SES method of bamCompare broken

[robertamezquita]

It seems like there's a small error in running bamCompare..seems to be an issue with the SES method being invoked, as it works with the readCounts method.

bamCompare \                                                                                       
    -b1 $BAM1 \                                                                                                                        
    -b2 $INPUT1 \                                                                                                                      
    --outFileName bamComp/K27Ac_MP_1.bw \                                                                                              
    --scaleFactorsMethod=SES \                                                                                                         
    --sampleLength=1000 \                                                                                                              
    --numberOfSamples=200000 \                                                                                                         
    --ratio=first \                                                                                                                    
    --binSize=10 \                                                                                                                     
    --smoothLength=30 \                                                                                                                
    --numberOfProcessors=8

Traceback (most recent call last):
  File "/home/ra364/.local/bin/bamCompare", line 7, in <module>
    main()
  File "/home/ra364/.local/lib/python2.7/site-packages/deeptools/bamCompare.py", line 309, in main
    scale_factors = get_scale_factors(args)
  File "/home/ra364/.local/lib/python2.7/site-packages/deeptools/bamCompare.py", line 199, in get_scale_factors
    mapped_reads = [bam1.mapped, bam2.mapped]
UnboundLocalError: local variable 'bam1' referenced before assignment

[dpryan79]

Oops, not sure how we missed that. I guess if you use -v then it works around the issue. That's not ideal, of course, but it'll work until we release a bugfix version.

[dpryan79]

Actually, can you try deleting line 199 in bamCompare.py and then changing theses lines: https://github.com/fidelram/deepTools/blob/master/deeptools/bamCompare.py#L233-L234

to this:

if mapped_reads is None:
    mapped_reads = get_num_kept_reads(args)

That should fix another issue there as well.

[dpryan79]

I've patched this in the hotfix/2.3.4 branch. The goal is to release a patched version early next week (it might take a while to get it on pypi and in bioconda, so you might have to install from github).