matefixer.py 文件源码

def fixmate(infile, outfile):
    inbam = pysam.Samfile(infile, 'rb')
    outbam = pysam.Samfile(outfile, 'wb', header=inbam.header, 
                           referencenames=inbam.references)
    qname = None    
    nTotal = 0
    nFixed = 0
    count = 0;        
    reads = []    
    gc.disable()    
    for rseq in inbam.fetch(until_eof=True):
        nTotal += 1        
        if qname is None or qname == rseq.qname:
            qname = rseq.qname
            reads.append(rseq)            
        else:            
            count = process(reads, inbam.getrname) 
            if count > 0:
                for r in reads:
                    outbam.write(r)
                nFixed += count                
            qname = rseq.qname
            del reads
            reads = [rseq]
        if nTotal % 200000 == 0:        
            logger.info('%d read(s) fixed' % nTotal)
            gc.enable()
            gc.disable()

    count = process(reads, inbam.getrname)
    if count > 0:
        for r in reads:
            outbam.write(r)
        nFixed += count
    logger.info('%d read(s) processed' % nTotal)
    logger.info('%d read(s) fixed and written to file' % nFixed)

    inbam.close()
    outbam.close()
    return (nTotal, nFixed)