Fixed "skipped intervals" bug on DiagnoseTargets
Problem ------- Diagnose targets was skipping intervals when they were not covered by any reads. Solution -------- Rework the interval iteration logic to output all intervals as they're skipped over by the traversal, as well as adding a loop on traversal done to finish outputting intervals past the coverage of teh BAM file. Summarized Changes ------------------ * Outputs all intervals it iterates over, even if uncovered * Outputs leftover intervals in the end of the traversal * Updated integration tests [fixes #47813825]
This commit is contained in:
Mauricio Carneiro
parent
ff430c821e
commit
cf7afc1ad4
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@ -152,11 +152,14 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
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@Argument(fullName = "print_debug_log", shortName = "dl", doc = "Used only for debugging the walker. Prints extra info to screen", required = false)
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private boolean debug = false;
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private HashMap<GenomeLoc, IntervalStatistics> intervalMap = null; // maps each interval => statistics
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private PeekableIterator<GenomeLoc> intervalListIterator; // an iterator to go over all the intervals provided as we traverse the genome
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private Set<String> samples = null; // all the samples being processed
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private final Allele SYMBOLIC_ALLELE = Allele.create("<DT>", false); // avoid creating the symbolic allele multiple times
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private ThresHolder thresholds = null;
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private Map<GenomeLoc, IntervalStatistics> intervalMap = null; // maps each interval => statistics
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private PeekableIterator<GenomeLoc> intervalListIterator; // an iterator to go over all the intervals provided as we traverse the genome
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private Set<String> samples = null; // all the samples being processed
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private static final Allele SYMBOLIC_ALLELE = Allele.create("<DT>", false); // avoid creating the symbolic allele multiple times
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private static final Allele UNCOVERED_ALLELE = Allele.create("A", true); // avoid creating the 'fake' ref allele for uncovered intervals multiple times
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private ThresHolder thresholds = null; // object that holds all the thresholds for Diagnose Targets (todo -- should become a plugin based system)
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private static final int INITIAL_HASH_SIZE = 500000;
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@Override
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public void initialize() {
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@ -165,24 +168,32 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
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if (getToolkit().getIntervals() == null)
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throw new UserException("This tool only works if you provide one or more intervals. ( Use the -L argument )");
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thresholds = new ThresHolder(minimumBaseQuality, minimumMappingQuality, minimumCoverage, maximumCoverage, minMedianDepth, maxInsertSize, votePercentage, lowMedianDepthPercentage, badMateStatusThreshold, coverageStatusThreshold, excessiveCoverageThreshold, qualityStatusThreshold);
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thresholds = new ThresHolder(minimumBaseQuality, minimumMappingQuality, minimumCoverage, maximumCoverage,
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minMedianDepth, maxInsertSize, votePercentage, lowMedianDepthPercentage,
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badMateStatusThreshold, coverageStatusThreshold, excessiveCoverageThreshold,
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qualityStatusThreshold);
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intervalMap = new HashMap<GenomeLoc, IntervalStatistics>();
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intervalMap = new HashMap<GenomeLoc, IntervalStatistics>(INITIAL_HASH_SIZE);
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intervalListIterator = new PeekableIterator<GenomeLoc>(getToolkit().getIntervals().iterator());
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samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()); // get all of the unique sample names for the VCF Header
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vcfWriter.writeHeader(new VCFHeader(ThresHolder.getHeaderInfo(), samples)); // initialize the VCF header
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// get all of the unique sample names for the VCF Header
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samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
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vcfWriter.writeHeader(new VCFHeader(ThresHolder.getHeaderInfo(), samples));
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}
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@Override
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public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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GenomeLoc refLocus = ref.getLocus();
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removePastIntervals(refLocus, ref.getBase()); // process and remove any intervals in the map that are don't overlap the current locus anymore
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addNewOverlappingIntervals(refLocus); // add all new intervals that may overlap this reference locus
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// process and remove any intervals in the map that are don't overlap the current locus anymore
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// and add all new intervals that may overlap this reference locus
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outputFinishedIntervals(refLocus, ref.getBase());
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addNewOverlappingIntervals(refLocus);
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// at this point, all intervals in intervalMap overlap with this locus, so update all of them
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for (IntervalStatistics intervalStatistics : intervalMap.values())
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intervalStatistics.addLocus(context, ref, thresholds); // Add current locus to stats
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intervalStatistics.addLocus(context, ref, thresholds);
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return 1L;
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}
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@ -212,53 +223,40 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
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@Override
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public void onTraversalDone(Long result) {
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for (GenomeLoc interval : intervalMap.keySet())
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outputStatsToVCF(intervalMap.get(interval), Allele.create("A", true));
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}
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outputStatsToVCF(intervalMap.get(interval), UNCOVERED_ALLELE);
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private GenomeLoc getIntervalMapSpan() {
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GenomeLoc loc = null;
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for (GenomeLoc interval : intervalMap.keySet()) {
