHelp (line 26) | class TestCommandHelp(unittest.TestCase):
    method test_help_parser_for_each_command (line 28) | def test_help_parser_for_each_command(self):
  class TestBwamemIdxstats (line 34) | class TestBwamemIdxstats(TestCaseWithTmp):
    method setUp (line 36) | def setUp(self):
    method test_bwamem_idxstats (line 45) | def test_bwamem_idxstats(self):
    method test_bwamem_idxstats_with_filtering (line 55) | def test_bwamem_idxstats_with_filtering(self):
    method test_bwamem_idxstats_no_bam_output (line 74) | def test_bwamem_idxstats_no_bam_output(self):
  class TestMinimap2Idxstats (line 83) | class TestMinimap2Idxstats(TestCaseWithTmp):
    method setUp (line 86) | def setUp(self):
    method test_minimap2_idxstats (line 92) | def test_minimap2_idxstats(self):
    method test_minimap2_idxstats_with_readlist (line 104) | def test_minimap2_idxstats_with_readlist(self):
  class TestFastqBam (line 129) | class TestFastqBam(TestCaseWithTmp):
    method test_fastq_bam (line 132) | def test_fastq_bam(self):
    method test_fastq_to_bam_empty_inputs (line 195) | def test_fastq_to_bam_empty_inputs(self):
  class TestRmdupUnaligned (line 243) | class TestRmdupUnaligned(TestCaseWithTmp):
    method test_mvicuna_canned_input (line 245) | def test_mvicuna_canned_input(self):
    method test_mvicuna_empty_input (line 259) | def test_mvicuna_empty_input(self):
    method test_cdhit_canned_input (line 270) | def test_cdhit_canned_input(self):
    method test_cdhit_empty_input (line 284) | def test_cdhit_empty_input(self):
  class TestReadIdStore (line 295) | class TestReadIdStore(TestCaseWithTmp):
    method test_add_from_fastq_paired (line 298) | def test_add_from_fastq_paired(self):
    method test_add_from_fastq_single_end (line 314) | def test_add_from_fastq_single_end(self):
    method test_deduplication (line 327) | def test_deduplication(self):
    method test_write_to_file (line 340) | def test_write_to_file(self):
    method test_write_to_file_with_downsampling (line 361) | def test_write_to_file_with_downsampling(self):
    method test_empty_fastq (line 382) | def test_empty_fastq(self):
    method test_add_single (line 394) | def test_add_single(self):
    method test_extend (line 407) | def test_extend(self):
    method test_extend_generator (line 421) | def test_extend_generator(self):
    method test_contains (line 430) | def test_contains(self):
    method test_iter (line 439) | def test_iter(self):
    method test_delitem (line 448) | def test_delitem(self):
    method test_discard (line 465) | def test_discard(self):
    method test_shrink_to_subsample_basic (line 479) | def test_shrink_to_subsample_basic(self):
    method test_shrink_to_subsample_larger_than_store (line 496) | def test_shrink_to_subsample_larger_than_store(self):
    method test_shrink_to_subsample_randomness (line 507) | def test_shrink_to_subsample_randomness(self):
    method test_filter_bam_by_ids_include (line 530) | def test_filter_bam_by_ids_include(self):
    method test_filter_bam_by_ids_exclude (line 555) | def test_filter_bam_by_ids_exclude(self):
    method test_filter_bam_by_ids_header_preserved (line 582) | def test_filter_bam_by_ids_header_preserved(self):
    method test_filter_bam_by_ids_empty_input (line 619) | def test_filter_bam_by_ids_empty_input(self):
    method test_filter_bam_by_ids_empty_store_include (line 633) | def test_filter_bam_by_ids_empty_store_include(self):
    method test_filter_bam_by_ids_empty_store_exclude (line 652) | def test_filter_bam_by_ids_empty_store_exclude(self):
  class TestRmdupBbnorm (line 669) | class TestRmdupBbnorm(TestCaseWithTmp):
    method setUp (line 672) | def setUp(self):
    method test_bbnorm_canned_input (line 676) | def test_bbnorm_canned_input(self):
    method test_bbnorm_empty_input (line 690) | def test_bbnorm_empty_input(self):
    method test_bbnorm_multi_library (line 700) | def test_bbnorm_multi_library(self):
    method test_bbnorm_single_end (line 715) | def test_bbnorm_single_end(self):
    method test_bbnorm_min_input_reads_skip (line 730) | def test_bbnorm_min_input_reads_skip(self):
    method test_bbnorm_min_input_reads_process (line 744) | def test_bbnorm_min_input_reads_process(self):
    method test_bbnorm_max_output_reads_downsample (line 760) | def test_bbnorm_max_output_reads_downsample(self):
  class TestMvicuna (line 780) | class TestMvicuna(TestCaseWithTmp):
    method test_mvicuna (line 793) | def test_mvicuna(self):
  class TestAlignAndFix (line 813) | class TestAlignAndFix(TestCaseWithTmp):
    method setUp (line 814) | def setUp(self):
    method test_novoalign (line 821) | def test_novoalign(self):
    method test_bwa (line 824) | def test_bwa(self):
    method test_minimap2 (line 827) | def test_minimap2(self):
    method simple_execution (line 830) | def simple_execution(self, aligner):
    method test_empty_reads (line 839) | def test_empty_reads(self):
    method test_dup_marker_sambamba (line 847) | def test_dup_marker_sambamba(self):
    method test_dup_marker_picard_explicit (line 861) | def test_dup_marker_picard_explicit(self):
    method test_dup_marker_default_is_sambamba (line 875) | def test_dup_marker_default_is_sambamba(self):
    method test_align_and_fix_full_sambamba_pipeline (line 881) | def test_align_and_fix_full_sambamba_pipeline(self):
  class TestDownsampleBams (line 900) | class TestDownsampleBams(TestCaseWithTmp):
    method setUp (line 901) | def setUp(self):
    method test_normalization_to_lowest_cardinality (line 915) | def test_normalization_to_lowest_cardinality(self):
    method test_downsample_to_target_count (line 929) | def test_downsample_to_target_count(self):
    method test_downsample_to_target_count_without_subdir (line 942) | def test_downsample_to_target_count_without_subdir(self):
    method test_downsample_with_dedup_after (line 954) | def test_downsample_with_dedup_after(self):
    method test_downsample_with_dedup_before (line 968) | def test_downsample_with_dedup_before(self):
    method test_downsample_to_too_large_target_count (line 981) | def test_downsample_to_too_large_target_count(self):
  class TestTrimRmdupSubsamp (line 991) | class TestTrimRmdupSubsamp(TestCaseWithTmp):
    method test_subsamp_empty (line 998) | def test_subsamp_empty(self):
    method test_subsamp_small_50 (line 1008) | def test_subsamp_small_50(self):
    method test_subsamp_small_90 (line 1018) | def test_subsamp_small_90(self):
    method test_subsamp_small_200 (line 1029) | def test_subsamp_small_200(self):
    method test_subsamp_big_500 (line 1039) | def test_subsamp_big_500(self):

