def merge_bam_files(bam_files, work_dir, config):
"""Merge multiple BAM files from a sample into a single BAM for processing.
"""
out_file = os.path.join(work_dir, os.path.basename(bam_files[0]))
if not os.path.exists(out_file):
picard = PicardRunner(config["program"]["picard"])
with utils.curdir_tmpdir() as tmp_dir:
opts = [("OUTPUT", out_file),
("SORT_ORDER", "coordinate"),
("TMP_DIR", tmp_dir)]
for b in bam_files:
opts.append(("INPUT", b))
picard.run("MergeSamFiles", opts)
return out_file
