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Updated documentation 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2365 348d0f76-0448-11de-a6fe-93d51630548a
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sjia 2009-12-15 20:45:19 +00:00
parent 5974c42468
commit 18f61d2586
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
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@ -1,6 +1,5 @@
/* /*
* To change this template, choose Tools | Templates * Calculates the probability of observing data for each genotype at every position. NOTE: run FindClosestAllele first to create .filter file. Usage: java -jar GenomeAnalysisTK.jar -T CalculateBaseLikelihoods -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval [-filter INPUT.filter -minAllowedMismatches 7] | grep -v "INFO" | grep -v "MISALIGNED" > OUTPUT.baselikelihoods
* and open the template in the editor.
*/ */
package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller; package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
@ -38,11 +37,12 @@ public class CalculateBaseLikelihoodsWalker extends LocusWalker<Integer, Pair<Lo
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 = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_CaucasiansUSA.freq"; String AlleleFrequencyFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_CaucasiansUSA.freq";
String UniqueAllelesFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/UniqueAlleles";
SAMFileReader HLADictionaryReader = new SAMFileReader(); SAMFileReader HLADictionaryReader = new SAMFileReader();
String[] HLAreads, HLAnames; String[] HLAreads, HLAnames;
Integer[] HLAstartpos, HLAstoppos; Integer[] HLAstartpos, HLAstoppos;
Hashtable AlleleFrequencies;
Hashtable AlleleFrequencies,UniqueAlleles;
int[][] LOD, LikelihoodScores; int[][] LOD, LikelihoodScores;
ArrayList<String> ReadsToDiscard = new ArrayList<String>(); ArrayList<String> ReadsToDiscard = new ArrayList<String>();
@ -74,7 +74,7 @@ public class CalculateBaseLikelihoodsWalker extends LocusWalker<Integer, Pair<Lo
} }
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());