def _run_minimap(reference_file, reads_files, num_proc, mode, out_file,
sam_output):
#SAM_HEADER = "\'@PG|@HD|@SQ|@RG|@CO\'"
work_dir = os.path.dirname(out_file)
stderr_file = os.path.join(work_dir, "minimap.stderr")
SORT_THREADS = "4"
SORT_MEM = "4G" if os.path.getsize(
reference_file) > 100 * 1024 * 1024 else "1G"
cmdline = [MINIMAP_BIN, reference_file]
cmdline.extend(reads_files)
cmdline.extend(["-x", mode, "-t", str(num_proc)])
#Produces gzipped SAM sorted by reference name. Since it's not sorted by
#read name anymore, it's important that all reads have SEQ.
#is sam_output not set, produces PAF alignment
#a = SAM output, p = min primary-to-seconday score
#N = max secondary alignments
#--sam-hit-only = don't output unmapped reads
#--secondary-seq = custom option to output SEQ for seqcondary alignment with hard clipping
#-L: move CIGAR strings for ultra-long reads to the separate tag
#-Q don't output fastq quality
if sam_output:
tmp_prefix = os.path.join(
os.path.dirname(out_file),
"sort_" + datetime.datetime.now().strftime("%y%m%d_%H%M%S"))
cmdline.extend([
"-a", "-p", "0.5", "-N", "10", "--sam-hit-only", "-L", "-Q",
"--secondary-seq"
])
cmdline.extend(
["|", SAMTOOLS_BIN, "view", "-T", reference_file, "-u", "-"])
cmdline.extend([
"|", SAMTOOLS_BIN, "sort", "-T", tmp_prefix, "-O", "bam", "-@",
SORT_THREADS, "-l", "1", "-m", SORT_MEM
])
else:
pass #paf output enabled by default
#cmdline.extend(["|", "grep", "-Ev", SAM_HEADER]) #removes headers
#cmdline.extend(["|", "sort", "-k", "3,3", "-T", work_dir,
# "--parallel=8", "-S", "4G"])
#cmdline.extend(["|", "gzip", "-1"])
#logger.debug("Running: " + " ".join(cmdline))
try:
devnull = open(os.devnull, "wb")
#env = os.environ.copy()
#env["LC_ALL"] = "C"
subprocess.check_call(
["/bin/bash", "-c", "set -o pipefail; " + " ".join(cmdline)],
stderr=open(stderr_file, "w"),
stdout=open(out_file, "w"))
os.remove(stderr_file)
except (subprocess.CalledProcessError, OSError) as e:
logger.error(
"Error running minimap2, terminating. See the alignment error log "
" for details: " + stderr_file)
raise AlignmentException(str(e))