From 4e6108f1695d39e2c21ed38675e0082119b77a32 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Thu, 19 Sep 2024 10:01:03 -0400 Subject: [PATCH] run aligners on sanitized fastas too --- read_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/read_utils.py b/read_utils.py index 5d5d2f19..8cb6a1a0 100755 --- a/read_utils.py +++ b/read_utils.py @@ -1197,7 +1197,7 @@ def align_and_fix( samtools = tools.samtools.SamtoolsTool() refFastaCopy = mkstempfname('.ref_copy.fasta') - shutil.copyfile(refFasta, refFastaCopy) + shutil.copyfile(util.file.fastas_with_sanitized_ids(refFasta, use_tmp=True)[0], refFastaCopy) tools.picard.CreateSequenceDictionaryTool().execute(refFastaCopy, overwrite=True, JVMmemory=JVMmemory) samtools.faidx(refFastaCopy, overwrite=True)