Merge pull request #4 from jiaan-yu/master

Typo fixes

Author: illusional

vcf_utils/add_bam_stats.py

@@ -84,7 +84,7 @@ def create_mpileup_dict(mpileup):
     elif not args.normal_id:
         sys.exit('normal sample id is required for somatic vcf')
     elif not args.tumor_id:
-        sys.exist('tumor sample id is required for somatic vcf')
+        sys.exit('tumor sample id is required for somatic vcf')
     else:
         try:
             f = open(args.normal_mpileup, 'r')

vcf_utils/extract_strelka_germline_DP_AF.py

@@ -15,9 +15,9 @@
 import sys
 from variant import Variant
 
-AF_HEADER_LINE='####INFO=<ID=AF,Number=A,Type=Float,Description="Allele \
+AF_HEADER_LINE='##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele \
 Frequency, for each ALT allele, in the same order as listed - Calculated By \
-Bioinformatics Dept">>\n'
+Bioinformatics Dept">\n'
 
 parser = argparse.ArgumentParser(description="Calculate AF for strelka germline vcf")
 parser.add_argument("-i", dest="input", help="Input strelka germline vcf", required=True)

vcf_utils/extract_strelka_somatic_DP_AF.py

@@ -18,10 +18,10 @@
 
 AD_HEADER_LINE='##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Extracted allelic \
 depths for the ref and alt alleles based on strelka recommendation \
-- Calculated By Bioinformatics Dept">>\n'
-AF_HEADER_LINE='####INFO=<ID=AF,Number=A,Type=Float,Description="Allele \
+- Calculated By Bioinformatics Dept">\n'
+AF_HEADER_LINE='##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele \
 Frequency, for each ALT allele, in the same order as listed - Calculated By \
-Bioinformatics Dept">>\n'
+Bioinformatics Dept">\n'
 
 parser = argparse.ArgumentParser(description="Calculate AF for strelka somatic vcf")
 parser.add_argument("-i", dest="input", help="Input strelka somatic vcf", required=True)