def _bowtie_for_innerdist(start,
fastq_file,
pair_file,
ref_file,
out_base,
out_dir,
config,
remove_workdir=False):
work_dir = os.path.join(out_dir, "innerdist_estimate")
if os.path.exists(work_dir):
shutil.rmtree(work_dir)
safe_makedir(work_dir)
extra_args = ["-s", str(start), "-u", "250000"]
bowtie_runner = _select_bowtie_version(config)
out_sam = bowtie_runner.align(fastq_file, pair_file, ref_file, out_base,
work_dir, config, extra_args)
runner = broad.runner_from_config(config)
metrics_file = runner.run_fn("picard_insert_metrics", out_sam)
if not file_exists(metrics_file):
return None, None
parser = PicardMetricsParser()
with open(metrics_file) as metrics_handle:
insert_metrics = parser._parse_insert_metrics(metrics_handle)
avg_read_length = _calculate_average_read_length(out_sam)
mean_insert = int(float(insert_metrics["MEAN_INSERT_SIZE"])) - int(
2 * avg_read_length)
std_deviation = int(float(insert_metrics["STANDARD_DEVIATION"]))
return mean_insert, std_deviation
def _bowtie_for_innerdist(start, fastq_file, pair_file, ref_file, out_base,
out_dir, config, remove_workdir=False):
work_dir = os.path.join(out_dir, "innerdist_estimate")
if os.path.exists(work_dir):
shutil.rmtree(work_dir)
safe_makedir(work_dir)
extra_args = ["-s", str(start), "-u", "250000"]
bowtie_runner = _select_bowtie_version(config)
out_sam = bowtie_runner.align(fastq_file, pair_file, ref_file, out_base,
work_dir, config, extra_args)
runner = broad.runner_from_config(config)
metrics_file = runner.run_fn("picard_insert_metrics", out_sam)
if not file_exists(metrics_file):
return None, None
parser = PicardMetricsParser()
with open(metrics_file) as metrics_handle:
insert_metrics = parser._parse_insert_metrics(metrics_handle)
avg_read_length = _calculate_average_read_length(out_sam)
mean_insert = int(float(insert_metrics["MEAN_INSERT_SIZE"])) - int(2 * avg_read_length)
std_deviation = int(float(insert_metrics["STANDARD_DEVIATION"]))
return mean_insert, std_deviation
