@Test(dataProvider = "testGetSamReadNameFromFastqHeader") public void testGetSamReadNameFromFastqHeader(final String fastqHeader, final String expectedSamReadName) { Assert.assertEquals(SequenceUtil.getSamReadNameFromFastqHeader(fastqHeader), expectedSamReadName); }
/** * Converts a {@link FastqRecord} into a simple unmapped {@link SAMRecord}. * * <p>This method allows to pass a {@link BiConsumer} to add the information from the record in * a customizable manner. * * @param record object to encode. * @param header header for the returned object. * @param custom function to customize encoding. Note that default information might be overriden. */ public static SAMRecord asSAMRecord(final FastqRecord record, final SAMFileHeader header, final BiConsumer<FastqRecord, SAMRecord> custom) { // construct the SAMRecord and set the unmapped flag final SAMRecord samRecord = new SAMRecord(header); samRecord.setReadUnmappedFlag(true); // get the read name from the FastqRecord correctly formatted final String readName = SequenceUtil.getSamReadNameFromFastqHeader(record.getReadName()); // set the basic information from the FastqRecord samRecord.setReadName(readName); samRecord.setReadBases(record.getReadBases()); samRecord.setBaseQualities(record.getBaseQualities()); custom.accept(record, samRecord); return samRecord; }
/** * Converts a {@link FastqRecord} into a simple unmapped {@link SAMRecord}. * * <p>This method allows to pass a {@link BiConsumer} to add the information from the record in * a customizable manner. * * @param record object to encode. * @param header header for the returned object. * @param custom function to customize encoding. Note that default information might be overriden. */ public static SAMRecord asSAMRecord(final FastqRecord record, final SAMFileHeader header, final BiConsumer<FastqRecord, SAMRecord> custom) { // construct the SAMRecord and set the unmapped flag final SAMRecord samRecord = new SAMRecord(header); samRecord.setReadUnmappedFlag(true); // get the read name from the FastqRecord correctly formatted final String readName = SequenceUtil.getSamReadNameFromFastqHeader(record.getReadName()); // set the basic information from the FastqRecord samRecord.setReadName(readName); samRecord.setReadBases(record.getReadBases()); samRecord.setBaseQualities(record.getBaseQualities()); custom.accept(record, samRecord); return samRecord; }
/** Creates a simple SAM file from a single fastq file. */ protected int doUnpaired(final FastqReader freader, final SAMFileWriter writer) { int readCount = 0; final ProgressLogger progress = new ProgressLogger(LOG); for ( ; freader.hasNext() ; readCount++) { final FastqRecord frec = freader.next(); final SAMRecord srec = createSamRecord(writer.getFileHeader(), SequenceUtil.getSamReadNameFromFastqHeader(frec.getReadHeader()) , frec, false) ; srec.setReadPairedFlag(false); writer.addAlignment(srec); progress.record(srec); } return readCount; }
/** Creates a simple SAM file from a single fastq file. */ protected int doUnpaired(final FastqReader freader, final SAMFileWriter writer) { int readCount = 0; final ProgressLogger progress = new ProgressLogger(LOG); for ( ; freader.hasNext() ; readCount++) { final FastqRecord frec = freader.next(); final SAMRecord srec = createSamRecord(writer.getFileHeader(), SequenceUtil.getSamReadNameFromFastqHeader(frec.getReadHeader()) , frec, false) ; srec.setReadPairedFlag(false); writer.addAlignment(srec); progress.record(srec); } return readCount; }
/** More complicated method that takes two fastq files and builds pairing information in the SAM. */ protected int doPaired(final FastqReader freader1, final FastqReader freader2, final SAMFileWriter writer) { int readCount = 0; final ProgressLogger progress = new ProgressLogger(LOG); for ( ; freader1.hasNext() && freader2.hasNext() ; readCount++) { final FastqRecord frec1 = freader1.next(); final FastqRecord frec2 = freader2.next(); final String frec1Name = SequenceUtil.getSamReadNameFromFastqHeader(frec1.getReadHeader()); final String frec2Name = SequenceUtil.getSamReadNameFromFastqHeader(frec2.getReadHeader()); final String baseName = getBaseName(frec1Name, frec2Name, freader1, freader2); final SAMRecord srec1 = createSamRecord(writer.getFileHeader(), baseName, frec1, true) ; srec1.setFirstOfPairFlag(true); srec1.setSecondOfPairFlag(false); writer.addAlignment(srec1); progress.record(srec1); final SAMRecord srec2 = createSamRecord(writer.getFileHeader(), baseName, frec2, true) ; srec2.setFirstOfPairFlag(false); srec2.setSecondOfPairFlag(true); writer.addAlignment(srec2); progress.record(srec2); } if (freader1.hasNext() || freader2.hasNext()) { throw new PicardException("Input paired fastq files must be the same length"); } return readCount; }
/** More complicated method that takes two fastq files and builds pairing information in the SAM. */ protected int doPaired(final FastqReader freader1, final FastqReader freader2, final SAMFileWriter writer) { int readCount = 0; final ProgressLogger progress = new ProgressLogger(LOG); for ( ; freader1.hasNext() && freader2.hasNext() ; readCount++) { final FastqRecord frec1 = freader1.next(); final FastqRecord frec2 = freader2.next(); final String frec1Name = SequenceUtil.getSamReadNameFromFastqHeader(frec1.getReadHeader()); final String frec2Name = SequenceUtil.getSamReadNameFromFastqHeader(frec2.getReadHeader()); final String baseName = getBaseName(frec1Name, frec2Name, freader1, freader2); final SAMRecord srec1 = createSamRecord(writer.getFileHeader(), baseName, frec1, true) ; srec1.setFirstOfPairFlag(true); srec1.setSecondOfPairFlag(false); writer.addAlignment(srec1); progress.record(srec1); final SAMRecord srec2 = createSamRecord(writer.getFileHeader(), baseName, frec2, true) ; srec2.setFirstOfPairFlag(false); srec2.setSecondOfPairFlag(true); writer.addAlignment(srec2); progress.record(srec2); } if (freader1.hasNext() || freader2.hasNext()) { throw new PicardException("Input paired fastq files must be the same length"); } return readCount; }