From cf664592a315944a207f25668b525142f9d45013 Mon Sep 17 00:00:00 2001
From: Sergey Koren <sergek@umd.edu>
Date: Wed, 25 Sep 2024 16:45:19 -0400
Subject: [PATCH] fix RG

---
 src/Snakefiles/7-combineConsensus.sm | 3 ++-
 src/scripts/bam_rename.py            | 5 +++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/Snakefiles/7-combineConsensus.sm b/src/Snakefiles/7-combineConsensus.sm
index 835529e..1c2627e 100644
--- a/src/Snakefiles/7-combineConsensus.sm
+++ b/src/Snakefiles/7-combineConsensus.sm
@@ -36,6 +36,7 @@ rule combineConsensus:
         tigmap    = rules.buildPackages.output.tigmap,
         scfmap    = rules.layoutContigs.output.scfmap,
         layout    = rules.layoutContigs.output.layout,
+        ontalns   = rules.generateLayoutContigsInputs.output.ontalns,
         hificov   = rules.verkko.input.hifi5cov,
         finished  = rules.buildPackages.output.finished,
         pathstsv  = rules.rukki.output.pathstsv if config['ruk_enable'] == "True" else rules.emptyfile.output,
@@ -122,7 +123,7 @@ if [ "{params.haveBAM}" = "True" ]; then
    echo ""
    mem_per_core=\`expr {resources.mem_gb} \/ {threads} | awk '{{if (\$1 < 1) print "1G"; else print \$1"G"}}'\`
 
-   {params.SAMTOOLS} merge -f -O bam --reference combined.fasta -@{threads} -u - {params.packbam} | {PYTHON} {VERKKO}/scripts/bam_rename.py ../{input.layout} ../6-layoutContigs/ont-gapfill.txt ../{input.scfmap} ../{input.tigmap} {params.packcns} | {params.SAMTOOLS} sort -m \$mem_per_core -@{threads} -o ../{output.bam}
+   {params.SAMTOOLS} merge -f -O bam --reference combined.fasta -@{threads} -u - {params.packbam} | {PYTHON} {VERKKO}/scripts/bam_rename.py ../{input.layout} ../{input.ontalns} ../{input.scfmap} ../{input.tigmap} {params.packcns} | {params.SAMTOOLS} sort -m \$mem_per_core -@{threads} -o ../{output.bam}
 else
    touch ../{output.bam}
 fi
diff --git a/src/scripts/bam_rename.py b/src/scripts/bam_rename.py
index 50e582b..a2b8132 100755
--- a/src/scripts/bam_rename.py
+++ b/src/scripts/bam_rename.py
@@ -22,11 +22,12 @@
    for l in f:
       parts = l.strip().split('\t')
       if len(parts) > 2:
-         readtorg[parts[0]] = "LA" if (int(parts[-1]) == 0) else "UL"
+         readtorg[parts[0]] = "LA" if (int(parts[-1]) == 0 or len(parts) == 3) else "UL"
 with open(gap_info) as f:
    for l in f:
       parts = l.strip().split('\t')
-      readtorg[parts[0]] = "UL-gap"
+      if parts[0] in readtorg and readtorg[parts[0]] == "LA":
+          readtorg[parts[0]] = "UL-gap"
 
 for filename in sys.argv[5:]:
   sys.stderr.write("Starting file %s\n"%(filename))