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now makes confident reference intervals. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@247 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-04-01 18:46:14 +00:00
parent 6994cca988
commit 675505646d
1 changed files with 58 additions and 8 deletions
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66
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
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@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate; import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.*;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import java.util.List; import java.util.List;
@ -15,7 +16,6 @@ import java.io.PrintStream;
public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate, String> public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate, String>
{ {
@Argument public int N; @Argument public int N;
@Argument public int DOWNSAMPLE; @Argument public int DOWNSAMPLE;
@Argument public String GFF_OUTPUT_FILE; @Argument public String GFF_OUTPUT_FILE;
@ -25,7 +25,6 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
public AlleleFrequencyEstimate map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) public AlleleFrequencyEstimate map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context)
{ {
// Convert context data into bases and 4-base quals
// Convert context data into bases and 4-base quals // Convert context data into bases and 4-base quals
String bases = getBases(context); String bases = getBases(context);
double quals[][] = getOneBaseQuals(context); double quals[][] = getOneBaseQuals(context);
@ -354,16 +353,67 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
return result; return result;
} }
private String confident_interval_start = ""; private String confident_ref_interval_start = "";
private double confident_interval_min_LOD = 0; private double confident_ref_interval_LOD_sum = 0;
private double confident_interval_max_LOD = 0; private double confident_ref_interval_length = 0;
private boolean inside_confident_interval = false; private boolean inside_confident_ref_interval = false;
public String reduceInit()
{
confident_ref_interval_start = "";
confident_ref_interval_LOD_sum = 0;
confident_ref_interval_length = 0;
inside_confident_ref_interval = false;
return "";
}
public String reduceInit() { return ""; }
public String reduce(AlleleFrequencyEstimate alleleFreq, String sum) public String reduce(AlleleFrequencyEstimate alleleFreq, String sum)
{ {
// Print RESULT data for confident calls // Print RESULT data for confident calls
if ((alleleFreq.lodVsRef >= 5) || (alleleFreq.lodVsRef <= -5)) { this.output.print(alleleFreq.asGFFString()); }
if (inside_confident_ref_interval && (alleleFreq.lodVsRef > -5.0))
{
// No longer hom-ref, so output a ref line.
String[] tokens;
tokens = confident_ref_interval_start.split(":");
String contig = tokens[0];
int start = Integer.parseInt(tokens[1]);
tokens = alleleFreq.location.split(":");
int end = Integer.parseInt(tokens[1])-1;
double lod = confident_ref_interval_LOD_sum / confident_ref_interval_length;
output.format("%s\tCALLER\tREFERENCE\t%d\t%d\t%f\t.\t.\tLENGTH %d\n",
contig,
start,
end,
lod,
(int)(confident_ref_interval_length));
inside_confident_ref_interval = false;
}
else if (inside_confident_ref_interval && (alleleFreq.lodVsRef <= -5.0))
{
// Still hom-ref so increment the counters.
confident_ref_interval_LOD_sum += alleleFreq.lodVsRef;
confident_ref_interval_length += 1;
}
else if ((!inside_confident_ref_interval) && (alleleFreq.lodVsRef > -5.0))
{
// do nothing.
}
else if ((!inside_confident_ref_interval) && (alleleFreq.lodVsRef <= -5.0))
{
// We moved into a hom-ref region so start a new interval.
confident_ref_interval_start = alleleFreq.location;
confident_ref_interval_LOD_sum = alleleFreq.lodVsRef;
confident_ref_interval_length = 1;
inside_confident_ref_interval = true;
}
if (alleleFreq.lodVsRef >= 5) { this.output.print(alleleFreq.asGFFString()); }
return ""; return "";
} }