computeGCBias.py can't handle --blackListFileName

[kashyapchhatbar]

The rest of the tools are fine with it, however computeGCBias is not considering --blackListFileName properly

Here's the error

~ @
❯ computeGCBias -b bowtie_sorted/Input_WT_rep1.bam -bl mm9-blacklist.bed -freq freq.txt --effectiveGenomeSize 2150570000 -g mm9.2bit -l 120
Traceback (most recent call last):
  File "/usr/bin/computeGCBias", line 7, in <module>
    main()
  File "/usr/lib/python2.7/site-packages/deeptools/computeGCBias.py", line 623, in main
    filter_out_file = args.BlackListFileName
AttributeError: 'Namespace' object has no attribute 'BlackListFileName'

It's showing the error here. I think it's a typo for blackListFileName argument and also since the new implementation of blacklist file, filterOut argument is not required.

Huge thanks for the awesome tool 👍

[dpryan79]

I've merged the fix for this. I'll try to coordinate getting version 2.2.3 on pypi/bioconda/Galaxy today.

[dpryan79]

Ping @bgruening @fidelram

[bgruening]

Okidoki!

[kashyapchhatbar]

Confirming that the fix is working! Thanks :)

[dpryan79]

Great, thanks for letting us know!