Totally revamped the MNP annotation and put it in its own walker: AnnotateMNPsWalker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4730 348d0f76-0448-11de-a6fe-93d51630548a
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/*
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* Copyright (c) 2010, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.phasing;
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import org.broad.tribble.util.variantcontext.Allele;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.vcf.*;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableFeature;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.AminoAcid;
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import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.AminoAcidTable;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.vcf.VCFUtils;
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import java.util.*;
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import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods;
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/**
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* Walks along all variant ROD loci, and dynamically annotates alleles at MNP records.
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*/
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@Allows(value = {DataSource.REFERENCE})
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@Requires(value = {DataSource.REFERENCE}, referenceMetaData = {@RMD(name = AnnotateMNPsWalker.REFSEQ_ROD_NAME, type = AnnotatorInputTableFeature.class), @RMD(name = AnnotateMNPsWalker.VARIANT_ROD_NAME, type = ReferenceOrderedDatum.class)})
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public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
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@Output(doc = "File to which variants should be written", required = true)
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protected VCFWriter writer = null;
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private ManualSortingVCFWriter sortingWriter = null;
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private LinkedList<String> rodNames = null;
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private GenomeLocParser locParser = null;
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private TreeMap<GenomeLoc, Set<GenomeLoc>> MNPstartToStops = null; // Must be TreeMap sorted by START sites!
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public final static String REFSEQ_ROD_NAME = "refseq";
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public final static String VARIANT_ROD_NAME = "variant";
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private LocusToFeatures locusToRefSeqFeatures = null;
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protected final static String MNP_ANNOTATION_KEY_PREFIX = "MNP.refseq.";
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protected final static String REFSEQ_NAME = "name";
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protected final static String REFSEQ_NAME2 = "name2";
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protected final static String REFSEQ_POSITION_TYPE = "positionType";
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protected final static String REFSEQ_CDS = "CDS";
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protected final static String REFSEQ_STRAND = "transcriptStrand";
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protected final static String REFSEQ_POS_STRAND = "+";
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protected final static String REFSEQ_NEG_STRAND = "-";
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protected final static String REFSEQ_CODON_COORD = "codonCoord";
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protected final static String REFSEQ_CODING_FRAME = "frame";
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protected final static String REFSEQ_REF_CODON = "referenceCodon";
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protected final static String REFSEQ_REF_AA = "referenceAA";
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protected final static String REFSEQ_ALT_BASE = "haplotypeAlternate";
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protected final static String REFSEQ_VARIANT_CODON = "variantCodon";
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protected final static String REFSEQ_VARIANT_AA = "variantAA";
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protected final static String REFSEQ_CHANGES_AA = "changesAA";
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protected final static String REFSEQ_FUNCTIONAL_CLASS = "functionalClass";
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protected final static String REFSEQ_PROTEIN_COORD_DESCRIPTION = "proteinCoordStr";
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protected final static String REFSEQ_CODING_ANNOTATIONS = "codingVariants";
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public void initialize() {
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rodNames = new LinkedList<String>();
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rodNames.add(VARIANT_ROD_NAME);
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locParser = getToolkit().getGenomeLocParser();
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MNPstartToStops = new TreeMap<GenomeLoc, Set<GenomeLoc>>(); // sorted by start sites
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initializeVcfWriter();
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locusToRefSeqFeatures = new LocusToFeatures();
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}
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private void initializeVcfWriter() {
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sortingWriter = new ManualSortingVCFWriter(writer);
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writer = sortingWriter;
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// setup the header fields:
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Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
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hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
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Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), rodNames);
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writer.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(rodNameToHeader.get(rodNames.get(0)).getGenotypeSamples())));
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}
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public boolean generateExtendedEvents() {
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return false;
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}
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public Integer reduceInit() {
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return 0;
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}
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/**
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* For each site of interest, annotate it if it's a MNP.
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*
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* @param tracker the meta-data tracker
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* @param ref the reference base
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* @param context the context for the given locus
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* @return count of MNPs observed
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*/
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if (tracker == null)
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return null;
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int numMNPsObserved = 0;
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GenomeLoc curLocus = ref.getLocus();
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clearOldLocusFeatures(curLocus);
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boolean requireStartHere = false; // see EVERY site of the MNP
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boolean takeFirstOnly = false; // take as many entries as the VCF file has
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for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, null, context.getLocation(), requireStartHere, takeFirstOnly)) {
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if (vc.getType() == VariantContext.Type.MNP) {
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GenomeLoc MNPloc = VariantContextUtils.getLocation(locParser, vc);
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boolean atStartOfMNP = curLocus.getStart() == MNPloc.getStart();
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boolean atEndOfMNP = curLocus.getStart() == MNPloc.getStop();
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logger.debug("Observed MNP at " + MNPloc);
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if (isChrM(vc)) {
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if (atStartOfMNP) {
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logger.warn("Skipping mitochondrial MNP at " + MNPloc + " due to complexity of coding table [need to know if first codon, etc.]...");
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writeVCF(vc);
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}
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continue;
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}
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GenomeLoc stopLoc = locParser.createGenomeLoc(curLocus.getContig(), MNPloc.getStop());
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final List<Object> refSeqRODs = tracker.getReferenceMetaData(REFSEQ_ROD_NAME);
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for (Object refSeqObject : refSeqRODs) {
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AnnotatorInputTableFeature refSeqAnnotation = (AnnotatorInputTableFeature) refSeqObject;
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locusToRefSeqFeatures.putLocusFeatures(curLocus, refSeqAnnotation, stopLoc);
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}
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if (atStartOfMNP) { // MNP is starting here, so register that we're waiting for it
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Set<GenomeLoc> stopLocs = MNPstartToStops.get(curLocus);
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if (stopLocs == null) {
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stopLocs = new HashSet<GenomeLoc>();
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MNPstartToStops.put(curLocus, stopLocs);
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}
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stopLocs.add(stopLoc);
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}
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if (atEndOfMNP) {
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numMNPsObserved++; // only count a MNP at its stop site
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logger.debug("Observed end of MNP at " + curLocus);
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logger.debug("Current list of per-locus features\n" + locusToRefSeqFeatures);
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Map<String, Object> MNPannotations = annotateMNP(vc);
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MNPannotations.putAll(vc.getAttributes());
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vc = VariantContext.modifyAttributes(vc, MNPannotations);
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writeVCF(vc);
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GenomeLoc startLoc = locParser.createGenomeLoc(curLocus.getContig(), MNPloc.getStart());
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Set<GenomeLoc> stopLocs = MNPstartToStops.get(startLoc);
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if (stopLocs != null) { // otherwise, just removed stopLocs due to another MNP that has the same (start, stop)
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stopLocs.remove(stopLoc);
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if (stopLocs.isEmpty()) // no longer waiting for startLoc
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MNPstartToStops.remove(startLoc);
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}
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}
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}
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else {
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writeVCF(vc);
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}
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}
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Integer mostUpstreamWritableLoc = null;
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if (!MNPstartToStops.isEmpty()) {
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GenomeLoc waitingForLoc = MNPstartToStops.entrySet().iterator().next().getKey();
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mostUpstreamWritableLoc = waitingForLoc.getStart() - 1;
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}
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sortingWriter.setmostUpstreamWritableLocus(mostUpstreamWritableLoc);
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return numMNPsObserved;
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}
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private static boolean isChrM(final VariantContext vc) {
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return vc.getChr().equals("chrM") || vc.getChr().equals("MT");
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}
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private Map<String, Object> annotateMNP(VariantContext vc) {
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Map<String, Object> annotations = new HashMap<String, Object>();
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RefSeqNameToFeatures nameToPositionalFeatures = new RefSeqNameToFeatures(vc);
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MNPannotationKeyBuilder kb = new MNPannotationKeyBuilder(nameToPositionalFeatures);
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for (Map.Entry<String, RefSeqFeatureList> nameToFeatureEntry : nameToPositionalFeatures.entrySet()) {
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String featureName = nameToFeatureEntry.getKey();
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RefSeqFeatureList feature = nameToFeatureEntry.getValue();
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CodonAnnotationsForAltAlleles codonAnnotationsForAlleles = new CodonAnnotationsForAltAlleles(vc, feature);
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annotations.put(kb.getKey(REFSEQ_CODING_ANNOTATIONS), codonAnnotationsForAlleles.toString());
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annotations.put(kb.getKey(REFSEQ_NAME), featureName);
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annotations.put(kb.getKey(REFSEQ_NAME2), feature.name2);
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annotations.put(kb.getKey(REFSEQ_POSITION_TYPE), REFSEQ_CDS);
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annotations.put(kb.getKey(REFSEQ_STRAND), (feature.positiveStrand ? REFSEQ_POS_STRAND : REFSEQ_NEG_STRAND));
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annotations.put(kb.getKey(REFSEQ_CODON_COORD), feature.getCodonCoordString());
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kb.incrementFeatureIndex();
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}
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return annotations;
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}
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private static class MNPannotationKeyBuilder {
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private int featureIndex;
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private boolean multipleEntries;
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public MNPannotationKeyBuilder(RefSeqNameToFeatures nameToPositionalFeatures) {
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this.featureIndex = 1;
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this.multipleEntries = nameToPositionalFeatures.nameToFeatures.size() > 1;
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}
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public void incrementFeatureIndex() {
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featureIndex++;
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}
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public String getKey(String type) {
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String annotationKey = MNP_ANNOTATION_KEY_PREFIX + type;
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if (multipleEntries)
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annotationKey += "_" + featureIndex;
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return annotationKey;
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}
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}
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private static byte[] ByteArrayToPrimitive(Byte[] nonNullArray) {
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byte[] primArray = new byte[nonNullArray.length];
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for (int i = 0; i < nonNullArray.length; i++) {
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if (nonNullArray[i] == null)
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throw new ReviewedStingException("nonNullArray[i] == null");
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primArray[i] = nonNullArray[i];
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}
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return primArray;
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}
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private void clearOldLocusFeatures(GenomeLoc curLoc) {
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Iterator<Map.Entry<GenomeLoc, PositionalRefSeqFeatures>> locusFeaturesIt = locusToRefSeqFeatures.entrySet().iterator();
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while (locusFeaturesIt.hasNext()) {
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Map.Entry<GenomeLoc, PositionalRefSeqFeatures> locusFeaturesEntry = locusFeaturesIt.next();
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if (curLoc.isPast(locusFeaturesEntry.getValue().getFurthestLocusUsingFeatures()))
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locusFeaturesIt.remove();
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}
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}
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public Integer reduce(Integer count, Integer total) {
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if (count != null)
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total = total + count;
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return total;
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}
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/**
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* @param result the number of MNPs processed.
