Examples of GATKSamRecordFactory

org.broadinstitute.gatk.utils.sam.GATKSamRecordFactory
Factory interface implementation used to create GATKSamRecords from SAMFileReaders with SAM-JDK @author Mark DePristo

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

                                                       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:

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

    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

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

    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 {

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