def process_sample(data):
"""Finalize processing for a sample, potentially multiplexed.
"""
if data["config"]["algorithm"]["snpcall"]:
logger.info("Finalizing variant calls: %s" % str(data["name"]))
data["vrn_file"] = finalize_genotyper(data["vrn_file"],
data["work_bam"],
data["sam_ref"], data["config"])
logger.info("Calculating variation effects for %s" % str(data["name"]))
ann_vrn_file, effects_file = variation_effects(data["vrn_file"],
data["sam_ref"],
data["genome_build"],
data["config"])
if ann_vrn_file:
data["vrn_file"] = ann_vrn_file
data["effects_file"] = effects_file
if data["config"]["algorithm"].get("transcript_assemble", False):
data["tx_file"] = assemble_transcripts(data["work_bam"],
data["sam_ref"], data["config"])
if data["sam_ref"] is not None:
logger.info("Generating summary files: %s" % str(data["name"]))
generate_align_summary(data["work_bam"], data["fastq2"] is not None,
data["sam_ref"], data["name"], data["config"],
data["dirs"])
return [[data]]
def process_sample(data):
"""Finalize processing for a sample, potentially multiplexed.
"""
if data["config"]["algorithm"]["snpcall"]:
logger.info("Finalizing variant calls: %s" % str(data["name"]))
data["vrn_file"] = finalize_genotyper(data["vrn_file"], data["work_bam"],
data["sam_ref"], data["config"])
logger.info("Calculating variation effects for %s" % str(data["name"]))
ann_vrn_file, effects_file = variation_effects(data["vrn_file"],
data["sam_ref"],
data["genome_build"],
data["config"])
if ann_vrn_file:
data["vrn_file"] = ann_vrn_file
data["effects_file"] = effects_file
if data["config"]["algorithm"].get("transcript_assemble", False):
data["tx_file"] = assemble_transcripts(data["work_bam"],
data["sam_ref"],
data["config"])
if data["sam_ref"] is not None:
logger.info("Generating summary files: %s" % str(data["name"]))
generate_align_summary(data["work_bam"], data["fastq2"] is not None,
data["sam_ref"], data["name"],
data["config"], data["dirs"])
return [[data]]
def postprocess_variants(data):
"""Provide post-processing of variant calls.
"""
if data["config"]["algorithm"]["snpcall"]:
logger.info("Finalizing variant calls: %s" % str(data["name"]))
data["vrn_file"] = finalize_genotyper(data["vrn_file"], data["work_bam"],
data["sam_ref"], data["config"])
logger.info("Calculating variation effects for %s" % str(data["name"]))
ann_vrn_file = variation_effects(data["vrn_file"], data["sam_ref"],
data["genome_build"], data["config"])
if ann_vrn_file:
data["vrn_file"] = ann_vrn_file
return [[data]]
def postprocess_variants(data):
"""Provide post-processing of variant calls.
"""
if data["config"]["algorithm"]["snpcall"]:
logger.info("Finalizing variant calls: %s" % str(data["name"]))
data["vrn_file"] = finalize_genotyper(data["vrn_file"],
data["work_bam"],
data["sam_ref"], data["config"])
logger.info("Calculating variation effects for %s" % str(data["name"]))
ann_vrn_file = variation_effects(data["vrn_file"], data["sam_ref"],
data["genome_build"], data["config"])
if ann_vrn_file:
data["vrn_file"] = ann_vrn_file
return [[data]]