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Forgot to change some direct references to variables in SSG. Fixed. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1009 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-15 14:16:18 +00:00
parent 9eeb5f79d4
commit 161c74716c
2 changed files with 4 additions and 4 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/ContrastiveGenotypers.java
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@ -26,7 +26,7 @@ public class ContrastiveGenotypers extends LocusWalker<Integer, Integer> {
caller_1b = new SingleSampleGenotyper();
caller_1b.METRICS_FILE = new File("/dev/stdout");
caller_1b.METRICS_INTERVAL = 6000;
caller_1b.NO_SECONDARY_BASES = false;
caller_1b.IGNORE_SECONDARY_BASES = true;
//caller_1b.retest = false;
//caller_1b.qHom = 0.04;
//caller_1b.qHet = 0.49;
@ -38,7 +38,7 @@ public class ContrastiveGenotypers extends LocusWalker<Integer, Integer> {
caller_4b = new SingleSampleGenotyper();
caller_4b.METRICS_FILE = new File("/dev/stdout");
caller_4b.METRICS_INTERVAL = caller_1b.METRICS_INTERVAL;
caller_4b.NO_SECONDARY_BASES = true;
caller_4b.IGNORE_SECONDARY_BASES = false;
//caller_4b.retest = true;
//caller_4b.qHom = 0.04;
//caller_4b.qHet = 0.49;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
View File

@ -88,8 +88,8 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
caller.VARIANTS_FILE = null;
caller.METRICS_FILE = null;
caller.LOD_THRESHOLD = lodThreshold;
caller.NO_SECONDARY_BASES = false;
caller.PRINT_METRICS = false;
caller.IGNORE_SECONDARY_BASES = true;
caller.SUPPRESS_METRICS = true;
caller.SAMPLE_NAME_REGEX = SAMPLE_NAME_REGEX;
caller.initialize();
caller.variantsOut = individual_output_file;