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*/
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public void onTraversalDone(Integer result) {
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System.out.println("Number of MNPs observed: " + result);
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writer.close();
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}
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private void writeVCF(VariantContext vc) {
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byte refBase;
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if (!vc.isIndel()) {
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Allele varAllele = vc.getReference();
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refBase = SNPallelePair.getSingleBase(varAllele);
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}
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else {
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refBase = vc.getReferenceBaseForIndel();
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}
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writer.add(vc, refBase);
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}
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/*
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Inner classes:
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*/
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// Maps: RefSeq entry name -> features for ALL positions of a particular VariantContext MNP:
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private class RefSeqNameToFeatures {
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private Map<String, RefSeqFeatureList> nameToFeatures;
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public RefSeqNameToFeatures(VariantContext vc) {
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this.nameToFeatures = new HashMap<String, RefSeqFeatureList>();
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int MNPstart = vc.getStart();
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int MNPstop = vc.getEnd();
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int MNPlength = MNPstop - MNPstart + 1;
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for (int i = 0; i < MNPlength; i++) {
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int genomicPosition = MNPstart + i;
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GenomeLoc posLoc = locParser.createGenomeLoc(vc.getChr(), genomicPosition);
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PositionalRefSeqFeatures locFeatures = locusToRefSeqFeatures.getLocusFeatures(posLoc);
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if (locFeatures == null) // no features for posLoc
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continue;
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for (Map.Entry<String, PositionalRefSeqFeature> nameToFeatureEntry : locFeatures.entrySet()) {
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String name = nameToFeatureEntry.getKey();
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PositionalRefSeqFeature posFeature = nameToFeatureEntry.getValue();
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RefSeqFeatureList featureList = nameToFeatures.get(name);
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if (featureList == null) {
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featureList = new RefSeqFeatureList(MNPlength);
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nameToFeatures.put(name, featureList);
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}
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featureList.updateFeatureAtPosition(i, posFeature);
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}
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}
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||||||
|
}
|
||||||
|
|
||||||
|
public Set<Map.Entry<String, RefSeqFeatureList>> entrySet() {
|
||||||
|
return nameToFeatures.entrySet();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// For a particular RefSeq entry, contains the features for ALL positions of a particular VariantContext MNP
|
||||||
|
|
||||||
|
private static class RefSeqFeatureList {
|
||||||
|
private final static String CODON_FRAME_START = "(";
|
||||||
|
private final static String CODON_FRAME_END = ")";
|
||||||
|
private final static String CODON_DELIM = "|";
|
||||||
|
|
||||||
|
private CodingRefSeqFeature[] refSeqFeatures;
|
||||||
|
private String name2;
|
||||||
|
private Boolean positiveStrand;
|
||||||
|
|
||||||
|
private Map<Integer, List<Integer>> codonToIndices; // Map of: codon index -> MNP indices that refer to codon
|
||||||
|
|
||||||
|
public RefSeqFeatureList(int MNPlength) {
|
||||||
|
this.refSeqFeatures = new CodingRefSeqFeature[MNPlength];
|
||||||
|
for (int i = 0; i < MNPlength; i++)
|
||||||
|
this.refSeqFeatures[i] = null;
|
||||||
|
|
||||||
|
this.name2 = null;
|
||||||
|
this.positiveStrand = null;
|
||||||
|
this.codonToIndices = new TreeMap<Integer, List<Integer>>();
|
||||||
|
}
|
||||||
|
|
||||||
|
public void updateFeatureAtPosition(int index, PositionalRefSeqFeature feature) {
|
||||||
|
if (name2 == null) {
|
||||||
|
name2 = feature.name2;
|
||||||
|
positiveStrand = feature.positiveStrand;
|
||||||
|
}
|
||||||
|
else if (!name2.equals(feature.name2) || positiveStrand != feature.positiveStrand) {
|
||||||
|
throw new UserException("Inconsistency between previous RefSeq entry and: " + feature);
|
||||||
|
}
|
||||||
|
|
||||||
|
CodingRefSeqFeature crsf = new CodingRefSeqFeature(feature);
|
||||||
|
refSeqFeatures[index] = crsf;
|
||||||
|
|
||||||
|
List<Integer> indicesWithCodon = codonToIndices.get(crsf.codonCoord);
|
||||||
|
if (indicesWithCodon == null) {
|
||||||
|
indicesWithCodon = new LinkedList<Integer>();
|
||||||
|
codonToIndices.put(crsf.codonCoord, indicesWithCodon);
|
||||||
|
}
|
||||||
|
indicesWithCodon.add(index);
|
||||||
|
}
|
||||||
|
|
||||||
|
public Set<Map.Entry<Integer, List<Integer>>> codonIndicesEntrySet() {
|
||||||
|
return codonToIndices.entrySet();
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getCodonCoordString() {
|
||||||
|
StringBuilder sb = new StringBuilder();
|
||||||
|
|
||||||
|
for (int i = 0; i < refSeqFeatures.length; i++) {
|
||||||
|
CodingRefSeqFeature crsf = refSeqFeatures[i];
|
||||||
|
if (crsf != null)
|
||||||
|
sb.append(crsf.codonCoord).append(CODON_FRAME_START).append(crsf.codingFrame).append(CODON_FRAME_END);
|
||||||
|
if (i < refSeqFeatures.length - 1)
|
||||||
|
sb.append(CODON_DELIM);
|
||||||
|
}
|
||||||
|
|
||||||
|
return sb.toString();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private static class CodingRefSeqFeature {
|
||||||
|
protected int codonCoord;
|
||||||
|
protected int codingFrame;
|
||||||
|
protected String referenceCodon;
|
||||||
|
protected String referenceAA;
|
||||||
|
|
||||||
|
