picard.illumina.IlluminaBasecallsToFastq Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2013 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.illumina;
import htsjdk.samtools.SAMRecordQueryNameComparator;
import htsjdk.samtools.SAMUtils;
import htsjdk.samtools.fastq.BasicFastqWriter;
import htsjdk.samtools.fastq.FastqReader;
import htsjdk.samtools.fastq.FastqRecord;
import htsjdk.samtools.fastq.FastqWriter;
import htsjdk.samtools.fastq.FastqWriterFactory;
import htsjdk.samtools.util.CollectionUtil;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.SortingCollection;
import htsjdk.samtools.util.StringUtil;
import picard.PicardException;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.Illumina;
import picard.fastq.Casava18ReadNameEncoder;
import picard.fastq.IlluminaReadNameEncoder;
import picard.fastq.ReadNameEncoder;
import picard.illumina.parser.ClusterData;
import picard.illumina.parser.IlluminaFileUtil;
import picard.illumina.parser.ReadData;
import picard.illumina.parser.ReadStructure;
import picard.illumina.parser.readers.BclQualityEvaluationStrategy;
import picard.util.IlluminaUtil;
import picard.util.TabbedTextFileWithHeaderParser;
import java.io.BufferedReader;
import java.io.File;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStream;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Set;
@CommandLineProgramProperties(
usage = IlluminaBasecallsToFastq.USAGE_SUMMARY + IlluminaBasecallsToFastq.USAGE_DETAILS,
usageShort = IlluminaBasecallsToFastq.USAGE_SUMMARY,
programGroup = Illumina.class
)
public class IlluminaBasecallsToFastq extends CommandLineProgram {
static final String USAGE_SUMMARY = "Generate FASTQ file(s) from Illumina basecall read data. ";
static final String USAGE_DETAILS = "This tool generates FASTQ files from data in an Illumina BaseCalls output directory. " +
"Separate FASTQ files are created for each template, barcode, and index (molecular barcode) read. Briefly, the template reads " +
"are the target sequence of your experiment, the barcode sequence reads facilitate sample demultiplexing, and the index reads " +
"help mitigate instrument phasing errors. For additional information on the read types, please see the following " +
"reference here.
" +
"" +
"In the absence of sample pooling (multiplexing) and/or barcodes, then an OUTPUT_PREFIX (file directory) must be " +
"provided as the sample identifier. For multiplexed samples, a MULTIPLEX_PARAMS file must be specified. " +
"The MULTIPLEX_PARAMS file contains the list of sample barcodes used to sort template, barcode, and index reads. " +
"It is essentially the same as the BARCODE_FILE used in the" +
"ExtractIlluminaBarcodes " +
"tool.
" +
"" +
"Files from this tool use the following naming format: {prefix}.{type}_{number}.fastq with the {prefix} indicating the sample " +
"barcode, the {type} indicating the types of reads e.g. index, barcode, or blank (if it contains a template read). " +
"The {number} indicates the read number, either first (1) or second (2) for paired-end sequencing.
" +
"Usage examples:
" +
"" +
"Example 1: Sample(s) with either no barcode or barcoded without multiplexing
" +
"java -jar picard.jar IlluminaBasecallsToFastq \\
" +
" READ_STRUCTURE=25T8B25T \\
" +
" BASECALLS_DIR=basecallDirectory \\
" +
" LANE=001 \\
" +
" OUTPUT_PREFIX=noBarcode.1 \\
" +
" RUN_BARCODE=run15 \\
" +
" FLOWCELL_BARCODE=abcdeACXX
" +
"Example 2: Multiplexed samples
" +
"java -jar picard.jar IlluminaBasecallsToFastq \\
" +
" READ_STRUCTURE=25T8B25T \\
" +
" BASECALLS_DIR=basecallDirectory \\
" +
" LANE=001 \\
" +
" MULTIPLEX_PARAMS=demultiplexed_output.txt \\
" +
" RUN_BARCODE=run15 \\
" +
" FLOWCELL_BARCODE=abcdeACXX
" +
"" +
"The FLOWCELL_BARCODE is required if emitting Casava 1.8-style read name headers.
