def sort_sams(sam_paths, output_dir):
sorted_sam_paths = list()
for sam_path in sam_paths:
sam_sorted_prefix = os.path.join(output_dir, "sorted_{}".format(libdcamp.common.get_base_name(sam_path)))
sam_sorted_path = "{}.sam".format(sam_sorted_prefix)
sorted_sam_paths.append(sam_sorted_path)
if os.path.exists(sam_sorted_path):
continue
picardtools.sort_sam(sam_path, sam_sorted_path, "coordinate")
assert len(sorted_sam_paths)
return sorted_sam_paths
def sort_bam(bam_path, output_dir):
sorted_bam_path = os.path.join(output_dir, "sorted_" + os.path.basename(bam_path))
if not os.path.exists(sorted_bam_path):
picardtools.sort_sam(bam_path, sorted_bam_path, "coordinate")
return sorted_bam_path
