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Remove REF_N status from DiagnoseTargets 

This is not really feasible with the current mandate of this walker. We would have to traverse by reference and that would make the runtime much higher, and we are not really interested in the status 99% of the time anyway. There are other walkers that can report this, and just this, status more cheaply.

[fixes #48442663]
This commit is contained in:
Mauricio Carneiro 2013-04-20 14:42:33 -04:00
parent 2b923f1568
commit b3c0abd9e8
4 changed files with 2 additions and 11 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java
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@ -54,8 +54,6 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
*/
public enum CallableStatus {
REF_N("the reference base was an N, which is not considered callable the GATK"),
PASS("the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE"),
COVERAGE_GAPS("absolutely no coverage was observed at a locus, regardless of the filtering parameters"),

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/IntervalStatistics.java
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@ -154,9 +154,6 @@ class IntervalStatistics {
output.add(status);
}
if (hasNref)
output.add(CallableStatus.REF_N);
// get median DP of each sample
final double minMedianDepth = thresholds.getLowMedianDepthThreshold() * samples.size();
final int nSamples = samples.size();

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java
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@ -139,10 +139,6 @@ class SampleStatistics {
if ((totals.get(CallableStatus.POOR_QUALITY) / intervalSize) >= thresholds.getQualityStatusThreshold())
output.add(CallableStatus.POOR_QUALITY);
if (totals.get(CallableStatus.REF_N) > 0)
output.add(CallableStatus.REF_N);
if (output.isEmpty()) {
output.add(CallableStatus.PASS);
}

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java
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@ -66,11 +66,11 @@ public class DiagnoseTargetsIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testSingleSample() {
DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "bd614643284a849724bf8ee6bc4df8bf");
DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "3d558ec8828c269774ee45e5df086a5f");
}
@Test(enabled = true)
public void testMultiSample() {
DTTest("testMultiSample ", "-I " + multiSample, "145f5d4641abfdeadbc59ee74ce1560f");
DTTest("testMultiSample ", "-I " + multiSample, "d40cf1f1daf68f2740cd411e2cf361fc");
}
}