def runBAMtoJunctionBED(paths_to_run):
bamfile_dir,bed_reference_dir,output_bedfile_path = paths_to_run
output_bedfile_path = string.replace(bamfile_dir,'.bam','__junction.bed')
#if os.path.exists(output_bedfile_path) == False: ### Only run if the file doesn't exist
results = BAMtoJunctionBED.parseJunctionEntries(bamfile_dir,multi=True)
#else: print output_bedfile_path, 'already exists.'
return results
def runBAMtoJunctionBED(paths_to_run):
bamfile_dir, bed_reference_dir, output_bedfile_path = paths_to_run
output_bedfile_path = string.replace(bamfile_dir, '.bam', '__junction.bed')
#if os.path.exists(output_bedfile_path) == False: ### Only run if the file doesn't exist
results = BAMtoJunctionBED.parseJunctionEntries(bamfile_dir, multi=True)
#else: print output_bedfile_path, 'already exists.'
return results
