Merge pull request #447 from broadinstitute/ak_diamonds

use diamond types <>

src/main/java/org/broadinstitute/hellbender/metrics/MultiLevelCollector.java

@@ -98,7 +98,7 @@ private abstract class Distributor {
         protected abstract PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE> makeUnknownCollector();
 
         public Distributor(final List<SAMReadGroupRecord> rgRecs) {
-            collectors = new LinkedHashMap<String, PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE>>();
+            collectors = new LinkedHashMap<>();
             for(final SAMReadGroupRecord rg : rgRecs) {
                 final String key = getKey(rg);
                 if(!collectors.containsKey(key)) {
@@ -150,7 +150,7 @@ public void addToFile(final MetricsFile<METRIC_TYPE, HISTOGRAM_KEY> file) {
     private class AllReadsDistributor extends Distributor {
 
         public AllReadsDistributor(final List<SAMReadGroupRecord> rgRecs) {
-            super(new ArrayList<SAMReadGroupRecord>());
+            super(new ArrayList<>());
             makeCollector(null);
         }
 
@@ -258,7 +258,7 @@ protected PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE> makeUnknow
      *                     readGroups found in the records depending on the accumulationLevels provided
      */
     protected void setup(final Set<MetricAccumulationLevel> accumulationLevels, final List<SAMReadGroupRecord> samRgRecords) {
-        outputOrderedDistributors = new ArrayList<Distributor>(4);
+        outputOrderedDistributors = new ArrayList<>(4);
         if(accumulationLevels.contains(MetricAccumulationLevel.ALL_READS)) {
             outputOrderedDistributors.add(new AllReadsDistributor(samRgRecords));
         }

src/main/java/org/broadinstitute/hellbender/tools/ClipReads.java

@@ -198,7 +198,7 @@ public final class ClipReads extends ReadWalker {
     /**
      * List of sequence that should be clipped from the reads
      */
-    private List<SeqToClip> sequencesToClip = new ArrayList<SeqToClip>();
+    private List<SeqToClip> sequencesToClip = new ArrayList<>();
 
     /**
      * List of cycle start / stop pairs (0-based, stop is included in the cycle to remove) to clip from the reads
@@ -259,7 +259,7 @@ public void onTraversalStart() {
         // Initialize the cycle ranges to clip
         //
         if (cyclesToClipArg != null) {
-            cyclesToClip = new ArrayList<Pair<Integer, Integer>>();
+            cyclesToClip = new ArrayList<>();
             for (String range : cyclesToClipArg.split(",")) {
                 try {
                     String[] elts = range.split("-");

src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/AlignmentSummaryMetricsCollector.java

@@ -73,7 +73,7 @@ public void acceptRecord(final SAMRecord rec, final ReferenceSequence ref) {
 
     /** Converts the supplied adapter sequences to byte arrays in both fwd and rc. */
     private byte [][] prepareAdapterSequences() {
-        final Set<String> kmers = new HashSet<String>();
+        final Set<String> kmers = new HashSet<>();
 
         // Make a set of all kmers of adapterMatchLength
         for (final String seq : adapterSequence) {
@@ -194,7 +194,7 @@ public void addMetricsToFile(final MetricsFile<AlignmentSummaryMetrics, Comparab
          */
         private class IndividualAlignmentSummaryMetricsCollector {
             private long numPositiveStrand = 0;
-            private final Histogram<Integer> readLengthHistogram = new Histogram<Integer>();
+            private final Histogram<Integer> readLengthHistogram = new Histogram<>();
             private AlignmentSummaryMetrics metrics;
             private long chimeras;
             private long chimerasDenominator;
@@ -203,9 +203,9 @@ private class IndividualAlignmentSummaryMetricsCollector {
 
             private long nonBisulfiteAlignedBases = 0;
             private long hqNonBisulfiteAlignedBases = 0;
-            private final Histogram<Long> mismatchHistogram = new Histogram<Long>();
-            private final Histogram<Long> hqMismatchHistogram = new Histogram<Long>();
-            private final Histogram<Integer> badCycleHistogram = new Histogram<Integer>();
+            private final Histogram<Long> mismatchHistogram = new Histogram<>();
+            private final Histogram<Long> hqMismatchHistogram = new Histogram<>();
+            private final Histogram<Integer> badCycleHistogram = new Histogram<>();
 
             public IndividualAlignmentSummaryMetricsCollector(final AlignmentSummaryMetrics.Category pairingCategory,
                                                               final String sample,

src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectMultipleMetrics.java

@@ -103,7 +103,7 @@ public SinglePassSamProgram makeInstance(final String outbase) {
 
