Cleaned up javadoc... (#1434)

- cleaned up javadoc so that there are no warnings and so that the links work properly.
- removed unneeded imports
- some IDE-recommended changes.

src/main/java/picard/analysis/CollectWgsMetrics.java

@@ -268,7 +268,7 @@ protected IntervalList getIntervalsToExamine() {
         return intervals;
     }
 
-    /** This method should only be called after {@link this.getSamReader()} is called. */
+    /** This method should only be called after {@link #getSamReader()} is called. */
     protected SAMFileHeader getSamFileHeader() {
         if (this.header == null) throw new IllegalStateException("getSamFileHeader() was called but this.header is null");
         return this.header;
@@ -360,10 +360,10 @@ protected long getBasesExcludedBy(final CountingFilter filter) {
     }
 
     /**
-     * Creates {@link htsjdk.samtools.util.AbstractLocusIterator} implementation according to {@link this#USE_FAST_ALGORITHM} value.
+     * Creates {@link htsjdk.samtools.util.AbstractLocusIterator} implementation according to {@link #USE_FAST_ALGORITHM} value.
      *
      * @param in inner {@link htsjdk.samtools.SamReader}
-     * @return if {@link this#USE_FAST_ALGORITHM} is enabled, returns {@link htsjdk.samtools.util.EdgeReadIterator} implementation,
+     * @return if {@link #USE_FAST_ALGORITHM} is enabled, returns {@link htsjdk.samtools.util.EdgeReadIterator} implementation,
      * otherwise default algorithm is used and {@link htsjdk.samtools.util.SamLocusIterator} is returned.
      */
     protected AbstractLocusIterator getLocusIterator(final SamReader in) {
@@ -378,11 +378,11 @@ protected AbstractLocusIterator getLocusIterator(final SamReader in) {
     }
 
     /**
-     * Creates {@link picard.analysis.AbstractWgsMetricsCollector} implementation according to {@link this#USE_FAST_ALGORITHM} value.
+     * Creates {@link picard.analysis.AbstractWgsMetricsCollector} implementation according to {@link #USE_FAST_ALGORITHM} value.
      *
      * @param coverageCap the maximum depth/coverage to consider.
      * @param intervals the intervals over which metrics are collected.
-     * @return if {@link this#USE_FAST_ALGORITHM} is enabled, returns {@link picard.analysis.FastWgsMetricsCollector} implementation,
+     * @return if {@link #USE_FAST_ALGORITHM} is enabled, returns {@link picard.analysis.FastWgsMetricsCollector} implementation,
      * otherwise default algorithm is used and {@link picard.analysis.CollectWgsMetrics.WgsMetricsCollector} is returned.
      */
     protected AbstractWgsMetricsCollector getCollector(final int coverageCap, final IntervalList intervals) {

src/main/java/picard/illumina/DistanceMetric.java

@@ -40,7 +40,7 @@ protected int distance0(final SingleBarcodeDistanceMetric editDistance) {
             "Unequal bases are considered mismatches. No-call read-bases, or those with low quality are not considered mismatches.") {
         @Override
         protected int distance0(final SingleBarcodeDistanceMetric editDistance) {
-            return editDistance.leniantHammingDistance();
+            return editDistance.lenientHammingDistance();
         }
     },
 

src/main/java/picard/sam/PositionBasedDownsampleSam.java

@@ -33,7 +33,7 @@
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.StandardOptionDefinitions;
 import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
-import picard.sam.markduplicates.util.OpticalDuplicateFinder;
+import picard.sam.markduplicates.MarkDuplicates;
 import picard.sam.util.PhysicalLocationInt;
 import picard.sam.util.ReadNameParser;
 

src/main/java/picard/sam/SamErrorMetric/BaseCalculator.java

@@ -28,8 +28,8 @@
 import htsjdk.samtools.util.SamLocusIterator;
 
 /**
- * An interface that can take a collection of bases (provided as {@link htsjdk.samtools.util.SamLocusIterator.RecordAndOffset RecordAndOffset}
- * and {@link SamLocusAndReferenceIterator.SAMLocusAndReference SAMLocusAndReference}) and generates a
+ * An interface that can take a collection of bases (provided as {@link SamLocusIterator.RecordAndOffset}
+ * and {@link SamLocusAndReferenceIterator.SAMLocusAndReference}) and generates a
  * {@link ErrorMetric} from them.
  * <p>
  * The Calculator has a suffix which will be used to generate the metric file suffixes.
@@ -47,7 +47,7 @@ public interface BaseCalculator {
     ErrorMetric getMetric();
 
