/** * Writes out the count of records without coordinates * * @param count */ @Override public void writeNoCoordinateRecordCount(final Long count) { codec.writeLong(count == null ? 0 : count); }
/** * Writes out the count of records without coordinates * * @param count */ public void writeNoCoordinateRecordCount(final Long count) { codec.writeLong(count == null ? 0 : count); }
private void writeNullContent() { codec.writeLong(0); // 0 bins , 0 intv } }
/** * Writes out the count of records without coordinates * * @param count */ @Override public void writeNoCoordinateRecordCount(final Long count) { codec.writeLong(count == null ? 0 : count); }
/** * Writes out the count of records without coordinates * * @param count */ @Override public void writeNoCoordinateRecordCount(final Long count) { codec.writeLong(count == null ? 0 : count); }
private void writeNullContent() { codec.writeLong(0); // 0 bins , 0 intv } }
/** * Writes out the count of records without coordinates * * @param count */ @Override public void writeNoCoordinateRecordCount(final Long count) { codec.writeLong(count == null ? 0 : count); }
private void writeNullContent() { codec.writeLong(0); // 0 bins , 0 intv } }
private void writeNullContent() { codec.writeLong(0); // 0 bins , 0 intv } }
private void writeNullContent() { codec.writeLong(0); // 0 bins , 0 intv } }
void writeVirtualOffset(final long virtualOffset) { if (prev > virtualOffset) { throw new IllegalArgumentException(String.format( "Offsets not in order: %#x > %#x", prev, virtualOffset)); } tempOffsetsCodec.writeLong(virtualOffset); virtualOffsetCount++; prev = virtualOffset; }
void writeVirtualOffset(final long virtualOffset) { if (prev > virtualOffset) { throw new IllegalArgumentException(String.format( "Offsets not in order: %#x > %#x", prev, virtualOffset)); } tempOffsetsCodec.writeLong(virtualOffset); virtualOffsetCount++; prev = virtualOffset; }
/** * Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450 * * @param metaData information describing numAligned records, numUnAligned, etc */ private void writeChunkMetaData(final BAMIndexMetaData metaData) { codec.writeInt(GenomicIndexUtil.MAX_BINS); final int nChunk = 2; codec.writeInt(nChunk); codec.writeLong(metaData.getFirstOffset()); codec.writeLong(metaData.getLastOffset()); codec.writeLong(metaData.getAlignedRecordCount()); codec.writeLong(metaData.getUnalignedRecordCount()); }
/** * Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450 * * @param metaData information describing numAligned records, numUnAligned, etc */ private void writeChunkMetaData(final BAMIndexMetaData metaData) { codec.writeInt(GenomicIndexUtil.MAX_BINS); final int nChunk = 2; codec.writeInt(nChunk); codec.writeLong(metaData.getFirstOffset()); codec.writeLong(metaData.getLastOffset()); codec.writeLong(metaData.getAlignedRecordCount()); codec.writeLong(metaData.getUnalignedRecordCount()); }
/** * Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450 * * @param metaData information describing numAligned records, numUnAligned, etc */ private void writeChunkMetaData(final BAMIndexMetaData metaData) { codec.writeInt(GenomicIndexUtil.MAX_BINS); final int nChunk = 2; codec.writeInt(nChunk); codec.writeLong(metaData.getFirstOffset()); codec.writeLong(metaData.getLastOffset()); codec.writeLong(metaData.getAlignedRecordCount()); codec.writeLong(metaData.getUnalignedRecordCount()); }
/** * Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450 * * @param metaData information describing numAligned records, numUnAligned, etc */ private void writeChunkMetaData(final BAMIndexMetaData metaData) { codec.writeInt(GenomicIndexUtil.MAX_BINS); final int nChunk = 2; codec.writeInt(nChunk); codec.writeLong(metaData.getFirstOffset()); codec.writeLong(metaData.getLastOffset()); codec.writeLong(metaData.getAlignedRecordCount()); codec.writeLong(metaData.getUnalignedRecordCount()); }
/** * Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450 * * @param metaData information describing numAligned records, numUnAligned, etc */ private void writeChunkMetaData(final BAMIndexMetaData metaData) { codec.writeInt(GenomicIndexUtil.MAX_BINS); final int nChunk = 2; codec.writeInt(nChunk); codec.writeLong(metaData.getFirstOffset()); codec.writeLong(metaData.getLastOffset()); codec.writeLong(metaData.getAlignedRecordCount()); codec.writeLong(metaData.getUnalignedRecordCount()); }
private void writeBin(final Bin bin) { final int binNumber = bin.getBinNumber(); if (binNumber >= GenomicIndexUtil.MAX_BINS){ throw new SAMException("Unexpected bin number when writing bam index " + binNumber); } codec.writeInt(binNumber); if (bin.getChunkList() == null){ codec.writeInt(0); return; } final List<Chunk> chunkList = bin.getChunkList(); final int n_chunk = chunkList.size(); codec.writeInt(n_chunk); for (final Chunk c : chunkList) { codec.writeLong(c.getChunkStart()); codec.writeLong(c.getChunkEnd()); } }
private void writeBin(final Bin bin) { final int binNumber = bin.getBinNumber(); if (binNumber >= GenomicIndexUtil.MAX_BINS){ throw new SAMException("Unexpected bin number when writing bam index " + binNumber); } codec.writeInt(binNumber); if (bin.getChunkList() == null){ codec.writeInt(0); return; } final List<Chunk> chunkList = bin.getChunkList(); final int n_chunk = chunkList.size(); codec.writeInt(n_chunk); for (final Chunk c : chunkList) { codec.writeLong(c.getChunkStart()); codec.writeLong(c.getChunkEnd()); } }
@Test public void testReadAndWriteLong() throws IOException { final long value = 42; final File outputFile = File.createTempFile(TEST_BASENAME, ".bin"); outputFile.deleteOnExit(); final OutputStream stream = new FileOutputStream(outputFile); final BinaryCodec codec = new BinaryCodec(stream); codec.writeLong(value); codec.close(); //Reading from file final InputStream instream = new FileInputStream(outputFile); final BinaryCodec readCodec = new BinaryCodec(instream); Assert.assertEquals(value, readCodec.readLong()); readCodec.close(); }