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multiBamSummary bins with --outRawCounts dies in an error. #407

@dpryan79

Description

@dpryan79
multiBamSummary bins -p 1 --region chr1 -b ENCFF001FWO.bam ENCFF030VNO.bam -o results.npz --outRawCounts readcounts.tab

Causes this:

Traceback (most recent call last):
  File "/home/ryan/.local/bin/multiBamSummary", line 11, in <module>
    main(args)
  File "/home/ryan/.local/lib/python2.7/site-packages/deeptools/multiBamSummary.py", line 225, in main
    num_reads_per_bin = c.run(allArgs=args)
  File "/home/ryan/.local/lib/python2.7/site-packages/deeptools/countReadsPerBin.py", line 296, in run
    transcript_id_designator=transcript_id_designator)
  File "/home/ryan/.local/lib/python2.7/site-packages/deeptools/mapReduce.py", line 144, in mapReduce
    res = list(map(func, TASKS))
  File "/home/ryan/.local/lib/python2.7/site-packages/deeptools/countReadsPerBin.py", line 27, in countReadsInRegions_wrapper
    return CountReadsPerBin.count_reads_in_region(*args)
  File "/home/ryan/.local/lib/python2.7/site-packages/deeptools/countReadsPerBin.py", line 438, in count_reads_in_region
    _file.write("\t".join(["{}".format(x) for x in subnum_reads_per_bin[idx, :]]) + "\n")
IndexError: index 24 is out of bounds for axis 0 with size 24

I'm not sure if this is only when bins is uses or if regions are specified too. This was first reported by Astrid Böhne on the mailing list.

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