public CodingRefSeqFeature(PositionalRefSeqFeature feature) {
|
||||||
|
this.codonCoord = feature.codonCoord;
|
||||||
|
this.codingFrame = feature.codingFrame;
|
||||||
|
this.referenceCodon = feature.referenceCodon.toUpperCase();
|
||||||
|
this.referenceAA = feature.referenceAA;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private static class CodonAnnotationsForAltAlleles {
|
||||||
|
protected final static int MIN_CODON_INDEX = 0;
|
||||||
|
protected final static int NUM_CODON_INDICES = 3;
|
||||||
|
private final static String CODON_ANNOTATION_DELIM = ",";
|
||||||
|
|
||||||
|
private List<SingleCodonAnnotationsForAlleles> alleleAnnotations;
|
||||||
|
|
||||||
|
public CodonAnnotationsForAltAlleles(VariantContext vc, RefSeqFeatureList feature) {
|
||||||
|
this.alleleAnnotations = new LinkedList<SingleCodonAnnotationsForAlleles>();
|
||||||
|
|
||||||
|
int MNPstart = vc.getStart();
|
||||||
|
int MNPstop = vc.getEnd();
|
||||||
|
int MNPlength = MNPstop - MNPstart + 1;
|
||||||
|
|
||||||
|
for (Map.Entry<Integer, List<Integer>> codonToIndicesEntry : feature.codonIndicesEntrySet()) {
|
||||||
|
int codonIndex = codonToIndicesEntry.getKey();
|
||||||
|
List<Integer> indices = codonToIndicesEntry.getValue();
|
||||||
|
if (indices.isEmpty())
|
||||||
|
throw new ReviewedStingException("indices should not exist if it's empty!");
|
||||||
|
|
||||||
|
for (int index : indices) {
|
||||||
|
int frame = feature.refSeqFeatures[index].codingFrame;
|
||||||
|
if (feature.refSeqFeatures[index].codonCoord != codonIndex)
|
||||||
|
throw new ReviewedStingException("LOGICAL ERROR: feature.refSeqFeatures[index].codonCoord != codonIndex");
|
||||||
|
if (frame < MIN_CODON_INDEX || frame >= NUM_CODON_INDICES)
|
||||||
|
throw new UserException("RefSeq codon frame not one of {0,1,2}");
|
||||||
|
}
|
||||||
|
CodingRefSeqFeature firstFeatureForCodon = feature.refSeqFeatures[indices.get(0)];
|
||||||
|
String refCodon = firstFeatureForCodon.referenceCodon;
|
||||||
|
|
||||||
|
SingleCodonAnnotationsForAlleles codonAnnotation = new SingleCodonAnnotationsForAlleles(codonIndex, vc.getAlternateAlleles(), MNPlength, refCodon, firstFeatureForCodon, indices, feature);
|
||||||
|
alleleAnnotations.add(codonAnnotation);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public String toString() {
|
||||||
|
StringBuilder sb = new StringBuilder();
|
||||||
|
|
||||||
|
int index = 0;
|
||||||
|
for (SingleCodonAnnotationsForAlleles codonToAlleles : alleleAnnotations) {
|
||||||
|
sb.append(codonToAlleles);
|
||||||
|
if (index < alleleAnnotations.size() - 1)
|
||||||
|
sb.append(CODON_ANNOTATION_DELIM);
|
||||||
|
index++;
|
||||||
|
}
|
||||||
|
|
||||||
|
return sb.toString();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private static class SingleCodonAnnotationsForAlleles {
|
||||||
|
private final static String CODON_MAP_SYMBOL = "->";
|
||||||
|
private final static String CODON_ANNOTATION_START = "[";
|
||||||
|
private final static String CODON_ANNOTATION_END = "]";
|
||||||
|
private final static String REF_CODON_INFO_DELIM = "|";
|
||||||
|
private final static String ALLELE_ANNOTATION_DELIM = ",";
|
||||||
|
private final static String ASSIGNMENT = ":";
|
||||||
|
|
||||||
|
private int codonIndex;
|
||||||
|
private String refCodon;
|
||||||
|
private String refAA;
|
||||||
|
|
||||||
|
private List<SingleCodonAnnotationsForAllele> annotationsForAlleles;
|
||||||
|
|
||||||
|
public SingleCodonAnnotationsForAlleles(int codonIndex, Collection<Allele> altAlleles, int MNPlength, String refCodon, CodingRefSeqFeature firstFeatureForCodon, List<Integer> indices, RefSeqFeatureList feature) {
|
||||||
|
if (refCodon.length() != CodonAnnotationsForAltAlleles.NUM_CODON_INDICES)
|
||||||
|
throw new UserException("RefSeq reference codon " + refCodon + " is not of length " + CodonAnnotationsForAltAlleles.NUM_CODON_INDICES);
|
||||||
|
|
||||||
|
AminoAcid refAA = AminoAcidTable.getEukaryoticAA(refCodon);
|
||||||
|
if (!refAA.getCode().equals(firstFeatureForCodon.referenceAA))
|
||||||
|
throw new UserException("RefSeq: translated reference codon= " + refAA + " != " + firstFeatureForCodon.referenceAA + " = reference AA");
|
||||||
|
|
||||||
|
this.codonIndex = codonIndex;
|
||||||
|
this.refCodon = refCodon;
|
||||||
|
this.refAA = refAA.getCode();
|
||||||
|
this.annotationsForAlleles = new LinkedList<SingleCodonAnnotationsForAllele>();
|
||||||
|
|
||||||
|
for (Allele altAllele : altAlleles) {
|
||||||
|
if (altAllele.length() != MNPlength)
|
||||||
|
throw new ReviewedStingException("length(altAllele) != length(MNP)");
|
||||||
|
byte[] altBases = altAllele.getBases();
|
||||||
|
|
||||||
|
Byte[] variantCodonArr = new Byte[CodonAnnotationsForAltAlleles.NUM_CODON_INDICES];
|
||||||
|
for (int i = CodonAnnotationsForAltAlleles.MIN_CODON_INDEX; i < CodonAnnotationsForAltAlleles.NUM_CODON_INDICES; i++)
|
||||||
|
variantCodonArr[i] = null;
|
||||||
|
|
||||||
|
for (int index : indices) {
|
||||||
|
int frame = feature.refSeqFeatures[index].codingFrame;
|
||||||
|
if (variantCodonArr[frame] != null)
|
||||||
|
throw new UserException("RefSeq assigns codon " + codonIndex + " twice at same frame: " + frame);
|
||||||
|
|
||||||
|
byte base = altBases[index];
|
||||||
|
if (!feature.positiveStrand) // negative strand codon
|
||||||
|
base = BaseUtils.simpleComplement(base);
|
||||||
|
|
||||||
|
variantCodonArr[frame] = base;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* For missing frames, there MUST exist AT LEAST one index that refers to this codon,
|
||||||
|
so use it to derive the missing bases [ALREADY complemented if on the negative strand]:
|
||||||
|
*/
|
||||||
|
for (int frame = CodonAnnotationsForAltAlleles.MIN_CODON_INDEX; frame < CodonAnnotationsForAltAlleles.NUM_CODON_INDICES; frame++) {
|
||||||
|
if (variantCodonArr[frame] == null)
|
||||||
|
variantCodonArr[frame] = (byte) refCodon.charAt(frame);
|
||||||
|
}
|
||||||
|
String variantCodon = new String(ByteArrayToPrimitive(variantCodonArr)).toUpperCase();
|
||||||
|
|
||||||
|
SingleCodonAnnotationsForAllele alleleAnnotation = new SingleCodonAnnotationsForAllele(variantCodon, refCodon, refAA, codonIndex);
|
||||||
|
annotationsForAlleles.add(alleleAnnotation);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public String toString() {
|
||||||
|
StringBuilder sb = new StringBuilder();
|
||||||
|
|
||||||
|
sb.append(codonIndex).append(CODON_MAP_SYMBOL).append(CODON_ANNOTATION_START);
|
||||||
|
sb.append(REFSEQ_REF_CODON).append(ASSIGNMENT).append(refCodon).append(REF_CODON_INFO_DELIM);
|
||||||
|
sb.append(REFSEQ_REF_AA).append(ASSIGNMENT).append(refAA).append(REF_CODON_INFO_DELIM);
|
||||||
|
|
||||||
|
int index = 0;
|
||||||
|
for (SingleCodonAnnotationsForAllele annotation : annotationsForAlleles) {
|
||||||
|
sb.append(annotation);
|
||||||
|
if (index < annotationsForAlleles.size() - 1)
|
||||||
|
sb.append(ALLELE_ANNOTATION_DELIM);
|
||||||
|
index++;
|
||||||
