Package htsjdk.samtools.fastq

Examples of htsjdk.samtools.fastq.FastqRecord

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        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, false, OUTPUT);

        int readCount = 0;
        final ProgressLogger progress = new ProgressLogger(LOG);
        for ( ; freader.hasNext()  ; readCount++) {
            final FastqRecord frec = freader.next();
            final SAMRecord srec = createSamRecord(header, getReadName(frec.getReadHeader(), false) , frec, false) ;
            srec.setReadPairedFlag(false);
            writer.addAlignment(srec);
            progress.record(srec);
        }
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        final SAMFileWriter writer = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(header, false, OUTPUT);

        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 = getReadName(frec1.getReadHeader(), true);
            final String frec2Name = getReadName(frec2.getReadHeader(), true);
            final String baseName = getBaseName(frec1Name, frec2Name, freader1, freader2);

            final SAMRecord srec1 = createSamRecord(header, baseName, frec1, true) ;
            srec1.setFirstOfPairFlag(true);
            srec1.setSecondOfPairFlag(false);
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                                      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())
                );
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        if (maxBasesToWrite != null && maxBasesToWrite < readString.length()) {
            readString = readString.substring(0, maxBasesToWrite);
            baseQualities = baseQualities.substring(0, maxBasesToWrite);
        }

        writer.write(new FastqRecord(seqHeader, readString, "", baseQualities));

    }
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                "SECOND_END_FASTQ=" + f2.getAbsolutePath(),
            });
        }

        Iterator<FastqRecord> it = new FastqReader(f1).iterator();
        FastqRecord first = it.next();
        Assert.assertEquals(first.getReadString(), bases1_1, testName);
        Assert.assertEquals(first.getBaseQualityString(), quals1_1, testName);
        FastqRecord second = it.next();
        Assert.assertEquals(second.getReadString(), bases1_2, testName);
        Assert.assertEquals(second.getBaseQualityString(), quals1_2, testName);
        it = new FastqReader(f2).iterator();
        first = it.next();
        Assert.assertEquals(first.getReadString(), bases2_1, testName);
        Assert.assertEquals(first.getBaseQualityString(), quals2_1, testName);
        second = it.next();
        Assert.assertEquals(second.getReadString(), bases2_2, testName);
        Assert.assertEquals(second.getBaseQualityString(), quals2_2, testName);
    }
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    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 ;
    }
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Related Classes of htsjdk.samtools.fastq.FastqRecord

  • picard.illumina.IlluminaBasecallsToFastq$ClusterToFastqRecordsForClusterConverter
  • picard.sam.FastqToSam
  • picard.sam.SamToFastq
  • picard.sam.SamToFastqTest
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