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Modifications to NQSClusteredZScoreWalker to output empirical mismatch rates on bins by both Z-score and reported Q-score, rather than averaging over all Q-score bins for each Z-score. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1773 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-07 13:45:12 +00:00
parent 8dd0924b37
commit 225b9bccc1
1 changed files with 15 additions and 20 deletions
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35
java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSClusteredZScoreWalker.java
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@ -21,8 +21,8 @@ import net.sf.samtools.SAMRecord;
*/
public class NQSClusteredZScoreWalker extends LocusWalker<LocalMapType, int[][][]> {
static final int WIN_SIDE_SIZE = 5;
static final int Z_SCORE_MAX = 7;
static final int Z_SCORE_MULTIPLIER = 30; // bins are Z_SCORE * (this) rounded to the nearst int
static final int Z_SCORE_MAX = 8;
static final int Z_SCORE_MULTIPLIER = 50; // bins are Z_SCORE * (this) rounded to the nearst int
static final int MM_OFFSET = 1;
static final int MATCH_OFFSET = 0;
static final int MAX_Q_SCORE = 2 + QualityUtils.MAX_REASONABLE_Q_SCORE;
@ -68,7 +68,9 @@ public class NQSClusteredZScoreWalker extends LocusWalker<LocalMapType, int[][][
public void onTraversalDone( int[][][] zScoreBins ) {
out.print( header() );
for ( int i = 0; i < Z_SCORE_MAX*Z_SCORE_MULTIPLIER; i ++ ) {
out.print( formatData(zScoreBins[i],i) );
for ( int j = 0; j < MAX_Q_SCORE; j ++ ) {
out.print( formatData(zScoreBins[i][j], i, j) );
}
}
}
@ -133,27 +135,20 @@ public class NQSClusteredZScoreWalker extends LocusWalker<LocalMapType, int[][][
return String.format(format, "ZScore", "N_obs", "Expected_Mismatch", "Empirical_Mismatch", "Expected_MM_As_Q", "Empirical_MM_As_Q");
}
public String formatData ( int[][] matchMismatchQ, int zScoreBin ) {
double zScore = ( (double) zScoreBin )/Z_SCORE_MULTIPLIER;
int match = 0;
int mismatch = 0;
double expMMR = 0.0;
public String formatData ( int[] matchMismatch, int zScoreBin, int q ) {
String format = "%f\t%d\t%f\t%f\t%d\t%d%n";
for ( int i = 0; i < MAX_Q_SCORE; i ++ ) {
match += matchMismatchQ[i][MATCH_OFFSET];
mismatch += matchMismatchQ[i][MM_OFFSET];
expMMR += QualityUtils.qualToErrorProb((byte)i)*matchMismatchQ[i][MATCH_OFFSET];
expMMR += QualityUtils.qualToErrorProb((byte)i)*matchMismatchQ[i][MM_OFFSET];
}
expMMR = (expMMR / ( match + mismatch ));
double empMMR = ((double) mismatch)/(match + mismatch);
int expMMRAsQ = QualityUtils.probToQual(1-expMMR);
int empMMRAsQ = QualityUtils.probToQual(1-empMMR);
String format = "%f\t%d\t%f\t%f\t%d\t%d%n";
}
double zScore = ( (double) zScoreBin )/Z_SCORE_MULTIPLIER;
int counts = matchMismatch[MATCH_OFFSET] + matchMismatch[MM_OFFSET];
double empMMR = (((double)matchMismatch[MM_OFFSET])/counts);
double expMMR = QualityUtils.qualToErrorProb((byte) q);
int empMMRAsQ = QualityUtils.probToQual(1-empMMR);
return String.format(format, zScore, match+mismatch, expMMR, empMMR, expMMRAsQ, empMMRAsQ);
return String.format(format, zScore, counts, expMMR, empMMR, q, empMMRAsQ);
}
}