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*
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package org.broad.igv.plugin.mongovariant;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SAMSequenceRecord;
import org.apache.log4j.Logger;
import org.broad.igv.annotations.ForTesting;
import org.broad.igv.feature.Chromosome;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.track.FeatureSource;
import org.broad.igv.track.Track;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.variant.VariantTrack;
import org.broad.igv.variant.vcf.VCFVariant;
import org.broadinstitute.gatk.tools.walkers.na12878kb.core.*;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.GenomeLocSortedSet;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.VariantContext;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
/**
* User: jacob
* Date: 2012-Dec-14
*/
public class VariantReviewSource implements FeatureSource<VCFVariant> {
private static Logger log = Logger.getLogger(VariantReviewSource.class);
private int featureWindowSize = 1000000;
private NA12878DBArgumentCollection args;
private NA12878KnowledgeBase kb;
private GenomeLocParser parser;
/**
* Whether to return consensus sites only, as opposed to all sites
*/
@ForTesting
boolean consensusOnly = true;
public VariantReviewSource(ResourceLocator locator) {
this.args = new NA12878DBArgumentCollection(locator.getPath());
parser = createGenomeLocParser();
}
private void initKB() {
kb = new NA12878KnowledgeBase(parser, this.args);
log.info("Connected to " + this.args.getLocator());
}
private void closeKB() {
if (kb != null) {
kb.close();
kb = null;
}
}
@Override
protected void finalize() throws Throwable {
super.finalize();
this.closeKB();
}
@Override
public Iterator<VCFVariant> getFeatures(String chr, int start, int end) throws IOException {
if (kb == null) {
initKB();
}
//Convert from 0-based to 1-based
GenomeLoc loc = this.parser.createGenomeLoc(chromoNameToStandard(chr), start + 1, end);
GenomeLocSortedSet glss = new GenomeLocSortedSet(this.parser, loc);
SiteManager manager = new SiteManager(parser, glss, parser.getContigs());
SiteIterator<MongoVariantContext> iterator;
if (consensusOnly) {
iterator = kb.getConsensusSites(manager);
} else {
iterator = kb.getCalls(manager);
}
List<VCFVariant> variants = new ArrayList<VCFVariant>();
while (iterator.hasNext()) {
MongoVariantContext mvc = iterator.next();
MongoVCFVariant vcf = new MongoVCFVariant(mvc, mvc.getChr());
variants.add(vcf);
}
return variants.iterator();
}
@Override
public List<LocusScore> getCoverageScores(String chr, int start, int end, int zoom) {
return null;
}
@Override
public int getFeatureWindowSize() {
return featureWindowSize;
}
@Override
public void setFeatureWindowSize(int size) {
this.featureWindowSize = size;
}
/**
* TODO This chromosome replacement is a hack
* The db uses digits (or X/Y, note the case), IGV uses "chr#"
*
* @param chromoName
* @return
*/
static String chromoNameToStandard(String chromoName) {
if(chromoName.toLowerCase().startsWith("chr")){
return chromoName.substring(3);
}else{
return chromoName;
}
}
private GenomeLocParser createGenomeLocParser() {
SAMSequenceDictionary dict = new SAMSequenceDictionary();
for (Chromosome chr : GenomeManager.getInstance().getCurrentGenome().getChromosomes()) {
dict.addSequence(new SAMSequenceRecord(chromoNameToStandard(chr.getName()), chr.getLength()));
}
return new GenomeLocParser(dict);
}
static MongoVariantContext createMVC(int allele0, int allele1, String callsetName, VariantContext variantContext, TruthStatus truthStatus, boolean isComplexEvent) {
List<Allele> alleleList = variantContext.getAlleles();
MongoGenotype mgt = new MongoGenotype(allele0, allele1);
Genotype gt = mgt.toGenotype(alleleList);
MongoVariantContext mvc = MongoVariantContext.create(callsetName, variantContext, truthStatus, gt);
mvc.setReviewed(true);
mvc.setChr(chromoNameToStandard(mvc.getChr()));
mvc.setIsComplexEvent(isComplexEvent);
mvc.setConfidence(NA12878KnowledgeBase.InputCallsetConfidence.REVIEW.confidence);
return mvc;
}
public static VariantTrack loadVariantReview(ResourceLocator locator, List<Track> newTracks) {
//TODO Figure out how to name the samples properly
List<String> allSamples = Collections.emptyList();
VariantReviewSource source = new VariantReviewSource(locator);
VariantTrack track = new VariantTrack(locator, source, allSamples, false);
track.setRenderer(new VariantReviewRenderer(track));
newTracks.add(track);
track.setMargin(0);
return track;
}
}