diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index a13801c7c..5713432b4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -112,6 +112,13 @@ public class UnifiedArgumentCollection { @Argument(fullName = "multiallelic", shortName = "multiallelic", doc = "Allow the discovery of multiple alleles (SNPs only)", required = false) public boolean MULTI_ALLELIC = false; + /** + * If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES), + * then this site will be skipped and a warning printed. Note that genotyping sites with many alternate alleles is both CPU and memory intensive. + */ + @Argument(fullName = "max_alternate_alleles", shortName = "maxAlleles", doc = "Maximum number of alternate alleles to genotype", required = false) + public int MAX_ALTERNATE_ALLELES = 5; + // indel-related arguments /** * A candidate indel is genotyped (and potentially called) if there are this number of reads with a consensus indel at a site. @@ -150,14 +157,6 @@ public class UnifiedArgumentCollection { @Argument(fullName = "ignoreSNPAlleles", shortName = "ignoreSNPAlleles", doc = "expt", required = false) public boolean IGNORE_SNP_ALLELES = false; - /** - * If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES), - * then this site will be skipped and a warning printed. Note that genotyping sites with many alternate alleles is both CPU and memory intensive. - */ - @Hidden - @Argument(fullName = "max_alternate_alleles", shortName = "maxAlleles", doc = "Maximum number of alternate alleles to genotype", required = false) - public int MAX_ALTERNATE_ALLELES = 5; - // Developers must remember to add any newly added arguments to the list here as well otherwise they won't get changed from their default value! public UnifiedArgumentCollection clone() {