FILE: tests/unit/core/test_tools.py
  function stub_conda (line 18) | def stub_conda():
  function tool_class (line 23) | def tool_class(request):
  function test_tool_install (line 27) | def test_tool_install(tool_class):

FILE: tests/unit/core/test_tools_bbmap.py
  class TestToolBBMap (line 15) | class TestToolBBMap(TestCaseWithTmp):
    method setUp (line 17) | def setUp(self):
    method test_align (line 23) | def test_align(self):
    method test_bbnorm_paired_interleaved (line 36) | def test_bbnorm_paired_interleaved(self):
    method test_bbnorm_single_end (line 71) | def test_bbnorm_single_end(self):

FILE: tests/unit/core/test_tools_bwa.py
  class TestToolBwa (line 13) | class TestToolBwa(TestCaseWithTmp):
    method setUp (line 15) | def setUp(self):
    method test_working_bam (line 30) | def test_working_bam(self):
    method test_corrupt_bam (line 40) | def test_corrupt_bam(self):

FILE: tests/unit/core/test_tools_fastqc.py
  class HTMLValidator (line 14) | class HTMLValidator(HTMLParser):
    method __init__ (line 16) | def __init__(self):
    method error (line 21) | def error(self, message):
  class TestToolFastQC (line 26) | class TestToolFastQC(TestCaseWithTmp):
    method _validate_html (line 28) | def _validate_html(self, html_path):
    method _validate_zip (line 40) | def _validate_zip(self, zip_path):
    method test_fastqc_nonempty_bam (line 50) | def test_fastqc_nonempty_bam(self):
    method test_fastqc_empty_bam (line 78) | def test_fastqc_empty_bam(self):
    method test_fastqc_without_zip (line 113) | def test_fastqc_without_zip(self):

FILE: tests/unit/core/test_tools_minimap2.py
  class TestToolMinimap2 (line 15) | class TestToolMinimap2(TestCaseWithTmp):
    method setUp (line 17) | def setUp(self):
    method test_human_bam (line 25) | def test_human_bam(self):
    method test_ebola_bam (line 31) | def test_ebola_bam(self):
    method test_corrupt_bam (line 38) | def test_corrupt_bam(self):
  class TestMinimap2Idxstats (line 45) | class TestMinimap2Idxstats(TestCaseWithTmp):
    method setUp (line 48) | def setUp(self):
    method test_idxstats_basic (line 55) | def test_idxstats_basic(self):
    method test_idxstats_with_readlist (line 85) | def test_idxstats_with_readlist(self):
    method test_idxstats_no_readlist (line 118) | def test_idxstats_no_readlist(self):
    method test_idxstats_empty_input (line 133) | def test_idxstats_empty_input(self):
    method test_idxstats_empty_reference (line 151) | def test_idxstats_empty_reference(self):
    method test_idxstats_multi_reference (line 165) | def test_idxstats_multi_reference(self):

FILE: tests/unit/core/test_tools_novoalign.py
  class TestToolNovoalign (line 21) | class TestToolNovoalign(TestCaseWithTmp):
    method setUp (line 23) | def setUp(self):
    method test_index (line 29) | def test_index(self):
    method test_align (line 39) | def test_align(self):
    method test_align_filter (line 51) | def test_align_filter(self):
    method test_multi_read_groups (line 63) | def test_multi_read_groups(self):
    method test_multi_read_groups_filter (line 130) | def test_multi_read_groups_filter(self):

FILE: tests/unit/core/test_tools_picard.py
  class TestToolPicard (line 18) | class TestToolPicard(TestCaseWithTmp):
    method test_fasta_index (line 20) | def test_fasta_index(self):
    method test_messy_fasta_index (line 39) | def test_messy_fasta_index(self):
    method test_sam_downsample (line 56) | def test_sam_downsample(self):
    method test_revert_bam_empty_input (line 72) | def test_revert_bam_empty_input(self):

FILE: tests/unit/core/test_tools_sambamba.py
  class TestToolSambamba (line 19) | class TestToolSambamba(TestCaseWithTmp):
    method setUp (line 22) | def setUp(self):
    method test_sambamba_installed (line 27) | def test_sambamba_installed(self):
    method test_version (line 32) | def test_version(self):
  class TestSambambaSort (line 40) | class TestSambambaSort(TestCaseWithTmp):
    method setUp (line 43) | def setUp(self):
    method test_sort_coordinate (line 48) | def test_sort_coordinate(self):
    method test_sort_queryname (line 64) | def test_sort_queryname(self):
    method test_sort_with_threads (line 80) | def test_sort_with_threads(self):
  class TestSambambaIndex (line 94) | class TestSambambaIndex(TestCaseWithTmp):
    method setUp (line 97) | def setUp(self):
    method test_index_basic (line 102) | def test_index_basic(self):
    method test_index_with_threads (line 119) | def test_index_with_threads(self):
    method test_index_file_exists (line 130) | def test_index_file_exists(self):
  class TestSambambaMerge (line 149) | class TestSambambaMerge(TestCaseWithTmp):
    method setUp (line 152) | def setUp(self):
    method test_merge_two_bams (line 157) | def test_merge_two_bams(self):
    method test_merge_preserves_reads (line 175) | def test_merge_preserves_reads(self):
  class TestSambambaFlagstat (line 195) | class TestSambambaFlagstat(TestCaseWithTmp):
    method setUp (line 198) | def setUp(self):
    method test_flagstat_basic (line 203) | def test_flagstat_basic(self):
    method test_flagstat_returns_dict (line 212) | def test_flagstat_returns_dict(self):
    method test_flagstat_empty_bam (line 221) | def test_flagstat_empty_bam(self):
  class TestSambambaMarkdup (line 231) | class TestSambambaMarkdup(TestCaseWithTmp):
    method setUp (line 234) | def setUp(self):
    method test_markdup_basic (line 239) | def test_markdup_basic(self):
    method test_markdup_with_threads (line 260) | def test_markdup_with_threads(self):
    method test_markdup_empty_input (line 272) | def test_markdup_empty_input(self):
    method test_markdup_removes_duplicates (line 287) | def test_markdup_removes_duplicates(self):

