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added "booster" metrics 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1375 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-08-04 20:53:45 +00:00
parent 3a8d923785
commit a5a7d7dab8
1 changed files with 24 additions and 4 deletions
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28
java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
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@ -13,12 +13,14 @@ import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
import java.util.List; import java.util.List;
import java.util.Collection; import java.util.Collection;
import java.io.IOException; import java.io.IOException;
import java.io.File;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.StringUtil; import net.sf.samtools.util.StringUtil;
import net.sf.picard.reference.ReferenceSequence; import net.sf.picard.reference.ReferenceSequence;
import edu.mit.broad.picard.util.Interval; import edu.mit.broad.picard.util.Interval;
import edu.mit.broad.picard.util.OverlapDetector; import edu.mit.broad.picard.util.OverlapDetector;
import edu.mit.broad.picard.directed.IntervalList;
@By(DataSource.REFERENCE) @By(DataSource.REFERENCE)
public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerformanceWalker.TargetInfo> { public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerformanceWalker.TargetInfo> {
@ -31,6 +33,11 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
@Argument(fullName="free_standing_distance", shortName="fsd", required=false, doc="minimum distance to next interval to consider freestanding") @Argument(fullName="free_standing_distance", shortName="fsd", required=false, doc="minimum distance to next interval to consider freestanding")
public Integer FREE_STANDING_DISTANCE = 500; public Integer FREE_STANDING_DISTANCE = 500;
@Argument(fullName="booster", required=false, doc="interval list of booster baits")
public File BOOSTER_FILE;
public Integer BOOSTER_DISTANCE = 250; // how far away can a booster be to "hit" its target?
public static class TargetInfo { public static class TargetInfo {
public int counts = 0; public int counts = 0;
@ -91,7 +98,7 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
@Override @Override
public void onTraversalDone(List<Pair<GenomeLoc, TargetInfo>> results) { public void onTraversalDone(List<Pair<GenomeLoc, TargetInfo>> results) {
out.println("location\tlength\tgc\tavg_coverage\tnormalized_coverage\thit_twice\tfreestanding"); out.println("location\tlength\tgc\tavg_coverage\tnormalized_coverage\thit_twice\tfreestanding\tboosted");
// first zip through and build an overlap detector of all the intervals, so later // first zip through and build an overlap detector of all the intervals, so later
// we can calculate if this interval is free-standing // we can calculate if this interval is free-standing
@ -102,6 +109,15 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
od.addLhs(interval, interval); od.addLhs(interval, interval);
} }
OverlapDetector<Interval> booster = new OverlapDetector<Interval>(-BOOSTER_DISTANCE,0);
if (BOOSTER_FILE != null) {
IntervalList il = IntervalList.fromFile(BOOSTER_FILE);
List<Interval> l = il.getUniqueIntervals();
booster.addAll(l, l);
}
// now zip through and calculate the total average coverage // now zip through and calculate the total average coverage
long totalCoverage = 0; long totalCoverage = 0;
@ -132,12 +148,16 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
double gc = calculateGC(target); double gc = calculateGC(target);
// if there is more than one hit on the overlap detector, it's not freestanding // if there is more than one hit on the overlap detector, it's not freestanding
Collection<Interval> hits = od.getOverlaps(makeInterval(target)); Interval targetInterval = makeInterval(target);
Collection<Interval> hits = od.getOverlaps(targetInterval);
boolean freestanding = (hits.size() == 1); boolean freestanding = (hits.size() == 1);
out.printf("%s:%d-%d\t%d\t%6.4f\t%6.4f\t%6.4f\t%d\t%d\n", boolean boosted = (booster.getOverlaps(targetInterval).size() > 0);
out.printf("%s:%d-%d\t%d\t%6.4f\t%6.4f\t%6.4f\t%d\t%d\t%d\n",
target.getContig(), target.getStart(), target.getStop(), length, gc, target.getContig(), target.getStart(), target.getStop(), length, gc,
avgCoverage, normCoverage, ((ti.hitTwice)?1:0), ((freestanding)?1:0) avgCoverage, normCoverage, ((ti.hitTwice)?1:0), ((freestanding)?1:0), ((boosted)?1:0)
); );