Package htsjdk.samtools

Examples of htsjdk.samtools.SAMRecord

58
59
60
61
62
63
64
65
66
67
68
69
        samFileHeader.setSequenceDictionary(sequenceDictionary);
    }

    @Test
    public void testSortedReadsBasic() {
        SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(samFileHeader,"read1",getContig(0).getSequenceIndex(),1,10);
        SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(samFileHeader,"read2",getContig(0).getSequenceIndex(),2,10);
        List<SAMRecord> reads = Arrays.asList(read1,read2);

        VerifyingSamIterator iterator = new VerifyingSamIterator(GATKSAMIteratorAdapter.adapt(reads.iterator()));

        Assert.assertTrue(iterator.hasNext(),"Insufficient reads");
View Full Code Here
73
74
75
76
77
78
79
80
81
82
83
84
        Assert.assertFalse(iterator.hasNext(),"Too many reads in iterator");
    }

    @Test
    public void testSortedReadsAcrossContigs() {
        SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(samFileHeader,"read1",getContig(0).getSequenceIndex(),2,10);
        SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(samFileHeader,"read2",getContig(1).getSequenceIndex(),1,10);
        List<SAMRecord> reads = Arrays.asList(read1,read2);

        VerifyingSamIterator iterator = new VerifyingSamIterator(GATKSAMIteratorAdapter.adapt(reads.iterator()));

        Assert.assertTrue(iterator.hasNext(),"Insufficient reads");
View Full Code Here
88
89
90
91
92
93
94
95
96
97
98
99
        Assert.assertFalse(iterator.hasNext(),"Too many reads in iterator");
    }

    @Test(expectedExceptions=UserException.MissortedBAM.class)
    public void testImproperlySortedReads() {
        SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(samFileHeader,"read1",getContig(0).getSequenceIndex(),2,10);
        SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(samFileHeader,"read2",getContig(0).getSequenceIndex(),1,10);
        List<SAMRecord> reads = Arrays.asList(read1,read2);

        VerifyingSamIterator iterator = new VerifyingSamIterator(GATKSAMIteratorAdapter.adapt(reads.iterator()));

        Assert.assertTrue(iterator.hasNext(),"Insufficient reads");
View Full Code Here
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
        new ReadGroupBlackListFilter(badFilters);
    }

    @Test
    public void testFilterReadGroup() {
        SAMRecord filteredRecord = ArtificialSAMUtils.createArtificialRead(getHeader(), "readUno", 0, 1, 20);
        filteredRecord.setAttribute("RG", getReadGroupId(1));

        SAMRecord unfilteredRecord = ArtificialSAMUtils.createArtificialRead(getHeader(), "readDos", 0, 2, 20);
        unfilteredRecord.setAttribute("RG", getReadGroupId(2));

        List<String> filterList = new ArrayList<String>();
        filterList.add("RG:" + getReadGroupId(1));

        ReadGroupBlackListFilter filter = new ReadGroupBlackListFilter(filterList);
View Full Code Here
105
106
107
108
109
110
111
112
113
114
115
116
    }

    @Test(expectedExceptions=UserException.MalformedBAM.class)
    public void testInvalidAlignment() {
        // Create an invalid alignment state.
        SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(samFileHeader,"read1",getContig(0).getSequenceIndex(),1,10);
        SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(samFileHeader,"read1",getContig(0).getSequenceIndex(),2,10);
        read1.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
        List<SAMRecord> reads = Arrays.asList(read1,read2);

        VerifyingSamIterator iterator = new VerifyingSamIterator(GATKSAMIteratorAdapter.adapt(reads.iterator()));
View Full Code Here
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
        Assert.assertFalse(filter.filterOut(unfilteredRecord));
    }

    @Test
    public void testFilterPlatformUnit() {
        SAMRecord filteredRecord = ArtificialSAMUtils.createArtificialRead(getHeader(), "readUno", 0, 1, 20);
        filteredRecord.setAttribute("RG", getReadGroupId(1));

        SAMRecord unfilteredRecord = ArtificialSAMUtils.createArtificialRead(getHeader(), "readDos", 0, 2, 20);
        unfilteredRecord.setAttribute("RG", getReadGroupId(2));

        List<String> filterList = new ArrayList<String>();
        filterList.add("PU:" + getPlatformUnit(1));

        ReadGroupBlackListFilter filter = new ReadGroupBlackListFilter(filterList);
View Full Code Here
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
        List<SAMRecord> records = new ArrayList<SAMRecord>();
        int alignmentStart = 0;
        for (int x = 1; x <= getReadGroupCount(); x++) {
            SAMReadGroupRecord groupRecord = getHeader().getReadGroup(getReadGroupId(x));
            for (int y = 1; y <= recordsPerGroup; y++) {
                SAMRecord record = ArtificialSAMUtils.createArtificialRead(getHeader(), "readUno", 0, ++alignmentStart, 20);
                record.setAttribute("RG", groupRecord.getReadGroupId());
                records.add(record);
            }
        }

        List<String> filterList = new ArrayList<String>();
        filterList.add("RG:" + getReadGroupId(1));
        filterList.add("RG:" + getReadGroupId(3));