FILE: tests/unit/core/test_tools_samtools.py
  class TestToolSamtools (line 17) | class TestToolSamtools(TestCaseWithTmp):
    method test_count_bam (line 19) | def test_count_bam(self):
    method test_fasta_index (line 24) | def test_fasta_index(self):
    method test_messy_fasta_index (line 35) | def test_messy_fasta_index(self):
    method test_isEmpty (line 51) | def test_isEmpty(self):
    method test_sam_downsample (line 58) | def test_sam_downsample(self):
    method test_filterByCigarString (line 73) | def test_filterByCigarString(self):
    method test_bam2fa (line 89) | def test_bam2fa(self):
  class TestSamtoolsImport (line 100) | class TestSamtoolsImport(TestCaseWithTmp):
    method test_import_paired_fastq_basic (line 103) | def test_import_paired_fastq_basic(self):
    method test_import_with_full_read_group (line 123) | def test_import_with_full_read_group(self):
    method test_import_rg_defaults (line 157) | def test_import_rg_defaults(self):
    method test_import_read_flags (line 185) | def test_import_read_flags(self):
    method test_import_read_rg_tag (line 205) | def test_import_read_rg_tag(self):
    method test_import_empty_fastq (line 225) | def test_import_empty_fastq(self):
    method test_import_multithreaded (line 259) | def test_import_multithreaded(self):

