Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileHeader

350
351
352
353
354
355
356
357
358
359
360
361
    // -------------------------------------------------------------------------------------

    @Test(enabled=true)
    public void testDistanceAcrossContigs() {
        final int chrSize = 1000;
        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(10, 0, chrSize);
        GenomeLocParser parser = new GenomeLocParser(header.getSequenceDictionary());
        GenomeLoc loc1 = parser.createGenomeLoc("chr3", 500);  // to check regular case
        GenomeLoc loc2 = parser.createGenomeLoc("chr7", 200);  // to check regular case
        GenomeLoc loc3 = parser.createGenomeLoc("chr0", 1);    // to check corner case
        GenomeLoc loc4 = parser.createGenomeLoc("chr9", 1000);// to check corner case
        GenomeLoc loc5 = parser.createGenomeLoc("chr7", 500);  // to make sure it does the right thing when in the same chromosome
View Full Code Here
62
63
64
65
66
67
68
69
70
71
72
73
74
    @Test
    public void testSplitByReadGroup() {
        SAMReadGroupRecord readGroupOne = new SAMReadGroupRecord("rg1");
        SAMReadGroupRecord readGroupTwo = new SAMReadGroupRecord("rg2");

        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
        header.addReadGroup(readGroupOne);
        header.addReadGroup(readGroupTwo);

        GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
        read1.setAttribute("RG",readGroupOne.getId());
        GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
        read2.setAttribute("RG",readGroupTwo.getId());
View Full Code Here
104
105
106
107
108
109
110
111
112
113
114
    /**
     * Ensure that splitting read groups still works when dealing with null read groups.
     */
    @Test
    public void testSplitByNullReadGroups() {
        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);

        GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
        GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
        GATKSAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);

View Full Code Here
135
136
137
138
139
140
141
142
143
144
145
146
147
        SAMReadGroupRecord readGroupOne = new SAMReadGroupRecord("rg1");
        readGroupOne.setSample("sample1");
        SAMReadGroupRecord readGroupTwo = new SAMReadGroupRecord("rg2");
        readGroupTwo.setSample("sample2");

        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
        header.addReadGroup(readGroupOne);
        header.addReadGroup(readGroupTwo);

        GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
        read1.setAttribute("RG",readGroupOne.getId());
        GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
        read2.setAttribute("RG",readGroupTwo.getId());
View Full Code Here
185
186
187
188
189
190
191
192
193
194
195
196
197
        SAMReadGroupRecord readGroupOne = new SAMReadGroupRecord("rg1");
        readGroupOne.setSample(sample1);
        SAMReadGroupRecord readGroupTwo = new SAMReadGroupRecord("rg2");
        readGroupTwo.setSample(sample2);

        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
        header.addReadGroup(readGroupOne);
        header.addReadGroup(readGroupTwo);

        GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
        read1.setAttribute("RG",readGroupOne.getId());
        GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
        read2.setAttribute("RG",readGroupTwo.getId());
View Full Code Here
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
        }
    }

    @DataProvider(name = "ArtificialSingleSampleReadStreamTestDataProvider")
    public Object[][] createArtificialSingleSampleReadStreamTests() {
        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(3, 1, 10000);
        String readGroupID = "testReadGroup";
        SAMReadGroupRecord readGroup = new SAMReadGroupRecord(readGroupID);
        readGroup.setSample("testSample");
        header.addReadGroup(readGroup);

        GenomeAnalysisEngine.resetRandomGenerator();

        // brute force testing!
        for ( int numContigs = 0; numContigs <= 2; numContigs++ ) {
View Full Code Here
127
128
129
130
131
132
133
134
135
136
137
138
139
        test.run();
    }

    @DataProvider(name = "ArtificialSingleSampleReadStreamInvalidArgumentsTestDataProvider")
    public Object[][] createInvalidArgumentsTests() {
        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(3, 1, 10000);
        String readGroupID = "testReadGroup";
        header.addReadGroup(new SAMReadGroupRecord(readGroupID));

        return new Object[][] {
            {"testNullHeader", null, readGroupID, 1, 1, 1, 2, 1, 2, 1, 2, 0},
            {"testNullReadGroup", header, null, 1, 1, 1, 2, 1, 2, 1, 2, 0},
            {"testInvalidReadGroup", header, "foo", 1, 1, 1, 2, 1, 2, 1, 2, 0},
View Full Code Here
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
    /**
     * A unit test that creates an artificial read for testing some code that uses reads
     */
    @Test(dataProvider = "TestMappings")
    public void testPLFromReadWithRG(final String plField, final NGSPlatform expected) {
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final String rgID = "ID";
        final SAMReadGroupRecord rg = new SAMReadGroupRecord(rgID);
        if ( plField != null )
            rg.setPlatform(plField);
        header.addReadGroup(rg);
        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 10);
        read.setAttribute("RG", rgID);
        Assert.assertEquals(NGSPlatform.fromRead(read), expected);
    }
View Full Code Here
147
148
149
150
151
152
153
154
155
156
157
158
159
        Assert.assertEquals(NGSPlatform.fromRead(read), expected);
    }

    @Test()
    public void testPLFromReadWithRGButNoPL() {
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final String rgID = "ID";
        final SAMReadGroupRecord rg = new SAMReadGroupRecord(rgID);
        header.addReadGroup(rg);
        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 10);
        read.setAttribute("RG", rgID);
        Assert.assertEquals(NGSPlatform.fromRead(read), NGSPlatform.UNKNOWN);
    }
View Full Code Here
158
159
160
161
162
163
164
165
166
        Assert.assertEquals(NGSPlatform.fromRead(read), NGSPlatform.UNKNOWN);
    }

    @Test
    public void testReadWithoutRG() {
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 10);
        Assert.assertEquals(NGSPlatform.fromRead(read), NGSPlatform.UNKNOWN);
    }
View Full Code Here
TOP

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
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.