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Base transition table now forces epsilon/3 (three-state) model for the unified genotyper. Verified to be identical with changing the default model to being epsilon/3. This of course changes the observed counts, so the integration test has been updated. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1897 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-21 21:18:26 +00:00
parent 55fa1cfa06
commit af761fb9bd
2 changed files with 11 additions and 8 deletions
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3
java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
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@ -55,7 +55,10 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
throw new StingException("You have opted to use a number of previous bases in excess of 3. In order to do this you must change the reference window size in the walker itself.");
}
ug = new UnifiedGenotyper();
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
ug.initialize();
uac.baseModel = BaseMismatchModel.THREE_STATE;
ug.setUnifiedArgumentCollection(uac);
// refWindow = new ReferenceContextWindow(nPreviousBases);
usePreviousBases = new ArrayList<Boolean>();
previousBaseLoci = new ArrayList<GenomeLoc>();

16
java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java
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@ -14,14 +14,14 @@ import java.util.Arrays;
*/
public class BaseTransitionTableCalculatorJavaIntegrationTest extends WalkerTest{
// MD5s last computed 10/20 at revision 1877
public static final String OUTPUT_MD5_STANDARD = "856a3124fb078b4d820f935369ec53cc";
public static final String OUTPUT_MD5_3MISMATCHES = "847375e3d40415d237c627a56d163760";
public static final String OUTPUT_MD5_LOWMAPPINGQUALITY = "d7e490168dfef8eb4185b596f55bfaa8";
public static final String OUTPUT_MD5_LOWQUALITYSCORE = "e3f3c3875936b0df7a8899c2ef5d1dd2";
public static final String OUTPUT_MD5_LOWCONFIDENTREFTHRESHOLD = "521a9fa7716ed22550c2ba3fe3409070";
public static final String OUTPUT_MD5_HIGHCONFIDENTREFTHRESHOLD = "8ab6d389fc494881736e9a58126c2f1b";
public static final String OUTPUT_MD5_ALLARGUMENTS = "f45481946d7a5c70078d432b0baff083";
public static final String OUTPUT_MD5_USEREADGROUP = "6dbf18e96f3367c8764b4d1e15eb956b";
public static final String OUTPUT_MD5_STANDARD = "e88f010ea842bcdb6503a4da24b90edc";
public static final String OUTPUT_MD5_3MISMATCHES = "46f9aadbfe260a286fb6c8cac137dddd";
public static final String OUTPUT_MD5_LOWMAPPINGQUALITY = "0b7447e0a271ffa5c8ff1719db3585e6";
public static final String OUTPUT_MD5_LOWQUALITYSCORE = "87d793f751328b0a9299a69b99cd0112";
public static final String OUTPUT_MD5_LOWCONFIDENTREFTHRESHOLD = "bc70acf997295a6cc13f3e88b254cc24";
public static final String OUTPUT_MD5_HIGHCONFIDENTREFTHRESHOLD = "17d49c12fc64926a71bc32ac1eec7f68";
public static final String OUTPUT_MD5_ALLARGUMENTS = "5599a4a577927fb9875adc26140dee7e";
public static final String OUTPUT_MD5_USEREADGROUP = "f6e8bd2101316deae93512dd09a69567";
public static final String LOCUS = "1:10,000,000-10,200,000";
public static final String BAM_FILE = "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam";
public static final String REFERENCE = "/broad/1KG/reference/human_b36_both.fasta";