FILE: tests/unit/core/test_tools_splitcode.py
  class TestSplitcodeLookupTable (line 21) | class TestSplitcodeLookupTable(TestCaseWithTmp):
    method test_basic_single_pool (line 24) | def test_basic_single_pool(self):
    method test_zero_reads_pool (line 87) | def test_zero_reads_pool(self):
    method test_multi_pool (line 119) | def test_multi_pool(self):
    method test_append_run_id (line 164) | def test_append_run_id(self):
    method test_unique_library_ids_per_sample (line 194) | def test_unique_library_ids_per_sample(self):
  class TestSplitcodeIntegration (line 255) | class TestSplitcodeIntegration(TestCaseWithTmp):
    method setUp (line 263) | def setUp(self):
    method tearDown (line 268) | def tearDown(self):
    method create_test_bam_with_inline_barcodes (line 272) | def create_test_bam_with_inline_barcodes(self, output_bam, num_reads=1...
    method test_run_splitcode_on_pool_basic (line 309) | def test_run_splitcode_on_pool_basic(self):
    method test_run_splitcode_on_pool_empty_output (line 388) | def test_run_splitcode_on_pool_empty_output(self):
    method test_splitcode_json_output_format (line 469) | def test_splitcode_json_output_format(self):
    method test_splitcode_output_file_locations (line 537) | def test_splitcode_output_file_locations(self):
    method test_splitcode_barcode_trimming (line 600) | def test_splitcode_barcode_trimming(self):
    method test_splitcode_with_append_run_id (line 661) | def test_splitcode_with_append_run_id(self):
  class TestGenerateSplitcodeConfigAndKeepFiles (line 728) | class TestGenerateSplitcodeConfigAndKeepFiles(TestCaseWithTmp):
    method setUp (line 736) | def setUp(self):
    method tearDown (line 740) | def tearDown(self):
    method test_basic_single_pool (line 744) | def test_basic_single_pool(self):
    method test_variable_barcode_lengths (line 802) | def test_variable_barcode_lengths(self):
    method test_hamming_distance_parameter (line 826) | def test_hamming_distance_parameter(self):
    method test_r1_trim_bp_right_of_barcode (line 859) | def test_r1_trim_bp_right_of_barcode(self):
    method test_multi_pool_filtering (line 892) | def test_multi_pool_filtering(self):
    method test_empty_pool_raises_error (line 925) | def test_empty_pool_raises_error(self):
    method test_config_keep_id_matching (line 944) | def test_config_keep_id_matching(self):
    method test_output_prefix_path_construction (line 981) | def test_output_prefix_path_construction(self):
    method test_complex_realistic_scenario (line 1006) | def test_complex_realistic_scenario(self):
  class TestSplitcodeSummaryJSONErrorHandling (line 1064) | class TestSplitcodeSummaryJSONErrorHandling(TestCaseWithTmp):
    method setUp (line 1072) | def setUp(self):
    method tearDown (line 1076) | def tearDown(self):
    method test_missing_json_file_provides_debugging_info (line 1080) | def test_missing_json_file_provides_debugging_info(self):
    method test_malformed_json_provides_file_preview (line 1116) | def test_malformed_json_provides_file_preview(self):
  class TestConvertSplitcodeMetricsToPicardStyle (line 1147) | class TestConvertSplitcodeMetricsToPicardStyle(TestCaseWithTmp):
    method setUp (line 1166) | def setUp(self):
    method tearDown (line 1170) | def tearDown(self):
    method test_basic_conversion (line 1174) | def test_basic_conversion(self):
    method test_missing_required_column_raises_error (line 1234) | def test_missing_required_column_raises_error(self):
