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Fixes / TODOs for meaningful results with AFCalculationResult 

-- Right now the state of the AFCaclulationResult can be corrupt (ie, log10 likelihoods can be -Infinity).  Forced me to disable reasonable contracts.  Needs to be thought through
-- exactCallsLog should be optional
-- Update UG integration tests as the calculation of the normalized posteriors is done in a marginally different way so the output is rounded slightly differently.
This commit is contained in:
Mark DePristo 2012-10-03 19:54:27 -07:00
parent 50e4a832ea
commit f6a2ca6e7f
3 changed files with 17 additions and 7 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
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@ -60,6 +60,6 @@ public class StandardCallerArgumentCollection {
public int MAX_ALTERNATE_ALLELES = 3; public int MAX_ALTERNATE_ALLELES = 3;
@Hidden @Hidden
@Argument(shortName = "logExactCalls", doc="x") @Argument(shortName = "logExactCalls", doc="x", required=false)
public File exactCallsLog = null; public File exactCallsLog = null;
} }

18
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationResult.java
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@ -84,7 +84,7 @@ public class AlleleFrequencyCalculationResult {
* *
* @return a log10 prob * @return a log10 prob
*/ */
@Ensures("result < 0") @Ensures("goodLog10Value(result)")
public double getLog10MLE() { public double getLog10MLE() {
return log10MLE; return log10MLE;
} }
@ -94,7 +94,7 @@ public class AlleleFrequencyCalculationResult {
* *
* @return a log10 prob * @return a log10 prob
*/ */
@Ensures("result < 0") @Ensures("goodLog10Value(result)")
public double getLog10MAP() { public double getLog10MAP() {
return log10MAP; return log10MAP;
} }
@ -185,7 +185,10 @@ public class AlleleFrequencyCalculationResult {
* Get the normalized -- across all AFs -- of AC == 0, NOT LOG10 * Get the normalized -- across all AFs -- of AC == 0, NOT LOG10
* @return * @return
*/ */
@Ensures({"result >= 0.0", "result <= 1.0"}) // TODO -- this ensure cannot be enabled right now because the log10 inputs can be infinity, etc.
// TODO -- we should own these values in a more meaningful way and return good values in the case
// TODO -- where this happens, or instead thrown an error and have a function to say "was this calculation successful
// @Ensures({"result >= 0.0", "result <= 1.0"})
public double getNormalizedPosteriorOfAFzero() { public double getNormalizedPosteriorOfAFzero() {
return getNormalizedPosteriors()[0]; return getNormalizedPosteriors()[0];
} }
@ -194,7 +197,10 @@ public class AlleleFrequencyCalculationResult {
* Get the normalized -- across all AFs -- of AC > 0, NOT LOG10 * Get the normalized -- across all AFs -- of AC > 0, NOT LOG10
* @return * @return
*/ */
@Ensures({"result >= 0.0", "result <= 1.0"}) // TODO -- this ensure cannot be enabled right now because the log10 inputs can be infinity, etc.
// TODO -- we should own these values in a more meaningful way and return good values in the case
// TODO -- where this happens, or instead thrown an error and have a function to say "was this calculation successful
//@Ensures({"result >= 0.0", "result <= 1.0"})
public double getNormalizedPosteriorOfAFGTZero() { public double getNormalizedPosteriorOfAFGTZero() {
return getNormalizedPosteriors()[1]; return getNormalizedPosteriors()[1];
} }
@ -285,4 +291,8 @@ public class AlleleFrequencyCalculationResult {
this.allelesUsedInGenotyping = allelesUsedInGenotyping; this.allelesUsedInGenotyping = allelesUsedInGenotyping;
} }
private static boolean goodLog10Value(final double result) {
return result <= 0.0 || Double.isInfinite(result) || Double.isNaN(result);
}
} }

4
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -182,12 +182,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test @Test
public void testOutputParameterAllConfident() { public void testOutputParameterAllConfident() {
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "da318257d25a02abd26a3348421c3c69"); testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "7bb6375fddc461c72d44f261f6d4b3c7");
} }
@Test @Test
public void testOutputParameterAllSites() { public void testOutputParameterAllSites() {
testOutputParameters("--output_mode EMIT_ALL_SITES", "13c4f01cffbbfac600318be95b3ca02f"); testOutputParameters("--output_mode EMIT_ALL_SITES", "2104dac76fa2a58a92c72b331c7f2095");
} }
private void testOutputParameters(final String args, final String md5) { private void testOutputParameters(final String args, final String md5) {