|
}
|
||||||
|
sb.append(CODON_ANNOTATION_END);
|
||||||
|
|
||||||
|
return sb.toString();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private static class SingleCodonAnnotationsForAllele {
|
||||||
|
private final static String ALLELE_START = "{";
|
||||||
|
private final static String ALLELE_END = "}";
|
||||||
|
private final static String CODON_INFO_DELIM = "|";
|
||||||
|
private final static String ASSIGNMENT = ":";
|
||||||
|
|
||||||
|
private String variantCodon;
|
||||||
|
private String variantAA;
|
||||||
|
private boolean changesAA;
|
||||||
|
private String functionalClass;
|
||||||
|
private String proteinCoordStr;
|
||||||
|
|
||||||
|
public SingleCodonAnnotationsForAllele(String variantCodon, String refCodon, AminoAcid refAA, int codonIndex) {
|
||||||
|
this.variantCodon = variantCodon;
|
||||||
|
AminoAcid variantAA = AminoAcidTable.getEukaryoticAA(this.variantCodon);
|
||||||
|
this.variantAA = variantAA.getCode();
|
||||||
|
|
||||||
|
this.changesAA = !refAA.equals(variantAA);
|
||||||
|
|
||||||
|
if (!this.variantCodon.equals(refCodon)) {
|
||||||
|
if (changesAA) {
|
||||||
|
if (variantAA.isStop()) {
|
||||||
|
functionalClass = "nonsense";
|
||||||
|
}
|
||||||
|
else if (refAA.isStop()) {
|
||||||
|
functionalClass = "readthrough";
|
||||||
|
}
|
||||||
|
else {
|
||||||
|
functionalClass = "missense";
|
||||||
|
}
|
||||||
|
}
|
||||||
|
else { // the same aa:
|
||||||
|
functionalClass = "silent";
|
||||||
|
}
|
||||||
|
}
|
||||||
|
else { // the same codon:
|
||||||
|
functionalClass = "no_change";
|
||||||
|
}
|
||||||
|
|
||||||
|
this.proteinCoordStr = "p." + refAA.getLetter() + codonIndex + variantAA.getLetter();
|
||||||
|
}
|
||||||
|
|
||||||
|
public String toString() {
|
||||||
|
StringBuilder sb = new StringBuilder();
|
||||||
|
|
||||||
|
sb.append(ALLELE_START);
|
||||||
|
sb.append(REFSEQ_VARIANT_CODON).append(ASSIGNMENT).append(variantCodon).append(CODON_INFO_DELIM);
|
||||||
|
sb.append(REFSEQ_VARIANT_AA).append(ASSIGNMENT).append(variantAA).append(CODON_INFO_DELIM);
|
||||||
|
sb.append(REFSEQ_CHANGES_AA).append(ASSIGNMENT).append(changesAA).append(CODON_INFO_DELIM);
|
||||||
|
sb.append(REFSEQ_FUNCTIONAL_CLASS).append(ASSIGNMENT).append(functionalClass).append(CODON_INFO_DELIM);
|
||||||
|
sb.append(REFSEQ_PROTEIN_COORD_DESCRIPTION).append(ASSIGNMENT).append(proteinCoordStr);
|
||||||
|
sb.append(ALLELE_END);
|
||||||
|
|
||||||
|
return sb.toString();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
// External classes:
|
||||||
|
|
||||||
|
class LocusToFeatures {
|
||||||
|
private Map<GenomeLoc, PositionalRefSeqFeatures> locusToFeatures;
|
||||||
|
|
||||||
|
public LocusToFeatures() {
|
||||||
|
this.locusToFeatures = new TreeMap<GenomeLoc, PositionalRefSeqFeatures>();
|
||||||
|
}
|
||||||
|
|
||||||
|
public PositionalRefSeqFeatures getLocusFeatures(GenomeLoc loc) {
|
||||||
|
return locusToFeatures.get(loc);
|
||||||
|
}
|
||||||
|
|
||||||
|
public void putLocusFeatures(GenomeLoc loc, AnnotatorInputTableFeature refSeqAnnotation, GenomeLoc locusUsingThis) {
|
||||||
|
PositionalRefSeqFeatures locFeatures = locusToFeatures.get(loc);
|
||||||
|
if (locFeatures == null) {
|
||||||
|
locFeatures = new PositionalRefSeqFeatures(locusUsingThis);
|
||||||
|
locusToFeatures.put(loc, locFeatures);
|
||||||
|
}
|
||||||
|
locFeatures.putFeature(refSeqAnnotation, locusUsingThis);
|
||||||
|
}
|
||||||
|
|
||||||
|
public Set<Map.Entry<GenomeLoc, PositionalRefSeqFeatures>> entrySet() {
|
||||||
|
return locusToFeatures.entrySet();
|
||||||
|
}
|
||||||
|
|
||||||
|
public String toString() { // INTERNAL use only
|
||||||
|
StringBuilder sb = new StringBuilder();
|
||||||
|
|
||||||
|
for (Map.Entry<GenomeLoc, PositionalRefSeqFeatures> locFeatures : entrySet()) {
|
||||||
|
GenomeLoc loc = locFeatures.getKey();
|
||||||
|
PositionalRefSeqFeatures features = locFeatures.getValue();
|
||||||
|
sb.append("Locus: ").append(loc).append("\n").append(features);
|
||||||
|
}
|
||||||
|
|
||||||
|
return sb.toString();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
class PositionalRefSeqFeatures {
|
||||||
|
private final static String[] REQUIRE_COLUMNS =
|
||||||
|
{AnnotateMNPsWalker.REFSEQ_NAME, AnnotateMNPsWalker.REFSEQ_POSITION_TYPE};
|
||||||
|
|
||||||
|
private Map<String, PositionalRefSeqFeature> nameToFeature;
|
||||||
|
private GenomeLoc furthestLocusUsingFeatures;
|
||||||
|
|
||||||
|
public PositionalRefSeqFeatures(GenomeLoc locusUsingThis) {
|
||||||
|
this.nameToFeature = new HashMap<String, PositionalRefSeqFeature>();
|
||||||
|
this.furthestLocusUsingFeatures = locusUsingThis;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void putFeature(AnnotatorInputTableFeature refSeqAnnotation, GenomeLoc locusUsingThis) {
|
||||||
|
for (String column : REQUIRE_COLUMNS) {
|
||||||
|
if (!refSeqAnnotation.containsColumnName(column))
|
||||||
|
throw new UserException("In RefSeq: " + refSeqAnnotation + " Missing column " + column);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (locusUsingThis.isPast(furthestLocusUsingFeatures))
|
||||||
|
furthestLocusUsingFeatures = locusUsingThis;
|
||||||
|
|
||||||
|
String posType = refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_POSITION_TYPE);
|
||||||
|
if (!posType.equals(AnnotateMNPsWalker.REFSEQ_CDS)) // only interested in coding sequence annotations
|
||||||
|
return;
|
||||||
|
|
||||||
|
PositionalRefSeqFeature newLocusFeature = new PositionalRefSeqFeature(refSeqAnnotation);
|
||||||
|
|
||||||
|
String refSeqName = refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_NAME);
|
||||||
|
PositionalRefSeqFeature locusFeature = nameToFeature.get(refSeqName);
|
||||||
|
if (locusFeature == null) {
|
||||||
|
locusFeature = newLocusFeature;
|
||||||
|
nameToFeature.put(refSeqName, locusFeature);
|
||||||
|
}
|
||||||
|
else if (!locusFeature.equals(newLocusFeature)) {
|
||||||
|
throw new UserException("Inconsistency between previous RefSeq entry and: " + refSeqAnnotation);
|
||||||
|
}
|
||||||
|
|
||||||
|
locusFeature.updateFeature(refSeqAnnotation);
|
||||||
|
}
|
||||||
|
|
||||||
|
public GenomeLoc getFurthestLocusUsingFeatures() {
|
||||||
|
return furthestLocusUsingFeatures;
|
||||||
|
}
|
||||||
|
|
||||||
|
public Set<Map.Entry<String, PositionalRefSeqFeature>> entrySet() {
|
||||||
|
return nameToFeature.entrySet();
|
||||||
|
}
|
||||||
|
|
||||||
|
public String toString() { // INTERNAL use only
|
||||||
|
StringBuilder sb = new StringBuilder();
|
||||||
|
|
||||||
|
for (Map.Entry<String, PositionalRefSeqFeature> nameFeatureEntry : entrySet()) {
|
||||||
|
String name = nameFeatureEntry.getKey();
|
||||||
|
PositionalRefSeqFeature feature = nameFeatureEntry.getValue();
|
||||||
|
sb.append(name).append(" -> [").append(feature).append("]\n");
|
||||||
|
}
|
||||||
|
|
||||||
|
return sb.toString();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
class PositionalRefSeqFeature {
|
||||||
|