" +
"
";
// The following attributes define the command-line arguments
@Option(doc = "The basecalls directory. ", shortName = "B")
public File BASECALLS_DIR;
@Option(doc = "The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If not set, use BASECALLS_DIR. ", shortName = "BCD", optional = true)
public File BARCODES_DIR;
@Option(doc = "Lane number. ", shortName = StandardOptionDefinitions.LANE_SHORT_NAME)
public Integer LANE;
@Option(doc = "The prefix for output FASTQs. Extensions as described above are appended. Use this option for a non-barcoded run, or" +
" for a barcoded run in which it is not desired to demultiplex reads into separate files by barcode.",
shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME,
mutex = {"MULTIPLEX_PARAMS"})
public File OUTPUT_PREFIX;
@Option(doc = "The barcode of the run. Prefixed to read names.")
public String RUN_BARCODE;
@Option(doc = "The name of the machine on which the run was sequenced; required if emitting Casava1.8-style read name headers", optional = true)
public String MACHINE_NAME;
@Option(doc = "The barcode of the flowcell that was sequenced; required if emitting Casava1.8-style read name headers", optional = true)
public String FLOWCELL_BARCODE;
@Option(doc = ReadStructure.PARAMETER_DOC, shortName = "RS")
public String READ_STRUCTURE;
@Option(doc = "Tab-separated file for creating all output FASTQs demultiplexed by barcode for a lane with single " +
"IlluminaBasecallsToFastq invocation. The columns are OUTPUT_PREFIX, and BARCODE_1, BARCODE_2 ... BARCODE_X " +
"where X = number of barcodes per cluster (optional). Row with BARCODE_1 set to 'N' is used to specify " +
"an output_prefix for no barcode match.",
mutex = {"OUTPUT_PREFIX"})
public File MULTIPLEX_PARAMS;
@Deprecated
@Option(doc = "Deprecated (No longer used). Which adapters to look for in the read.")
public List ADAPTERS_TO_CHECK = null;
@Option(doc = "The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is automatically set to " +
"the number of cores available on the machine. If NUM_PROCESSORS < 0, then the number of cores used will" +
" be the number available on the machine less NUM_PROCESSORS.")
public Integer NUM_PROCESSORS = 0;
@Option(doc = "If set, this is the first tile to be processed (used for debugging). Note that tiles are not processed" +
" in numerical order.",
optional = true)
public Integer FIRST_TILE;
@Option(doc = "If set, process no more than this many tiles (used for debugging).", optional = true)
public Integer TILE_LIMIT;
@Option(doc = "Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of reads" +
" and convert their quality scores to Q2.")
public boolean APPLY_EAMSS_FILTER = true;
@Option(doc = "If true, call System.gc() periodically. This is useful in cases in which the -Xmx value passed " +
"is larger than the available memory.")
public Boolean FORCE_GC = true;
@Option(doc = "Configure SortingCollections to store this many records before spilling to disk. For an indexed" +
" run, each SortingCollection gets this value/number of indices.")
public int MAX_READS_IN_RAM_PER_TILE = 1200000;
@Option(doc = "The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are lower than this value, an error is thrown." +
"The default of 2 is what the Illumina's spec describes as the minimum, but in practice the value has been observed lower.")
public int MINIMUM_QUALITY = BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY;
@Option(doc = "Whether to include non-PF reads", shortName = "NONPF", optional = true)
public boolean INCLUDE_NON_PF_READS = true;
@Option(doc = "Whether to ignore reads whose barcodes are not found in MULTIPLEX_PARAMS. Useful when outputting " +
"FASTQs for only a subset of the barcodes in a lane.", shortName = "INGORE_UNEXPECTED")
public boolean IGNORE_UNEXPECTED_BARCODES = false;
@Option(doc = "The read name header formatting to emit. Casava1.8 formatting has additional information beyond Illumina, including: " +
"the passing-filter flag value for the read, the flowcell name, and the sequencer name.")
public ReadNameFormat READ_NAME_FORMAT = ReadNameFormat.CASAVA_1_8;
@Option(shortName = "GZIP", doc = "Compress output FASTQ files using gzip and append a .gz extension to the file names.")
public boolean COMPRESS_OUTPUTS = false;
/**
* Simple switch to control the read name format to emit.
