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Updated documentation 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2362 348d0f76-0448-11de-a6fe-93d51630548a
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sjia 2009-12-15 20:33:38 +00:00
parent 4148991d81
commit 4322beeb35
1 changed files with 4 additions and 3 deletions
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7
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java
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@ -1,5 +1,5 @@
/* /**
* FindClosestAlleleWalker finds the most similar HLA allele per read * Finds the most similar HLA allele for each read. Usage: java -jar GenomeAnalysisTK.jar -T FindClosestAllele -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L INPUT.interval -findFirst | grep -v INFO | sort -k1 > OUTPUT
*/ */
package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller; package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
@ -37,6 +37,7 @@ public class FindClosestAlleleWalker extends ReadWalker<Integer, Integer> {
String CaucasianAlleleFrequencyFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_CaucasiansUSA.freq"; String CaucasianAlleleFrequencyFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_CaucasiansUSA.freq";
String BlackAlleleFrequencyFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_BlackUSA.freq"; String BlackAlleleFrequencyFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_BlackUSA.freq";
String AlleleFrequencyFile; String AlleleFrequencyFile;
String UniqueAllelesFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/UniqueAlleles";
String PolymorphicSitesFile = "/humgen/gsa-scr1/GSA/sjia/Sting/HLA.polymorphic.sites"; String PolymorphicSitesFile = "/humgen/gsa-scr1/GSA/sjia/Sting/HLA.polymorphic.sites";
@ -88,7 +89,7 @@ public class FindClosestAlleleWalker extends ReadWalker<Integer, Integer> {
} }
out.printf("INFO Reading HLA allele frequencies ... "); out.printf("INFO Reading HLA allele frequencies ... ");
FrequencyFileReader HLAfreqReader = new FrequencyFileReader(); FrequencyFileReader HLAfreqReader = new FrequencyFileReader();
HLAfreqReader.ReadFile(AlleleFrequencyFile); HLAfreqReader.ReadFile(AlleleFrequencyFile,UniqueAllelesFile);
AlleleFrequencies = HLAfreqReader.GetAlleleFrequencies(); AlleleFrequencies = HLAfreqReader.GetAlleleFrequencies();
out.printf("Done! Frequencies for %s HLA alleles loaded.\n",AlleleFrequencies.size()); out.printf("Done! Frequencies for %s HLA alleles loaded.\n",AlleleFrequencies.size());