private final static String[] REQUIRE_COLUMNS =
|
||||||
|
{AnnotateMNPsWalker.REFSEQ_NAME2, AnnotateMNPsWalker.REFSEQ_STRAND,
|
||||||
|
AnnotateMNPsWalker.REFSEQ_CODON_COORD, AnnotateMNPsWalker.REFSEQ_CODING_FRAME,
|
||||||
|
AnnotateMNPsWalker.REFSEQ_REF_CODON, AnnotateMNPsWalker.REFSEQ_REF_AA};
|
||||||
|
|
||||||
|
protected String name2;
|
||||||
|
protected boolean positiveStrand;
|
||||||
|
protected int codonCoord;
|
||||||
|
protected int codingFrame;
|
||||||
|
protected String referenceCodon;
|
||||||
|
protected String referenceAA;
|
||||||
|
|
||||||
|
private Map<String, BaseAnnotations> baseToAnnotations;
|
||||||
|
|
||||||
|
public PositionalRefSeqFeature(AnnotatorInputTableFeature refSeqAnnotation) {
|
||||||
|
for (String column : REQUIRE_COLUMNS) {
|
||||||
|
if (!refSeqAnnotation.containsColumnName(column))
|
||||||
|
throw new UserException("In RefSeq: " + refSeqAnnotation + " Missing column " + column);
|
||||||
|
}
|
||||||
|
this.name2 = refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_NAME2);
|
||||||
|
this.positiveStrand = (refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_STRAND).equals(AnnotateMNPsWalker.REFSEQ_POS_STRAND));
|
||||||
|
this.codonCoord = Integer.parseInt(refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_CODON_COORD));
|
||||||
|
this.codingFrame = Integer.parseInt(refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_CODING_FRAME));
|
||||||
|
this.referenceCodon = refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_REF_CODON);
|
||||||
|
this.referenceAA = refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_REF_AA);
|
||||||
|
|
||||||
|
this.baseToAnnotations = new HashMap<String, BaseAnnotations>();
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean equals(PositionalRefSeqFeature that) {
|
||||||
|
return this.name2.equals(that.name2) && this.positiveStrand == that.positiveStrand && this.codonCoord == that.codonCoord && this.codingFrame == that.codingFrame
|
||||||
|
&& this.referenceCodon.equals(that.referenceCodon) && this.referenceAA.equals(that.referenceAA);
|
||||||
|
}
|
||||||
|
|
||||||
|
public void updateFeature(AnnotatorInputTableFeature refSeqAnnotation) {
|
||||||
|
if (!refSeqAnnotation.containsColumnName(AnnotateMNPsWalker.REFSEQ_ALT_BASE))
|
||||||
|
throw new UserException("In RefSeq: " + refSeqAnnotation + " Missing column " + AnnotateMNPsWalker.REFSEQ_ALT_BASE);
|
||||||
|
String base = refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_ALT_BASE);
|
||||||
|
|
||||||
|
baseToAnnotations.put(base, new BaseAnnotations(refSeqAnnotation));
|
||||||
|
}
|
||||||
|
|
||||||
|
public String toString() { // INTERNAL use only
|
||||||
|
StringBuilder sb = new StringBuilder();
|
||||||
|
|
||||||
|
sb.append("name2= ").append(name2);
|
||||||
|
sb.append(", positiveStrand= ").append(positiveStrand);
|
||||||
|
sb.append(", codonCoord= ").append(codonCoord);
|
||||||
|
sb.append(", codingFrame= ").append(codingFrame);
|
||||||
|
sb.append(", referenceCodon= ").append(referenceCodon);
|
||||||
|
sb.append(", referenceAA= ").append(referenceAA);
|
||||||
|
|
||||||
|
sb.append(", baseAnnotations= {");
|
||||||
|
for (Map.Entry<String, BaseAnnotations> baseToAnnotationsEntry : baseToAnnotations.entrySet()) {
|
||||||
|
String base = baseToAnnotationsEntry.getKey();
|
||||||
|
BaseAnnotations annotations = baseToAnnotationsEntry.getValue();
|
||||||
|
sb.append(" ").append(base).append(" -> {").append(annotations).append("}");
|
||||||
|
}
|
||||||
|
sb.append(" }");
|
||||||
|
|
||||||
|
return sb.toString();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
class BaseAnnotations {
|
||||||
|
private final static String[] REQUIRE_COLUMNS =
|
||||||
|
{AnnotateMNPsWalker.REFSEQ_VARIANT_CODON, AnnotateMNPsWalker.REFSEQ_VARIANT_AA,
|
||||||
|
AnnotateMNPsWalker.REFSEQ_CHANGES_AA, AnnotateMNPsWalker.REFSEQ_FUNCTIONAL_CLASS,
|
||||||
|
AnnotateMNPsWalker.REFSEQ_PROTEIN_COORD_DESCRIPTION};
|
||||||
|
|
||||||
|
protected String variantCodon;
|
||||||
|
protected String variantAA;
|
||||||
|
protected boolean changesAA;
|
||||||
|
protected String functionalClass;
|
||||||
|
protected String proteinCoordStr;
|
||||||
|
|
||||||
|
public BaseAnnotations(AnnotatorInputTableFeature refSeqAnnotation) {
|
||||||
|
for (String column : REQUIRE_COLUMNS) {
|
||||||
|
if (!refSeqAnnotation.containsColumnName(column))
|
||||||
|
throw new UserException("In RefSeq: " + refSeqAnnotation + " Missing column " + column);
|
||||||
|
}
|
||||||
|
this.variantCodon = refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_VARIANT_CODON);
|
||||||
|
this.variantAA = refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_VARIANT_AA);
|
||||||
|
this.changesAA = Boolean.parseBoolean(refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_CHANGES_AA));
|
||||||
|
this.functionalClass = refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_FUNCTIONAL_CLASS);
|
||||||
|
this.proteinCoordStr = refSeqAnnotation.getColumnValue(AnnotateMNPsWalker.REFSEQ_PROTEIN_COORD_DESCRIPTION);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
public String toString() { // INTERNAL use only
|
||||||
|
StringBuilder sb = new StringBuilder();
|
||||||
|
|
||||||
|
sb.append("variantCodon= ").append(variantCodon);
|
||||||
|
sb.append(", variantAA= ").append(variantAA);
|
||||||
|
sb.append(", changesAA= ").append(changesAA);
|
||||||
|
sb.append(", functionalClass= ").append(functionalClass);
|
||||||
|
sb.append(", proteinCoordStr= ").append(proteinCoordStr);
|
||||||
|
|
||||||
|
return sb.toString();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -169,14 +169,8 @@ public class MergePhasedSegregatingAlternateAllelesVCFWriter implements VCFWrite
|
||||||
if (shouldMerge) {
|
if (shouldMerge) {
|
||||||
numRecordsSatisfyingMergeRule++;
|
numRecordsSatisfyingMergeRule++;
|
||||||
VariantContext mergedVc = VariantContextUtils.mergeIntoMNP(genomeLocParser, vcfrWaitingToMerge.vc, vc, referenceFileForMNPmerging);
|
VariantContext mergedVc = VariantContextUtils.mergeIntoMNP(genomeLocParser, vcfrWaitingToMerge.vc, vc, referenceFileForMNPmerging);
|
||||||
|
|
||||||
if (mergedVc != null) {
|
if (mergedVc != null) {
|
||||||
mergedRecords = true;
|
mergedRecords = true;
|
||||||
|
|
||||||
Map<String, Object> updatedAttribs = RefSeqData.getMergedRefSeqAttributes(vcfrWaitingToMerge.vc, vc);
|
|
||||||
updatedAttribs.putAll(mergedVc.getAttributes());
|
|
||||||
mergedVc = VariantContext.modifyAttributes(mergedVc, updatedAttribs);
|
|
||||||
|
|
||||||
vcfrWaitingToMerge = new VCFRecord(mergedVc, vcfrWaitingToMerge.refBase, true);
|
vcfrWaitingToMerge = new VCFRecord(mergedVc, vcfrWaitingToMerge.refBase, true);
|
||||||
numMergedRecords++;
|
numMergedRecords++;
|
||||||
}
|
}
|
||||||
|
|
@ -446,132 +440,4 @@ public class MergePhasedSegregatingAlternateAllelesVCFWriter implements VCFWrite
|
||||||
return sb.toString();
|
return sb.toString();
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
