zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

max_alternate_alleles also ready to be made public

This commit is contained in:
Eric Banks 2011-12-20 12:59:02 -05:00
parent 6f52bd580b
commit 8ade2d6ac2
1 changed files with 7 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

15
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
View File

@ -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() {