def align_pipe(fastq_file, pair_file, ref_file, names, align_dir, config):
"""Perform piped alignment of fastq input files, generating sorted output BAM.
"""
pair_file = pair_file if pair_file else ""
out_file = os.path.join(align_dir, "{0}-sort.bam".format(names["lane"]))
samtools = config_utils.get_program("samtools", config)
bwa = config_utils.get_program("bwa", config)
resources = config_utils.get_resources("samtools", config)
num_cores = config["algorithm"].get("num_cores", 1)
# adjust memory for samtools since used alongside alignment
max_mem = config_utils.adjust_memory(resources.get("memory", "2G"),
3, "decrease")
rg_info = novoalign.get_rg_info(names)
if not utils.file_exists(out_file):
novoalign.check_samtools_version(config)
with utils.curdir_tmpdir() as work_dir:
with file_transaction(out_file) as tx_out_file:
tx_out_prefix = os.path.splitext(tx_out_file)[0]
cmd = ("{bwa} mem -M -t {num_cores} -R '{rg_info}' -v 1 {ref_file} "
"{fastq_file} {pair_file} "
"| {samtools} view -b -S -u - "
"| {samtools} sort -@ {num_cores} -m {max_mem} - {tx_out_prefix}")
cmd = cmd.format(**locals())
do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
[do.file_nonempty(tx_out_file)])
return out_file
def align_bam(in_bam, ref_file, names, align_dir, config):
"""Perform direct alignment of an input BAM file with BWA using pipes.
This avoids disk IO by piping between processes:
- samtools sort of input BAM to queryname
- bedtools conversion to interleaved FASTQ
- bwa-mem alignment
- samtools conversion to BAM
- samtools sort to coordinate
"""
out_file = os.path.join(align_dir, "{0}-sort.bam".format(names["lane"]))
samtools = config_utils.get_program("samtools", config)
bedtools = config_utils.get_program("bedtools", config)
bwa = config_utils.get_program("bwa", config)
resources = config_utils.get_resources("samtools", config)
num_cores = config["algorithm"].get("num_cores", 1)
max_mem = resources.get("memory", "768M")
rg_info = novoalign.get_rg_info(names)
if not utils.file_exists(out_file):
novoalign.check_samtools_version()
with utils.curdir_tmpdir() as work_dir:
with file_transaction(out_file) as tx_out_file:
tx_out_prefix = os.path.splitext(tx_out_file)[0]
prefix1 = "%s-in1" % tx_out_prefix
cmd = ("{samtools} sort -n -o -l 0 -@ {num_cores} -m {max_mem} {in_bam} {prefix1} "
"| {bedtools} bamtofastq -i /dev/stdin -fq /dev/stdout -fq2 /dev/stdout "
"| {bwa} mem -p -M -t {num_cores} -R '{rg_info}' -v 1 {ref_file} - "
"| {samtools} view -b -S -u - "
"| {samtools} sort -@ {num_cores} -m {max_mem} - {tx_out_prefix}")
cmd = cmd.format(**locals())
do.run(cmd, "bwa mem alignment from BAM: %s" % names["sample"], None,
[do.file_nonempty(tx_out_file)])
return out_file
def align_bam(in_bam, ref_file, names, align_dir, config):
"""Perform direct alignment of an input BAM file with BWA using pipes.
This avoids disk IO by piping between processes:
- samtools sort of input BAM to queryname
- bedtools conversion to interleaved FASTQ
- bwa-mem alignment
- samtools conversion to BAM
- samtools sort to coordinate
"""
out_file = os.path.join(align_dir, "{0}-sort.bam".format(names["lane"]))
samtools = config_utils.get_program("samtools", config)
bedtools = config_utils.get_program("bedtools", config)
bwa = config_utils.get_program("bwa", config)
resources = config_utils.get_resources("samtools", config)
num_cores = config["algorithm"].get("num_cores", 1)
# adjust memory for samtools since used for input and output
max_mem = config_utils.adjust_memory(resources.get("memory", "1G"),
3, "decrease")
rg_info = novoalign.get_rg_info(names)
if not utils.file_exists(out_file):
novoalign.check_samtools_version(config)
with utils.curdir_tmpdir() as work_dir:
with file_transaction(out_file) as tx_out_file:
tx_out_prefix = os.path.splitext(tx_out_file)[0]
prefix1 = "%s-in1" % tx_out_prefix
cmd = ("{samtools} sort -n -o -l 0 -@ {num_cores} -m {max_mem} {in_bam} {prefix1} "
"| {bedtools} bamtofastq -i /dev/stdin -fq /dev/stdout -fq2 /dev/stdout "
"| {bwa} mem -p -M -t {num_cores} -R '{rg_info}' -v 1 {ref_file} - "
"| {samtools} view -b -S -u - "
"| {samtools} sort -@ {num_cores} -m {max_mem} - {tx_out_prefix}")
cmd = cmd.format(**locals())
do.run(cmd, "bwa mem alignment from BAM: %s" % names["sample"], None,
[do.file_nonempty(tx_out_file)])
return out_file