From 6bb7f7e9d815acfd6344e1c161f8ca32565535b2 Mon Sep 17 00:00:00 2001 From: kiran Date: Wed, 10 Jun 2009 14:06:33 +0000 Subject: [PATCH] Commented some stuff out so that things compile. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@963 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/ContrastiveGenotypers.java | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ContrastiveGenotypers.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ContrastiveGenotypers.java index 33a9ffdb1..511a9f187 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ContrastiveGenotypers.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ContrastiveGenotypers.java @@ -30,10 +30,10 @@ public class ContrastiveGenotypers extends LocusWalker { caller_1b.metricsInterval = 6000; caller_1b.printMetrics = false; caller_1b.fourBaseMode = false; - caller_1b.retest = false; - caller_1b.qHom = 0.04; - caller_1b.qHet = 0.49; - caller_1b.qHomNonRef = 0.97; + //caller_1b.retest = false; + //caller_1b.qHom = 0.04; + //caller_1b.qHet = 0.49; + //caller_1b.qHomNonRef = 0.97; caller_1b.lodThreshold = 5.0; caller_1b.initialize(); caller_1b.reduceInit(); @@ -43,10 +43,10 @@ public class ContrastiveGenotypers extends LocusWalker { caller_4b.metricsInterval = caller_1b.metricsInterval; caller_4b.printMetrics = false; caller_4b.fourBaseMode = true; - caller_4b.retest = true; - caller_4b.qHom = 0.04; - caller_4b.qHet = 0.49; - caller_4b.qHomNonRef = 0.97; + //caller_4b.retest = true; + //caller_4b.qHom = 0.04; + //caller_4b.qHet = 0.49; + //caller_4b.qHomNonRef = 0.97; caller_4b.lodThreshold = 5.0; caller_4b.initialize(); caller_4b.reduceInit();