suggestions from copliot review implemented

holmeso · holmeso · commit 90793912a303 · 2025-05-15T16:04:03.000+10:00
diff --git a/qannotate/src/au/edu/qimr/qannotate/nanno/Annotate.java b/qannotate/src/au/edu/qimr/qannotate/nanno/Annotate.java
@@ -161,6 +161,10 @@ public int engage() throws Exception {
         return exitStatus;
     }
 
+    private boolean isStandardContig(ChrPosition thisVcfsCP) {
+        return thisVcfsCP.getChromosome().startsWith("chr") ? STANDARD_GRCH38_CONTIGS.contains(thisVcfsCP.getChromosome().substring(3)) : STANDARD_GRCH38_CONTIGS.contains(thisVcfsCP.getChromosome());
+    }
+
 
     private static List<String> getAnnotationsForPosition(ChrPosition cp, List<AnnotationSource> annotationSources, Executor executor) {
         long contigAndPosition = ((ChrPositionUtils.convertContigAndPositionToLong(cp.getChromosome().startsWith("chr") ? cp.getChromosome().substring(3) : cp.getChromosome(), cp.getStartPosition())));

Original file line number	Diff line number	Diff line change
`@@ -161,6 +161,10 @@ public int engage() throws Exception {`
`161`	`161`	`return exitStatus;`
`162`	`162`	`}`
`163`	`163`
	`164`	`+ private boolean isStandardContig(ChrPosition thisVcfsCP) {`
	`165`	`+ return thisVcfsCP.getChromosome().startsWith("chr") ? STANDARD_GRCH38_CONTIGS.contains(thisVcfsCP.getChromosome().substring(3)) : STANDARD_GRCH38_CONTIGS.contains(thisVcfsCP.getChromosome());`
	`166`	`+ }`
	`167`	`+`
`164`	`168`
`165`	`169`	`private static List<String> getAnnotationsForPosition(ChrPosition cp, List<AnnotationSource> annotationSources, Executor executor) {`
`166`	`170`	`long contigAndPosition = ((ChrPositionUtils.convertContigAndPositionToLong(cp.getChromosome().startsWith("chr") ? cp.getChromosome().substring(3) : cp.getChromosome(), cp.getStartPosition())));`