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Intermediate checking for evaluation -- now supports transition / transversion evaluation 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@793 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-05-22 17:05:06 +00:00
parent f2ea193149
commit 7a979859a9
4 changed files with 74 additions and 13 deletions
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26
java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
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@ -73,11 +73,12 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
*
* @return reference allele, forward strand
*/
public String getRefBasesFWD() {
if ( onFwdStrand() )
return refBases;
else
return SequenceUtil.reverseComplement(refBases);
public String getRefBasesFWD() {
return getAllelesFWD().get(0);
//if ( onFwdStrand() )
// return refBases;
//else
// return SequenceUtil.reverseComplement(refBases);
}
/**
@ -87,9 +88,11 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
* @return reference base on the forward strand
*/
public char getRefSnpFWD() throws IllegalStateException {
//System.out.printf("refbases is %s but %s%n", refBases, toString());
if ( isIndel() ) throw new IllegalStateException("Variant is not a SNP");
if ( onFwdStrand() ) return refBases.charAt(0);
else return SequenceUtil.reverseComplement(refBases).charAt(0);
return getAllelesFWD().get(0).charAt(0);
// if ( onFwdStrand() ) return refBases.charAt(0);
// else return SequenceUtil.reverseComplement(refBases).charAt(0);
}
public List<String> getAllelesFWD() {
@ -187,8 +190,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
@Override
public char getAltSnpFWD() throws IllegalStateException {
// TODO Auto-generated method stub
return 0;
return getAllelesFWD().get(1).charAt(0);
}
@Override
@ -205,8 +207,8 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
@Override
public double getMAF() {
// TODO Auto-generated method stub
return 0;
// Fixme: update to actually get MAF
return avHet;
}
@Override
@ -218,7 +220,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
@Override
public double getVariationConfidence() {
// TODO Auto-generated method stub
return 0;
return 100;
}
@Override

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicateQualsWalker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers;
package org.broadinstitute.sting.playground.gatk.duplicates.walkers;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.walkers.DuplicateWalker;

32
java/src/org/broadinstitute/sting/utils/BaseUtils.java
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@ -6,6 +6,38 @@ package org.broadinstitute.sting.utils;
* @author Kiran Garimella
*/
public class BaseUtils {
/// In genetics, a transition is a mutation changing a purine to another purine nucleotide (A <-> G) or
// a pyrimidine to another pyrimidine nucleotide (C <-> T).
// Approximately two out of every three single nucleotide polymorphisms (SNPs) are transitions.
public enum BaseSubstitutionType {
TRANSITION, // A <-> G or C <-> T
TRANSVERSION
}
/**
* Returns the base substitution type of the 2 state SNP
* @param base1
* @param base2
* @return
*/
public static BaseSubstitutionType SNPSubstitutionType( char base1, char base2 ) {
BaseSubstitutionType t = isTransition(base1, base2) ? BaseSubstitutionType.TRANSITION : BaseSubstitutionType.TRANSVERSION;
//System.out.printf("SNPSubstitutionType( char %c, char %c ) => %s%n", base1, base2, t);
return t;
}
public static boolean isTransition( char base1, char base2 ) {
int b1 = simpleBaseToBaseIndex(base1);
int b2 = simpleBaseToBaseIndex(base2);
return b1 == 0 && b2 == 2 || b1 == 2 && b2 == 0 ||
b1 == 1 && b2 == 3 || b1 == 3 && b2 == 1;
}
public static boolean isTransversion( char base1, char base2 ) {
return ! isTransition(base1, base2);
}
/** Private constructor. No instantiating this class! */
private BaseUtils() {}

27
java/test/org/broadinstitute/sting/utils/BaseUtilsTest.java
View File

@ -18,6 +18,33 @@ public class BaseUtilsTest extends BaseTest {
compareFrequentBaseFractionToExpected("ACCCCTTTTG", 4.0/10.0);
}
@Test
public void testTransitionTransversion() {
logger.warn("Executing testTransitionTransversion");
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'G' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'C', 'A' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'C', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'C', 'G' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'T', 'A' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'T', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'T', 'G' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'G', 'A' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'G', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'G', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'a', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'a', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 't' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'c' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'a', 't' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'a', 'c' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
}
private void compareFrequentBaseFractionToExpected(String sequence, double expected) {
double fraction = BaseUtils.mostFrequentBaseFraction(sequence.getBytes());
Assert.assertTrue(MathUtils.compareDoubles(fraction, expected) == 0);