    method test_empty_required_column_raises_error (line 1261) | def test_empty_required_column_raises_error(self):
    method test_barcode_combination_without_inline (line 1288) | def test_barcode_combination_without_inline(self):
    method test_library_name_fallback (line 1322) | def test_library_name_fallback(self):
    method test_library_name_uses_barcode_name_fallback (line 1353) | def test_library_name_uses_barcode_name_fallback(self):
    method test_combine_innerbarcode_unmatched_false (line 1383) | def test_combine_innerbarcode_unmatched_false(self):
    method test_combine_innerbarcode_unmatched_true_with_report_within_pools_true (line 1417) | def test_combine_innerbarcode_unmatched_true_with_report_within_pools_...
    method test_combine_innerbarcode_unmatched_true_with_report_within_pools_false (line 1460) | def test_combine_innerbarcode_unmatched_true_with_report_within_pools_...
    method test_stats_computation_global (line 1498) | def test_stats_computation_global(self):
    method test_stats_computation_within_pools (line 1536) | def test_stats_computation_within_pools(self):
    method test_pct_matches_computation (line 1583) | def test_pct_matches_computation(self):
    method test_normalized_matches_excludes_all_n (line 1621) | def test_normalized_matches_excludes_all_n(self):
    method test_custom_demux_function_name (line 1657) | def test_custom_demux_function_name(self):
    method test_zero_reads_handling (line 1686) | def test_zero_reads_handling(self):

FILE: tests/unit/core/test_tools_trimmomatic.py
  class TestTrimmomatic (line 12) | class TestTrimmomatic(TestCaseWithTmp):
    method test_trimmomatic_paired (line 14) | def test_trimmomatic_paired(self):
    method test_trimmomatic_paired_maxinfo (line 30) | def test_trimmomatic_paired_maxinfo(self):
    method test_trimmomatic_single (line 46) | def test_trimmomatic_single(self):

FILE: tests/unit/core/test_util_file.py
  function testTempFiles (line 29) | def testTempFiles():
  function test_check_paths (line 71) | def test_check_paths(tmpdir):
  function test_uncompressed_file_type (line 93) | def test_uncompressed_file_type():
  function test_string_to_file_name (line 108) | def test_string_to_file_name():
  function compressed_input_file (line 129) | def compressed_input_file(request):
  function expected_plaintext (line 133) | def expected_plaintext():
  function test_decompress_shutil_copyfileobj (line 136) | def test_decompress_shutil_copyfileobj(request, expected_plaintext, comp...
  function test_decompress_line_by_line (line 142) | def test_decompress_line_by_line(request, expected_plaintext, compressed...
  class TestExtractTarball (line 150) | class TestExtractTarball(TestCaseWithTmp):
    method setUp (line 151) | def setUp(self):
    method test_simple_extract (line 159) | def test_simple_extract(self):
  class TestTarballMerger (line 167) | class TestTarballMerger(TestCaseWithTmp):
    method setUp (line 168) | def setUp(self):
    method test_simple_merge (line 177) | def test_simple_merge(self):
    method test_merge_with_extract (line 197) | def test_merge_with_extract(self):
    method test_merge_with_extract_repack_from_disk (line 227) | def test_merge_with_extract_repack_from_disk(self):
    method test_piped_in_merge (line 258) | def test_piped_in_merge(self):
    method capsys (line 282) | def capsys(self, capsys):
    method test_piped_out_merge (line 285) | def test_piped_out_merge(self):
    method test_merge_piped_in_and_out (line 309) | def test_merge_piped_in_and_out(self):

