Fix bcftools running path

bbimber · bbimber · commit 5a8cee6f3903 · 2021-12-15T14:19:48.000-08:00
diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/BcftoolsRunner.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/BcftoolsRunner.java
@@ -18,8 +18,8 @@ public BcftoolsRunner(@Nullable Logger logger)
         super(logger);
     }
 
-    public File getSamtoolsPath()
+    public File getBcfToolsPath()
     {
-        return SequencePipelineService.get().getExeForPackage("SAMTOOLSPATH", "samtools");
+        return SequencePipelineService.get().getExeForPackage("BCFTOOLSPATH", "bcftools");
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -18,8 +18,8 @@ public BcftoolsRunner(@Nullable Logger logger)`
`18`	`18`	`super(logger);`
`19`	`19`	`}`
`20`	`20`
`21`		`- public File getSamtoolsPath()`
	`21`	`+ public File getBcfToolsPath()`
`22`	`22`	`{`
`23`		`- return SequencePipelineService.get().getExeForPackage("SAMTOOLSPATH", "samtools");`
	`23`	`+ return SequencePipelineService.get().getExeForPackage("BCFTOOLSPATH", "bcftools");`
`24`	`24`	`}`
`25`	`25`	`}`