     /**
-     * the function by which new loci are "shown" to the calculator
+     * The function by which new loci are "shown" to the calculator
      **/
     void addBase(final SamLocusIterator.RecordAndOffset recordAndOffset,
                  final SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo);

src/main/java/picard/sam/SamErrorMetric/ReadBaseStratification.java

@@ -231,10 +231,10 @@ public String getSuffix() {
      *
      * @param <T>             the type of the left Stratifier
      * @param <S>             the type of the right Stratifier
-     * @param leftStratifier  a {@link RecordAndOffsetStratifier<T>} to use
-     * @param rightStratifier a {@link RecordAndOffsetStratifier<S>} to use
+     * @param leftStratifier  a {@link RecordAndOffsetStratifier} to use
+     * @param rightStratifier a {@link RecordAndOffsetStratifier} to use
      * @param suffix          the suffix to use for the new stratifier
-     * @return an instance of {@link  PairStratifier>} that will stratify according to both <code>leftStratifier</code>
+     * @return an instance of {@link  PairStratifier} that will stratify according to both <code>leftStratifier</code>
      * and <code>rightStratifier</code>
      */
     public static <T extends Comparable<T>, S extends Comparable<S>> PairStratifier<T, S> PairStratifierFactory(

src/main/java/picard/util/BaitDesigner.java

@@ -385,12 +385,6 @@ int estimateBaits(final int start, final int end) {
         return Math.max(MINIMUM_BAITS_PER_TARGET, (int) (Math.ceil(length - BAIT_SIZE) / (double) BAIT_OFFSET) + 1);
     }
 
-    /**
-     * Main method that coordinates the checking of inputs, designing of baits and then
-     * the writing out of all necessary files.
-     *
-     * @return
-     */
     @Override
     protected int doWork() {
         // Input parameter munging and checking

src/main/java/picard/util/SingleBarcodeDistanceMetric.java

@@ -84,11 +84,17 @@ public int hammingDistance() {
         return numMismatches;
     }
 
-    /**
-     * Similar to Hamming distance but this version doesn't penalize matching bases with low quality for the read.
-     * @return
-     */
+
+    @Deprecated //(due to typo in original name. 1/9/2020)
     public int leniantHammingDistance() {
+        return lenientHammingDistance();
+    }
+        /**
+         * Similar to Hamming distance but this version doesn't penalize matching bases with low quality for the read.
+
+         * @return the edit distance between the barcode(s) and the read(s)
+         */
+    public int lenientHammingDistance() {
         int numMismatches = 0;
         for (int i = 0; i < barcodeBases.length && i < maskedBases.length && numMismatches <= maximalInterestingDistance; ++i) {
 

src/main/java/picard/vcf/MendelianViolations/FindMendelianViolations.java

@@ -44,9 +44,9 @@
 import htsjdk.variant.vcf.VCFHeaderLineType;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.cmdline.CommandLineProgram;
-import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import picard.cmdline.StandardOptionDefinitions;
 import picard.cmdline.programgroups.VariantEvaluationProgramGroup;
 import picard.pedigree.PedFile;
@@ -209,24 +209,22 @@ private Set<Interval> parseIntervalLists(final Set<String> intervalLists){
         }
         return intervals;
     }
-     /**
+
+    /**
      * Validates that the sex chromosomes don't overlap and parses the pseudo-autosomal regions into usable
      * objects to ensure their parsability
-     *
-     * @return
      */
     @Override
     protected String[] customCommandLineValidation() {
         final List<String> errors = new ArrayList<>();
 
         // Check that the sex chromosomes are not overlapping
-        final Set<String> sexChroms = new HashSet<>();
-        sexChroms.addAll(FEMALE_CHROMS);
+        final Set<String> sexChroms = new HashSet<>(FEMALE_CHROMS);
         sexChroms.retainAll(MALE_CHROMS);
         if (!sexChroms.isEmpty()) errors.add("The following chromosomes were listed as both male and female sex chromosomes: " + sexChroms);
 
         if (errors.isEmpty()) return null;
-        else return errors.toArray(new String[errors.size()]);
+        else return errors.toArray(new String[0]);
     }
 
     @Override