From 275850fbd367ffb7b8637f6d105ed1993c41b8bb Mon Sep 17 00:00:00 2001 From: Takuto Sato Date: Mon, 5 Aug 2024 20:46:57 -0400 Subject: [PATCH] small changes --- src/main/java/picard/sam/RevertSam.java | 2 +- src/test/java/picard/sam/MergeBamAlignmentTest.java | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/src/main/java/picard/sam/RevertSam.java b/src/main/java/picard/sam/RevertSam.java index ab1ffd70b1..558bc22d86 100644 --- 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 index 216b97ac6c..affbe24c00 100644 --- 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");