*/
public enum ReadNameFormat {
CASAVA_1_8, ILLUMINA
}
private final Map sampleBarcodeFastqWriterMap = new HashMap<>();
private ReadStructure readStructure;
private BasecallsConverter basecallsConverter;
private static final Log log = Log.getInstance(IlluminaBasecallsToFastq.class);
private final FastqWriterFactory fastqWriterFactory = new FastqWriterFactory();
private ReadNameEncoder readNameEncoder;
private static final Comparator queryNameComparator = (r1, r2) -> SAMRecordQueryNameComparator.compareReadNames(r1.templateRecords[0].getReadHeader(),
r2.templateRecords[0].getReadHeader());
@Override
protected int doWork() {
initialize();
basecallsConverter.doTileProcessing();
return 0;
}
@Override
protected String[] customCommandLineValidation() {
final LinkedList errors = new LinkedList<>();
if (READ_NAME_FORMAT == ReadNameFormat.CASAVA_1_8 && MACHINE_NAME == null) {
errors.add("MACHINE_NAME is required when using Casava1.8-style read name headers.");
}
if (READ_NAME_FORMAT == ReadNameFormat.CASAVA_1_8 && FLOWCELL_BARCODE == null) {
errors.add("FLOWCELL_BARCODE is required when using Casava1.8-style read name headers.");
}
if (ADAPTERS_TO_CHECK != null) {
log.warn("ADAPTERS_TO_CHECK is not used");
}
if (errors.isEmpty()) {
return null;
} else {
return errors.toArray(new String[errors.size()]);
}
}
/**
* Prepares loggers, initiates garbage collection thread, parses arguments and initialized variables appropriately/
*/
private void initialize() {
fastqWriterFactory.setCreateMd5(CREATE_MD5_FILE);
switch (READ_NAME_FORMAT) {
case CASAVA_1_8:
readNameEncoder = new Casava18ReadNameEncoder(MACHINE_NAME, RUN_BARCODE, FLOWCELL_BARCODE);
break;
case ILLUMINA:
readNameEncoder = new IlluminaReadNameEncoder(RUN_BARCODE);
break;
}
final BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY);
readStructure = new ReadStructure(READ_STRUCTURE);
if (MULTIPLEX_PARAMS != null) {
IOUtil.assertFileIsReadable(MULTIPLEX_PARAMS);
}
final boolean demultiplex;
if (OUTPUT_PREFIX != null) {
sampleBarcodeFastqWriterMap.put(null, buildWriter(OUTPUT_PREFIX));
demultiplex = false;
} else {
populateWritersFromMultiplexParams();
demultiplex = true;
}
final int readsPerCluster = readStructure.templates.length() + readStructure.sampleBarcodes.length();
if (IlluminaFileUtil.hasCbcls(BASECALLS_DIR, LANE)) {
if (BARCODES_DIR == null) BARCODES_DIR = BASECALLS_DIR;
basecallsConverter = new NewIlluminaBasecallsConverter<>(BASECALLS_DIR, BARCODES_DIR, LANE, readStructure,
sampleBarcodeFastqWriterMap, demultiplex, Math.max(1, MAX_READS_IN_RAM_PER_TILE / readsPerCluster),
TMP_DIR, NUM_PROCESSORS,
FIRST_TILE, TILE_LIMIT, queryNameComparator,
new FastqRecordsForClusterCodec(readStructure.templates.length(),
readStructure.sampleBarcodes.length(), readStructure.molecularBarcode.length()),
FastqRecordsForCluster.class, bclQualityEvaluationStrategy, IGNORE_UNEXPECTED_BARCODES);
} else {
basecallsConverter = new IlluminaBasecallsConverter<>(BASECALLS_DIR, BARCODES_DIR, LANE, readStructure,
sampleBarcodeFastqWriterMap, demultiplex, Math.max(1, MAX_READS_IN_RAM_PER_TILE / readsPerCluster), TMP_DIR, NUM_PROCESSORS,
