3eea3791dc36fbfc521b45b9eebd854c73908b62,dataPrepScripts/CreateTensor.py,,OutputAlnTensor,#Any#,52

Before Change

    beginToEnd = {}
    with open(can_fn) as f:
        for row in f.readlines():
            row = row.split()
            pos = int(row[1])
            if ctgStart != None and pos < ctgStart: continue
            if ctgEnd != None and pos > ctgEnd: continue
            if args.considerleftedge == False:
                beginToEnd[ pos - (param.flankingBaseNum+1) ] = (pos + (param.flankingBaseNum+1), pos)
            elif args.considerleftedge == True:
                for i in range(pos - (param.flankingBaseNum+1), pos + (param.flankingBaseNum+1)):
                    beginToEnd[ i ] = (pos + (param.flankingBaseNum+1), pos)

    p = subprocess.Popen(shlex.split("%s view %s %s:%d-%d" % (samtools, bam_fn, ctgName, ctgStart, ctgEnd) ), stdout=subprocess.PIPE, bufsize=8388608)\
        if ctgStart and ctgEnd\
        else subprocess.Popen(shlex.split("%s view %s %s" % (samtools, bam_fn, ctgName) ), stdout=subprocess.PIPE, bufsize=8388608)

After Change

    centerToAln = {}

    tensor_fpo = open(tensor_fn, "wb")
    tensor_fp = subprocess.Popen(shlex.split("gzip -c"), stdin=subprocess.PIPE, stdout=tensor_fpo, stderr=sys.stderr, bufsize=8388608)

    for l in p.stdout:
        l = l.split()
        if l[0][0] == "@":

Instances