Examples of it.unimi.dsi.fastutil.ints.IntArrayList.clear()

Class it.unimi.dsi.fastutil.ints.IntArrayList

Examples of it.unimi.dsi.fastutil.ints.IntArrayList.clear()

it.unimi.dsi.fastutil.ints.IntArrayList.clear()

          
          pl.expectedUpdates = numberOfTerms[ i ];
          pl.start("Verifying all skips in " + index[i] + "...");


          for (t = 0; t < numberOfTerms[ i ]; t++) {
            l.clear();
            positions.clear();
            IndexIterator documents = termLists ? indexReader[ i ].documents( terms[ i ].get( t ) ) : indexReader[ i ].documents( t );
            int d;
            while( ( d = documents.nextDocument() ) != -1 ) {
              l.add( d );

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        final IntArrayList buffer = new IntArrayList(200);
        final int referenceIndex = overlap.getContigIndex();
        final int overlapStart = overlap.getStart();
        final int overlapEnd = overlap.getStop();
        for (int s = 0; s < sampleCount; s++) {
            buffer.clear();
            final GATKSAMRecord[] sampleReads = readsBySampleIndex[s];
            final int sampleReadCount = sampleReads.length;
            buffer.ensureCapacity(sampleReadCount);
            for (int r = 0; r < sampleReadCount; r++)
                if (unclippedReadOverlapsRegion(sampleReads[r], referenceIndex, overlapStart, overlapEnd))

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            final int sampleReadCount = sampleReads.length;
            for (int r = 0; r < sampleReadCount; r++)
                if (!unclippedReadOverlapsRegion(sampleReads[r], locContig, locStart, locEnd))
                    removeIndices.add(r);
            removeSampleReads(s,removeIndices,alleleCount);
            removeIndices.clear();
        }
    }


    // Compare the read coordinates to the location of interest.
    private boolean readOverlapsLocation(final String contig, final int locStart,

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                final GATKSAMRecord read = sampleReads[r];
                if (readIsPoorlyModelled(s,r,read, maximumErrorPerBase))
                    removeIndices.add(r);
            }
            removeSampleReads(s, removeIndices, alleleCount);
            removeIndices.clear();
        }
    }


    // Check whether the read is poorly modelled.
    protected boolean readIsPoorlyModelled(final int sampleIndex, final int readIndex, final GATKSAMRecord read, final double maxErrorRatePerBase) {

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                final int sampleReadCount = readsBySampleIndex[s].length;
                readsToRemove.ensureCapacity(sampleReadCount);
                for (int r = 0; r < sampleReadCount; r++)
                    readsToRemove.add(r);
                removeSampleReads(s,readsToRemove,alleleCount);
                readsToRemove.clear();
            }
            else {
                final Map<A,List<GATKSAMRecord>> readsByBestAllelesMap = readsByBestAlleleMap(s);
                removeSampleReads(s,AlleleBiasedDownsamplingUtils.selectAlleleBiasedReads(readsByBestAllelesMap, fraction),alleleCount);
            }

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