Examples of SAMReadGroupRecord

Examples of htsjdk.samtools.SAMReadGroupRecord

48
49
50
51
52
53
54
55
56
57
58
59
        Object pu_attr = samRecord.getAttribute("PU");

        if ( pu_attr == null ) {
            // no platform unit in the record, go get from read group
            SAMReadGroupRecord rgr = samRecord.getReadGroup();
            if ( rgr == null ) throw new UserException.MalformedBAM(samRecord, "Read " + samRecord.getReadName() +" has NO associated read group record");
            pu_attr = rgr.getAttribute("PU") ;
        }
        if ( pu_attr == null ) return false; // could not get PU, forget about the filtering...
        return blackListedLanes.contains((String)pu_attr);
    }
View Full Code Here

Examples of htsjdk.samtools.SAMReadGroupRecord

53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
    public boolean filterOut(SAMRecord samRecord) {
        for (Entry<String, Collection<String>> filterEntry : filterEntries) {
            String attributeType = filterEntry.getKey();

            SAMReadGroupRecord samReadGroupRecord = samRecord.getReadGroup();
            if (samReadGroupRecord != null) {
                Object attribute;
                if ("ID".equals(attributeType) || "RG".equals(attributeType))
                    attribute = samReadGroupRecord.getId();
                else
                    attribute = samReadGroupRecord.getAttribute(attributeType);
                if (attribute != null && filterEntry.getValue().contains(attribute))
                    return true;
            }
        }
View Full Code Here

Examples of htsjdk.samtools.SAMReadGroupRecord

41
42
43
44
45
46
47
48
public class LibraryReadFilter extends ReadFilter {
    @Argument(fullName = "library", shortName = "library", doc="The name of the library to keep, filtering out all others", required=true)
    private String LIBRARY_TO_KEEP = null;

    public boolean filterOut( final SAMRecord read ) {
        final SAMReadGroupRecord readGroup = read.getReadGroup();
        return ( readGroup == null || readGroup.getLibrary() == null || !readGroup.getLibrary().equals( LIBRARY_TO_KEEP ) );
    }
View Full Code Here

Examples of htsjdk.samtools.SAMReadGroupRecord

37
38
39
40
41
42
43
44
public class SampleFilter extends ReadFilter {
    @Argument(fullName = "sample_to_keep", shortName = "goodSM", doc="The name of the sample(s) to keep, filtering out all others", required=true)
    private Set SAMPLES_TO_KEEP = null;

    public boolean filterOut( final SAMRecord read ) {
        final SAMReadGroupRecord readGroup = read.getReadGroup();
        return !( readGroup != null && SAMPLES_TO_KEEP.contains(readGroup.getSample()) );
    }
View Full Code Here

Examples of htsjdk.samtools.SAMReadGroupRecord

59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
    /**
     * Ensure that basic read group splitting works.
     */
    @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());
        GATKSAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
        read3.setAttribute("RG",readGroupOne.getId());
        GATKSAMRecord read4 = ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,10);
        read4.setAttribute("RG",readGroupTwo.getId());
        GATKSAMRecord read5 = ArtificialSAMUtils.createArtificialRead(header,"read5",0,1,10);
        read5.setAttribute("RG",readGroupTwo.getId());
        GATKSAMRecord read6 = ArtificialSAMUtils.createArtificialRead(header,"read6",0,1,10);
        read6.setAttribute("RG",readGroupOne.getId());
        GATKSAMRecord read7 = ArtificialSAMUtils.createArtificialRead(header,"read7",0,1,10);
        read7.setAttribute("RG",readGroupOne.getId());

View Full Code Here

Examples of htsjdk.samtools.SAMReadGroupRecord

130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
    /**
     * Ensure that splitting read groups still works when dealing with a sample-split pileup.
     */
    @Test
    public void testSplitBySample() {
        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());
        GATKSAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
        read3.setAttribute("RG",readGroupOne.getId());
        GATKSAMRecord read4 = ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,10);
        read4.setAttribute("RG",readGroupTwo.getId());

        ReadBackedPileupImpl sample1Pileup = new ReadBackedPileupImpl(null,
                                                                      Arrays.asList(read1,read3),
                                                                      Arrays.asList(1,1));
        ReadBackedPileupImpl sample2Pileup = new ReadBackedPileupImpl(null,
                                                                      Arrays.asList(read2,read4),
                                                                      Arrays.asList(1,1));
        Map<String,ReadBackedPileupImpl> sampleToPileupMap = new HashMap<String,ReadBackedPileupImpl>();
        sampleToPileupMap.put(readGroupOne.getSample(),sample1Pileup);
        sampleToPileupMap.put(readGroupTwo.getSample(),sample2Pileup);

        ReadBackedPileup compositePileup = new ReadBackedPileupImpl(null,sampleToPileupMap);

        ReadBackedPileup rg1Pileup = compositePileup.getPileupForReadGroup("rg1");
        List<GATKSAMRecord> rg1Reads = rg1Pileup.getReads();
View Full Code Here

Examples of htsjdk.samtools.SAMReadGroupRecord

180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
    @Test
    public void testGetPileupForSample() {
        String sample1 = "sample1";
        String sample2 = "sample2";

        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());

        Map<String,ReadBackedPileupImpl> sampleToPileupMap = new HashMap<String,ReadBackedPileupImpl>();
        sampleToPileupMap.put(sample1,new ReadBackedPileupImpl(null,Collections.singletonList(read1),0));
        sampleToPileupMap.put(sample2,new ReadBackedPileupImpl(null,Collections.singletonList(read2),0));
View Full Code Here

Examples of htsjdk.samtools.SAMReadGroupRecord

70
71
72
73
74
75
76
77
78
79
80
81
    @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!
View Full Code Here

Examples of htsjdk.samtools.SAMReadGroupRecord

129
130
131
132
133
134
135
136
137
138
139
    @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

Examples of htsjdk.samtools.SAMReadGroupRecord

136
137
138
139
140
141
142
143
144
145
146
147
148
     */
    @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
TOP
Copyright © 2018 www.massapi.com. 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.