Examples with TraversalParameters org.broadinstitute.hellbender.engine.TraversalParameters used on opensource projects

Example 1 with TraversalParameters

use of org.broadinstitute.hellbender.engine.TraversalParameters in project gatk by broadinstitute.

the class IntervalArgumentCollection method parseIntervals.

private void parseIntervals(final GenomeLocParser genomeLocParser) {
    // return if no interval arguments at all
    if (!intervalsSpecified()) {
        throw new GATKException("Cannot call parseIntervals() without specifying either intervals to include or exclude.");
    }
    GenomeLocSortedSet includeSortedSet;
    if (getIntervalStrings().isEmpty()) {
        // the -L argument isn't specified, which means that -XL was, since we checked intervalsSpecified()
        // therefore we set the include set to be the entire reference territory
        includeSortedSet = GenomeLocSortedSet.createSetFromSequenceDictionary(genomeLocParser.getSequenceDictionary());
    } else {
        try {
            includeSortedSet = IntervalUtils.loadIntervals(getIntervalStrings(), intervalSetRule, intervalMerging, intervalPadding, genomeLocParser);
        } catch (UserException.EmptyIntersection e) {
            throw new CommandLineException.BadArgumentValue("-L, --interval_set_rule", getIntervalStrings() + "," + intervalSetRule, "The specified intervals had an empty intersection");
        }
    }
    final GenomeLocSortedSet excludeSortedSet = IntervalUtils.loadIntervals(excludeIntervalStrings, IntervalSetRule.UNION, intervalMerging, intervalExclusionPadding, genomeLocParser);
    if (excludeSortedSet.contains(GenomeLoc.UNMAPPED)) {
        throw new UserException("-XL unmapped is not currently supported");
    }
    GenomeLocSortedSet intervals;
    // if no exclude arguments, can return the included set directly
    if (excludeSortedSet.isEmpty()) {
        intervals = includeSortedSet;
    } else // otherwise there are exclude arguments => must merge include and exclude GenomeLocSortedSets
    {
        intervals = includeSortedSet.subtractRegions(excludeSortedSet);
        if (intervals.isEmpty()) {
            throw new CommandLineException.BadArgumentValue("-L,-XL", getIntervalStrings().toString() + ", " + excludeIntervalStrings.toString(), "The intervals specified for exclusion with -XL removed all territory specified by -L.");
        }
        // logging messages only printed when exclude (-XL) arguments are given
        final long toPruneSize = includeSortedSet.coveredSize();
        final long toExcludeSize = excludeSortedSet.coveredSize();
        final long intervalSize = intervals.coveredSize();
        logger.info(String.format("Initial include intervals span %d loci; exclude intervals span %d loci", toPruneSize, toExcludeSize));
        logger.info(String.format("Excluding %d loci from original intervals (%.2f%% reduction)", toPruneSize - intervalSize, (toPruneSize - intervalSize) / (0.01 * toPruneSize)));
    }
    logger.info(String.format("Processing %d bp from intervals", intervals.coveredSize()));
    // Separate out requests for unmapped records from the rest of the intervals.
    boolean traverseUnmapped = false;
    if (intervals.contains(GenomeLoc.UNMAPPED)) {
        traverseUnmapped = true;
        intervals.remove(GenomeLoc.UNMAPPED);
    }
    traversalParameters = new TraversalParameters(IntervalUtils.convertGenomeLocsToSimpleIntervals(intervals.toList()), traverseUnmapped);
}

Example 2 with TraversalParameters

use of org.broadinstitute.hellbender.engine.TraversalParameters in project gatk by broadinstitute.

the class IntervalArgumentCollectionTest method testUnmappedAndMappedInclusion.

@Test(dataProvider = "optionalOrNot")
public void testUnmappedAndMappedInclusion(IntervalArgumentCollection iac) {
    iac.addToIntervalStrings("1:10-20");
    iac.addToIntervalStrings("2:1-5");
    iac.addToIntervalStrings("unmapped");
    final TraversalParameters traversalParameters = iac.getTraversalParameters(hg19GenomeLocParser.getSequenceDictionary());
    Assert.assertTrue(traversalParameters.traverseUnmappedReads());
    Assert.assertEquals(traversalParameters.getIntervalsForTraversal().size(), 2);
    Assert.assertEquals(traversalParameters.getIntervalsForTraversal().get(0), new SimpleInterval("1", 10, 20));
    Assert.assertEquals(traversalParameters.getIntervalsForTraversal().get(1), new SimpleInterval("2", 1, 5));
}

Example 3 with TraversalParameters

use of org.broadinstitute.hellbender.engine.TraversalParameters in project gatk by broadinstitute.

the class IntervalArgumentCollectionTest method testMultipleUnmappedInclusion.

@Test(dataProvider = "optionalOrNot")
public void testMultipleUnmappedInclusion(IntervalArgumentCollection iac) {
    iac.addToIntervalStrings("unmapped");
    iac.addToIntervalStrings("1:10-20");
    iac.addToIntervalStrings("unmapped");
    iac.addToIntervalStrings("unmapped");
    final TraversalParameters traversalParameters = iac.getTraversalParameters(hg19GenomeLocParser.getSequenceDictionary());
    Assert.assertTrue(traversalParameters.traverseUnmappedReads());
    Assert.assertEquals(traversalParameters.getIntervalsForTraversal().size(), 1);
    Assert.assertEquals(traversalParameters.getIntervalsForTraversal().get(0), new SimpleInterval("1", 10, 20));
}

Example 4 with TraversalParameters

use of org.broadinstitute.hellbender.engine.TraversalParameters in project gatk by broadinstitute.

the class IntervalArgumentCollectionTest method testUnmappedAndMappedInclusionPlusMappedExclusion.

@Test(dataProvider = "optionalOrNot")
public void testUnmappedAndMappedInclusionPlusMappedExclusion(IntervalArgumentCollection iac) {
    iac.addToIntervalStrings("1:10-20");
    iac.addToIntervalStrings("2:1-5");
    iac.addToIntervalStrings("unmapped");
    iac.excludeIntervalStrings.addAll(Arrays.asList("1"));
    final TraversalParameters traversalParameters = iac.getTraversalParameters(hg19GenomeLocParser.getSequenceDictionary());
    Assert.assertTrue(traversalParameters.traverseUnmappedReads());
    Assert.assertEquals(traversalParameters.getIntervalsForTraversal().size(), 1);
    Assert.assertEquals(traversalParameters.getIntervalsForTraversal().get(0), new SimpleInterval("2", 1, 5));
}

Example 5 with TraversalParameters

use of org.broadinstitute.hellbender.engine.TraversalParameters in project gatk by broadinstitute.

the class IntervalArgumentCollectionTest method testUnmappedInclusion.

@Test(dataProvider = "optionalOrNot")
public void testUnmappedInclusion(IntervalArgumentCollection iac) {
    iac.addToIntervalStrings("unmapped");
    final TraversalParameters traversalParameters = iac.getTraversalParameters(hg19GenomeLocParser.getSequenceDictionary());
    Assert.assertTrue(traversalParameters.traverseUnmappedReads());
    Assert.assertTrue(traversalParameters.getIntervalsForTraversal().isEmpty());
}