NIO output support for multiple tools (broadinstitute#4695)

ClipReads, LeftAlignIndels, RevertBaseQualityScores, UnmarkDuplicates, SplitNCigarReds
cwhelan · May 25, 2018 · 1404c8c · 1404c8c
1 parent 2da13da
commit 1404c8c
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Showing 5 changed files with 15 additions and 10 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/ClipReads.java b/src/main/java/org/broadinstitute/hellbender/tools/ClipReads.java
@@ -13,6 +13,7 @@
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
+import org.broadinstitute.hellbender.utils.io.IOUtils;
 import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
 import org.broadinstitute.hellbender.engine.FeatureContext;
 import org.broadinstitute.hellbender.engine.ReadWalker;
@@ -161,7 +162,7 @@ public final class ClipReads extends ReadWalker {
      * The output SAM/BAM/CRAM file will be written here
      */
     @Argument(doc = "BAM output file", shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME)
-    File OUTPUT;
+    String OUTPUT;
 
     /**
      * If provided, ClipReads will write summary statistics about the clipping operations applied to the reads in this file.
@@ -291,7 +292,7 @@ public void onTraversalStart() {
         }
 
         final boolean presorted = EnumSet.of(ClippingRepresentation.WRITE_NS, ClippingRepresentation.WRITE_NS_Q0S, ClippingRepresentation.WRITE_Q0S).contains(clippingRepresentation);
-        outputBam = createSAMWriter(OUTPUT, presorted);
+        outputBam = createSAMWriter(IOUtils.getPath(OUTPUT), presorted);
 
         accumulator = new ClippingData(sequencesToClip);
         try {

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/LeftAlignIndels.java b/src/main/java/org/broadinstitute/hellbender/tools/LeftAlignIndels.java
@@ -5,6 +5,7 @@
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
+import org.broadinstitute.hellbender.utils.io.IOUtils;
 import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
 import org.broadinstitute.hellbender.engine.FeatureContext;
 import org.broadinstitute.hellbender.engine.ReadWalker;
@@ -51,7 +52,7 @@
 public final class LeftAlignIndels extends ReadWalker {
 
     @Argument(doc="Output BAM")
-    private File OUTPUT;
+    private String OUTPUT;
 
     private SAMFileGATKReadWriter outputWriter = null;
 
@@ -62,7 +63,7 @@ public boolean requiresReference() {
 
     @Override
     public void onTraversalStart() {
-        outputWriter = createSAMWriter(OUTPUT, true);
+        outputWriter = createSAMWriter(IOUtils.getPath(OUTPUT), true);
     }
 
     @Override

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/RevertBaseQualityScores.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/RevertBaseQualityScores.java
@@ -4,6 +4,7 @@
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
+import org.broadinstitute.hellbender.utils.io.IOUtils;
 import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
 import org.broadinstitute.hellbender.engine.FeatureContext;
 import org.broadinstitute.hellbender.engine.ReadWalker;
@@ -30,13 +31,13 @@
 public class RevertBaseQualityScores extends ReadWalker {
 
     @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, doc="Write output to this file")
-    public File OUTPUT;
+    public String OUTPUT;
 
     private SAMFileGATKReadWriter outputWriter;
 
     @Override
     public void onTraversalStart() {
-        outputWriter = createSAMWriter(OUTPUT, true);
+        outputWriter = createSAMWriter(IOUtils.getPath(OUTPUT), true);
     }
 
     @Override

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/UnmarkDuplicates.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/UnmarkDuplicates.java
@@ -4,6 +4,7 @@
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
+import org.broadinstitute.hellbender.utils.io.IOUtils;
 import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
 import org.broadinstitute.hellbender.engine.FeatureContext;
 import org.broadinstitute.hellbender.engine.ReadWalker;
@@ -66,13 +67,13 @@ public class UnmarkDuplicates extends ReadWalker {
             "Clears the 0x400 SAM flag bit on all reads.";
 
     @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, doc="Write output to this file")
-    public File OUTPUT;
+    public String OUTPUT;
 
     private SAMFileGATKReadWriter outputWriter;
 
     @Override
     public void onTraversalStart() {
-        outputWriter = createSAMWriter(OUTPUT, true);
+        outputWriter = createSAMWriter(IOUtils.getPath(OUTPUT), true);
     }
 
     @Override

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReads.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReads.java
@@ -6,6 +6,7 @@
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
+import org.broadinstitute.hellbender.utils.io.IOUtils;
 import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
 import org.broadinstitute.hellbender.engine.FeatureContext;
 import org.broadinstitute.hellbender.engine.ReferenceContext;
@@ -74,7 +75,7 @@ public final class SplitNCigarReads extends TwoPassReadWalker {
     static final String MATE_CIGAR_TAG = "MC";
 
     @Argument(fullName = OUTPUT_LONG_NAME, shortName = OUTPUT_SHORT_NAME, doc="Write output to this BAM filename")
-    File OUTPUT;
+    String OUTPUT;
 
     /**
      * This flag tells GATK to refactor cigar string with NDN elements to one element. It intended primarily for use in
@@ -166,7 +167,7 @@ public void onTraversalStart() {
         try {
             referenceReader = new CachingIndexedFastaSequenceFile(referenceArguments.getReferencePath());
             GenomeLocParser genomeLocParser = new GenomeLocParser(getBestAvailableSequenceDictionary());
-            outputWriter = createSAMWriter(OUTPUT, false);
+            outputWriter = createSAMWriter(IOUtils.getPath(OUTPUT), false);
             overhangManager = new OverhangFixingManager(header, outputWriter, genomeLocParser, referenceReader, MAX_RECORDS_IN_MEMORY, MAX_MISMATCHES_IN_OVERHANG, MAX_BASES_TO_CLIP, doNotFixOverhangs, processSecondaryAlignments);
 
         } catch (FileNotFoundException ex) {