Bugfix to bbmap

bbimber · bbimber · commit c4a59ea1fe5c · 2025-05-17T12:36:25.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BBMapWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BBMapWrapper.java
@@ -105,7 +105,7 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
 
             List<String> params = new ArrayList<>();
 
-            String ambig = StringUtils.trimToNull(getProvider().getParameterByName("ambig").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class));
+            String ambig = StringUtils.trimToNull(getProvider().getParameterByName("ambiguous").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class));
             if (ambig != null)
             {
                 params.add("ambig=" + ambig);

Original file line number	Diff line number	Diff line change
`@@ -105,7 +105,7 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu`
`105`	`105`
`106`	`106`	`List<String> params = new ArrayList<>();`
`107`	`107`
`108`		`- String ambig = StringUtils.trimToNull(getProvider().getParameterByName("ambig").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class));`
	`108`	`+ String ambig = StringUtils.trimToNull(getProvider().getParameterByName("ambiguous").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class));`
`109`	`109`	`if (ambig != null)`
`110`	`110`	`{`
`111`	`111`	`params.add("ambig=" + ambig);`