fix

broadinstitute · Sep 19, 2024 · 393c8ab · 393c8ab
1 parent 17c4872
commit 393c8ab
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/read_utils.py b/read_utils.py
@@ -1197,7 +1197,8 @@ def align_and_fix(
  samtools = tools.samtools.SamtoolsTool()
 
  refFastaCopy = mkstempfname('.ref_copy.fasta')
- shutil.copyfile(util.file.fastas_with_sanitized_ids(refFasta, use_tmp=True).next(), refFastaCopy)
+ with util.file.fastas_with_sanitized_ids(refFasta, use_tmp=True) as sanitized_fastas:
+ shutil.copyfile(sanitized_fastas[0], refFastaCopy)
 
  tools.picard.CreateSequenceDictionaryTool().execute(refFastaCopy, overwrite=True, JVMmemory=JVMmemory)
  samtools.faidx(refFastaCopy, overwrite=True)