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fixed estimated Q reported calculation in the gatherer

This commit is contained in:
Mauricio Carneiro 2012-03-29 09:53:47 -04:00
parent 8a9fb514b6
commit f80bd4276a
3 changed files with 8 additions and 8 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java
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@ -109,7 +109,6 @@ public class RecalDatum extends RecalDatumOptimized {
public final void resetCalculatedQualities() {
empiricalQuality = 0.0;
estimatedQReported = 0.0;
}
private double calcExpectedErrors() {

13
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java
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@ -24,7 +24,7 @@ public class RecalibrationReport {
GATKReportTable argumentTable; // keep the argument table untouched just for output purposes
RecalibrationArgumentCollection RAC; // necessary for quantizing qualities with the same parameter | todo -- this should be a new parameter, not necessarily coming from the original table parameter list
private static String UNRECOGNIZED_REPORT_TABLE_EXCEPTION = "Unrecognized table. Did you add an extra required covariate? This is a hard check that needs propagate through the code";
private static String UNRECOGNIZED_REPORT_TABLE_EXCEPTION = "Unrecognized table. Did you add an extra required covariate? This is a hard check.";
public RecalibrationReport(final File RECAL_FILE) {
GATKReport report = new GATKReport(RECAL_FILE);
@ -77,10 +77,11 @@ public class RecalibrationReport {
/**
* Combines two recalibration reports by adding all observations and errors
*
* Note: This method DOES NOT recalculate the empirical qualities and quantized qualities. You have to recalculate them
* after combining. The reason for not calculating it is because this function is inteded for combining a series of
* recalibration reports, and it only makes sense to calculate the empirical qualities and quantized qualities after all
* the recalibration reports have been combined. Having the user recalculate when appropriate, makes this method faster
* Note: This method DOES NOT recalculate the empirical qualities and quantized qualities. You have to recalculate
* them after combining. The reason for not calculating it is because this function is inteded for combining a
* series of recalibration reports, and it only makes sense to calculate the empirical qualities and quantized
* qualities after all the recalibration reports have been combined. Having the user recalculate when appropriate,
* makes this method faster
*
* Note2: The empirical quality reported, however, is recalculated given its simplicity.
*
@ -97,7 +98,7 @@ public class RecalibrationReport {
if (thisDatum == null)
thisDatum = otherDatum; // sometimes the datum in other won't be present in 'this'. So just assign it!
else
thisDatum.increment(otherDatum); // add the two datum objects into 'this'
thisDatum.combine(otherDatum); // add the two datum objects into 'this'
thisDatum.resetCalculatedQualities(); // reset the empirical quality to make sure the user doesn't forget to recalculate it
}
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java
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@ -60,7 +60,7 @@ public class BQSRGathererUnitTest {
* @param factor 1 to test for equality, any other value to multiply the original value and match with the calculated
*/
private void testTablesWithColumnsAndFactor(GATKReportTable original, GATKReportTable calculated, List<String> columnsToTest, int factor) {
for (Object primaryKey : original.getPrimaryKeys()) { // tables don't necessarily have the same primary keys
for (Object primaryKey : original.getPrimaryKeys()) { // tables don't necessarily have the same primary keys
for (String column : columnsToTest) {
Object actual = calculated.get(primaryKey, column);
Object expected = original.get(primaryKey, column);