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added conversion from iupac format and new rod to deal with FLT file format 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1254 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-15 18:34:41 +00:00
parent 702cdd087f
commit 5be5e1d45f
2 changed files with 113 additions and 0 deletions
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52
java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java 100755
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@ -0,0 +1,52 @@
package org.broadinstitute.sting.gatk.refdata;
import java.util.*;
import org.broadinstitute.sting.utils.*;
/**
* 1 469 C S 51 52 0.00 44 1 C 0 M
* 1 492 C Y 130 51 0.00 46 1 C 0 T
* 1 20786 G K 5 6 0.00 46 1 T 38 G
*
*/
public class rodFLT extends TabularROD implements SNPCallFromGenotypes {
public rodFLT(final String name) {
super(name);
}
public GenomeLoc getLocation() {
loc = GenomeLocParser.createGenomeLoc(this.get("0"), Long.parseLong(this.get("1")));
return loc;
}
public String getRefBasesFWD() { return this.get("2"); }
public char getRefSnpFWD() throws IllegalStateException { return getRefBasesFWD().charAt(0); }
public String getAltBasesFWD() { return new String(BaseUtils.iupacToBases(this.get("3").charAt(0))); }
public char getAltSnpFWD() throws IllegalStateException {
char[] bases = BaseUtils.iupacToBases(this.get("3").charAt(0));
if ( bases[0] != getRefSnpFWD() )
return bases[0];
else
return bases[1];
}
public boolean isReference() { return false; }
public boolean isSNP() { return true; }
public boolean isInsertion() { return false; }
public boolean isDeletion() { return false; }
public boolean isIndel() { return false; }
public double getMAF() { return 0.0; }
public double getHeterozygosity() { return 0.0; }
public boolean isGenotype() { return false; }
public double getVariationConfidence() { return Double.parseDouble(this.get("6")); }
public double getConsensusConfidence() { return -1; }
public List<String> getGenotype() throws IllegalStateException { throw new IllegalStateException(); }
public int getPloidy() throws IllegalStateException { return 2; }
public boolean isBiallelic() { return true; }
// SNPCallFromGenotypes interface
public int nIndividuals() { return -1; }
public int nHomRefGenotypes() { return -1; }
public int nHetGenotypes() { return -1; }
public int nHomVarGenotypes() { return -1; }
public List<Genotype> getGenotypes() { return null; }
}

61
java/src/org/broadinstitute/sting/utils/BaseUtils.java
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@ -46,6 +46,67 @@ public class BaseUtils {
}
/**
* Converts a IUPAC nucleotide code to a pair of bases
*
* @param code
* @return 0, 1, 2, 3, or -1 if the base can't be understood
*/
static public char[] iupacToBases(char code) {
char[] bases = new char[2];
switch (code) {
case '*': // the wildcard character counts as an A
case 'A':
case 'a':
bases[0] = bases[1] = 'A';
break;
case 'C':
case 'c':
bases[0] = bases[1] = 'C';
break;
case 'G':
case 'g':
bases[0] = bases[1] = 'G';
break;
case 'T':
case 't':
bases[0] = bases[1] = 'T';
break;
case 'R':
case 'r':
bases[0] = 'A';
bases[1] = 'G';
break;
case 'Y':
case 'y':
bases[0] = 'C';
bases[1] = 'T';
break;
case 'S':
case 's':
bases[0] = 'G';
bases[1] = 'C';
break;
case 'W':
case 'w':
bases[0] = 'A';
bases[1] = 'T';
break;
case 'K':
case 'k':
bases[0] = 'G';
bases[1] = 'T';
break;
case 'M':
case 'm':
bases[0] = 'A';
bases[1] = 'C';
break;
default:
bases[0] = bases[1] = 'N';
}
return bases;
}
/**
* Converts a simple base to a base index
*