merge change to extract_haplotype_read_counts.py from development branch

bmvdgeijn · Apr 21, 2016 · b0bd0ba · b0bd0ba
1 parent 0ce63eb
commit b0bd0ba
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/CHT/extract_haplotype_read_counts.py b/CHT/extract_haplotype_read_counts.py
@@ -376,7 +376,9 @@ def set_snp_counts(data_files, region_list, snps, test_snp, options):
  snp.ref_hap_count = alt_count
  snp.alt_hap_count = ref_count
  else:
- raise ValueError("expected haplotype to be defined")
+ # haplotypes are undefined at this position
+ snp.ref_hap_count = 0
+ snp.alt_hap_count = 0