TEMP local commit for samtools location. Do not merge.

cmnbroad · cmnbroad · commit e368acefe7b8 · 2025-03-24T09:08:44.000-04:00
diff --git a/src/testUtils/java/org/broadinstitute/hellbender/testutils/SamtoolsTestUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/SamtoolsTestUtils.java
@@ -45,6 +45,7 @@ public static void assertSamtoolsAvailable() {
     public static String getSamtoolsBin() {
         final String samtoolsPath = System.getenv(SAMTOOLS_BINARY_ENV_VARIABLE);
         return samtoolsPath == null ? "/usr/bin/samtools" : samtoolsPath;
+        //return samtoolsPath == null ? "/opt/homebrew/bin/samtools" : samtoolsPath;
     }
 
     /**

Original file line number	Diff line number	Diff line change
`@@ -45,6 +45,7 @@ public static void assertSamtoolsAvailable() {`
`45`	`45`	`public static String getSamtoolsBin() {`
`46`	`46`	`final String samtoolsPath = System.getenv(SAMTOOLS_BINARY_ENV_VARIABLE);`
`47`	`47`	`return samtoolsPath == null ? "/usr/bin/samtools" : samtoolsPath;`
	`48`	`+ //return samtoolsPath == null ? "/opt/homebrew/bin/samtools" : samtoolsPath;`
`48`	`49`	`}`
`49`	`50`
`50`	`51`	`/**`