     @Override
     protected String[] customCommandLineValidation() {
-        programsToRun = new ArrayList<ProgramInterface>(PROGRAM);
+        programsToRun = new ArrayList<>(PROGRAM);
         return super.customCommandLineValidation();
     }
 
@@ -121,8 +121,8 @@ public Object doWork() {
             OUTPUT = OUTPUT.substring(0, OUTPUT.length() - 1);
         }
 
-        final List<SinglePassSamProgram> programs = new ArrayList<SinglePassSamProgram>();
-        for (ProgramInterface program : new HashSet<ProgramInterface>(programsToRun)) {
+        final List<SinglePassSamProgram> programs = new ArrayList<>();
+        for (ProgramInterface program : new HashSet<>(programsToRun)) {
             SinglePassSamProgram instance = program.makeInstance(OUTPUT);
 
             // Generally programs should not be accessing these directly but it might make things smoother

src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectOxoGMetrics.java

@@ -83,7 +83,7 @@ public class CollectOxoGMetrics extends PicardCommandLineProgram {
     public int CONTEXT_SIZE = 1;
 
     @Argument(doc = "The optional set of sequence contexts to restrict analysis to. If not supplied all contexts are analyzed.")
-    public Set<String> CONTEXTS = new HashSet<String>();
+    public Set<String> CONTEXTS = new HashSet<>();
 
     @Argument(doc = "For debugging purposes: stop after visiting this many sites with at least 1X coverage.")
     public int STOP_AFTER = Integer.MAX_VALUE;
@@ -159,7 +159,7 @@ public static final class CpcgMetrics extends MetricBase {
     @Override
     protected String[] customCommandLineValidation() {
         final int size = 1 + 2 * CONTEXT_SIZE;
-        final List<String> messages = new ArrayList<String>();
+        final List<String> messages = new ArrayList<>();
 
         for (final String ctx : CONTEXTS) {
             if (ctx.length() != size) {
@@ -188,16 +188,16 @@ protected Object doWork() {
         final ReferenceSequenceFileWalker refWalker = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE);
         final SamReader in = SamReaderFactory.makeDefault().open(INPUT);
 
-        final Set<String> samples = new HashSet<String>();
-        final Set<String> libraries = new HashSet<String>();
+        final Set<String> samples = new HashSet<>();
+        final Set<String> libraries = new HashSet<>();
         for (final SAMReadGroupRecord rec : in.getFileHeader().getReadGroups()) {
             samples.add(getOrElse(rec.getSample(), UNKNOWN_SAMPLE));
             libraries.add(getOrElse(rec.getLibrary(), UNKNOWN_LIBRARY));
         }
 
         // Setup the calculators
         final Set<String> contexts = CONTEXTS.isEmpty() ? makeContextStrings(CONTEXT_SIZE) : CONTEXTS;
-        final ListMap<String, Calculator> calculators = new ListMap<String, Calculator>();
+        final ListMap<String, Calculator> calculators = new ListMap<>();
         for (final String context : contexts) {
             for (final String library : libraries) {
                 calculators.add(context, new Calculator(library, context));
@@ -221,7 +221,7 @@ protected Object doWork() {
         iterator.setEmitUncoveredLoci(false);
         iterator.setMappingQualityScoreCutoff(MINIMUM_MAPPING_QUALITY);
 
