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minor changes for --noSLOD 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2074 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-11-18 18:48:01 +00:00
parent a70cf2b763
commit 087e01a439
2 changed files with 4 additions and 4 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EMGenotypeCalculationModel.java
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@ -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

6
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
View File

@ -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)