/** * A unit test that creates an artificial read for testing some code that uses reads */ @Test() 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 SamReader reader = SamReaderFactory.makeDefault().open(bam); final Iterator<SAMRecord> bamIt = reader.iterator(); while ( bamIt.hasNext() ) { final SAMRecord read = bamIt.next(); // all reads are actually GATKSAMRecords // TODO -- add some tests that use reads from a BAM } try { reader.close(); } catch ( IOException ex ) { throw new ReviewedGATKException("Unable to close " + bam , ex); } }
walker.setStates(readStates); final Map<GenomeLoc, ActiveRegion> activeRegionsMap = getActiveRegions(traversal, walker, intervals, bamBuilder.makeTemporarilyBAMFile());
final File bam = bamBuilder.makeTemporarilyBAMFile(); final SamReader reader = SamReaderFactory.makeDefault().open(bam); Assert.assertTrue(reader.hasIndex());
final Map<GenomeLoc, ActiveRegion> activeRegionsMap = getActiveRegions(traversal, walker, intervals, bamBuilder.makeTemporarilyBAMFile());