-        final List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
+        final List<SamRecordFilter> filters = new ArrayList<>();
         filters.add(new NotPrimaryAlignmentFilter());
         filters.add(new DuplicateReadFilter());
         if (MINIMUM_INSERT_SIZE > 0 || MAXIMUM_INSERT_SIZE > 0) {
@@ -275,7 +275,7 @@ protected Object doWork() {
         for (final List<Calculator> calcs : calculators.values()) {
             for (final Calculator calc : calcs) {
                 final CpcgMetrics m = calc.finish();
-                m.SAMPLE_ALIAS = StringUtil.join(",", new ArrayList<String>(samples));
+                m.SAMPLE_ALIAS = StringUtil.join(",", new ArrayList<>(samples));
                 file.addMetric(m);
             }
         }
@@ -286,7 +286,7 @@ protected Object doWork() {
     }
 
     private Set<String> makeContextStrings(final int contextSize) {
-        final Set<String> contexts = new HashSet<String>();
+        final Set<String> contexts = new HashSet<>();
 
         for (final byte[] kmer : generateAllKmers(2 * contextSize + 1)) {
             if (kmer[contextSize] == 'C') {

src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/InsertSizeMetricsCollector.java

@@ -70,7 +70,7 @@ public void acceptRecord(final SAMRecord record, final ReferenceSequence refSeq)
 
     /** A Collector for individual InsertSizeMetrics for a given SAMPLE or SAMPLE/LIBRARY or SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels) */
     public class PerUnitInsertSizeMetricsCollector implements PerUnitMetricCollector<InsertSizeMetrics, Integer, InsertSizeCollectorArgs> {
-        final EnumMap<SamPairUtil.PairOrientation, Histogram<Integer>> Histograms = new EnumMap<SamPairUtil.PairOrientation, Histogram<Integer>>(SamPairUtil.PairOrientation.class);
+        final EnumMap<SamPairUtil.PairOrientation, Histogram<Integer>> Histograms = new EnumMap<>(SamPairUtil.PairOrientation.class);
         final String sample;
         final String library;
         final String readGroup;
@@ -93,9 +93,9 @@ else if (this.sample != null) {
             else {
                 prefix = "All_Reads.";
             }
-            Histograms.put(SamPairUtil.PairOrientation.FR,     new Histogram<Integer>("insert_size", prefix + "fr_count"));
-            Histograms.put(SamPairUtil.PairOrientation.TANDEM, new Histogram<Integer>("insert_size", prefix + "tandem_count"));
-            Histograms.put(SamPairUtil.PairOrientation.RF,     new Histogram<Integer>("insert_size", prefix + "rf_count"));
+            Histograms.put(SamPairUtil.PairOrientation.FR,     new Histogram<>("insert_size", prefix + "fr_count"));
+            Histograms.put(SamPairUtil.PairOrientation.TANDEM, new Histogram<>("insert_size", prefix + "tandem_count"));
+            Histograms.put(SamPairUtil.PairOrientation.RF,     new Histogram<>("insert_size", prefix + "rf_count"));
         }
 
         public void acceptRecord(final InsertSizeCollectorArgs args) {

src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/MeanQualityByCycle.java

@@ -100,7 +100,7 @@ private void ensureArraysBigEnough(final int length) {
 
         Histogram<Integer> getMeanQualityHistogram() {
             final String label = useOriginalQualities ? "MEAN_ORIGINAL_QUALITY" : "MEAN_QUALITY";
-            final Histogram<Integer> meanQualities = new Histogram<Integer>("CYCLE", label);
+            final Histogram<Integer> meanQualities = new Histogram<>("CYCLE", label);
 
             int firstReadLength = 0;
 

src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/QualityScoreDistribution.java

@@ -92,8 +92,8 @@ protected void acceptRead(final SAMRecord rec, final ReferenceSequence ref) {
     @Override
     protected void finish() {
         // Built the Histograms out of the long[]s
-        final Histogram<Byte> qHisto  = new Histogram<Byte>("QUALITY", "COUNT_OF_Q");
-        final Histogram<Byte> oqHisto = new Histogram<Byte>("QUALITY", "COUNT_OF_OQ");
+        final Histogram<Byte> qHisto  = new Histogram<>("QUALITY", "COUNT_OF_Q");
+        final Histogram<Byte> oqHisto = new Histogram<>("QUALITY", "COUNT_OF_OQ");
 
         for (int i=0; i< qCounts.length; ++i) {
             if (qCounts[i]  > 0) qHisto.increment( (byte) i, (double) qCounts[i]);

src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/ArtifactCounter.java

@@ -36,7 +36,7 @@ public ArtifactCounter(final String sampleAlias, final String library, final int
         this.library = library;
 
