Package org.broadinstitute.gatk.utils.sam

Examples of org.broadinstitute.gatk.utils.sam.GATKSamRecordFactory

304
305
306
307
308
309
310
311
312
313
314
                                                       1, Arrays.asList(""));  // No MD5s; we only want to check the cigar

        final File outputBam = executeTest("testGATKEngineConsolidatesCigars", spec).first.get(0);
        final SAMFileReader reader = new SAMFileReader(outputBam);
        reader.setValidationStringency(ValidationStringency.SILENT);
        reader.setSAMRecordFactory(new GATKSamRecordFactory());

        final SAMRecord read = reader.iterator().next();
        reader.close();

        // Original cigar was 0M3M0M8M. Check that it's been consolidated after running through the GATK engine:
View Full Code Here
217
218
219
220
221
222
223
224
225
226
227
    public void testWithBAMFile() {
        // create a fake BAM file, and iterate through it
        final ArtificialBAMBuilder bamBuilder = new ArtificialBAMBuilder(seq, 20, 10);
        final File bam = bamBuilder.makeTemporarilyBAMFile();
        final SAMFileReader reader = new SAMFileReader(bam);
        reader.setSAMRecordFactory(new GATKSamRecordFactory());

        final Iterator<SAMRecord> bamIt = reader.iterator();
        while ( bamIt.hasNext() ) {
            final GATKSAMRecord read = (GATKSAMRecord)bamIt.next(); // all reads are actually GATKSAMRecords
            // TODO -- add some tests that use reads from a BAM
View Full Code Here
70
71
72
73
74
75
76
77
78
79
80
    public int execute() throws IOException {
        final IndexedFastaSequenceFile reference = new CachingIndexedFastaSequenceFile(referenceFile);
        final GenomeLocParser genomeLocParser = new GenomeLocParser(reference);

        final SAMFileReader reader = new SAMFileReader(samFile);
        reader.setSAMRecordFactory(new GATKSamRecordFactory());

        SAMRecordIterator rawIterator;
        if ( location == null )
            rawIterator = reader.iterator();
        else {
View Full Code Here
TOP

Related Classes of org.broadinstitute.gatk.utils.sam.GATKSamRecordFactory

  • org.broadinstitute.gatk.engine.EngineFeaturesIntegrationTest
  • org.broadinstitute.gatk.utils.ExampleToCopyUnitTest
  • org.broadinstitute.gatk.utils.locusiterator.LIBSPerformance
    • 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.