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Updating default value for -mindel to the one used by Khalid in the pipeline and me in my tests.

This commit is contained in:
Eric Banks 2012-07-10 02:04:26 -04:00
parent 7eb45b4038
commit d7bf74fb7e
2 changed files with 3 additions and 3 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
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@ -173,7 +173,7 @@ public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, Red
* considered consensus. * considered consensus.
*/ */
@Argument(fullName = "minimum_del_proportion_to_trigger_variant", shortName = "mindel", doc = "", required = false) @Argument(fullName = "minimum_del_proportion_to_trigger_variant", shortName = "mindel", doc = "", required = false)
protected double minIndelProportionToTriggerVariant = 0.01; protected double minIndelProportionToTriggerVariant = 0.05;
/** /**
* Downsamples the coverage of a variable region approximately (guarantees the minimum to be equal to this). * Downsamples the coverage of a variable region approximately (guarantees the minimum to be equal to this).

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
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@ -21,13 +21,13 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
@Test(enabled = true) @Test(enabled = true)
public void testDefaultCompression() { public void testDefaultCompression() {
RRTest("testDefaultCompression ", L, "887d05e3bdbe831a2584305088806a39"); RRTest("testDefaultCompression ", L, "323dd4deabd7767efa0f2c6e7fa4189f");
} }
@Test(enabled = true) @Test(enabled = true)
public void testMultipleIntervals() { public void testMultipleIntervals() {
String intervals = "-L 20:10,100,000-10,100,500 -L 20:10,200,000-10,200,500 -L 20:10,300,000-10,300,500 -L 20:10,400,000-10,500,000 -L 20:10,500,050-10,500,060 -L 20:10,600,000-10,600,015 -L 20:10,700,000-10,700,110"; String intervals = "-L 20:10,100,000-10,100,500 -L 20:10,200,000-10,200,500 -L 20:10,300,000-10,300,500 -L 20:10,400,000-10,500,000 -L 20:10,500,050-10,500,060 -L 20:10,600,000-10,600,015 -L 20:10,700,000-10,700,110";
RRTest("testMultipleIntervals ", intervals, "04208b8e2c2e65bcb9d0eb038702b006"); RRTest("testMultipleIntervals ", intervals, "c437fb160547ff271f8eba30e5f3ff76");
} }
@Test(enabled = true) @Test(enabled = true)