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if (loc == null) {
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loc = interval;
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} else
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loc = interval.union(loc);
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GenomeLoc interval = intervalListIterator.peek();
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while (interval != null) {
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outputStatsToVCF(createIntervalStatistic(interval), UNCOVERED_ALLELE);
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intervalListIterator.next();
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interval = intervalListIterator.peek();
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}
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return loc;
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}
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private GenomeLoc getFinishedIntervalSpan(GenomeLoc pos) {
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GenomeLoc loc = null;
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for (GenomeLoc interval : intervalMap.keySet()) {
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if (interval.isBefore(pos)) {
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if (loc == null)
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loc = interval;
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else
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loc = interval.union(loc);
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}
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}
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return loc;
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}
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/**
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* Removes all intervals that are behind the current reference locus from the intervalMap
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* Outputs all intervals that are behind the current reference locus
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*
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* @param refLocus the current reference locus
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* @param refBase the reference allele
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*/
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private void removePastIntervals(GenomeLoc refLocus, byte refBase) {
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// if there are statistics to output/ check to see that we can output them in order
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if (getFinishedIntervalSpan(refLocus) != null &&
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getIntervalMapSpan().getStart() == getFinishedIntervalSpan(refLocus).getStart()) {
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private void outputFinishedIntervals(final GenomeLoc refLocus, final byte refBase) {
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GenomeLoc interval = intervalListIterator.peek();
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for (GenomeLoc interval : intervalMap.keySet()) {
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if (interval.isBefore(refLocus)) {
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outputStatsToVCF(intervalMap.get(interval), Allele.create(refBase, true));
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intervalMap.remove(interval);
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}
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// output empty statistics for uncovered intervals
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while (interval != null && interval.isBefore(refLocus)) {
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final IntervalStatistics stats = intervalMap.get(interval);
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outputStatsToVCF(stats != null ? stats : createIntervalStatistic(interval), UNCOVERED_ALLELE);
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if (stats != null) intervalMap.remove(interval);
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intervalListIterator.next();
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interval = intervalListIterator.peek();
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}
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// remove any potential leftover interval in intervalMap (this will only happen when we have overlapping intervals)
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for (GenomeLoc key : intervalMap.keySet()) {
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if (key.isBefore(refLocus)) {
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outputStatsToVCF(intervalMap.get(key), Allele.create(refBase, true));
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intervalMap.remove(key);
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}
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}
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}
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@ -269,17 +267,9 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
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*/
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private void addNewOverlappingIntervals(GenomeLoc refLocus) {
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GenomeLoc interval = intervalListIterator.peek();
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// skip any intervals with no coverage that we have passed
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while (interval != null && interval.isBefore(refLocus)) {
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intervalListIterator.next(); // discard the interval (we've already added it to the map)
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interval = intervalListIterator.peek();
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}
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// add any intervals that overlap this one
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while (interval != null && !interval.isPast(refLocus)) {
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intervalMap.put(interval, createIntervalStatistic(interval));
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intervalListIterator.next(); // discard the interval (we've already added it to the map)
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intervalListIterator.next();
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interval = intervalListIterator.peek();
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}
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}
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@ -66,11 +66,11 @@ public class DiagnoseTargetsIntegrationTest extends WalkerTest {
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@Test(enabled = true)
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public void testSingleSample() {
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DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "9954b21163d3e66db232938ec509067f");
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DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "9b51561bcf248da70a4d711380b04f7b");
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}
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@Test(enabled = true)
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public void testMultiSample() {
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DTTest("testMultiSample ", "-I " + multiSample, "7c5277261e8e9dd74666f04843ffb09c");
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DTTest("testMultiSample ", "-I " + multiSample, "925f88f0c41c6a9ac479be34e052dc5d");
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}
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}
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