Bump AMBER to 3.3

hartwigmedical · Apr 27, 2020 · 8a47315 · 8a47315
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Showing 3 changed files with 10 additions and 2 deletions.
diff --git a/amber/README.md b/amber/README.md
@@ -143,7 +143,7 @@ REFERENCE.amber.snp.vcf.gz | Entry at each SNP location in the reference.
 
 # Version History and Download Links
 To see arguments and usages of AMBER 2 please refer to the old [README](./README_2.md)
-- Upcoming
+- [3.3](https://github.com/hartwigmedical/hmftools/releases/tag/amber-v3.3)
   - Improved contamination check for very shallow sequencing
   - Support for multiple references
 - [3.2](https://github.com/hartwigmedical/hmftools/releases/tag/amber-v3.2)

diff --git a/pom.xml b/pom.xml
@@ -61,7 +61,7 @@
         <sig-analyser.version>1.0</sig-analyser.version>
         <sv-tools.version>1.0</sv-tools.version>
         <isofox.version>1.0</isofox.version>
-        <amber.version>3.2</amber.version>
+        <amber.version>3.3</amber.version>
         <cobalt.version>1.8</cobalt.version>
         <purple.version>2.41</purple.version>
         <sage.version>2.2</sage.version>

diff --git a/sage/src/main/java/com/hartwig/hmftools/sage/read/ReadContext.java b/sage/src/main/java/com/hartwig/hmftools/sage/read/ReadContext.java
@@ -227,4 +227,12 @@ public byte[] refTrinucleotideContext(int position) {
         return refBases.trinucleotideContext(position);
     }
 
+    public int length() {
+        return readBasesRightFlankIndex() - readBasesLeftFlankIndex() + 1;
+    }
+
+    public int coreLength() {
+        return readBasesRightCentreIndex() - readBasesLeftCentreIndex() + 1;
+    }
+
 }