From d7bf74fb7eed48f018cd2c45b88eb69ab694ddad Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 10 Jul 2012 02:04:26 -0400 Subject: [PATCH] Updating default value for -mindel to the one used by Khalid in the pipeline and me in my tests. --- .../walkers/compression/reducereads/ReduceReadsWalker.java | 2 +- .../compression/reducereads/ReduceReadsIntegrationTest.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java index 51993e1f2..095149bae 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java @@ -173,7 +173,7 @@ public class ReduceReadsWalker extends ReadWalker, Red * considered consensus. */ @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). diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java index 0a62afdc0..08f7ddd37 100755 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java @@ -21,13 +21,13 @@ public class ReduceReadsIntegrationTest extends WalkerTest { @Test(enabled = true) public void testDefaultCompression() { - RRTest("testDefaultCompression ", L, "887d05e3bdbe831a2584305088806a39"); + RRTest("testDefaultCompression ", L, "323dd4deabd7767efa0f2c6e7fa4189f"); } @Test(enabled = true) 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"; - RRTest("testMultipleIntervals ", intervals, "04208b8e2c2e65bcb9d0eb038702b006"); + RRTest("testMultipleIntervals ", intervals, "c437fb160547ff271f8eba30e5f3ff76"); } @Test(enabled = true)