00_rmChr.py "dupread" error

[dustin-mullaney]

The script 00_rmChr.py produces the following error:

Traceback (most recent call last):
  File "/Users/usr/programs/ATACgraph/script/ATACgraph", line 38, in <module>
    module.main()
  File "/Users/usr/programs/ATACgraph/script/00_rmChr.py", line 80, in main
    rmChr(infile,outfile,targetChr)
  File "/Users/usr/programs/ATACgraph/script/00_rmChr.py", line 49, in rmChr
    dupread += 1
UnboundLocalError: local variable 'dupread' referenced before assignment

I resolved this issue by editing the script:

def rmChr (infile,outfile,targetChr):
    samfile = openBamFile(infile)
    samout = pysam.AlignmentFile(outfile, "wb", template=samfile)
    chrs = samfile.references
    chrs_keep,chrs_rm = processInput (targetChr,chrs)
    keepread = 0
    dupread = 0 #added to fix error
    for chrom in chrs_keep:
        fetchread = samfile.fetch(chrom)
        for read in fetchread:
            samout.write(read)
            keepread += 1
            if read.is_duplicate:
                dupread += 1

    totalread = sum([x.total for x in samfile.get_index_statistics()])
    removeread = totalread - keepread
    removeratio = float(removeread) / totalread

    for chrom in samfile.get_index_statistics():
        if chrom.contig in chrs_rm:
            rmcount = chrom.total
            print "Remove %s %d reads" % (chrom.contig,rmcount)

    print "Remove total %d out of %d (%.3f)" % (removeread,totalread,removeratio) 

    samout.close()
    samfile.close()

Not 100% sure this was an appropriate solution.