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

Package org.broadinstitute.gatk.utils.sam

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

org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStream
An artificial stream of reads from a single read group/sample with configurable characteristics such as: -the number of contigs that the reads should be distributed across -number of "stacks" of reads sharing the same alignment start position per contig -the min/max number of reads in each stack (exact values chosen randomly from this range) -the min/max distance between stack start positions (exact values chosen randomly from this range) -the min/max length of each read (exact values chosen randomly from this range) -the number of unmapped reads The cigar string for all reads will be *M, where * is the length of the read. @author David Roazen

                int thisSampleNumContigs = MathUtils.randomIntegerInRange(minContigs, maxContigs);
                int thisSampleStacksPerContig = MathUtils.randomIntegerInRange(streamStacksPerContig.minStacksPerContig, streamStacksPerContig.maxStacksPerContig);


                int thisSampleNumUnmappedReads = GenomeAnalysisEngine.getRandomGenerator().nextDouble() < unmappedReadsFraction ? unmappedReadsCount : 0;


                ArtificialSingleSampleReadStream thisSampleStream = new ArtificialSingleSampleReadStream(header,
                                                                                                         readGroupID,
                                                                                                         thisSampleNumContigs,
                                                                                                         thisSampleStacksPerContig,
                                                                                                         streamStackDepth.minReadsPerStack,
                                                                                                         streamStackDepth.maxReadsPerStack,

View Full Code Here

                for ( int minReadsPerStack : Arrays.asList(1, targetCoverage / 2, targetCoverage, targetCoverage - 1, targetCoverage + 1, targetCoverage * 2) ) {
                    for ( int maxReadsPerStack : Arrays.asList(1, targetCoverage / 2, targetCoverage, targetCoverage - 1, targetCoverage + 1, targetCoverage * 2) ) {
                        for ( int numUnmappedReads : Arrays.asList(0, 1, targetCoverage, targetCoverage * 2) ) {
                            // Only interested in sane read stream configurations here
                            if ( minReadsPerStack <= maxReadsPerStack ) {
                                new DownsamplingReadsIteratorTest(new ArtificialSingleSampleReadStream(header,
                                                                                                       readGroupID,
                                                                                                       numContigs,
                                                                                                       stacksPerContig,
                                                                                                       minReadsPerStack,
                                                                                                       maxReadsPerStack,

View Full Code Here

        private void createTestBAM() {
            header = ArtificialSAMUtils.createArtificialSamHeader(numContigs, 1, 100000);
            SAMReadGroupRecord readGroup = new SAMReadGroupRecord("foo");
            readGroup.setSample("testSample");
            header.addReadGroup(readGroup);
            ArtificialSingleSampleReadStream artificialReads = new ArtificialSingleSampleReadStream(header,
                                                                                                    "foo",
                                                                                                    numContigs,
                                                                                                    numStacksPerContig,
                                                                                                    stackSize,
                                                                                                    stackSize,

View Full Code Here

TOP

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

htsjdk.samtools.SAMRecord

org.broadinstitute.gatk.engine.datasources.reads.ReadShardBalancerUnitTest$ReadShardBalancerTest

org.broadinstitute.gatk.engine.downsampling.DownsamplingReadsIteratorUnitTest

org.broadinstitute.gatk.engine.downsampling.PerSampleDownsamplingReadsIteratorUnitTest$PerSampleDownsamplingReadsIteratorTest

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException

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.