def picard_insert_gc_flagstat(input_bam,
ref_genome,
gc_metrics,
gc_metrics_summary,
gc_metrics_pdf,
tempdir,
flagstat_metrics,
insert_metrics,
insert_pdf,
picard_docker=None,
samtools_docker=None):
bamutils.bam_flagstat(input_bam,
flagstat_metrics,
docker_image=samtools_docker)
gc_tempdir = os.path.join(tempdir, 'gc')
helpers.makedirs(gc_tempdir)
picardutils.bam_collect_gc_metrics(input_bam,
ref_genome,
gc_metrics,
gc_metrics_summary,
gc_metrics_pdf,
gc_tempdir,
docker_image=picard_docker)
insert_tempdir = os.path.join(tempdir, 'insert')
helpers.makedirs(insert_tempdir)
picardutils.bam_collect_insert_metrics(input_bam,
flagstat_metrics,
insert_metrics,
insert_pdf,
insert_tempdir,
docker_image=picard_docker)
def bam_collect_gc_metrics(bam_filename, ref_genome, metrics_filename,
summary_filename, chart_filename, tempdir, config):
container_ctx = helpers.get_container_ctx(config['containers'],
'picard',
docker_only=True)
picardutils.bam_collect_gc_metrics(bam_filename, ref_genome,
metrics_filename, summary_filename,
chart_filename, tempdir,
**container_ctx)
def picard_insert_gc_flagstat(
input_bam,
ref_genome,
gc_metrics,
gc_metrics_summary,
gc_metrics_pdf,
tempdir,
flagstat_metrics,
insert_metrics,
insert_pdf,
):
bamutils.bam_flagstat(
input_bam,
flagstat_metrics,
)
gc_tempdir = os.path.join(tempdir, 'gc')
helpers.makedirs(gc_tempdir)
picardutils.bam_collect_gc_metrics(
input_bam,
ref_genome,
gc_metrics,
gc_metrics_summary,
gc_metrics_pdf,
gc_tempdir,
)
insert_tempdir = os.path.join(tempdir, 'insert')
helpers.makedirs(insert_tempdir)
picardutils.bam_collect_insert_metrics(
input_bam,
flagstat_metrics,
insert_metrics,
insert_pdf,
insert_tempdir,
)