Module Import alias Import alias ImportFrom alias If CompareEq Call NameLoad AttributeLoad NameLoad attr Num body Assert Call AttributeLoad SubscriptLoad AttributeLoad NameLoad attr Index Num attr Str Assign NameStore Call NameLoad Str Str SubscriptLoad AttributeLoad NameLoad attr Index Num Print Str NameLoad Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Num Str Assign NameStore Call AttributeLoad NameLoad attr NameLoad Str keyword NameLoad Assign NameStore Dict For NameStore Call AttributeLoad NameLoad attr keyword NameLoad body If CompareIn AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad SubscriptLoad NameLoad Index AttributeLoad NameLoad attr attr NameLoad orelse Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr ListLoad Expr Call AttributeLoad SubscriptLoad NameLoad Index AttributeLoad NameLoad attr attr NameLoad If CompareEq Call NameLoad SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Num body For NameStore SubscriptLoad NameLoad Index AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr NameLoad Delete SubscriptDel NameLoad Index AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr orelse Print Str SubscriptLoad AttributeLoad NameLoad attr Index Num Str
N/A N/A pysam N/A sys re sub N/A N/A N/A len N/A sys argv 2 N/A N/A N/A N/A N/A N/A sys argv N/A 1 endswith .bam N/A outname N/A sub bam$ fixed.bam N/A N/A sys argv N/A 1 N/A output bam: outname N/A inbam N/A N/A pysam Samfile N/A N/A sys argv N/A 1 rb N/A outbam N/A N/A pysam Samfile outname wb template inbam N/A reads N/A N/A read N/A N/A inbam fetch until_eof True N/A N/A N/A N/A read qname reads N/A N/A N/A N/A N/A reads N/A N/A read qname append read N/A N/A N/A reads N/A N/A read qname N/A N/A N/A N/A N/A reads N/A N/A read qname append read N/A N/A N/A len N/A reads N/A N/A read qname 2 N/A N/A outread N/A reads N/A N/A read qname N/A N/A N/A N/A outbam write outread N/A N/A reads N/A N/A read qname N/A N/A N/A inbam close N/A N/A N/A outbam close N/A N/A usage: N/A N/A sys argv N/A 0 <BAM file>