Bugfix to bbmap

bbimber · bbimber · commit 2eda1ad27424 · 2025-05-18T07:16:12.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BBMapWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BBMapWrapper.java
@@ -246,7 +246,7 @@ public File doAlignment(File inputFastq1, @Nullable File inputFastq2, File outpu
         Integer maxRam = SequencePipelineService.get().getMaxRam();
         if (maxRam != null)
         {
-            args.add("-Xmx=" + maxRam);
+            args.add("-Xmx=" + maxRam + "g");
         }
 
         Integer maxThreads = SequencePipelineService.get().getMaxThreads(getLogger());

Original file line number	Diff line number	Diff line change
`@@ -246,7 +246,7 @@ public File doAlignment(File inputFastq1, @Nullable File inputFastq2, File outpu`
`246`	`246`	`Integer maxRam = SequencePipelineService.get().getMaxRam();`
`247`	`247`	`if (maxRam != null)`
`248`	`248`	`{`
`249`		`- args.add("-Xmx=" + maxRam);`
	`249`	`+ args.add("-Xmx=" + maxRam + "g");`
`250`	`250`	`}`
`251`	`251`
`252`	`252`	`Integer maxThreads = SequencePipelineService.get().getMaxThreads(getLogger());`