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Allows callers to handle HLA reference files as input (rather than hard-coded paths) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3552 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
sjia 2010-06-14 18:56:08 +00:00
parent 266a47d83d
commit b3c3023c3c
3 changed files with 14 additions and 18 deletions
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11
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
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@ -58,17 +58,6 @@ public class CalculateBaseLikelihoodsWalker extends LocusWalker<Integer, Pair<Lo
@Argument(fullName = "minRequiredMatches", shortName = "minRequiredMatches", doc = "Min number of matches required per read (default 7)", required = false)
public int MINREQUIREDMATCHES = 0;
String HLAdatabaseFile ="/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_DICTIONARY.sam";
String CaucasianAlleleFrequencyFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_Caucasians.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 UniqueAllelesFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/UniqueAlleles";
SAMFileReader HLADictionaryReader = new SAMFileReader();
String[] HLAreads, HLAnames;
Integer[] HLAstartpos, HLAstoppos;
Hashtable AlleleFrequencies,UniqueAlleles;
int[][] LOD, LikelihoodScores;
ArrayList<String> ReadsToDiscard = new ArrayList<String>();

11
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestHLAWalker.java
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@ -60,10 +60,15 @@ public class FindClosestHLAWalker extends ReadWalker<Integer, Integer> {
@Argument(fullName = "onlyfrequent", shortName = "onlyfrequent", doc = "Only consider alleles with frequency > 0.0001", required = false)
public boolean ONLYFREQUENT = false;
String HLAdatabaseFile = "/humgen/gsa-scr1/GSA/sjia/HLA_CALLER/HLA_DICTIONARY.txt";
String PolymorphicSitesFile = "/humgen/gsa-scr1/GSA/sjia/HLA_CALLER/HLA_POLYMORPHIC_SITES.txt";
String AlleleFrequencyFile = "/humgen/gsa-scr1/GSA/sjia/HLA_CALLER/HLA_FREQUENCIES.txt";
@Argument(fullName = "HLAfrequencies", shortName = "HLAfrequencies", doc = "HLA allele frequencies file", required = true)
public String AlleleFrequencyFile = "HLA_FREQUENCIES.txt";
@Argument(fullName = "HLAdictionary", shortName = "HLAdictionary", doc = "HLA dictionary file", required = true)
public String HLAdatabaseFile = "HLA_DICTIONARY.txt";
@Argument(fullName = "PolymorphicSites", shortName = "PolymorphicSites", doc = "file containing polymorphic sites within the HLA", required = true)
public String PolymorphicSitesFile = "HLA_POLYMORPHIC_SITES.txt";
HLAFileReader HLADictionaryReader = new HLAFileReader();
boolean DatabaseLoaded = false;

10
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerWalker.java
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@ -69,12 +69,14 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
@Argument(fullName = "minRequiredMatches", shortName = "minRequiredMatches", doc = "Min number of matches required per read (default 7)", required = false)
public int MINREQUIREDMATCHES = 5;
@Argument(fullName = "HLAfrequencies", shortName = "HLAfrequencies", doc = "HLA allele frequencies file", required = true)
public String AlleleFrequencyFile = "HLA_FREQUENCIES.txt";
@Argument(fullName = "HLAdictionary", shortName = "HLAdictionary", doc = "HLA dictionary file", required = true)
public String HLAdatabaseFile = "HLA_DICTIONARY.txt";
GATKArgumentCollection args = this.getToolkit().getArguments();
String AlleleFrequencyFile = "/humgen/gsa-scr1/GSA/sjia/HLA_CALLER/HLA_FREQUENCIES.txt";
String PolymorphicSitesfile = "/humgen/gsa-scr1/GSA/sjia/HLA_CALLER/HLA_POLYMORPHIC_SITES.txt";
String HLAdatabaseFile = "/humgen/gsa-scr1/GSA/sjia/HLA_CALLER/HLA_DICTIONARY.txt";
// Initializing variables
HLAFileReader HLADictionaryReader = new HLAFileReader();