Refactoring / housekeeping Mutect2IntegrationTest (#6184)

Author: davidbenjamin

src/main/java/org/broadinstitute/hellbender/engine/spark/AssemblyRegionArgumentCollection.java

@@ -2,30 +2,31 @@
 
 import org.broadinstitute.barclay.argparser.Advanced;
 import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.hellbender.engine.AssemblyRegionWalker;
 
 import java.io.Serializable;
 
 public abstract class AssemblyRegionArgumentCollection implements Serializable {
     private static final long serialVersionUID = 1L;
 
-    @Argument(fullName = "min-assembly-region-size", doc = "Minimum size of an assembly region", optional = true)
+    @Argument(fullName = AssemblyRegionWalker.MIN_ASSEMBLY_LONG_NAME, doc = "Minimum size of an assembly region", optional = true)
     public int minAssemblyRegionSize = defaultMinAssemblyRegionSize();
 
-    @Argument(fullName = "max-assembly-region-size", doc = "Maximum size of an assembly region", optional = true)
+    @Argument(fullName = AssemblyRegionWalker.MAX_ASSEMBLY_LONG_NAME, doc = "Maximum size of an assembly region", optional = true)
     public int maxAssemblyRegionSize = defaultMaxAssemblyRegionSize();
 
-    @Argument(fullName = "assembly-region-padding", doc = "Number of additional bases of context to include around each assembly region", optional = true)
+    @Argument(fullName = AssemblyRegionWalker.ASSEMBLY_PADDING_LONG_NAME, doc = "Number of additional bases of context to include around each assembly region", optional = true)
     public int assemblyRegionPadding = defaultAssemblyRegionPadding();
 
-    @Argument(fullName = "max-reads-per-alignment-start", doc = "Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable.", optional = true)
+    @Argument(fullName = AssemblyRegionWalker.MAX_STARTS_LONG_NAME, doc = "Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable.", optional = true)
     public int maxReadsPerAlignmentStart = defaultMaxReadsPerAlignmentStart();
 
     @Advanced
-    @Argument(fullName = "active-probability-threshold", doc="Minimum probability for a locus to be considered active.", optional = true)
+    @Argument(fullName = AssemblyRegionWalker.THRESHOLD_LONG_NAME, doc="Minimum probability for a locus to be considered active.", optional = true)
     public double activeProbThreshold = defaultActiveProbThreshold();
 
     @Advanced
-    @Argument(fullName = "max-prob-propagation-distance", doc="Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions", optional = true)
+    @Argument(fullName = AssemblyRegionWalker.PROPAGATION_LONG_NAME, doc="Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions", optional = true)
     public int maxProbPropagationDistance = defaultMaxProbPropagationDistance();
 
     /**

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

@@ -21,6 +21,8 @@ public abstract class ReadThreadingAssemblerArgumentCollection implements Serial
     public static final String ERROR_CORRECT_READS_LONG_NAME = "error-correct-reads";
 
     public static final String CAPTURE_ASSEMBLY_FAILURE_BAM_LONG_NAME = "capture-assembly-failure-bam";
+    public static final String KMER_SIZE_LONG_NAME = "kmer-size";
+    public static final String DONT_INCREASE_KMER_SIZE_LONG_NAME = "dont-increase-kmer-sizes-for-cycles";
 
 
     //---------------------------------------------------------------------------------------------------------------
@@ -58,15 +60,15 @@ public abstract class ReadThreadingAssemblerArgumentCollection implements Serial
      * Multiple kmer sizes can be specified, using e.g. `--kmer-size 10 --kmer-size 25`.
      */
     @Advanced
-    @Argument(fullName="kmer-size", doc="Kmer size to use in the read threading assembler", optional = true)
+    @Argument(fullName= KMER_SIZE_LONG_NAME, doc="Kmer size to use in the read threading assembler", optional = true)
     public List<Integer> kmerSizes = Lists.newArrayList(10,25);
 
     /**
      * When graph cycles are detected, the normal behavior is to increase kmer sizes iteratively until the cycles are
      * resolved. Disabling this behavior may cause the program to give up on assembling the ActiveRegion.
      */
     @Advanced
-    @Argument(fullName="dont-increase-kmer-sizes-for-cycles", doc="Disable iterating over kmer sizes when graph cycles are detected", optional = true)
+    @Argument(fullName= DONT_INCREASE_KMER_SIZE_LONG_NAME, doc="Disable iterating over kmer sizes when graph cycles are detected", optional = true)
     public boolean dontIncreaseKmerSizesForCycles = false;
 
     /**

src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java

@@ -62,6 +62,10 @@ public class M2ArgumentCollection extends AssemblyBasedCallerArgumentCollection
 
     public static final double DEFAULT_MITO_PRUNING_LOG_ODDS_THRESHOLD = MathUtils.log10ToLog(-4);
     public static final String INDEPENDENT_MATES_LONG_NAME = "independent-mates";
+    public static final String MINIMUM_ALLELE_FRACTION_LONG_NAME = "minimum-allele-fraction";
+    public static final String MINIMUM_ALLELE_FRACTION_SHORT_NAME = "min-AF";
+    public static final String LOD_BAND_LONG_NAME = "gvcf-lod-band";
+    public static final String LOD_BAND_SHORT_NAME = "LODB";
 