FILE: tests/unit/core/test_util_misc.py
  class TestRunAndPrint (line 13) | class TestRunAndPrint(unittest.TestCase):
    method testBasicRunSuccess (line 15) | def testBasicRunSuccess(self):
    method testBasicRunFailDontCare (line 33) | def testBasicRunFailDontCare(self):
    method testBasicRunFailAndCatch (line 43) | def testBasicRunFailAndCatch(self):
  class TestFeatureSorter (line 58) | class TestFeatureSorter(unittest.TestCase):
    method testBasicSortingWithOverlap (line 60) | def testBasicSortingWithOverlap(self):
    method testBasicIntervalsWithOverlap (line 75) | def testBasicIntervalsWithOverlap(self):
    method testDisjointAndOverlappingIntervals (line 92) | def testDisjointAndOverlappingIntervals(self):
    method testMultiChrWindowedFeatures (line 112) | def testMultiChrWindowedFeatures(self):
    method testOpenWindowRight (line 128) | def testOpenWindowRight(self):
    method testOpenWindowLeft (line 145) | def testOpenWindowLeft(self):
    method testMultiChrWithPayloadIntervals (line 161) | def testMultiChrWithPayloadIntervals(self):
  class TestConfigIncludes (line 184) | class TestConfigIncludes(unittest.TestCase):
    method testConfigIncludes (line 186) | def testConfigIncludes(self):
  function test_as_type (line 213) | def test_as_type():
  function test_subdict (line 251) | def test_subdict(iter_d, iter_subset):
  function test_chk (line 275) | def test_chk():
  function test_available_cpu_count (line 285) | def test_available_cpu_count(monkeypatch_function_result):

FILE: tests/unit/phylo/test_interhost.py
  class TestCommandHelp (line 14) | class TestCommandHelp(unittest.TestCase):
    method test_help_parser_for_each_command (line 16) | def test_help_parser_for_each_command(self):
  function makeTempFasta (line 22) | def makeTempFasta(seqs):
  class TestCoordMapper (line 30) | class TestCoordMapper(TestCaseWithTmp):
    method setUp (line 32) | def setUp(self):
    method test_no_indels (line 39) | def test_no_indels(self):
    method test_map_indels (line 44) | def test_map_indels(self):
    method test_side_param (line 56) | def test_side_param(self):
    method test_oob_errors (line 66) | def test_oob_errors(self):
    method test_invalid_pos_error (line 72) | def test_invalid_pos_error(self):
    method test_invalid_chr_error (line 78) | def test_invalid_chr_error(self):
    method test_unequal_genomes_error (line 84) | def test_unequal_genomes_error(self):
    method test_map_chr_only (line 91) | def test_map_chr_only(self):
  class TestCoordMapperMultipleSeqs (line 100) | class TestCoordMapperMultipleSeqs(TestCaseWithTmp):
    method setUp (line 102) | def setUp(self):
    method test_legacy_call (line 117) | def test_legacy_call(self):
    method test_no_indels (line 125) | def test_no_indels(self):
    method test_map_indels (line 130) | def test_map_indels(self):
    method test_side_param (line 142) | def test_side_param(self):
    method test_oob_errors (line 152) | def test_oob_errors(self):
    method test_invalid_pos_error (line 158) | def test_invalid_pos_error(self):
    method test_invalid_chr_error (line 164) | def test_invalid_chr_error(self):
    method test_unequal_genomes_error (line 168) | def test_unequal_genomes_error(self):
    method test_duplicate_chr_names_error (line 175) | def test_duplicate_chr_names_error(self):
    method test_multiple_input_genomes (line 182) | def test_multiple_input_genomes(self):
    method test_single_chr_error (line 191) | def test_single_chr_error(self):
    method test_map_chr_only (line 198) | def test_map_chr_only(self):
  class TestSpecificAlignments (line 208) | class TestSpecificAlignments(TestCaseWithTmp):
    method test_basic_alignment (line 214) | def test_basic_alignment(self):
    method test_unequal_len (line 219) | def test_unequal_len(self):
    method test_no_real_bases_in_sample (line 225) | def test_no_real_bases_in_sample(self):
    method test_no_real_bases_at_position (line 238) | def test_no_real_bases_at_position(self):
    method test_aligned_gaps (line 250) | def test_aligned_gaps(self):
    method test_adjacent_gaps (line 264) | def test_adjacent_gaps(self):
    method test_one_real_base (line 291) | def test_one_real_base(self):
    method test_exactly_two_pairs (line 300) | def test_exactly_two_pairs(self):

