zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fix for concordance: samples found only in truth no longer kill it. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3160 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-13 21:33:49 +00:00
parent 8573b0bc6f
commit 0b575596f8
1 changed files with 8 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

15
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/GenotypeConcordance.java
View File

@ -5,7 +5,6 @@ import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.contexts.variantcontext.*; import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis; import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.tags.Param;
import org.broadinstitute.sting.playground.utils.report.utils.TableType; import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
@ -369,9 +368,10 @@ class SampleStats implements TableType {
* @param called the called type * @param called the called type
*/ */
public void incrValue(String sample, Genotype.Type truth, Genotype.Type called) { public void incrValue(String sample, Genotype.Type truth, Genotype.Type called) {
if (!concordanceStats.containsKey(sample)) if ( concordanceStats.containsKey(sample) )
concordanceStats.get(sample)[truth.ordinal()][called.ordinal()]++;
else if ( called != Genotype.Type.NO_CALL )
throw new StingException("Sample " + sample + " has not been seen in a previous eval; this analysis module assumes that all samples are present in each variant context"); throw new StingException("Sample " + sample + " has not been seen in a previous eval; this analysis module assumes that all samples are present in each variant context");
concordanceStats.get(sample)[truth.ordinal()][called.ordinal()]++;
} }
/** /**
@ -398,19 +398,20 @@ class SampleStats implements TableType {
Genotype.Type type = Genotype.Type.values()[(y/6)+1]; // get the row type Genotype.Type type = Genotype.Type.values()[(y/6)+1]; // get the row type
// save some repeat work, get the total every time // save some repeat work, get the total every time
long total = 0; long total = 0;
Object[] rowKeys = getRowKeys();
for (int called = 0; called < nGenotypeTypes; called++) for (int called = 0; called < nGenotypeTypes; called++)
total += concordanceStats.get((String) getRowKeys()[x])[type.ordinal()][called]; total += concordanceStats.get(rowKeys[x])[type.ordinal()][called];
// now get the cell they're interested in // now get the cell they're interested in
switch (y % 6) { switch (y % 6) {
case (0): // get the total_true for this type case (0): // get the total_true for this type
return total; return total;
case (1): case (1):
return concordanceStats.get((String)getRowKeys()[x])[type.ordinal()][type.ordinal()]; return concordanceStats.get(rowKeys[x])[type.ordinal()][type.ordinal()];
case (2): case (2):
return total == 0 ? 0.0 : (100.0 * (double) concordanceStats.get((String)getRowKeys()[x])[type.ordinal()][type.ordinal()] / (double) total); return total == 0 ? 0.0 : (100.0 * (double) concordanceStats.get(rowKeys[x])[type.ordinal()][type.ordinal()] / (double) total);
default: default:
return concordanceStats.get((String)getRowKeys()[x])[type.ordinal()][(y % 6) - 3]; return concordanceStats.get(rowKeys[x])[type.ordinal()][(y % 6) - 3];
} }
} }