/* Some methods for extracting and merging RefSeq-related data from annotated VCF INFO fields:
|
|
||||||
*/
|
|
||||||
|
|
||||||
class RefSeqData {
|
|
||||||
private static String REFSEQ_PREFIX = "refseq.";
|
|
||||||
|
|
||||||
private static String NUM_RECORDS_KEY = REFSEQ_PREFIX + "numMatchingRecords";
|
|
||||||
private static String NAME_KEY = REFSEQ_PREFIX + "name";
|
|
||||||
private static String NAME2_KEY = REFSEQ_PREFIX + "name2";
|
|
||||||
|
|
||||||
private static String CODON_KEY = REFSEQ_PREFIX + "codonCoord";
|
|
||||||
|
|
||||||
private static Map<String, String> getRefSeqEntriesToNames(VariantContext vc, boolean getName2) {
|
|
||||||
Map<String, String> entriesToNames = new HashMap<String, String>();
|
|
||||||
|
|
||||||
Integer numRecords = vc.getAttributeAsIntegerNoException(NUM_RECORDS_KEY);
|
|
||||||
if (numRecords != null) {
|
|
||||||
for (int i = 1; i <= numRecords; i++) {
|
|
||||||
String key = NAME_KEY + "_" + i;
|
|
||||||
String name = vc.getAttributeAsStringNoException(key);
|
|
||||||
if (name != null)
|
|
||||||
entriesToNames.put(key, name);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
else {
|
|
||||||
String name = vc.getAttributeAsStringNoException(NAME_KEY);
|
|
||||||
if (name != null) {
|
|
||||||
entriesToNames.put(NAME_KEY, name);
|
|
||||||
}
|
|
||||||
else { // Check all INFO fields for a match:
|
|
||||||
for (Map.Entry<String, Object> entry : vc.getAttributes().entrySet()) {
|
|
||||||
String key = entry.getKey();
|
|
||||||
if (getName2 && key.startsWith(NAME2_KEY))
|
|
||||||
entriesToNames.put(key, entry.getValue().toString());
|
|
||||||
else if (key.startsWith(NAME_KEY) && !key.startsWith(NAME2_KEY))
|
|
||||||
entriesToNames.put(key, entry.getValue().toString());
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
return entriesToNames;
|
|
||||||
}
|
|
||||||
|
|
||||||
private static Map<String, String> getRefSeqEntriesToNames(VariantContext vc) {
|
|
||||||
return getRefSeqEntriesToNames(vc, false);
|
|
||||||
}
|
|
||||||
|
|
||||||
public static Set<String> getRefSeqNames(VariantContext vc, boolean getName2) {
|
|
||||||
return new TreeSet<String>(getRefSeqEntriesToNames(vc, getName2).values());
|
|
||||||
}
|
|
||||||
|
|
||||||
public static Set<String> getRefSeqNames(VariantContext vc) {
|
|
||||||
return getRefSeqNames(vc, false);
|
|
||||||
}
|
|
||||||
|
|
||||||
public static Map<String, Object> getMergedRefSeqAttributes(VariantContext vc1, VariantContext vc2) {
|
|
||||||
Map<String, Object> refSeqAttribs = new HashMap<String, Object>();
|
|
||||||
|
|
||||||
List<RefSeqEntry> list1 = getAllRefSeqEntries(vc1);
|
|
||||||
List<RefSeqEntry> list2 = getAllRefSeqEntries(vc2);
|
|
||||||
boolean addSuffix = list1.size() > 1 || list2.size() > 1;
|
|
||||||
int count = 1;
|
|
||||||
|
|
||||||
for (RefSeqEntry refseq1 : list1) {
|
|
||||||
for (RefSeqEntry refseq2 : list2) {
|
|
||||||
Set<String> keys = new HashSet<String>();
|
|
||||||
keys.addAll(refseq1.info.keySet());
|
|
||||||
keys.addAll(refseq2.info.keySet());
|
|
||||||
|
|
||||||
String keySuffix = "";
|
|
||||||
if (addSuffix)
|
|
||||||
keySuffix = "_" + count++;
|
|
||||||
|
|
||||||
Object name1 = refseq1.info.get(NAME_KEY);
|
|
||||||
Object name2 = refseq2.info.get(NAME_KEY);
|
|
||||||
boolean sameGene = name1 != null && name2 != null && name1.equals(name2);
|
|
||||||
|
|
||||||
for (String key : keys) {
|
|
||||||
Object obj1 = refseq1.info.get(key);
|
|
||||||
Object obj2 = refseq2.info.get(key);
|
|
||||||
if (obj1 == null)
|
|
||||||
obj1 = "";
|
|
||||||
if (obj2 == null)
|
|
||||||
obj2 = "";
|
|
||||||
|
|
||||||
if (sameGene && key.equals(CODON_KEY) && obj1.equals(obj2)) // vc1 and vc2 have variants in the same codon in the same gene
|
|
||||||
System.out.println(vc1.getChr() + ":" + vc1.getStart() + " --> CODON: obj1 = " + obj1);
|
|
||||||
|
|
||||||
String useKey = key + keySuffix;
|
|
||||||
String mergedVal = obj1 + "\\" + obj2;
|
|
||||||
refSeqAttribs.put(useKey, mergedVal);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
return refSeqAttribs;
|
|
||||||
}
|
|
||||||
|
|
||||||
private static List<RefSeqEntry> getAllRefSeqEntries(VariantContext vc) {
|
|
||||||
List<RefSeqEntry> allRefSeq = new LinkedList<RefSeqEntry>();
|
|
||||||
|
|
||||||
for (Map.Entry<String, String> entryToName : getRefSeqEntriesToNames(vc).entrySet()) {
|
|
||||||
String entry = entryToName.getKey();
|
|
||||||
String entrySuffix = entry.replaceFirst(NAME_KEY, "");
|
|
||||||
allRefSeq.add(new RefSeqEntry(vc, entrySuffix));
|
|
||||||
}
|
|
||||||
|
|
||||||
return allRefSeq;
|
|
||||||
}
|
|
||||||
|
|
||||||
private static class RefSeqEntry {
|
|
||||||
public Map<String, Object> info;
|
|
||||||
|
|
||||||
public RefSeqEntry(VariantContext vc, String entrySuffix) {
|
|
||||||
this.info = new HashMap<String, Object>();
|
|
||||||
|
|
||||||
for (Map.Entry<String, Object> attribEntry : vc.getAttributes().entrySet()) {
|
|
||||||
String key = attribEntry.getKey();
|
|
||||||
if (key.startsWith(REFSEQ_PREFIX) && key.endsWith(entrySuffix)) {
|
|
||||||
String genericKey = key.replaceAll(entrySuffix, "");
|
|
||||||
this.info.put(genericKey, attribEntry.getValue());
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
@ -70,12 +70,12 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
|
||||||
@Argument(fullName = "disablePrintAltAlleleStats", shortName = "noAlleleStats", doc = "Should the print-out of alternate allele statistics be disabled?; [default:false]", required = false)
|
@Argument(fullName = "disablePrintAltAlleleStats", shortName = "noAlleleStats", doc = "Should the print-out of alternate allele statistics be disabled?; [default:false]", required = false)
|
||||||
protected boolean disablePrintAlternateAlleleStatistics = false;
|
protected boolean disablePrintAlternateAlleleStatistics = false;
|
||||||
|
|
||||||
public final static String IGNORE_CODING = "IGNORE";
|
public final static String IGNORE_REFSEQ = "IGNORE";
|
||||||
public final static String UNION_CODING = "UNION";
|
public final static String UNION_REFSEQ = "UNION";
|
||||||
public final static String INTERSECT_CODING = "INTERSECT";
|
public final static String INTERSECT_REFSEQ = "INTERSECT";
|
||||||
|
|
||||||
@Argument(fullName = "mergeBasedOnCodingAnnotation", shortName = "mergeBasedOnCodingAnnotation", doc = "'Should merging be performed if two sites lie on the same coding sequence in the INFO field {" + IGNORE_CODING + ", " + UNION_CODING + ", " + INTERSECT_CODING + "}; [default:"+ IGNORE_CODING + "]", required = false)
|
@Argument(fullName = "mergeBasedOnRefSeqAnnotation", shortName = "mergeBasedOnRefSeqAnnotation", doc = "'Should merging be performed if two sites lie on the same RefSeq sequence in the INFO field {" + IGNORE_REFSEQ + ", " + UNION_REFSEQ + ", " + INTERSECT_REFSEQ + "}; [default:"+ IGNORE_REFSEQ + "]", required = false)
|
||||||
protected String mergeBasedOnCodingAnnotation = IGNORE_CODING;
