Java FastqReader.hasNext方法代码示例

import htsjdk.samtools.fastq.FastqReader; //导入方法依赖的package包/类
/** 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;
}
 

import htsjdk.samtools.fastq.FastqReader; //导入方法依赖的package包/类
/** 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;
}
 

import htsjdk.samtools.fastq.FastqReader; //导入方法依赖的package包/类
private Set<String> createFastqReadHeaderSet(final File file) {
    final Set<String> set = new HashSet<String>();
    final FastqReader freader = new FastqReader(file);
    while (freader.hasNext()) {
        final FastqRecord frec = freader.next();
        set.add(frec.getReadHeader());
    }
    return set ;
}
 

import htsjdk.samtools.fastq.FastqReader; //导入方法依赖的package包/类
/**
 *
 * @param fastqReader a FastqReader object
 * @param out - the output fastq reads
 * @param mappedReads a HashSet of mapped reads
 */
public static void writeRecords(FastqReader fastqReader, FastqWriter out, HashSet<String> mappedReads) {
    while (fastqReader.hasNext()) {
        FastqRecord record = fastqReader.next();
        String readName = record.getReadHeader();
        int hashIndex = readName.indexOf(" ");
        readName = readName.substring(0, hashIndex);
        if (mappedReads.contains(readName)) {
            out.write(record);
        }
    }
    out.close();
}
 

import htsjdk.samtools.fastq.FastqReader; //导入方法依赖的package包/类
/**
 * Extract paired-end fastq sequences from a list of sequence names
 *
 * @param list a HashSet of read names
 * @param fastqLeft all left-handed reads
 * @param fastqRight all right-handed reads
 * @param fastqLeftOut the left-handed reads in the list
 * @param fastqRightOut the right-handed reads in the list
 * @throws FileNotFoundException
 * @throws IOException
 */
public void getPairedFastqSeqsFromHashSet(HashSet list, File fastqLeft, File fastqRight,
        File fastqLeftOut, File fastqRightOut) throws FileNotFoundException, IOException {
    final FastqReader readerLeft = new FastqReader(fastqLeft);
    final FastqReader readerRight = new FastqReader(fastqRight);

    FastqWriterFactory writer = new FastqWriterFactory();
    FastqWriter outLeft = writer.newWriter(fastqLeftOut);
    FastqWriter outRight = writer.newWriter(fastqRightOut);
    int recordsfound = 0;

    while (readerLeft.hasNext()) {
        FastqRecord recordLeft = readerLeft.next();
        FastqRecord recordRight = readerRight.next();
        String leftRead = recordLeft.getReadHeader();

        int hashIndex = leftRead.indexOf(" ");
        leftRead = leftRead.substring(0, hashIndex);
        if (list.contains(leftRead)) {
            recordsfound++;
            outLeft.write(recordLeft);
            outRight.write(recordRight);
        }
    }
    System.out.println("Processed " + list.size() + " , found " + recordsfound);

}
 

import htsjdk.samtools.fastq.FastqReader; //导入方法依赖的package包/类
/**
 * Turns a fastq file into fasta format
 *
 * @param fastqIn the fastq intput file
 * @param fastaOut the fasta output file
 * @throws IOException
 */
public void fastqToFastaFile(File fastqIn, File fastaOut) throws IOException {
    final FastqReader reader = new FastqReader(fastqIn);
    Writer out = new BufferedWriter(new FileWriter(fastaOut));
    while (reader.hasNext()) {
        FastqRecord record = reader.next();
        out.write(fastqToFastaSeq(record).toString());
    }
    out.close();
}