        ReadGroupBlackListFilter filter = new ReadGroupBlackListFilter(filterList);
        int filtered = 0;
        int unfiltered = 0;
        for (SAMRecord record : records) {
            String readGroupName = record.getReadGroup().getReadGroupId();
            if (filter.filterOut(record)) {
                if (!filterList.contains("RG:" + readGroupName))
                    Assert.fail("Read group " + readGroupName + " was filtered");
                filtered++;
            } else {
View Full Code Here
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
        List<SAMRecord> records = new ArrayList<SAMRecord>();
        int alignmentStart = 0;
        for (int x = 1; x <= getReadGroupCount(); x++) {
            SAMReadGroupRecord groupRecord = getHeader().getReadGroup(getReadGroupId(x));
            for (int y = 1; y <= recordsPerGroup; y++) {
                SAMRecord record = ArtificialSAMUtils.createArtificialRead(getHeader(), "readUno", 0, ++alignmentStart, 20);
                record.setAttribute("RG", groupRecord.getReadGroupId());
                records.add(record);
            }
        }

        List<String> filterList = new ArrayList<String>();
        filterList.add("PU:" + getPlatformUnit(1));

        ReadGroupBlackListFilter filter = new ReadGroupBlackListFilter(filterList);
        int filtered = 0;
        int unfiltered = 0;
        for (SAMRecord record : records) {
            String platformUnit = (String) record.getReadGroup().getAttribute("PU");
            if (filter.filterOut(record)) {
                if (!filterList.contains("PU:" + platformUnit))
                    Assert.fail("Platform unit " + platformUnit + " was filtered");
                filtered++;
            } else {
View Full Code Here
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
        List<SAMRecord> records = new ArrayList<SAMRecord>();
        int alignmentStart = 0;
        for (int x = 1; x <= getReadGroupCount(); x++) {
            SAMReadGroupRecord groupRecord = getHeader().getReadGroup(getReadGroupId(x));
            for (int y = 1; y <= recordsPerGroup; y++) {
                SAMRecord record = ArtificialSAMUtils.createArtificialRead(getHeader(), "readUno", 0, ++alignmentStart, 20);
                record.setAttribute("RG", groupRecord.getReadGroupId());
                records.add(record);
            }
        }

        List<String> filterList = new ArrayList<String>();
        filterList.add(privateTestDir + "readgroupblacklisttest.txt");

        ReadGroupBlackListFilter filter = new ReadGroupBlackListFilter(filterList);
        int filtered = 0;
        int unfiltered = 0;
        for (SAMRecord record : records) {
            String readGroup = record.getReadGroup().getReadGroupId();
            if (filter.filterOut(record)) {
                if (!("ReadGroup3".equals(readGroup) || "ReadGroup4".equals(readGroup)))
                    Assert.fail("Read group " + readGroup + " was filtered");
                filtered++;
            } else {
View Full Code Here
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
        List<SAMRecord> records = new ArrayList<SAMRecord>();
        int alignmentStart = 0;
        for (int x = 1; x <= getReadGroupCount(); x++) {
            SAMReadGroupRecord groupRecord = getHeader().getReadGroup(getReadGroupId(x));
            for (int y = 1; y <= recordsPerGroup; y++) {
                SAMRecord record = ArtificialSAMUtils.createArtificialRead(getHeader(), "readUno", 0, ++alignmentStart, 20);
                record.setAttribute("RG", groupRecord.getReadGroupId());
                records.add(record);
            }
        }

        List<String> filterList = new ArrayList<String>();
        filterList.add(privateTestDir + "readgroupblacklisttestlist.txt");

        ReadGroupBlackListFilter filter = new ReadGroupBlackListFilter(filterList);
        int filtered = 0;
        int unfiltered = 0;
        for (SAMRecord record : records) {
            String readGroup = record.getReadGroup().getReadGroupId();
            if (filter.filterOut(record)) {
                if (!("ReadGroup3".equals(readGroup) || "ReadGroup4".equals(readGroup)))
                    Assert.fail("Read group " + readGroup + " was filtered");
                filtered++;
            } else {
View Full Code Here
TOP

Related Classes of htsjdk.samtools.SAMRecord

  • org.broad.igv.sam.PicardAlignment
  • org.broad.igv.sam.reader.SAMFileGroup$SamGroupIterator
  • org.broad.igv.sam.reader.SAMQueryIterator
  • org.broadinstitute.gatk.engine.datasources.reads.IntervalOverlapFilteringIterator
  • org.broadinstitute.gatk.engine.datasources.reads.IntervalOverlapFilteringIteratorUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.PicardBaselineBenchmark
  • org.broadinstitute.gatk.engine.datasources.reads.TheoreticalMinimaBenchmark
  • org.broadinstitute.gatk.engine.downsampling.DownsamplingReadsIterator
  • org.broadinstitute.gatk.engine.downsampling.PerSampleDownsamplingReadsIterator
  • org.broadinstitute.gatk.engine.downsampling.PerSampleDownsamplingReadsIteratorUnitTest$PerSampleDownsamplingReadsIteratorTest
    • 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.