Merge pull request #5 from treangenlab/main_orphan

Main orphan
treangenlab · May 16, 2023 · 70cff08 · 70cff08
2 parents f9588ba + 4f84b71
commit 70cff08
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/meth_phaser_post_processing b/meth_phaser_post_processing
@@ -301,15 +301,17 @@ def get_altered_vcf(original_vcf, output_vcf, block_relationship_dfs):
  if "1|0" in rec:
  if "PS" in rec.split("\t")[-2]:
  split_rec = rec.split("\t")
- start_loc = split_rec[-1].split(":")[-3]
+ ps_tag_location = split_rec[-2].split(":").index("PS")
+ start_loc = split_rec[-1].split(":")[ps_tag_location]
  # print(split_rec, start_loc)
  split_rec[-1] = split_rec[-1].replace(start_loc, get_altered_block_start_loc(current_chrom_final_block, int(start_loc))) # type: ignore
  rec = "\t".join(split_rec)
  altered_vcf_file.writelines(rec.replace("1|0", "0|1"))
  elif "0|1" in rec:
  if "PS" in rec.split("\t")[-2]:
  split_rec = rec.split("\t")
- start_loc = split_rec[-1].split(":")[-3]
+ ps_tag_location = split_rec[-2].split(":").index("PS")
+ start_loc = split_rec[-1].split(":")[ps_tag_location]
  # print(split_rec, start_loc)
  split_rec[-1] = split_rec[-1].replace(start_loc, get_altered_block_start_loc(current_chrom_final_block, int(start_loc))) # type: ignore
  rec = "\t".join(split_rec)