     @Override
     protected int getDefaultMaxMnpDistance() { return 1; }
@@ -239,7 +243,7 @@ public double getInitialLogOdds() {
      * Note that, unlike the GQ used by HaplotypeCaller GVCFs, here the reference calls with the highest confidence are the most negative.
      */
     @Advanced
-    @Argument(fullName = "gvcf-lod-band", shortName = "LODB", doc = "Exclusive upper bounds for reference confidence LOD bands " +
+    @Argument(fullName = LOD_BAND_LONG_NAME, shortName = LOD_BAND_SHORT_NAME, doc = "Exclusive upper bounds for reference confidence LOD bands " +
             "(must be specified in increasing order)", optional = true)
     public List<Double> GVCFGQBands = new ArrayList<>(70);
     {
@@ -249,7 +253,7 @@ public double getInitialLogOdds() {
     }
 
     @Advanced
-    @Argument(fullName = "minimum-allele-fraction", shortName = "min-AF", doc = "Lower bound of variant allele fractions to consider when calculating variant LOD", optional = true)
+    @Argument(fullName = MINIMUM_ALLELE_FRACTION_LONG_NAME, shortName = MINIMUM_ALLELE_FRACTION_SHORT_NAME, doc = "Lower bound of variant allele fractions to consider when calculating variant LOD", optional = true)
     public double minAF = 0.00;
 
     @Advanced

src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2TestingUtils.java

@@ -24,39 +24,27 @@ public class M2TestingUtils {
      */
     private static final int DEFAULT_ALIGNMENT_START = 99_991;
     private static final int DEFAULT_CHROM_INDEX = 0;
-    private static final byte DEFAULT_BASEQ = 26;
     private static final int DEFAULT_MAPQ = 60;
     private static final int DEFAULT_NUM_CHROMOSOMES = 1;
     private static final int DEFAULT_STARTING_CHROM = 1;
     private static final int DEFAULT_CHROMOSOME_SIZE = 1_000_000;
     public static final byte[] DEFAULT_REF_BASES = "CATCACACTCACTAAGCACACAGAGAATAAT".getBytes();
-    // Bases for C->T SNP at position 100,000                *
-    public static final byte[] DEFAULT_ALT_BASES = "CATCACACTTACTAAGCACACAGAGAATAAT".getBytes();
-    public static final int DEFAULT_START_POSITION = 99_991;
-    public static final int DEFAULT_END_POSITION = 100_021;
-    public static final int DEFAULT_SNP_POSITION = 100_000;
-    public static final int DEFAULT_READ_LENGTH = DEFAULT_REF_BASES.length;
-    public static final String DEFAULT_SAMPLE_NAME = "sample1";
 
     public static SAMFileGATKReadWriter getBareBonesSamWriter(final File samFile, final SAMFileHeader samHeader) {
         return new SAMFileGATKReadWriter(ReadUtils.createCommonSAMWriter(samFile, null, samHeader, true, true, false));
     }
 
-    public static byte[] getUniformBQArray(final byte quality, final int readLength){
-        final byte[] quals = new byte[readLength];
-        Arrays.fill(quals, quality);
-        return quals;
-    }
-
     public static List<GATKRead> createReads(final int numReads, final byte[] bases, final SAMFileHeader samHeader,
                                              final byte baseQuality, final String namePrefix){
         final int readLength = bases.length;
 
         final List<GATKRead> reads = new ArrayList<>(numReads);
         for (int i = 0; i < numReads; i++) {
             final String cigar = bases.length + "M";
+            final byte[] quals = new byte[readLength];
+            Arrays.fill(quals, baseQuality);
             final GATKRead read = ArtificialReadUtils.createArtificialRead(samHeader, namePrefix + i, DEFAULT_CHROM_INDEX,
-                    DEFAULT_ALIGNMENT_START, bases, getUniformBQArray(baseQuality, readLength), cigar);
+                    DEFAULT_ALIGNMENT_START, bases, quals, cigar);
             read.setReadGroup(DEFAULT_READ_GROUP_NAME);
             read.setMappingQuality(DEFAULT_MAPQ);
             read.setIsFirstOfPair();
@@ -67,14 +55,6 @@ public static List<GATKRead> createReads(final int numReads, final byte[] bases,
         return reads;
     }
 
-    public static List<GATKRead> createReads(final int numReads, final byte[] bases, final SAMFileHeader samHeader){
-        return createReads(numReads, bases, samHeader, DEFAULT_BASEQ, "read");
-    }
-
-    public static SAMFileHeader createSamHeader(){
-        return createSamHeader(DEFAULT_SAMPLE_NAME);
-    }
-
     public static SAMFileHeader createSamHeader(final String sampleName){
         final SAMFileHeader samHeader = ArtificialReadUtils.createArtificialSamHeader(
                 DEFAULT_NUM_CHROMOSOMES, DEFAULT_STARTING_CHROM, DEFAULT_CHROMOSOME_SIZE);