FORCE_GC, FIRST_TILE, TILE_LIMIT, queryNameComparator,
new FastqRecordsForClusterCodec(readStructure.templates.length(),
readStructure.sampleBarcodes.length(), readStructure.molecularBarcode.length()), FastqRecordsForCluster.class, bclQualityEvaluationStrategy,
this.APPLY_EAMSS_FILTER, INCLUDE_NON_PF_READS, IGNORE_UNEXPECTED_BARCODES);
}
basecallsConverter.setConverter(
new ClusterToFastqRecordsForClusterConverter(
basecallsConverter.getFactory().getOutputReadStructure()));
log.info("READ STRUCTURE IS " + readStructure.toString());
}
/**
* Assert that expectedCols are present
*
* @param actualCols The columns present in the MULTIPLEX_PARAMS file
* @param expectedCols The columns that are REQUIRED
*/
private void assertExpectedColumns(final Set actualCols, final Set expectedCols) {
final Set missingColumns = new HashSet<>(expectedCols);
missingColumns.removeAll(actualCols);
if (!missingColumns.isEmpty()) {
throw new PicardException(String.format(
"MULTIPLEX_PARAMS file %s is missing the following columns: %s.",
MULTIPLEX_PARAMS.getAbsolutePath(), StringUtil.join(", ", missingColumns
)));
}
}
/**
* For each line in the MULTIPLEX_PARAMS file create a FastqRecordsWriter and put it in the sampleBarcodeFastqWriterMap map,
* where the key to the map is the concatenation of all sampleBarcodes in order for the given line.
*/
private void populateWritersFromMultiplexParams() {
final TabbedTextFileWithHeaderParser libraryParamsParser = new TabbedTextFileWithHeaderParser(MULTIPLEX_PARAMS);
final Set expectedColumnLabels = CollectionUtil.makeSet("OUTPUT_PREFIX");
final List sampleBarcodeColumnLabels = new ArrayList<>();
for (int i = 1; i <= readStructure.sampleBarcodes.length(); i++) {
sampleBarcodeColumnLabels.add("BARCODE_" + i);
}
expectedColumnLabels.addAll(sampleBarcodeColumnLabels);
assertExpectedColumns(libraryParamsParser.columnLabels(), expectedColumnLabels);
for (final TabbedTextFileWithHeaderParser.Row row : libraryParamsParser) {
List sampleBarcodeValues = null;
if (!sampleBarcodeColumnLabels.isEmpty()) {
sampleBarcodeValues = new ArrayList<>();
for (final String sampleBarcodeLabel : sampleBarcodeColumnLabels) {
sampleBarcodeValues.add(row.getField(sampleBarcodeLabel));
}
}
final String key = (sampleBarcodeValues == null || sampleBarcodeValues.contains("N")) ? null : StringUtil.join("", sampleBarcodeValues);
if (sampleBarcodeFastqWriterMap.containsKey(key)) { //This will catch the case of having more than 1 line in a non-barcoded MULTIPLEX_PARAMS file
throw new PicardException("Row for barcode " + key + " appears more than once in MULTIPLEX_PARAMS file " +
MULTIPLEX_PARAMS);
}
final FastqRecordsWriter writer = buildWriter(new File(row.getField("OUTPUT_PREFIX")));
sampleBarcodeFastqWriterMap.put(key, writer);
}
if (sampleBarcodeFastqWriterMap.isEmpty()) {
throw new PicardException("MULTIPLEX_PARAMS file " + MULTIPLEX_PARAMS + " does have any data rows.");
}
libraryParamsParser.close();
}
/**
* @return FastqRecordsWriter that contains one or more FastqWriters (amount depends on read structure), all using
* outputPrefix to determine the filename(s).
