cleaning up

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/".

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<String, Path> readOutputMap(final Path outputMapFile) {
     }
 
     // Create an output map file to be written to a specified directory
-    // tsto: remove prefix?
     public static Map<String, Path> createOutputMapFromReadGroups(final List<SAMReadGroupRecord> readGroups, final Path outputDir, final String extension) {
         final Map<String, Path> outputMap = new HashMap<>();
         for (final SAMReadGroupRecord readGroup : readGroups) {

src/test/java/picard/sam/RevertSamTest.java

@@ -702,7 +702,7 @@ private List<SAMReadGroupRecord> 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,