From 087e01a439f223bd0089adb926c07cf4323a4675 Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 18 Nov 2009 18:48:01 +0000 Subject: [PATCH] minor changes for --noSLOD git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2074 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/genotyper/EMGenotypeCalculationModel.java | 2 +- .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EMGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EMGenotypeCalculationModel.java index 8a50d2a94..976deaedd 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EMGenotypeCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EMGenotypeCalculationModel.java @@ -58,7 +58,7 @@ public abstract class EMGenotypeCalculationModel extends GenotypeCalculationMode if ( dbsnp != null ) ((IDBacked)locusdata).setID(dbsnp.getRS_ID()); } - if ( locusdata instanceof SLODBacked ) { + if ( locusdata instanceof SLODBacked && REPORT_SLOD ) { // calculate strand score diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 4102dd64b..902caffc5 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -44,9 +44,6 @@ public class UnifiedArgumentCollection { @Argument(fullName = "poolSize", shortName = "ps", doc = "Number of individuals in the pool (for POOLED model only)", required = false) public int POOLSIZE = 0; - @Argument(fullName = "noSLOD", shortName = "nsl", doc = "If provided, we will not calculate the SLOD", required = false) - public boolean NO_SLOD = false; - // control the output @Argument(fullName = "variant_output_format", shortName = "vf", doc = "Format to be used to represent variants; default is VCF", required = false) public GenotypeWriterFactory.GENOTYPE_FORMAT VAR_FORMAT = GenotypeWriterFactory.GENOTYPE_FORMAT.VCF; @@ -60,6 +57,9 @@ public class UnifiedArgumentCollection { @Argument(fullName = "verbose_mode", shortName = "verbose", doc = "File to print all of the annotated and detailed debugging output", required = false) public String VERBOSE = null; + @Argument(fullName = "noSLOD", shortName = "nsl", doc = "If provided, we will not calculate the SLOD", required = false) + public boolean NO_SLOD = false; + // control the error modes @Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)