diff --git a/src/main/java/picard/nio/PicardBucketUtils.java b/src/main/java/picard/nio/PicardBucketUtils.java index 88ee005ed7..f46e012fb7 100644 --- a/src/main/java/picard/nio/PicardBucketUtils.java +++ b/src/main/java/picard/nio/PicardBucketUtils.java @@ -83,17 +83,11 @@ public static PicardHtsPath getLocalTempFilePath(final String prefix, final Stri return getTempFilePath((String) null, prefix, extension); } - // Move to BucktUtils - // "directory" - // Signaled by the trailing "/" - // Shouldn't be used for other FileSystems - /** * Creates a path to a "directory" on a Google Cloud System filesystem with a randomly generated URI. * Since the notion of directories does not exist in GCS, it creates a path to a URI ending in "/". * Calling this method will not create a directory/file on GCS. It merely returns a path to a non-directory. * - * * See: https://stackoverflow.com/questions/51892343/google-gsutil-create-folder * * @param parentDir The root path where the new "directory" is to live e.g. "gs://hellbender-test-logs/staging/picard/test/RevertSam/". diff --git a/src/main/java/picard/sam/RevertSam.java b/src/main/java/picard/sam/RevertSam.java index 459195fc39..ab1ffd70b1 100644 --- a/src/main/java/picard/sam/RevertSam.java +++ b/src/main/java/picard/sam/RevertSam.java @@ -242,9 +242,6 @@ public String getHelpDoc() { "same library name.", shortName = StandardOptionDefinitions.LIBRARY_NAME_SHORT_NAME, optional = true) public String LIBRARY_NAME; -// @Argument(doc = "The prefix to be prepended to the output files, when OUTPUT_BY_READ_GROUP is true but the OUTPUT_MAP was not provided", optional = true) -// public String PREFIX = null; - private final static Log log = Log.getInstance(RevertSam.class); /** @@ -272,7 +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 + 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 SAMFileHeader inHeader = in.getFileHeader(); ValidationUtil.validateHeaderOverrides(inHeader, SAMPLE_ALIAS, LIBRARY_NAME); @@ -593,7 +590,6 @@ public static Map readOutputMap(final Path outputMapFile) { } // Create an output map file to be written to a specified directory - // tsto: remove prefix? public static Map createOutputMapFromReadGroups(final List readGroups, final Path outputDir, final String extension) { final Map outputMap = new HashMap<>(); for (final SAMReadGroupRecord readGroup : readGroups) { diff --git a/src/test/java/picard/sam/RevertSamTest.java b/src/test/java/picard/sam/RevertSamTest.java index 4456b75133..a4d2af3720 100755 --- a/src/test/java/picard/sam/RevertSamTest.java +++ b/src/test/java/picard/sam/RevertSamTest.java @@ -702,7 +702,7 @@ private List getReadGroups(final Path sam){ * @param outputPath The path to a directory, when output by read group is true and the map isn't provided. * The path to a single output SAM file, when output by read group is turned off. May be null. * @param outputByReadGroup Whether to output by read group - * @param outputMapDir The location for a dynamically created output map file. Maybe null. + * @param outputMapDir The location for a dynamically created output map file. May be null. */ @Test(dataProvider = "cloudTestData", groups = "cloud") public void testCloud(final PicardHtsPath inputSAM, final PicardHtsPath outputPath, final boolean outputByReadGroup,