|
protected String mergeBasedOnRefSeqAnnotation = IGNORE_REFSEQ;
|
||||||
|
|
||||||
private LinkedList<String> rodNames = null;
|
private LinkedList<String> rodNames = null;
|
||||||
|
|
||||||
|
|
@ -90,10 +90,10 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
|
||||||
GenomeLocParser genomeLocParser = getToolkit().getGenomeLocParser();
|
GenomeLocParser genomeLocParser = getToolkit().getGenomeLocParser();
|
||||||
|
|
||||||
MergeRule mergeRule = null;
|
MergeRule mergeRule = null;
|
||||||
if (mergeBasedOnCodingAnnotation.equals(IGNORE_CODING))
|
if (mergeBasedOnRefSeqAnnotation.equals(IGNORE_REFSEQ))
|
||||||
mergeRule = new DistanceMergeRule(maxGenomicDistanceForMNP, genomeLocParser);
|
mergeRule = new DistanceMergeRule(maxGenomicDistanceForMNP, genomeLocParser);
|
||||||
else
|
else
|
||||||
mergeRule = new SameGenePlusWithinDistanceMergeRule(maxGenomicDistanceForMNP, genomeLocParser, mergeBasedOnCodingAnnotation);
|
mergeRule = new SameGenePlusWithinDistanceMergeRule(maxGenomicDistanceForMNP, genomeLocParser, mergeBasedOnRefSeqAnnotation);
|
||||||
|
|
||||||
// false <-> don't take control of writer, since didn't create it:
|
// false <-> don't take control of writer, since didn't create it:
|
||||||
vcMergerWriter = new MergePhasedSegregatingAlternateAllelesVCFWriter(writer,genomeLocParser, getToolkit().getArguments().referenceFile, mergeRule, useSingleSample, emitOnlyMergedRecords, logger, false, !disablePrintAlternateAlleleStatistics);
|
vcMergerWriter = new MergePhasedSegregatingAlternateAllelesVCFWriter(writer,genomeLocParser, getToolkit().getArguments().referenceFile, mergeRule, useSingleSample, emitOnlyMergedRecords, logger, false, !disablePrintAlternateAlleleStatistics);
|
||||||
|
|
@ -175,7 +175,7 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
enum MergeBasedOnCodingAnnotation {
|
enum MergeBasedOnRefSeqAnnotation {
|
||||||
UNION_WITH_DIST, INTERSECT_WITH_DIST
|
UNION_WITH_DIST, INTERSECT_WITH_DIST
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -206,45 +206,45 @@ class DistanceMergeRule implements MergeRule {
|
||||||
}
|
}
|
||||||
|
|
||||||
class SameGenePlusWithinDistanceMergeRule extends DistanceMergeRule {
|
class SameGenePlusWithinDistanceMergeRule extends DistanceMergeRule {
|
||||||
private MergeBasedOnCodingAnnotation mergeBasedOnCodingAnnotation;
|
private MergeBasedOnRefSeqAnnotation mergeBasedOnRefSeqAnnotation;
|
||||||
|
|
||||||
public SameGenePlusWithinDistanceMergeRule(int maxGenomicDistanceForMNP, GenomeLocParser genomeLocParser, String mergeBasedOnCodingAnnotation) {
|
public SameGenePlusWithinDistanceMergeRule(int maxGenomicDistanceForMNP, GenomeLocParser genomeLocParser, String mergeBasedOnRefSeqAnnotation) {
|
||||||
super(maxGenomicDistanceForMNP, genomeLocParser);
|
super(maxGenomicDistanceForMNP, genomeLocParser);
|
||||||
|
|
||||||
if (mergeBasedOnCodingAnnotation.equals(MergeSegregatingAlternateAllelesWalker.UNION_CODING))
|
if (mergeBasedOnRefSeqAnnotation.equals(MergeSegregatingAlternateAllelesWalker.UNION_REFSEQ))
|
||||||
this.mergeBasedOnCodingAnnotation = MergeBasedOnCodingAnnotation.UNION_WITH_DIST;
|
this.mergeBasedOnRefSeqAnnotation = MergeBasedOnRefSeqAnnotation.UNION_WITH_DIST;
|
||||||
else if (mergeBasedOnCodingAnnotation.equals(MergeSegregatingAlternateAllelesWalker.INTERSECT_CODING))
|
else if (mergeBasedOnRefSeqAnnotation.equals(MergeSegregatingAlternateAllelesWalker.INTERSECT_REFSEQ))
|
||||||
this.mergeBasedOnCodingAnnotation = MergeBasedOnCodingAnnotation.INTERSECT_WITH_DIST;
|
this.mergeBasedOnRefSeqAnnotation = MergeBasedOnRefSeqAnnotation.INTERSECT_WITH_DIST;
|
||||||
else
|
else
|
||||||
throw new UserException("Must provide " + MergeSegregatingAlternateAllelesWalker.IGNORE_CODING + ", " + MergeSegregatingAlternateAllelesWalker.UNION_CODING + ", or " + MergeSegregatingAlternateAllelesWalker.INTERSECT_CODING + " as argument to mergeBasedOnCodingAnnotation!");
|
throw new UserException("Must provide " + MergeSegregatingAlternateAllelesWalker.IGNORE_REFSEQ + ", " + MergeSegregatingAlternateAllelesWalker.UNION_REFSEQ + ", or " + MergeSegregatingAlternateAllelesWalker.INTERSECT_REFSEQ + " as argument to mergeBasedOnRefSeqAnnotation!");
|
||||||
}
|
}
|
||||||
|
|
||||||
public boolean shouldMerge(VariantContext vc1, VariantContext vc2) {
|
public boolean shouldMerge(VariantContext vc1, VariantContext vc2) {
|
||||||
boolean withinDistance = super.shouldMerge(vc1, vc2);
|
boolean withinDistance = super.shouldMerge(vc1, vc2);
|
||||||
|
|
||||||
if (mergeBasedOnCodingAnnotation == MergeBasedOnCodingAnnotation.UNION_WITH_DIST)
|
if (mergeBasedOnRefSeqAnnotation == MergeBasedOnRefSeqAnnotation.UNION_WITH_DIST)
|
||||||
return withinDistance || sameGene(vc1, vc2);
|
return withinDistance || sameGene(vc1, vc2);
|
||||||
else // mergeBasedOnCodingAnnotation == MergeBasedOnCodingAnnotation.INTERSECT_WITH_DIST
|
else // mergeBasedOnRefSeqAnnotation == MergeBasedOnRefSeqAnnotation.INTERSECT_WITH_DIST
|
||||||
return withinDistance && sameGene(vc1, vc2);
|
return withinDistance && sameGene(vc1, vc2);
|
||||||
}
|
}
|
||||||
|
|
||||||
private boolean sameGene(VariantContext vc1, VariantContext vc2) {
|
private boolean sameGene(VariantContext vc1, VariantContext vc2) {
|
||||||
Set<String> names_vc1 = RefSeqData.getRefSeqNames(vc1);
|
Set<String> names_vc1 = RefSeqDataParser.getRefSeqNames(vc1);
|
||||||
Set<String> names_vc2 = RefSeqData.getRefSeqNames(vc2);
|
Set<String> names_vc2 = RefSeqDataParser.getRefSeqNames(vc2);
|
||||||
names_vc1.retainAll(names_vc2);
|
names_vc1.retainAll(names_vc2);
|
||||||
|
|
||||||
if (!names_vc1.isEmpty())
|
if (!names_vc1.isEmpty())
|
||||||
return true;
|
return true;
|
||||||
|
|
||||||
// Check refseq.name2:
|
// Check refseq.name2:
|
||||||
Set<String> names2_vc1 = RefSeqData.getRefSeqNames(vc1, true);
|
Set<String> names2_vc1 = RefSeqDataParser.getRefSeqNames(vc1, true);
|
||||||
Set<String> names2_vc2 = RefSeqData.getRefSeqNames(vc2, true);
|
Set<String> names2_vc2 = RefSeqDataParser.getRefSeqNames(vc2, true);
|
||||||
names2_vc1.retainAll(names2_vc2);
|
names2_vc1.retainAll(names2_vc2);
|
||||||
|
|
||||||
return !names2_vc1.isEmpty();
|
return !names2_vc1.isEmpty();
|
||||||
}
|
}
|
||||||
|
|
||||||
public String toString() {
|
public String toString() {
|
||||||
return super.toString() + " " + (mergeBasedOnCodingAnnotation == MergeBasedOnCodingAnnotation.UNION_WITH_DIST ? "OR" : "AND") + " on the same gene";
|
return super.toString() + " " + (mergeBasedOnRefSeqAnnotation == MergeBasedOnRefSeqAnnotation.UNION_WITH_DIST ? "OR" : "AND") + " on the same gene";
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
@ -543,7 +543,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
|
||||||
}
|
}
|
||||||
|
|
||||||
private class EdgeToReads {
|
private class EdgeToReads {
|
||||||
private Map<GraphEdge, List<String>> edgeReads;
|
private TreeMap<GraphEdge, List<String>> edgeReads;
|
||||||
|
|
||||||
public EdgeToReads() {
