repsonding to review comments and reenabling the test

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java

@@ -105,10 +105,9 @@ public final class LikelihoodEngineArgumentCollection implements Serializable {
     public double readDisqualificationThresholdConstant = PairHMMLikelihoodCalculationEngine.DEFAULT_DYNAMIC_DISQUALIFICATION_SCALE_FACTOR;
 
     /**
-     * Argument for generating a file of all of the inputs and ouptus for the pair hmm
+     * Argument for generating a file of all of the inputs and outputs for the pair hmm
      */
     @Advanced
-    @Hidden
     @Argument(fullName="pair-hmm-results-file", doc="File to write exact pairHMM inputs/outputs to for debugging purposes", optional = true)
     public GATKPath pairHmmResultsFile = null;
 

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java

@@ -114,6 +114,7 @@ public PairHMMLikelihoodCalculationEngine(final byte constantGCP,
      *
      * @param constantGCP the gap continuation penalty to use with the PairHMM
      * @param hmmType the type of the HMM to use
+     * @param resultsFile output file to dump per-read, per-haplotype inputs and outputs for debugging purposes (null if not enabled).
      * @param log10globalReadMismappingRate the global mismapping probability, in log10(prob) units.  A value of
      *                                      -3 means that the chance that a read doesn't actually belong at this
      *                                      location in the genome is 1 in 1000.  The effect of this parameter is

src/main/java/org/broadinstitute/hellbender/utils/pairhmm/PairHMM.java

@@ -371,7 +371,7 @@ public void setAndInitializeDebugOutputStream(final OutputStreamWriter writer) {
     }
 
     /**
-     * Method to be invoked implementing HMM engines to be used for storing results for various debugging purposes
+     * Method to be invoked by implementing HMM engines to output the various hmm inputs/outputs with uniform formatting.
      */
     protected void writeToResultsFileIfApplicable(byte[] readBases, byte[] readQuals, byte[] readInsQuals, byte[] readDelQuals, byte[] overallGCP, byte[] alleleBases, double lk) {
 

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -1612,7 +1612,7 @@ private static boolean isGVCFReferenceBlock( final VariantContext vc ) {
     @DataProvider(name="PairHMMResultsModes")
     public Object[][] PairHMMResultsModes() {
         return new Object[][] {
-                //{PairHMM.Implementation.AVX_LOGLESS_CACHING, new File(TEST_FILES_DIR, "expected.AVX.hmmresults.txt")}, //TODO disabled because of failures on travis
+                {PairHMM.Implementation.AVX_LOGLESS_CACHING, new File(TEST_FILES_DIR, "expected.AVX.hmmresults.txt")}, //TODO disabled because of failures on travis
                 {PairHMM.Implementation.LOGLESS_CACHING, new File(TEST_FILES_DIR, "expected.Java.hmmresults.txt")},
                 {PairHMM.Implementation.ORIGINAL, new File(TEST_FILES_DIR, "expected.Original.hmmresults.txt")},
                 {PairHMM.Implementation.EXACT, new File(TEST_FILES_DIR, "expected.Exact.hmmresults.txt")},