Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileHeader

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                    getClass().getSimpleName(), targetCoverage, numStacks, stackSizes, expectedStackSizes, multipleContigs));
        }

        public Collection<SAMRecord> createReads() {
            Collection<SAMRecord> reads = new ArrayList<SAMRecord>();
            SAMFileHeader header = multipleContigs ?
                                   ArtificialSAMUtils.createArtificialSamHeader(2, 1, 1000000) :
                                   ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000);

            int refIndex = 0;
            int alignmentStart = 1;
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            setName(String.format("%s: targetCoverage=%d numSamples=%d minContigs=%d maxContigs=%d %s %s %s unmappedReadsFraction=%.2f unmappedReadsCount=%d verifySortedness=%b",
                    getClass().getSimpleName(), targetCoverage, numSamples, minContigs, maxContigs, streamDensity, streamStackDepth, streamStacksPerContig, unmappedReadsFraction, unmappedReadsCount, verifySortedness));
        }

        private SAMFileHeader createHeader() {
            SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(maxContigs, 1, (streamDensity.maxDistanceBetweenStacks + MAX_READ_LENGTH) * streamStacksPerContig.maxStacksPerContig + 100000);
            List<String> readGroups = new ArrayList<String>(numSamples);
            List<String> sampleNames = new ArrayList<String>(numSamples);

            for ( int i = 0; i < numSamples; i++ ) {
                readGroups.add("ReadGroup" + i);
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        }

        public Collection<SAMRecord> createReads() {
            Collection<SAMRecord> reads = new ArrayList<SAMRecord>(totalReads);

            SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000);
            reads.addAll(ArtificialSAMUtils.createStackOfIdenticalArtificialReads(totalReads, header, "foo", 0, 1, 100));

            return reads;
        }
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        }

        public Collection<SAMRecord> createReads() {
            Collection<SAMRecord> reads = new ArrayList<SAMRecord>(totalReads);

            SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000);
            reads.addAll(ArtificialSAMUtils.createStackOfIdenticalArtificialReads(totalReads, header, "foo", 0, 1, 100));

            return reads;
        }
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    @DataProvider(name = "BiasedDownsamplingTest")
    public Object[][] makeBiasedDownsamplingTest() {
        final List<Object[]> tests = new LinkedList<Object[]>();

        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);

        for ( final int originalCount : Arrays.asList(1, 2, 10, 1000) ) {
            for ( final int toRemove : Arrays.asList(0, 1, 2, 10, 1000) ) {
                if ( toRemove <= originalCount )
                    tests.add(new Object[]{header, originalCount, toRemove});
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        }
    }

    @DataProvider(name = "DownsamplingReadsIteratorTestDataProvider")
    public Object[][] createDownsamplingReadsIteratorTests() {
        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(5, 1, 10000);
        String readGroupID = "testReadGroup";
        SAMReadGroupRecord readGroup = new SAMReadGroupRecord(readGroupID);
        readGroup.setSample("testSample");
        header.addReadGroup(readGroup);

        // Values that don't vary across tests
        int targetCoverage = 10;
        int minReadLength = 50;
        int maxReadLength = 100;
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        SampleDB db = builder.getFinalSampleDB();
        Assert.assertEquals(testPEDSamplesAsSet, db.getSamples());
    }

    private static final void addSAMHeader() {
        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10);
        ArtificialSAMUtils.createEnumeratedReadGroups(header, Arrays.asList("1", "2", "3"),
                Arrays.asList("kid", "mom", "dad"));
        builder.addSamplesFromSAMHeader(header);
    }
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    public void init() {
        SAMSequenceDictionary sequenceDictionary = new SAMSequenceDictionary();
        sequenceDictionary.addSequence(new SAMSequenceRecord("1",500));
        sequenceDictionary.addSequence(new SAMSequenceRecord("2",500));

        samFileHeader = new SAMFileHeader();
        samFileHeader.setSequenceDictionary(sequenceDictionary);
    }
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    private GenomeLocParser genomeLocParser;

    @BeforeClass
    public void init() throws FileNotFoundException {
        // sequence
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 100);
        genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
    }
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    }

    @DataProvider(name = "ActiveRegionReads")
    public Object[][] makeActiveRegionReads() {
        List<Object[]> tests = new ArrayList<Object[]>();
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        for ( final int start : Arrays.asList(1, 10, 100, contigLength - 10, contigLength - 1) ) {
            for ( final int readStartOffset : Arrays.asList(-100, -10, 0, 10, 100) ) {
                for ( final int readSize : Arrays.asList(10, 100, 1000) ) {
                    final GenomeLoc loc = genomeLocParser.createGenomeLocOnContig(contig, start, start + 10);
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Related Classes of htsjdk.samtools.SAMFileHeader

  • org.broad.igv.sam.PicardAlignment
  • org.broad.igv.sam.reader.BAMFileReader
  • org.broad.igv.sam.reader.BAMHttpQueryReaderTest
  • org.broad.igv.sam.reader.BAMHttpReader
  • org.broad.igv.sam.reader.MergedAlignmentReader
  • org.broad.igv.sam.reader.SAMFileGroup
  • org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancerUnitTest
  • org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtilsUnitTest
  • org.broadinstitute.gatk.engine.downsampling.DownsamplingReadsIteratorUnitTest
  • org.broadinstitute.gatk.engine.downsampling.FractionalDownsamplerUnitTest$FractionalDownsamplerTest
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