Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fixing argument namespace issue introduced with hguturu:hg-fix-pre-convert-gvcf #135

Merged
merged 2 commits into from
Mar 18, 2021
Merged

Fixing argument namespace issue introduced with hguturu:hg-fix-pre-convert-gvcf #135

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
3c1e7ba
fixing pre.py convert argument fix hap.py bug.
Mar 10, 2021
5f5b042
fixing convert_gvcf_truth missing from namespace.
Mar 12, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
25 changes: 18 additions & 7 deletions src/python/hap.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -83,6 +83,10 @@ def main():

# control preprocessing
pre.updateArgs(parser)
parser.add_argument('--convert-gvcf-truth', dest='convert_gvcf_truth', action="store_true", default=False,
help='Convert the truth set from genome VCF format to a VCF before processing.')
parser.add_argument('--convert-gvcf-query', dest='convert_gvcf_query', action="store_true", default=False,
help='Convert the query set from genome VCF format to a VCF before processing.')
parser.add_argument("--preprocess-truth", dest="preprocessing_truth", action="store_true", default=False,
help="Preprocess truth file with same settings as query (default is to accept truth in original format).")
parser.add_argument("--usefiltered-truth", dest="usefiltered_truth", action="store_true", default=False,
Expand Down Expand Up @@ -282,10 +286,13 @@ def main():
if args.preprocessing_truth:
if args.filter_nonref:
logging.info("Filtering out any variants genotyped as <NON_REF>")

if args.convert_gvcf_truth:

## Only converting truth gvcf to vcf if both arguments are true
convert_gvcf_truth = False
if args.convert_gvcf_truth or args.convert_gvcf_to_vcf:
logging.info("Converting genome VCF to VCF")

convert_gvcf_truth=True

tempfiles.append(ttf.name)
tempfiles.append(ttf.name + ".csi")
tempfiles.append(ttf.name + ".tbi")
Expand All @@ -306,7 +313,7 @@ def main():
args.somatic_allele_conversion,
"TRUTH",
filter_nonref=args.filter_nonref if args.preprocessing_truth else False,
convert_gvcf_to_vcf=args.convert_gvcf_truth)
convert_gvcf_to_vcf=convert_gvcf_truth)

args.vcf1 = ttf.name

Expand Down Expand Up @@ -337,8 +344,12 @@ def main():
logging.info("Preprocessing query: %s" % args.vcf2)
if args.filter_nonref:
logging.info("Filtering out any variants genotyped as <NON_REF>")
if args.convert_gvcf_query:
logging.info("Converting genome VCF to VCF")

## Only converting truth gvcf to vcf if both arguments are true
convert_gvcf_query = False
if args.convert_gvcf_query or args.convert_gvcf_to_vcf:
logging.info("Converting genome VCF to VCF")
convert_gvcf_query=True

starttime = time.time()

Expand Down Expand Up @@ -380,7 +391,7 @@ def main():
args.somatic_allele_conversion,
"QUERY",
filter_nonref=args.filter_nonref,
convert_gvcf_to_vcf=args.convert_gvcf_query)
convert_gvcf_to_vcf=convert_gvcf_query)

args.vcf2 = qtf.name
h2 = vcfextract.extractHeadersJSON(args.vcf2)
Expand Down