Module Import alias alias Import alias FunctionDef arguments args defaults body Print Call AttributeLoad NameLoad attr Str decorator_list If CompareEq Call NameLoad AttributeLoad NameLoad attr Num body Expr Call NameLoad Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Num For NameStore NameLoad body If Call AttributeLoad NameLoad attr Str body With Call NameLoad BinOpAdd BinOpAdd SubscriptLoad AttributeLoad NameLoad attr Index Num Str NameLoad Str NameStore body For NameStore NameLoad body If Call AttributeLoad NameLoad attr Str body Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr attr Assign NameStore SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Str Index Num Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore SubscriptLoad NameLoad Index Num Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Str Print Call AttributeLoad Str attr TupleLoad NameLoad NameLoad Str NameLoad NameLoad Str Str BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str NameLoad Str Str orelse Print Str SubscriptLoad AttributeLoad NameLoad attr Index Num Str
N/A N/A sys os N/A textwrap print_header N/A N/A N/A N/A N/A N/A N/A textwrap dedent     ##fileformat=VCFv4.1
    ##phasing=none
    ##INDIVIDUAL=TRUTH
    ##SAMPLE=<ID=TRUTH,Individual="TRUTH",Description="bamsurgeon spike-in">
    ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
    ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
    ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
    ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
    ##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation in primary">
    ##INFO=<ID=VAF,Number=1,Type=Float,Description="Variant Allele Frequency">
    ##INFO=<ID=DPR,Number=1,Type=Float,Description="Avg Depth in Region (+/- 1bp)">
    ##INFO=<ID=MATEID,Number=1,Type=String,Description="Breakend mate">
    ##ALT=<ID=INV,Description="Inversion">
    ##ALT=<ID=DUP,Description="Duplication">
    ##ALT=<ID=DEL,Description="Deletion">
    ##ALT=<ID=INS,Description="Insertion">
    ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
    #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SPIKEIN N/A N/A N/A N/A len N/A sys argv 2 N/A N/A N/A print_header N/A logdir_files N/A N/A os listdir N/A N/A sys argv N/A 1 N/A filename logdir_files N/A N/A N/A N/A filename endswith .log N/A N/A N/A open N/A N/A N/A N/A sys argv N/A 1 / filename r infile N/A N/A line infile N/A N/A N/A N/A line startswith snv N/A N/A c N/A N/A N/A N/A line strip split N/A chrom N/A N/A N/A N/A c N/A 1 split : N/A 0 N/A pos N/A c N/A 3 N/A mut N/A c N/A 4 N/A dpr N/A c N/A 6 N/A vaf N/A c N/A 7 N/A N/A ref alt N/A N/A mut split --> N/A N/A N/A join N/A chrom pos . ref alt 100 PASS N/A N/A N/A SOMATIC;VAF= vaf ;DPR= dpr GT 0/1 N/A N/A usage: N/A N/A sys argv N/A 0 <log directory>