small changes

broadinstitute · Aug 6, 2024 · 275850f · 275850f
1 parent 95de314
commit 275850f
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Showing 2 changed files with 1 addition and 2 deletions.
diff --git a/src/main/java/picard/sam/RevertSam.java b/src/main/java/picard/sam/RevertSam.java
@@ -269,7 +269,7 @@ protected int doWork() {
         }
 
         final boolean sanitizing = SANITIZE;
-        final SamReader in = SamReaderFactory.makeDefault().referenceSequence(referenceSequence.getReferencePath()).validationStringency(VALIDATION_STRINGENCY).open(SamInputResource.of(INPUT.toPath())); // tsato: confirm this won't break piped input
+        final SamReader in = SamReaderFactory.makeDefault().referenceSequence(referenceSequence.getReferencePath()).validationStringency(VALIDATION_STRINGENCY).open(SamInputResource.of(INPUT.toPath()));
         final SAMFileHeader inHeader = in.getFileHeader();
         ValidationUtil.validateHeaderOverrides(inHeader, SAMPLE_ALIAS, LIBRARY_NAME);
 

diff --git a/src/test/java/picard/sam/MergeBamAlignmentTest.java b/src/test/java/picard/sam/MergeBamAlignmentTest.java
@@ -77,7 +77,6 @@ public class MergeBamAlignmentTest extends CommandLineProgramTest {
 
     public static final File unmappedBam = new File(DATA_DIR, "unmapped.sam");
     private static final File alignedBam = new File(DATA_DIR, "aligned.sam");
-    public static final File alignedQuerySortedBam = new File(DATA_DIR, "aligned_query_name_sorted.sam");
     private static final File oneHalfAlignedBam = new File(DATA_DIR, "onehalfaligned.sam");
     private static final File otherHalfAlignedBam = new File(DATA_DIR, "otherhalfaligned.sam");
     private static final File mergingUnmappedBam = new File(TEST_DATA_DIR, "unmapped.sam");