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Can just give PickSequenomProbes a dbsnp rod to mask 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2920 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-03-03 16:50:58 +00:00
parent ca2cd9d4f5
commit 6ca6c98980
1 changed files with 7 additions and 3 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java
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@ -33,9 +33,13 @@ public class PickSequenomProbes extends RefWalker<String, String> {
public void initialize() {
if ( SNP_MASK != null ) {
logger.info("Loading SNP mask... ");
ReferenceOrderedData<TabularROD> snp_mask = new ReferenceOrderedData<TabularROD>("snp_mask",
new java.io.File(SNP_MASK), TabularROD.class);
ReferenceOrderedData snp_mask;
if ( SNP_MASK.contains("dbsnp")) {
snp_mask = new ReferenceOrderedData<rodDbSNP>("snp_mask",new java.io.File(SNP_MASK),rodDbSNP.class);
} else {
snp_mask = new ReferenceOrderedData<TabularROD>("snp_mask",
new java.io.File(SNP_MASK), TabularROD.class);
}
snpMaskIterator = snp_mask.iterator();
}
}