def reMergeBamfiles(infiles, sentinel):
infiles = [P.snip(x, ".sentinel") + ".bam" for x in infiles]
outfile = P.snip(sentinel, ".sentinel") + ".bam"
bad_samples = PARAMS["options_to_remove"].split(",")
to_merge = IDR.filterBadLibraries(infiles, bad_samples)
IDR.mergeBams(to_merge, outfile)
P.touch(sentinel)
def poolSampleBamfiles(infiles, sentinel):
"""
Merge filtered sample files for each tissue
"""
infiles = [P.snip(x, ".sentinel") + ".bam" for x in infiles]
outfile = P.snip(sentinel, ".sentinel") + ".bam"
IDR.mergeBams(infiles, outfile)
P.touch(sentinel)
def poolInputBamfiles(infiles, sentinel):
"""
Merge filtered input files for each tissue, with the option of excluding
undesirable libraries.
"""
infiles = [P.snip(x, ".sentinel") + ".bam" for x in infiles]
outfile = P.snip(sentinel, ".sentinel") + ".bam"
bad_samples = PARAMS["filter_remove_inputs"].split(",")
if len(infiles) > 1:
to_merge = IDR.filterBadLibraries(infiles, bad_samples)
IDR.mergeBams(to_merge, outfile)
else:
os.symlink(os.path.abspath(infiles[0]), outfile)
os.symlink(os.path.abspath(infiles[0]) + ".bai", outfile + ".bai")
P.touch(sentinel)