FILE: tests/unit/phylo/test_intrahost.py
  class TestCommandHelp (line 29) | class TestCommandHelp(unittest.TestCase):
    method test_help_parser_for_each_command (line 31) | def test_help_parser_for_each_command(self):
  function makeTempFasta (line 37) | def makeTempFasta(seqs):
  class MockVphaserOutput (line 45) | class MockVphaserOutput:
    method __init__ (line 50) | def __init__(self):
    method add_snp (line 54) | def add_snp(self, chrom, pos, acounts, libinfo=None):
    method add_indel (line 77) | def add_indel(self, chrom, pos, acounts, libinfo=None):
    method __iter__ (line 119) | def __iter__(self):
  class TestIntrahostFilters (line 132) | class TestIntrahostFilters(unittest.TestCase):
    method test_single_strand_bias_hard_filter (line 141) | def test_single_strand_bias_hard_filter(self):
  class TestPerSample (line 156) | class TestPerSample(TestCaseWithTmp):
    method test_vphaser_one_sample (line 163) | def test_vphaser_one_sample(self):
  class VcfMergeRunner (line 185) | class VcfMergeRunner:
    method __init__ (line 189) | def __init__(self, ref_genome=None):
    method set_ref (line 199) | def set_ref(self, genome):
    method add_genome (line 202) | def add_genome(self, sample_name, genome):
    method add_snp (line 209) | def add_snp(self, sample, chrom, pos, acounts, libinfo=None):
    method add_indel (line 216) | def add_indel(self, sample, chrom, pos, acounts, libinfo=None):
    method dump_isnv_tmp_file (line 225) | def dump_isnv_tmp_file(self, sample):
    method run_and_get_vcf_rows (line 232) | def run_and_get_vcf_rows(self, retree=1, omit_samplenames=False):
    method multi_align_samples (line 249) | def multi_align_samples(self, retree=1):
  class TestVcfMerge (line 293) | class TestVcfMerge(TestCaseWithTmp):
    method test_empty_output (line 300) | def test_empty_output(self):
    method test_headers_with_two_samps (line 319) | def test_headers_with_two_samps(self):
    method test_simple_snps (line 337) | def test_simple_snps(self):
    method test_simple_snps_guess_samplenames (line 365) | def test_simple_snps_guess_samplenames(self):
    method test_snps_with_varying_read_depth (line 393) | def test_snps_with_varying_read_depth(self):
    method test_snps_downstream_of_indels (line 421) | def test_snps_downstream_of_indels(self):
    method test_sample_major_allele_not_ref_allele (line 439) | def test_sample_major_allele_not_ref_allele(self):
    method test_backfill_sample_from_assembly (line 453) | def test_backfill_sample_from_assembly(self):
    method test_simple_insertions (line 475) | def test_simple_insertions(self):
    method test_simple_deletions (line 502) | def test_simple_deletions(self):
    method test_deletion_spans_deletion (line 528) | def test_deletion_spans_deletion(self):
    method test_insertion_spans_deletion (line 545) | def test_insertion_spans_deletion(self):
    method test_snp_within_insertion (line 570) | def test_snp_within_insertion(self):
    method test_2snps_within_insertion_same_sample (line 594) | def test_2snps_within_insertion_same_sample(self):
    method test_deletion_past_end_of_some_consensus (line 609) | def test_deletion_past_end_of_some_consensus(self):
    method test_snp_past_end_of_some_consensus (line 639) | def test_snp_past_end_of_some_consensus(self):
    method test_deletion_within_insertion (line 660) | def test_deletion_within_insertion(self):
    method test_insertion_within_insertion (line 690) | def test_insertion_within_insertion(self):
    method test_indel_collapse (line 714) | def test_indel_collapse(self):

