Rmats compatibility with gzipped fastq files.

[serenolopezdarwin]

Rmats uses STAR as its aligner, and STAR works with gzipped fastq files, but this functionality isn't included in the rmats implementation of STAR. This is because STAR requires the additional argument "--readFilesCommand zcat" in order to process compressed files. I believe this can be fixed in rmats_wrapper.py by adding a conditional that checks if the "sample" argument ends in ".gz" and adding " --readFilesCommand zcat" to doSTARMapping. Something like

if sample[0].endswith('.gz'):
    cmd += ' --readFilesCommand zcat'

at line 146 should work, though I'm not sure of the exact format of the sample list object (I assume it's file name strings).

If there are instances of STAR commands elsewhere in the pipeline they must be remedied in the same fashion.