*/
private FastqRecordsWriter buildWriter(final File outputPrefix) {
final File outputDir = outputPrefix.getAbsoluteFile().getParentFile();
IOUtil.assertDirectoryIsWritable(outputDir);
final String prefixString = outputPrefix.getName();
final String suffixString = COMPRESS_OUTPUTS ? "fastq.gz" : "fastq";
final FastqWriter[] templateWriters = new FastqWriter[readStructure.templates.length()];
final FastqWriter[] sampleBarcodeWriters = new FastqWriter[readStructure.sampleBarcodes.length()];
final FastqWriter[] molecularBarcodeWriters = new FastqWriter[readStructure.molecularBarcode.length()];
for (int i = 0; i < templateWriters.length; ++i) {
final String filename = String.format("%s.%d.%s", prefixString, i + 1, suffixString);
templateWriters[i] = fastqWriterFactory.newWriter(new File(outputDir, filename));
}
for (int i = 0; i < sampleBarcodeWriters.length; ++i) {
final String filename = String.format("%s.barcode_%d.%s", prefixString, i + 1, suffixString);
sampleBarcodeWriters[i] = fastqWriterFactory.newWriter(new File(outputDir, filename));
}
for (int i = 0; i < molecularBarcodeWriters.length; ++i) {
final String filename = String.format("%s.index_%d.%s", prefixString, i + 1, suffixString);
molecularBarcodeWriters[i] = fastqWriterFactory.newWriter(new File(outputDir, filename));
}
return new FastqRecordsWriter(templateWriters, sampleBarcodeWriters, molecularBarcodeWriters);
}
public static void main(final String[] args) {
new IlluminaBasecallsToFastq().instanceMainWithExit(args);
}
/**
* Container for various FastqWriters, one for each template read, one for each sample barcode read,
* and one for each molecular barcode read.
*/
private static final class FastqRecordsWriter implements BasecallsConverter.ConvertedClusterDataWriter {
final FastqWriter[] templateWriters;
final FastqWriter[] sampleBarcodeWriters;
final FastqWriter[] molecularBarcodeWriters;
/**
* @param templateWriters Writers for template reads in order, e,g. 0th element is for template read 1.
* @param sampleBarcodeWriters Writers for sample barcode reads in order, e,g. 0th element is for sample barcode read 1.
* @param molecularBarcodeWriters Writers for molecular barcode reads in order, e,g. 0th element is for molecualr barcode read 1.
*/
private FastqRecordsWriter(final FastqWriter[] templateWriters, final FastqWriter[] sampleBarcodeWriters, final FastqWriter[] molecularBarcodeWriters) {
this.templateWriters = templateWriters;
this.sampleBarcodeWriters = sampleBarcodeWriters;
this.molecularBarcodeWriters = molecularBarcodeWriters;
}
@Override
public void write(final FastqRecordsForCluster records) {
write(templateWriters, records.templateRecords);
write(sampleBarcodeWriters, records.sampleBarcodeRecords);
write(molecularBarcodeWriters, records.molecularBarcodeRecords);
}
private void write(final FastqWriter[] writers, final FastqRecord[] records) {
for (int i = 0; i < writers.length; ++i) {
writers[i].write(records[i]);
}
}
@Override
public void close() {
for (final FastqWriter writer : templateWriters) {
writer.close();
}
for (final FastqWriter writer : sampleBarcodeWriters) {
writer.close();
}
for (final FastqWriter writer : molecularBarcodeWriters) {
writer.close();
}
}
}
/**
* Contains the results of transforming one cluster into the record(s) to be written to output file(s).
*/
static class FastqRecordsForCluster {
// These are accessed directly by converter and writer rather than through getters and setters.
final FastqRecord[] templateRecords;
final FastqRecord[] sampleBarcodeRecords;
final FastqRecord[] molecularBarcodeRecords;
FastqRecordsForCluster(final int numTemplates, final int numSampleBarcodes, final int numMolecularBarcodes) {
templateRecords = new FastqRecord[numTemplates];
sampleBarcodeRecords = new FastqRecord[numSampleBarcodes];
molecularBarcodeRecords = new FastqRecord[numMolecularBarcodes];
}
}
/**
* Passed to IlluminaBaseCallsConverter to do the conversion from input format to output format.
