Examples of htsjdk.samtools.fastq.FastqReader

htsjdk.samtools.fastq.FastqReader

    }


    /* Simply invokes the right method for unpaired or paired data. */
    protected int doWork() {
            final QualityEncodingDetector detector = new QualityEncodingDetector();
            final FastqReader reader = new FastqReader(FASTQ,ALLOW_AND_IGNORE_EMPTY_LINES);
            if (FASTQ2 == null) {
                detector.add(QualityEncodingDetector.DEFAULT_MAX_RECORDS_TO_ITERATE, reader);
            } else {
                final FastqReader reader2 = new FastqReader(FASTQ2,ALLOW_AND_IGNORE_EMPTY_LINES);
                detector.add(QualityEncodingDetector.DEFAULT_MAX_RECORDS_TO_ITERATE, reader, reader2);
                reader2.close();
            }
            reader.close();
            
            QUALITY_FORMAT = detector.generateBestGuess(QualityEncodingDetector.FileContext.FASTQ, QUALITY_FORMAT);
            if (detector.isDeterminationAmbiguous())

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    /** Creates a simple SAM file from a single fastq file. */
    protected int doUnpaired() {
        IOUtil.assertFileIsReadable(FASTQ);
        IOUtil.assertFileIsWritable(OUTPUT);
        
        final FastqReader freader = new FastqReader(FASTQ,ALLOW_AND_IGNORE_EMPTY_LINES);
        final SAMFileHeader header = createFileHeader();
        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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    protected int doPaired() {
        IOUtil.assertFileIsReadable(FASTQ);
        IOUtil.assertFileIsReadable(FASTQ2);
        IOUtil.assertFileIsWritable(OUTPUT);
        
        final FastqReader freader1 = new FastqReader(FASTQ,ALLOW_AND_IGNORE_EMPTY_LINES);
        final FastqReader freader2 = new FastqReader(FASTQ2,ALLOW_AND_IGNORE_EMPTY_LINES);
        final SAMFileHeader header = createFileHeader() ;
        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);
            writer.addAlignment(srec1);
            progress.record(srec1);


            final SAMRecord srec2 = createSamRecord(header, baseName, frec2, true) ;
            srec2.setFirstOfPairFlag(false);
            srec2.setSecondOfPairFlag(true);
            writer.addAlignment(srec2);
            progress.record(srec2);
        }


        writer.close();


        if (freader1.hasNext() || freader2.hasNext()) {
            throw new PicardException("Input paired fastq files must be the same length");
        }


        return readCount;
    }

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            writer = new BasicFastqWriter(new PrintStream(os));
        }


        @Override
        public void setInputStream(final InputStream is) {
            reader = new FastqReader(new BufferedReader(new InputStreamReader(is)));
        }

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    private static FastqReader freader2 ;


    @BeforeClass
    public static void beforeClass() throws IOException {
        final File dummyFile = newTempFile("dummy");
        freader1 = new FastqReader(dummyFile);
        freader2 = new FastqReader(dummyFile);
    }

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                "FASTQ="            + f1.getAbsolutePath(),
                "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);

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              "READ1_MAX_BASES_TO_WRITE=" + read1MaxBases,
              "READ2_TRIM=" + read2Trim,
              "READ2_MAX_BASES_TO_WRITE=" + read2MaxBases
        });


        for (final FastqRecord first : new FastqReader(pair1File)) {
            Assert.assertEquals(first.getReadString().length(), expectedRead1Length, "Incorrect read length");
            Assert.assertEquals(first.getBaseQualityString().length(), expectedRead1Length, "Incorrect quality string length");
        }
        for (final FastqRecord second : new FastqReader(pair2File)) {
            Assert.assertEquals(second.getReadString().length(), expectedRead2Length, "Incorrect read length");
            Assert.assertEquals(second.getBaseQualityString().length(), expectedRead2Length, "Incorrect quality string length");
        }
    }

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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.FastqReader

picard.illumina.IlluminaBasecallsToFastq$FastqRecordsForClusterCodec

picard.sam.FastqToSam

picard.sam.FastqToSamTest

picard.sam.SamToFastqTest

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