FILE: tests/unit/phylo/test_ncbi.py
  class TestCommandHelp (line 19) | class TestCommandHelp(unittest.TestCase):
    method test_help_parser_for_each_command (line 21) | def test_help_parser_for_each_command(self):
  class TestFeatureReader (line 26) | class TestFeatureReader(TestCaseWithTmp):
    method setUp (line 27) | def setUp(self):
    method test_read_seq_id_simple (line 31) | def test_read_seq_id_simple(self):
    method test_read_seq_id_different_fnames (line 37) | def test_read_seq_id_different_fnames(self):
    method test_read_seq_id_refseq (line 43) | def test_read_seq_id_refseq(self):
    method test_read_seq_id_ddbj (line 47) | def test_read_seq_id_ddbj(self):
    method test_seq_location_str_format (line 51) | def test_seq_location_str_format(self):
  class TestFeatureTransfer (line 63) | class TestFeatureTransfer(TestCaseWithTmp):
    method setUp (line 64) | def setUp(self):
    method test_synthetic_feature_table (line 68) | def test_synthetic_feature_table(self):
    method test_synthetic_feature_table_oob_clip (line 85) | def test_synthetic_feature_table_oob_clip(self):
    method test_synthetic_feature_table_ignore_ambiguous_edges (line 111) | def test_synthetic_feature_table_ignore_ambiguous_edges(self):
    method test_severely_truncated_assembly_oob_clip (line 129) | def test_severely_truncated_assembly_oob_clip(self):
    method test_partial_symbols_column_placement (line 180) | def test_partial_symbols_column_placement(self):
    method test_internal_partials_dropped (line 229) | def test_internal_partials_dropped(self):
    method test_lasv_oob_clip (line 264) | def test_lasv_oob_clip(self):

FILE: tests/unit/phylo/test_tools.py
  function tool_class (line 10) | def tool_class(request):
  function test_tool_install (line 14) | def test_tool_install(tool_class):

FILE: tests/unit/phylo/test_tools_vphaser2.py
  class TestVPhaser2 (line 16) | class TestVPhaser2(TestCaseWithTmp):
    method test_vphaser2 (line 18) | def test_vphaser2(self):

FILE: tests/unit/phylo/test_util_vcf.py
  class StubGenome (line 22) | class StubGenome:
    method __init__ (line 28) | def __init__(self, chromlist):
    method chrlens (line 33) | def chrlens(self):
  class TestGenomePosition (line 37) | class TestGenomePosition(unittest.TestCase):
    method test_fail_OOB_get_gpos (line 40) | def test_fail_OOB_get_gpos(self):
    method test_fail_OOB_get_chr_pos (line 48) | def test_fail_OOB_get_chr_pos(self):
    method test_fail_non_int_pos (line 55) | def test_fail_non_int_pos(self):
    method test_spotcheck_edges (line 63) | def test_spotcheck_edges(self):
    method test_equality_1chrGenome (line 72) | def test_equality_1chrGenome(self):
    method test_equality_3chrGenome (line 80) | def test_equality_3chrGenome(self):
    method test_gpos_inbounds (line 96) | def test_gpos_inbounds(self):
    method test_chr_pos_inbounds (line 107) | def test_chr_pos_inbounds(self):
    method test_unique_gpos (line 119) | def test_unique_gpos(self):
    method test_unique_chr_pos (line 130) | def test_unique_chr_pos(self):
  class TestVcfReaderPositions (line 141) | class TestVcfReaderPositions(unittest.TestCase):
    method setUp (line 144) | def setUp(self):
    method test_sample_names (line 152) | def test_sample_names(self):
    method test_get_one_base (line 159) | def test_get_one_base(self):
    method test_get_positions_edges (line 168) | def test_get_positions_edges(self):
    method test_get_range_edges (line 174) | def test_get_range_edges(self):