Merge pull request #113 from hguturu/hg-fix-pre-convert-gvcf

changed pre.py params to work with single gvcf
Illumina · Mar 1, 2021 · 214ec68 · 214ec68
2 parents 9d128a9 + bdfd80a
commit 214ec68
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Showing 2 changed files with 5 additions and 9 deletions.
diff --git a/doc/normalisation.md b/doc/normalisation.md
@@ -17,7 +17,7 @@ usage: VCF preprocessor [-h] [--location LOCATIONS] [--pass-only]
                         [--fixchr] [--no-fixchr] [--bcf] [-v] [-r REF]
                         [-w WINDOW] [--threads THREADS] [--force-interactive]
                         [--logfile LOGFILE] [--verbose | --quiet] [--filter-nonref]
-                        [--convert-gvcf-truth] [--convert-gvcf-query]
+                        [--convert-gvcf-to-vcf]
                         input output
 ```
 
@@ -148,8 +148,7 @@ be used on genome VCFs since attempting to convert a standard VCF will
 cause all biallelic variants to be filtered out (most of them).
 
 ```
-  --convert-gvcf-truth Convert the truth genome VCF to a standard VCF.
-  --convert-gvcf-query Convert the query genome VCF to a standard VCF.          
+  --convert-gvcf-to-vcf Convert the input genome VCF to a standard VCF.
 ```
 
 Runtime behaviour can also be controlled as follows:

diff --git a/src/python/pre.py b/src/python/pre.py
@@ -242,7 +242,7 @@ def preprocessWrapper(args):
                args.threads,
                args.gender,
                args.somatic_allele_conversion,
-               convert_gvcf_to_vcf=args.convert_gvcf)
+               convert_gvcf_to_vcf=args.convert_gvcf_to_vcf)
 
     elapsed = time.time() - starttime
     logging.info("preprocess for %s -- time taken %.2f" % (args.input, elapsed))
@@ -316,12 +316,9 @@ def updateArgs(parser):
     parser.add_argument('--filter-nonref', dest='filter_nonref', action="store_true", default=False,
                         help='Remove any variants genotyped as <NON_REF>.')  
 
-    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-to-vcf', dest='convert_gvcf_to_vcf', action="store_true", default=False,
+                        help='Convert the input 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.')                          
-
     # genotype handling on chrX.
     parser.add_argument("--gender", dest="gender", choices=["male", "female", "auto", "none"], default="auto",
                         help="Specify sex. This determines how haploid calls on chrX get treated: for male samples,"