Support additional options for mGAP tracks

bbimber · bbimber · commit 5110798cf98b · 2025-02-02T18:04:36.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/SVTyperStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/SVTyperStep.java
@@ -113,7 +113,6 @@ else if (!svVcf.exists())
                 jsonArgs.add("-l");
                 jsonArgs.add(coverageJson.getPath());
 
-
                 if (threads != null)
                 {
                     jsonArgs.add("--max_reads");

Original file line number	Diff line number	Diff line change
`@@ -113,7 +113,6 @@ else if (!svVcf.exists())`
`113`	`113`	`jsonArgs.add("-l");`
`114`	`114`	`jsonArgs.add(coverageJson.getPath());`
`115`	`115`
`116`		`-`
`117`	`116`	`if (threads != null)`
`118`	`117`	`{`
`119`	`118`	`jsonArgs.add("--max_reads");`