MarkDups: remove unmapping coord delim from alt contig

hartwigmedical · Mar 21, 2024 · 7d3f9ed · 7d3f9ed
1 parent 9e32d3f
commit 7d3f9ed
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/mark-dups/src/main/java/com/hartwig/hmftools/markdups/common/ReadUnmapper.java b/mark-dups/src/main/java/com/hartwig/hmftools/markdups/common/ReadUnmapper.java
@@ -725,7 +725,10 @@ public static String[] parseUnmappedCoords(final String mateCoordsStr)
 
     private static void setUnmapCoordsAttribute(final SAMRecord read, final String chromosome, final int position)
     {
-        read.setAttribute(UNMAP_ATTRIBUTE, chromosome + UNMAPP_COORDS_DELIM + position);
+        // some alt contigs have the delimiter in their name, hence the replace
+        read.setAttribute(
+                UNMAP_ATTRIBUTE,
+                chromosome.replaceAll(UNMAPP_COORDS_DELIM, "") + UNMAPP_COORDS_DELIM + position);
     }
 
     public static void unmapMateAlignment(final SAMRecord read, final boolean readUnmapped, final boolean unmapRead)

diff --git a/pom.xml b/pom.xml
@@ -76,7 +76,7 @@
         <isofox.version>1.7.1</isofox.version>
         <lilac.version>1.6</lilac.version>
         <linx.version>2.0</linx.version>
-        <mark-dups.version>1.1.2</mark-dups.version>
+        <mark-dups.version>1.1.3</mark-dups.version>
         <neo.version>1.2</neo.version>
         <orange.version>3.1.0</orange.version>
         <orange-datamodel.version>2.2.0</orange-datamodel.version>