|
public EdgeToReads() {
|
||||||
this.edgeReads = new TreeMap<GraphEdge, List<String>>(); // implemented GraphEdge.compareTo()
|
this.edgeReads = new TreeMap<GraphEdge, List<String>>(); // implemented GraphEdge.compareTo()
|
||||||
|
|
@ -1196,7 +1196,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
|
||||||
}
|
}
|
||||||
|
|
||||||
public static PhasingTable marginalizeAsNewTable(PhasingTable table) {
|
public static PhasingTable marginalizeAsNewTable(PhasingTable table) {
|
||||||
Map<Haplotype, PreciseNonNegativeDouble> hapMap = new TreeMap<Haplotype, PreciseNonNegativeDouble>();
|
TreeMap<Haplotype, PreciseNonNegativeDouble> hapMap = new TreeMap<Haplotype, PreciseNonNegativeDouble>();
|
||||||
for (PhasingTable.PhasingTableEntry pte : table) {
|
for (PhasingTable.PhasingTableEntry pte : table) {
|
||||||
Haplotype rep = pte.getHaplotypeClass().getRepresentative();
|
Haplotype rep = pte.getHaplotypeClass().getRepresentative();
|
||||||
PreciseNonNegativeDouble score = hapMap.get(rep);
|
PreciseNonNegativeDouble score = hapMap.get(rep);
|
||||||
|
|
@ -1383,7 +1383,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
|
||||||
|
|
||||||
private class MultipleBaseCountsWriter {
|
private class MultipleBaseCountsWriter {
|
||||||
private BufferedWriter writer = null;
|
private BufferedWriter writer = null;
|
||||||
private Map<SampleReadLocus, MultipleBaseCounts> multipleBaseCounts = null;
|
private TreeMap<SampleReadLocus, MultipleBaseCounts> multipleBaseCounts = null;
|
||||||
|
|
||||||
public MultipleBaseCountsWriter(File outputMultipleBaseCountsFile) {
|
public MultipleBaseCountsWriter(File outputMultipleBaseCountsFile) {
|
||||||
FileOutputStream output;
|
FileOutputStream output;
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,109 @@
|
||||||
|
/*
|
||||||
|
* Copyright (c) 2010, The Broad Institute
|
||||||
|
*
|
||||||
|
* Permission is hereby granted, free of charge, to any person
|
||||||
|
* obtaining a copy of this software and associated documentation
|
||||||
|
* files (the "Software"), to deal in the Software without
|
||||||
|
* restriction, including without limitation the rights to use,
|
||||||
|
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||||
|
* copies of the Software, and to permit persons to whom the
|
||||||
|
* Software is furnished to do so, subject to the following
|
||||||
|
* conditions:
|
||||||
|
*
|
||||||
|
* The above copyright notice and this permission notice shall be
|
||||||
|
* included in all copies or substantial portions of the Software.
|
||||||
|
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||||
|
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||||
|
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||||
|
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||||
|
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||||
|
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||||
|
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||||
|
* OTHER DEALINGS IN THE SOFTWARE.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package org.broadinstitute.sting.gatk.walkers.phasing;
|
||||||
|
|
||||||
|
import org.broad.tribble.util.variantcontext.VariantContext;
|
||||||
|
import java.util.*;
|
||||||
|
|
||||||
|
/* Some methods for extracting RefSeq-related data from annotated VCF INFO fields:
|
||||||
|
*/
|
||||||
|
public class RefSeqDataParser {
|
||||||
|
private static String REFSEQ_PREFIX = "refseq.";
|
||||||
|
|
||||||
|
private static String NUM_RECORDS_KEY = REFSEQ_PREFIX + "numMatchingRecords";
|
||||||
|
private static String NAME_KEY = REFSEQ_PREFIX + "name";
|
||||||
|
private static String NAME2_KEY = REFSEQ_PREFIX + "name2";
|
||||||
|
|
||||||
|
private static Map<String, String> getRefSeqEntriesToNames(VariantContext vc, boolean getName2) {
|
||||||
|
String nameKeyToUse = getName2 ? NAME2_KEY : NAME_KEY;
|
||||||
|
String nameKeyToUseMultiplePrefix = nameKeyToUse + "_";
|
||||||
|
|
||||||
|
Map<String, String> entriesToNames = new HashMap<String, String>();
|
||||||
|
Integer numRecords = vc.getAttributeAsIntegerNoException(NUM_RECORDS_KEY);
|
||||||
|
if (numRecords != null) {
|
||||||
|
for (int i = 1; i <= numRecords; i++) {
|
||||||
|
String key = nameKeyToUseMultiplePrefix + i;
|
||||||
|
String name = vc.getAttributeAsStringNoException(key);
|
||||||
|
if (name != null)
|
||||||
|
entriesToNames.put(key, name);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
else { // no entry with the # of records:
|
||||||
|
String name = vc.getAttributeAsStringNoException(nameKeyToUse);
|
||||||
|
if (name != null) {
|
||||||
|
entriesToNames.put(nameKeyToUse, name);
|
||||||
|
}
|
||||||
|
else { // Check all INFO fields for a match (if there are multiple entries):
|
||||||
|
for (Map.Entry<String, Object> entry : vc.getAttributes().entrySet()) {
|
||||||
|
String key = entry.getKey();
|
||||||
|
if (key.startsWith(nameKeyToUseMultiplePrefix))
|
||||||
|
entriesToNames.put(key, entry.getValue().toString());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return entriesToNames;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Map<String, String> getRefSeqEntriesToNames(VariantContext vc) {
|
||||||
|
return getRefSeqEntriesToNames(vc, false);
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Set<String> getRefSeqNames(VariantContext vc, boolean getName2) {
|
||||||
|
return new TreeSet<String>(getRefSeqEntriesToNames(vc, getName2).values());
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Set<String> getRefSeqNames(VariantContext vc) {
|
||||||
|
return getRefSeqNames(vc, false);
|
||||||
|
}
|
||||||
|
|
||||||
|
// Returns a List of SEPARATE Map<refseq.ENTRY, refseq.VALUE> for EACH RefSeq annotation (i.e., each gene), stripping out the "_1", "_2", etc.
|
||||||
|
private static List<RefSeqEntry> getAllRefSeqEntries(VariantContext vc) {
|
||||||
|
List<RefSeqEntry> allRefSeq = new LinkedList<RefSeqEntry>();
|
||||||
|
|
||||||
|
for (Map.Entry<String, String> entryToName : getRefSeqEntriesToNames(vc).entrySet()) {
|
||||||
|
String entry = entryToName.getKey();
|
||||||
|
String entrySuffix = entry.replaceFirst(NAME_KEY, "");
|
||||||
|
allRefSeq.add(new RefSeqEntry(vc, entrySuffix));
|
||||||
|
}
|
||||||
|
|
||||||
|
return allRefSeq;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static class RefSeqEntry {
|
||||||
|
public Map<String, Object> info;
|
||||||
|
|
||||||
|
public RefSeqEntry(VariantContext vc, String entrySuffix) {
|
||||||
|
this.info = new HashMap<String, Object>();
|
||||||
|
|
||||||
|
for (Map.Entry<String, Object> attribEntry : vc.getAttributes().entrySet()) {
|
||||||
|
String key = attribEntry.getKey();
|
||||||
|
if (key.startsWith(REFSEQ_PREFIX) && key.endsWith(entrySuffix)) {
|
||||||
|
String genericKey = key.replaceAll(entrySuffix, "");
|
||||||
|
this.info.put(genericKey, attribEntry.getValue());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
Loading…
Reference in New Issue