         // define the contexts
-        this.fullContexts = new HashSet<String>();
+        this.fullContexts = new HashSet<>();
         for (final byte[] kmer : SequenceUtil.generateAllKmers(2 * contextSize + 1)) {
             this.fullContexts.add(StringUtil.bytesToString(kmer));
         }
@@ -45,9 +45,9 @@ public ArtifactCounter(final String sampleAlias, final String library, final int
         // NB: we use N to represent a wildcard base, rather than an ambiguous base. It's assumed that all of the input
         // contexts are unambiguous, and that any actual N's in the data have been dealt with elsewhere.
         final String padding = StringUtil.repeatCharNTimes('N', contextSize);
-        this.leadingContextMap = new HashMap<String, String>();
-        this.trailingContextMap = new HashMap<String, String>();
-        this.zeroContextMap = new HashMap<String, String>();
+        this.leadingContextMap = new HashMap<>();
+        this.trailingContextMap = new HashMap<>();
+        this.zeroContextMap = new HashMap<>();
         for (final String context : this.fullContexts) {
             final String leading = context.substring(0, contextSize);
             final String trailing = context.substring(contextSize + 1, context.length());
@@ -58,21 +58,21 @@ public ArtifactCounter(final String sampleAlias, final String library, final int
         }
 
         // set up the accumulators
-        final Set<String> halfContexts = new HashSet<String>();
+        final Set<String> halfContexts = new HashSet<>();
         halfContexts.addAll(leadingContextMap.values());
         halfContexts.addAll(trailingContextMap.values());
-        final Set<String> zeroContexts = new HashSet<String>();
+        final Set<String> zeroContexts = new HashSet<>();
         zeroContexts.addAll(zeroContextMap.values());
 
         this.fullContextAccumulator = new ContextAccumulator(fullContexts, expectedTandemReads);
         this.halfContextAccumulator = new ContextAccumulator(halfContexts, expectedTandemReads);
         this.zeroContextAccumulator = new ContextAccumulator(zeroContexts, expectedTandemReads);
 
         // these will get populated in the final step
-        preAdapterSummaryMetricsList = new ArrayList<PreAdapterSummaryMetrics>();
-        preAdapterDetailMetricsList = new ArrayList<PreAdapterDetailMetrics>();
-        baitBiasSummaryMetricsList = new ArrayList<BaitBiasSummaryMetrics>();
-        baitBiasDetailMetricsList = new ArrayList<BaitBiasDetailMetrics>();
+        preAdapterSummaryMetricsList = new ArrayList<>();
+        preAdapterDetailMetricsList = new ArrayList<>();
+        baitBiasSummaryMetricsList = new ArrayList<>();
+        baitBiasDetailMetricsList = new ArrayList<>();
     }
 
     /**
@@ -118,7 +118,7 @@ public void finish() {
      *
      */
     private Map<Transition, SummaryPair> getSummaryMetrics() {
-        final Map<Transition, SummaryPair> summaryMetricsMap = new HashMap<Transition, SummaryPair>();
+        final Map<Transition, SummaryPair> summaryMetricsMap = new HashMap<>();
 
         // extract the detail metrics from each accumulator
         final ListMap<Transition, DetailPair> fullMetrics = this.fullContextAccumulator.calculateMetrics(sampleAlias, library);
@@ -134,8 +134,8 @@ private Map<Transition, SummaryPair> getSummaryMetrics() {
             }
 
             // we want to report on leading / trailing contexts separately
-            final List<DetailPair> leadingMetricsForTransition = new ArrayList<DetailPair>();
-            final List<DetailPair> trailingMetricsForTransition = new ArrayList<DetailPair>();
+            final List<DetailPair> leadingMetricsForTransition = new ArrayList<>();
+            final List<DetailPair> trailingMetricsForTransition = new ArrayList<>();
             for (final DetailPair metrics : halfMetrics.get(transition)) {
                 // first make sure they're the same context
                 if (!metrics.preAdapterMetrics.CONTEXT.equals(metrics.baitBiasMetrics.CONTEXT)) {

src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/CollectSequencingArtifactMetrics.java

