Package it.unimi.dsi.fastutil.bytes

Examples of it.unimi.dsi.fastutil.bytes.ByteArrayList.clear()

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                if (chunk.size() > outputBuffer.length) {
                    outputBuffer = new byte[chunk.size()];
                }
                processor.doChunck(chunk.size(), chunk.toByteArray(outputBuffer));
                d.setDownloaded(d.getDownloaded() + chunk.size());
                chunk.clear();
                bufferWatch.add();
                //System.out.print(bufferWatch);
                long maxTime = getdSettings().getBufferTime() * 1000000;
                if (bufferWatch.getTime() < maxTime) {
                    growCount++;
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            final int sequenceVariationLength = Math.max(fromLength, toLength);
            final ByteString toQuality = var.getToQuality();

            if (hasReadInsertion(from)) {
                bases.clear();
                scores.clear();
                for (int i = 0; i < sequenceVariationLength; i++) {
                    final char toChar = i >= toLength ? '-' : to.charAt(i);
                    int size = toQuality.size();
                    final byte qual = size > 0 && i < size ? toQuality.byteAt(i) : 40;
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                    deletedBases++;

                }
                addBlock(insertionBlocks, alignmentEntry.getPosition() + var.getPosition(), bases, scores);
                bases.clear();
                scores.clear();
            } else if (!to.contains("-")) {
                for (int i = 0; i < toLength; i++) {
                    final int offset = j + var.getPosition() + i - 1 + leftPadding - insertedBases;
                    if (offset > 0 && offset < readBases.length) {
                        readBases[offset] = (byte) to.charAt(i);
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        int pos = start;
        int matchLength = alignmentEntry.getQueryAlignedLength() - deletedBases;
        int endAlignmentRefPosition = matchLength + start;
        bases.clear();
        scores.clear();
        int maxIndex = Math.min(readBases.length, readQual.length);
        while (pos < endAlignmentRefPosition) {
            final int index = pos - start + leftPadding;
            if (index < maxIndex) {
                bases.add(readBases[index]);
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