fix PS tag output issue

treangenlab · May 18, 2023 · 4369947 · 4369947
1 parent 4f84b71
commit 4369947
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Showing 3 changed files with 6 additions and 2 deletions.
diff --git a/meth_phaser_parallel b/meth_phaser_parallel
diff --git a/meth_phaser_post_processing b/meth_phaser_post_processing
@@ -306,7 +306,9 @@ def get_altered_vcf(original_vcf, output_vcf, block_relationship_dfs):
  # 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"))
+ rec = f"{rec}\n"
+ print(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")
@@ -315,7 +317,9 @@ def get_altered_vcf(original_vcf, output_vcf, block_relationship_dfs):
  # 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("0|1", "1|0"))
+ rec = f"{rec}\n"
+ print(rec)
+ altered_vcf_file.writelines(rec.replace("0|1", "1|0"))
  else:
  altered_vcf_file.writelines(rec)
  flpl = [x[0] for x in flipping_list]

diff --git a/methphasing b/methphasing