zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Bugfix - this walker was never changed to work with the new PoolUtils methods after those methods were changed to return ReadOffsetQuad objects rather than nested pairs. This broke the build :(. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1608 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-09-13 19:39:23 +00:00
parent c669e8d5ad
commit 5cf1d6c104
1 changed files with 3 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/AnalyzePowerWalker.java
View File

@ -9,6 +9,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.walkers.By; import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.playground.utils.PoolUtils; import org.broadinstitute.sting.playground.utils.PoolUtils;
import org.broadinstitute.sting.playground.utils.ReadOffsetQuad;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
import java.io.FileReader; import java.io.FileReader;
@ -73,8 +74,8 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{
Pair<List<SAMRecord>,List<Integer>> readsFilteredByQuality = filterByQuality(rawContext.getReads(),rawContext.getOffsets(), super.getMinQualityScore()); Pair<List<SAMRecord>,List<Integer>> readsFilteredByQuality = filterByQuality(rawContext.getReads(),rawContext.getOffsets(), super.getMinQualityScore());
context = new AlignmentContext(rawContext.getLocation(),readsFilteredByQuality.getFirst(),readsFilteredByQuality.getSecond()); context = new AlignmentContext(rawContext.getLocation(),readsFilteredByQuality.getFirst(),readsFilteredByQuality.getSecond());
} }
ReadOffsetQuad readsByDirection = PoolUtils.splitReadsByReadDirection(context.getReads(),context.getOffsets());
Pair<Pair<List<SAMRecord>, List<SAMRecord>>,Pair<List<Integer>,List<Integer>>> splitReads = PoolUtils.splitReadsByReadDirection(context.getReads(),context.getOffsets()); Pair<Pair<List<SAMRecord>, List<SAMRecord>>,Pair<List<Integer>,List<Integer>>> splitReads = new Pair(new Pair(readsByDirection.getFirstReads(),readsByDirection.getSecondReads()),new Pair(readsByDirection.getFirstOffsets(),readsByDirection.getSecondOffsets()));
if ( !super.suppress_printing ) if ( !super.suppress_printing )
{ {
Pair<double[],byte[]> powPair = super.calculatePower(splitReads,false,context); Pair<double[],byte[]> powPair = super.calculatePower(splitReads,false,context);