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Updated documentation 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2363 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
sjia 2009-12-15 20:35:18 +00:00
parent 4322beeb35
commit d8cfd707bc
1 changed files with 17 additions and 4 deletions
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21
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FrequencyFileReader.java
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@ -1,6 +1,5 @@
/* /**
* To change this template, choose Tools | Templates * File reader used by other Walkers to read HLA allele frequencies.
* and open the template in the editor.
*/ */
package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller; package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
@ -13,12 +12,16 @@ import java.util.Hashtable;
*/ */
public class FrequencyFileReader { public class FrequencyFileReader {
Hashtable AlleleFrequencies = new Hashtable(); Hashtable AlleleFrequencies = new Hashtable();
Hashtable UniqueAlleles = new Hashtable();
public Hashtable GetAlleleFrequencies(){ public Hashtable GetAlleleFrequencies(){
return AlleleFrequencies; return AlleleFrequencies;
} }
public void ReadFile(String filename){ public Hashtable GetUniqueAlleles(){
return UniqueAlleles;
}
public void ReadFile(String filename, String uniqueAllelesFile){
try{ try{
FileInputStream fstream = new FileInputStream(filename); FileInputStream fstream = new FileInputStream(filename);
DataInputStream in = new DataInputStream(fstream); DataInputStream in = new DataInputStream(fstream);
@ -31,6 +34,16 @@ public class FrequencyFileReader {
//System.out.printf("Loaded: %s\t%s\n",s[0],AlleleFrequencies.get(s[0]).toString()); //System.out.printf("Loaded: %s\t%s\n",s[0],AlleleFrequencies.get(s[0]).toString());
} }
in.close(); in.close();
fstream = new FileInputStream(uniqueAllelesFile);
in = new DataInputStream(fstream);
br = new BufferedReader(new InputStreamReader(in));
//Read File Line By Line
while ((strLine = br.readLine()) != null) {
UniqueAlleles.put(strLine,strLine);
//System.out.printf("Loaded: %s\t%s\n",s[0],AlleleFrequencies.get(s[0]).toString());
}
in.close();
}catch (Exception e){//Catch exception if any }catch (Exception e){//Catch exception if any
System.err.println("FrequencyFileReader Error: " + e.getMessage()); System.err.println("FrequencyFileReader Error: " + e.getMessage());
} }