def concatenate_sort_and_index_bams(out_bam, bams): tmp_bam = out_bam.replace('.bam', '_tmp.bam') # Drop the UMI tag since it's useless vdj_utils.concatenate_and_fix_bams(tmp_bam, bams, drop_tags=[PROCESSED_UMI_TAG]) # Wrap filenames in str() to prevent pysam crash on unicode input tk_bam.sort_and_index(str(tmp_bam), str(out_bam.replace('.bam', ''))) cr_utils.remove(tmp_bam, allow_nonexisting=True)
def concatenate_bams(out_bam, bams): # Drop the UMI tag since it's useless vdj_utils.concatenate_and_fix_bams(out_bam, bams, drop_tags=[PROCESSED_UMI_TAG])