Remove unused parameter

Author: Lenbok

src/com/rtg/position/output/GappedOutput.java

@@ -58,26 +58,21 @@ public class GappedOutput <G extends AbstractGappedRegion<G>> extends AbstractPo
 
   private final boolean mReverseFrame;
 
-  private final int mRepeatThreshold;
-
   //hang on to these for clone calls
 
   private final GapBucketsInfo mBucketInfo;
 
   /**
-   *
    * @param params parameters.
    * @param regionFactory factory for creating regions
    * @param scorer scoring implementation used
    * @param buildLengths lengths of sequences.
    * @param out where to write the output.
    * @param writer where to write output for unmapped reads
    * @param bucketInfo bucket info
-   * @param repeatFreq the repeat frequency threshold
    */
-  GappedOutput(final PositionParams params, GappedRegionFactory<G> regionFactory, GapScorer scorer, final ImmutableIntArray buildLengths, final Appendable out, final PositionWriter writer, final GapBucketsInfo bucketInfo, int repeatFreq) {
+  GappedOutput(final PositionParams params, GappedRegionFactory<G> regionFactory, GapScorer scorer, final ImmutableIntArray buildLengths, final Appendable out, final PositionWriter writer, final GapBucketsInfo bucketInfo) {
     super(params, out);
-    mRepeatThreshold = repeatFreq;
     mBucketInfo = bucketInfo;
     mBuildLengths = buildLengths;
     final Integer maxGap = params.output().maxGap();
@@ -436,7 +431,7 @@ public void nextQuery(final Frame frame, final int seqId) {
 
   @Override
   public PositionOutput reverseClone() {
-    return new GappedOutput<>(mParams, mRegionFactory, mProbabilities, mBuildLengths, mOut, mWriter.reverseClone(), mBucketInfo, mRepeatThreshold);
+    return new GappedOutput<>(mParams, mRegionFactory, mProbabilities, mBuildLengths, mOut, mWriter.reverseClone(), mBucketInfo);
   }
 
 }

src/com/rtg/position/output/OutputFormatType.java

@@ -49,7 +49,7 @@ private static class NgsOutputFormatType extends OutputFormatType {
     public
     PositionOutput output(final PositionParams params, final GapBucketsInfo bucketInfo, final ImmutableIntArray readLengths, final Appendable out, final Appendable unmappedOut, PositionWriter writer, int repeatFreq) {
       final GapScorer gs = new MismatchScores(params.output().maxGap(), params.output().distribution().maxIndel(), params.build().windowSize(), params.build().stepSize());
-      return new GappedOutput<>(params, GappedScoreLongRead.FACTORY, gs, readLengths, out, writer, bucketInfo, repeatFreq);
+      return new GappedOutput<>(params, GappedScoreLongRead.FACTORY, gs, readLengths, out, writer, bucketInfo);
     }
 
   }

test/com/rtg/position/output/GappedOutputTest.java

@@ -50,7 +50,7 @@ public GappedRegion region(int id, GapScorer distribution, PositionParams params
         return new GappedRegion(id, params.build(), distribution);
       }
     };
-    return new GappedOutput<>(params, regionFactory, new GappedDistribution(params).probabilities(), null, out, writer, bucketInfo, params.hashCountThreshold());
+    return new GappedOutput<>(params, regionFactory, new GappedDistribution(params).probabilities(), null, out, writer, bucketInfo);
   }
 
   protected static PositionParams makeParams(final int[] seqLengths, final int stepSize, final int windowSize, final int gapSize) throws IOException {