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BTTC is now Tree Reducible allowing for parallelization. 

Integration test comment changed to reflect actual date of last md5 update.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1901 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-22 23:19:29 +00:00
parent 2e552eb5a1
commit a6dc8cd44e
2 changed files with 6 additions and 2 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
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@ -24,7 +24,7 @@ import net.sf.samtools.SAMRecord;
*/
@By(DataSource.REFERENCE)
@Reference(window=@Window(start=-3,stop=3))
public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<BaseTransitionTable>,Set<BaseTransitionTable>> {
public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<BaseTransitionTable>,Set<BaseTransitionTable>> implements TreeReducible<Set<BaseTransitionTable>> {
@Argument(fullName="usePreviousBases", doc="Use previous bases of the reference as part of the calculation, uses the specified number, defaults to 0", required=false)
int nPreviousBases = 0;
@Argument(fullName="useSecondaryBase",doc="Use the secondary base of a read as part of the calculation", required=false)
@ -111,6 +111,10 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
return reduce;
}
public Set<BaseTransitionTable> treeReduce( Set<BaseTransitionTable> reduce1, Set<BaseTransitionTable> reduce2 ) {
return reduce(reduce1,reduce2);
}
public void onTraversalDone( Set<BaseTransitionTable> conditionalTables ) {
out.print(createHeaderFromConditions());
for ( BaseTransitionTable t : conditionalTables )

2
java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java
View File

@ -13,7 +13,7 @@ import java.util.Arrays;
* To change this template use File | Settings | File Templates.
*/
public class BaseTransitionTableCalculatorJavaIntegrationTest extends WalkerTest{
// MD5s last computed 10/20 at revision 1877
// MD5s last computed 10/21 at revision 1897
public static final String OUTPUT_MD5_STANDARD = "e88f010ea842bcdb6503a4da24b90edc";
public static final String OUTPUT_MD5_3MISMATCHES = "46f9aadbfe260a286fb6c8cac137dddd";
public static final String OUTPUT_MD5_LOWMAPPINGQUALITY = "0b7447e0a271ffa5c8ff1719db3585e6";