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Misc. debugging functionality to FS calculation (disabled by default)

This commit is contained in:
Mark DePristo 2013-07-24 11:40:28 -04:00
parent 1f86cf13d1
commit ccf0df0fea
1 changed files with 17 additions and 0 deletions
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17
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -81,6 +81,7 @@ import java.util.*;
* <p>The Fisher Strand test may not be calculated for certain complex indel cases or for multi-allelic sites.</p> * <p>The Fisher Strand test may not be calculated for certain complex indel cases or for multi-allelic sites.</p>
*/ */
public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
private final static boolean ENABLE_DEBUGGING = false;
private final static Logger logger = Logger.getLogger(FisherStrand.class); private final static Logger logger = Logger.getLogger(FisherStrand.class);
private static final String FS = "FS"; private static final String FS = "FS";
@ -99,6 +100,8 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
if (vc.isSNP() && stratifiedContexts != null) { if (vc.isSNP() && stratifiedContexts != null) {
final int[][] tableNoFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), -1); final int[][] tableNoFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), -1);
final int[][] tableFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), MIN_QUAL_FOR_FILTERED_TEST); final int[][] tableFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), MIN_QUAL_FOR_FILTERED_TEST);
printTable("unfiltered", tableNoFiltering);
printTable("filtered", tableFiltering);
return pValueForBestTable(tableFiltering, tableNoFiltering); return pValueForBestTable(tableFiltering, tableNoFiltering);
} }
else if (stratifiedPerReadAlleleLikelihoodMap != null) { else if (stratifiedPerReadAlleleLikelihoodMap != null) {
@ -203,6 +206,20 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
logger.info(String.format("%d %d; %d %d : %f", table[0][0], table[0][1], table[1][0], table[1][1], pValue)); logger.info(String.format("%d %d; %d %d : %f", table[0][0], table[0][1], table[1][0], table[1][1], pValue));
} }
/**
* Printing information to logger.info for debugging purposes
*
* @param name the name of the table
* @param table the table itself
*/
private void printTable(final String name, final int[][] table) {
if ( ENABLE_DEBUGGING ) {
final String pValue = (String)annotationForOneTable(pValueForContingencyTable(table)).get(FS);
logger.info(String.format("FS %s (REF+, REF-, ALT+, ALT-) = (%d, %d, %d, %d) = %s",
name, table[0][0], table[0][1], table[1][0], table[1][1], pValue));
}
}
private static boolean rotateTable(int[][] table) { private static boolean rotateTable(int[][] table) {
table[0][0] -= 1; table[0][0] -= 1;
table[1][0] += 1; table[1][0] += 1;