*/
class ClusterToFastqRecordsForClusterConverter
implements IlluminaBasecallsConverter.ClusterDataConverter {
private final int[] templateIndices;
private final int[] sampleBarcodeIndicies;
private final int[] molecularBarcodeIndicies;
ClusterToFastqRecordsForClusterConverter(final ReadStructure outputReadStructure) {
this.templateIndices = outputReadStructure.templates.getIndices();
this.sampleBarcodeIndicies = outputReadStructure.sampleBarcodes.getIndices();
this.molecularBarcodeIndicies = outputReadStructure.molecularBarcode.getIndices();
}
@Override
public FastqRecordsForCluster convertClusterToOutputRecord(final ClusterData cluster) {
final FastqRecordsForCluster ret = new FastqRecordsForCluster(readStructure.templates.length(), readStructure.sampleBarcodes.length(), readStructure.molecularBarcode.length());
final boolean appendTemplateNumberSuffix = ret.templateRecords.length > 1;
final boolean appendMolecularBarcodeNumber = ret.molecularBarcodeRecords.length > 1;
makeFastqRecords(ret.templateRecords, templateIndices, cluster, appendTemplateNumberSuffix);
makeFastqRecords(ret.sampleBarcodeRecords, sampleBarcodeIndicies, cluster, false);
makeFastqRecords(ret.molecularBarcodeRecords, molecularBarcodeIndicies, cluster, appendMolecularBarcodeNumber);
return ret;
}
private void makeFastqRecords(final FastqRecord[] recs, final int[] indices,
final ClusterData cluster, final boolean appendReadNumberSuffix) {
for (short i = 0; i < indices.length; ++i) {
final ReadData readData = cluster.getRead(indices[i]);
final String readBases = StringUtil.bytesToString(readData.getBases()).replace('.', 'N');
final String readName = readNameEncoder.generateReadName(cluster, appendReadNumberSuffix ? i + 1 : null);
recs[i] = new FastqRecord(
readName,
readBases,
null,
SAMUtils.phredToFastq(readData.getQualities())
);
}
}
}
/**
* Codec passed to IlluminaBasecallsConverter for use in SortingCollections of output records.
*/
static class FastqRecordsForClusterCodec implements SortingCollection.Codec {
private final int numTemplates;
private final int numSampleBarcodes;
private final int numMolecularBarcodes;
private BasicFastqWriter writer = null;
private FastqReader reader = null;
FastqRecordsForClusterCodec(final int numTemplates, final int numSampleBarcodes, final int numMolecularBarcodes) {
this.numTemplates = numTemplates;
this.numSampleBarcodes = numSampleBarcodes;
this.numMolecularBarcodes = numMolecularBarcodes;
}
@Override
public void setOutputStream(final OutputStream os) {
writer = new BasicFastqWriter(new PrintStream(os));
}
@Override
public void setInputStream(final InputStream is) {
reader = new FastqReader(new BufferedReader(new InputStreamReader(is)));
}
//TODO: add tests to encode and decode
@Override
public void encode(final FastqRecordsForCluster val) {
if (numTemplates != val.templateRecords.length) throw new IllegalStateException();
if (numSampleBarcodes != val.sampleBarcodeRecords.length) throw new IllegalStateException();
encodeArray(val.templateRecords);
encodeArray(val.sampleBarcodeRecords);
encodeArray(val.molecularBarcodeRecords);
writer.flush();
}
private void encodeArray(final FastqRecord[] recs) {
for (final FastqRecord rec : recs) {
writer.write(rec);
}
}
@Override
public FastqRecordsForCluster decode() {
if (!reader.hasNext()) return null;
final FastqRecordsForCluster ret = new FastqRecordsForCluster(numTemplates, numSampleBarcodes, numMolecularBarcodes);
decodeArray(ret.templateRecords);
decodeArray(ret.sampleBarcodeRecords);
decodeArray(ret.molecularBarcodeRecords);
return ret;
}
private void decodeArray(final FastqRecord[] recs) {
for (int i = 0; i < recs.length; ++i) {
recs[i] = reader.next();
}
}
@Override
public SortingCollection.Codec clone() {
return new FastqRecordsForClusterCodec(numTemplates, numSampleBarcodes, numMolecularBarcodes);
}
}
}
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