@@ -89,7 +89,7 @@ public class CollectSequencingArtifactMetrics extends SinglePassSamProgram {
 
     @Argument(doc = "If specified, only print results for these contexts in the detail metrics output. " +
                   "However, the summary metrics output will still take all contexts into consideration.", optional = true)
-    public Set<String> CONTEXTS_TO_PRINT = new HashSet<String>();
+    public Set<String> CONTEXTS_TO_PRINT = new HashSet<>();
 
     private static final String UNKNOWN_LIBRARY = "UnknownLibrary";
     private static final String UNKNOWN_SAMPLE = "UnknownSample";
@@ -103,13 +103,13 @@ public class CollectSequencingArtifactMetrics extends SinglePassSamProgram {
     private DbSnpBitSetUtil dbSnpMask;
     private SamRecordFilter recordFilter;
 
-    private final Set<String> samples = new HashSet<String>();
-    private final Set<String> libraries = new HashSet<String>();
-    private final Map<String, ArtifactCounter> artifactCounters = new HashMap<String, ArtifactCounter>();
+    private final Set<String> samples = new HashSet<>();
+    private final Set<String> libraries = new HashSet<>();
+    private final Map<String, ArtifactCounter> artifactCounters = new HashMap<>();
 
     @Override
     protected String[] customCommandLineValidation() {
-        final List<String> messages = new ArrayList<String>();
+        final List<String> messages = new ArrayList<>();
 
         final int contextFullLength = 2 * CONTEXT_SIZE + 1;
         if (CONTEXT_SIZE < 0) messages.add("CONTEXT_SIZE cannot be negative");
@@ -156,7 +156,7 @@ protected void setup(final SAMFileHeader header, final File samFile) {
         }
 
         // set record-level filters
-        final List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
+        final List<SamRecordFilter> filters = new ArrayList<>();
         filters.add(new FailsVendorReadQualityFilter());
         filters.add(new NotPrimaryAlignmentFilter());
         filters.add(new DuplicateReadFilter());
@@ -169,7 +169,7 @@ protected void setup(final SAMFileHeader header, final File samFile) {
         recordFilter = new AggregateFilter(filters);
 
         // set up the artifact counters
-        final String sampleAlias = StringUtil.join(",", new ArrayList<String>(samples));
+        final String sampleAlias = StringUtil.join(",", new ArrayList<>(samples));
         for (final String library : libraries) {
             artifactCounters.put(library, new ArtifactCounter(sampleAlias, library, CONTEXT_SIZE, TANDEM_READS));
         }

src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/ContextAccumulator.java

@@ -20,9 +20,9 @@ class ContextAccumulator {
 
     public ContextAccumulator(final Set<String> contexts, final boolean expectedTandemReads) {
         this.expectedTandemReads = expectedTandemReads;
-        this.artifactMap = new HashMap<Transition, Map<String, AlignmentAccumulator>>();
+        this.artifactMap = new HashMap<>();
         for (final Transition transition : Transition.values()) {
-            this.artifactMap.put(transition, new HashMap<String, AlignmentAccumulator>());
+            this.artifactMap.put(transition, new HashMap<>());
         }
         for (final String context : contexts) {
             final char refBase = getCentralBase(context);
@@ -43,7 +43,7 @@ public void countRecord(final String refContext, final char calledBase, final SA
      * Core method to compute detailed (i.e. context-by-context) metrics from this accumulator.
      */
     public ListMap<Transition, DetailPair> calculateMetrics(final String sampleAlias, final String library) {
-        final ListMap<Transition, DetailPair> detailMetricsMap = new ListMap<Transition, DetailPair>();
+        final ListMap<Transition, DetailPair> detailMetricsMap = new ListMap<>();
         for (final Transition altTransition : Transition.altValues()) {
             final Transition refTransition = altTransition.matchingRef();
             for (final String context : this.artifactMap.get(altTransition).keySet()) {