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Alteration to CoverageAndPowerWalker. It can now be flagged with -uc which will cause it to print not only the coverage on each strand that exceeds the quality score threshold, but also the total coverage on each strand as well. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1588 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-09-11 17:55:44 +00:00
parent 702ba553d6
commit c3f77acd5e
1 changed files with 19 additions and 2 deletions
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21
java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/CoverageAndPowerWalker.java
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@ -40,6 +40,9 @@ public class CoverageAndPowerWalker extends LocusWalker<Pair<Integer, Integer>,
@Argument(fullName="minQScore", shortName="qm", doc="Threshold for the minimum quality score, filter out bases below",required=false) @Argument(fullName="minQScore", shortName="qm", doc="Threshold for the minimum quality score, filter out bases below",required=false)
public byte minQScore = 0; public byte minQScore = 0;
@Argument(fullName="outputUnthresholdedCoverage", shortName = "uc", doc="Print out the total coverage as well as the coverage above the quality threshold", required = false)
public boolean outputUnthreshCvg = false;
private static final int BOOTSTRAP_ITERATIONS = 300; private static final int BOOTSTRAP_ITERATIONS = 300;
@ -69,11 +72,19 @@ public class CoverageAndPowerWalker extends LocusWalker<Pair<Integer, Integer>,
filteredContext = new AlignmentContext(context.getLocation(),readsFilteredByQuality.getFirst(),readsFilteredByQuality.getSecond()); filteredContext = new AlignmentContext(context.getLocation(),readsFilteredByQuality.getFirst(),readsFilteredByQuality.getSecond());
} }
Pair<Pair<List<SAMRecord>,List<SAMRecord>>,Pair<List<Integer>,List<Integer>>> readsByDirection = PoolUtils.splitReadsByReadDirection(filteredContext.getReads(),filteredContext.getOffsets()); Pair<Pair<List<SAMRecord>,List<SAMRecord>>,Pair<List<Integer>,List<Integer>>> readsByDirection = PoolUtils.splitReadsByReadDirection(filteredContext.getReads(),filteredContext.getOffsets());
if ( ! suppress_printing) { if ( ! suppress_printing && ! outputUnthreshCvg ) {
Pair<double[],byte[]> powers = calculatePower(readsByDirection, useBootstrap, filteredContext); Pair<double[],byte[]> powers = calculatePower(readsByDirection, useBootstrap, filteredContext);
out.printf("%s %d %d %d %d %d %d %f %f %f%n", filteredContext.getLocation(), readsByDirection.getFirst().getFirst().size(), readsByDirection.getFirst().getSecond().size(), out.printf("%s %d %d %d %d %d %d %f %f %f%n", filteredContext.getLocation(), readsByDirection.getFirst().getFirst().size(), readsByDirection.getFirst().getSecond().size(),
filteredContext.getReads().size(), powers.getSecond()[0], powers.getSecond()[1], powers.getSecond()[2], filteredContext.getReads().size(), powers.getSecond()[0], powers.getSecond()[1], powers.getSecond()[2],
powers.getFirst()[0], powers.getFirst()[1], powers.getFirst()[2]); powers.getFirst()[0], powers.getFirst()[1], powers.getFirst()[2]);
} else if (! suppress_printing && outputUnthreshCvg) {
Pair<double[],byte[]> powers = calculatePower(readsByDirection, useBootstrap, filteredContext);
Pair<Pair<List<SAMRecord>,List<SAMRecord>>,Pair<List<Integer>,List<Integer>>> ufReadsByDirection = PoolUtils.splitReadsByReadDirection(context.getReads(),context.getOffsets());
out.printf("%s %d %d %d %d %d %d %d %d %d %f %f %f%n", filteredContext.getLocation(), ufReadsByDirection.getFirst().getFirst().size(),
ufReadsByDirection.getFirst().getSecond().size(), context.getReads().size(),
readsByDirection.getFirst().getFirst().size(), readsByDirection.getFirst().getSecond().size(),
filteredContext.getReads().size(), powers.getSecond()[0], powers.getSecond()[1], powers.getSecond()[2],
powers.getFirst()[0], powers.getFirst()[1], powers.getFirst()[2]);
} }
return new Pair(readsByDirection.getFirst().getFirst().size(),readsByDirection.getFirst().getSecond().size()); return new Pair(readsByDirection.getFirst().getFirst().size(),readsByDirection.getFirst().getSecond().size());
} }
@ -172,7 +183,13 @@ public class CoverageAndPowerWalker extends LocusWalker<Pair<Integer, Integer>,
} }
public String createHeaderString() { public String createHeaderString() {
return "Chrom:Pos ForwardCoverage ReverseCoverage CombinedCoverage ForwardMedianQ ReverseMedianQ CombinedMedianQ PowerForward PowerReverse PowerCombined"; String headString;
if(! outputUnthreshCvg ) {
headString = "Chrom:Pos ForwardCoverage ReverseCoverage CombinedCoverage ForwardMedianQ ReverseMedianQ CombinedMedianQ PowerForward PowerReverse PowerCombined";
} else {
headString = "Chrom:Pos ForwardCoverage ReverseCoverage CombinedCoverage ForwardCoverageAboveThreshold ReverseCoverageAboveThreshold CombinedCoverageAboveThreshold ForwardMedianQ ReverseMedianQ CombinedMedianQ PowerForward PowerReverse PowerCombined";
}
return headString;
} }
public byte getMinQualityScore() { public byte getMinQualityScore() {