From f05d7cb427d00a85994391b0e2829cc704bb3314 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 17 Jan 2022 09:08:56 +0100
Subject: [PATCH] Use set_tag call from pysam
---
umi.wdl | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/umi.wdl b/umi.wdl
index e149caf..5916968 100644
--- a/umi.wdl
+++ b/umi.wdl
@@ -62,8 +62,7 @@ task BamReadNameToUmiTag {
for segment in in_bam: # type: pysam.AlignedSegment
new_name, umi = split_umi_from_name(segment.query_name)
segment.query_name = new_name
- # append does not work. (Pysam is not Pythonic.)
- segment.tags = segment.tags + [(bam_tag, umi)]
+ segment.set_tag("RX", umi, value_type="Z")
out_bam.write(segment)
if __name__ == "__main__":
--
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