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Removed MAG entirely 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5474 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-03-18 19:43:23 +00:00
parent 55897631ad
commit 22ff2573d5
2 changed files with 3 additions and 6 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidateBAQWalker.java
View File

@ -108,9 +108,8 @@ public class ValidateBAQWalker extends ReadWalker<Integer, Integer> {
baqReadTimer.stop();
glocalTimer.restart();
BAQ.MAG = magnification;
baqHMM.baqRead(read, refReader, BAQ.CalculationMode.RECALCULATE, BAQ.QualityMode.DONT_MODIFY);
BAQ.MAG = 1;
for ( int i = 0; i < magnification; i++ )
baqHMM.baqRead(read, refReader, BAQ.CalculationMode.RECALCULATE, BAQ.QualityMode.DONT_MODIFY);
glocalTimer.stop();
}

4
java/src/org/broadinstitute/sting/utils/baq/BAQ.java
View File

@ -39,7 +39,6 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
*/
public class BAQ {
private final static boolean DEBUG = false;
public static int MAG = 1; // todo -- remove me for performance testing only
public enum CalculationMode {
OFF, // don't apply a BAQ at all, the default
@ -506,8 +505,7 @@ public class BAQ {
// note -- assumes ref is offset from the *CLIPPED* start
BAQCalculationResult baqResult = new BAQCalculationResult(query, quals, ref);
int queryLen = queryEnd - queryStart;
for ( int i = 0; i < MAG; i++ )
hmm_glocal(baqResult.refBases, baqResult.readBases, queryStart, queryLen, baqResult.rawQuals, baqResult.state, baqResult.bq);
hmm_glocal(baqResult.refBases, baqResult.readBases, queryStart, queryLen, baqResult.rawQuals, baqResult.state, baqResult.bq);
return baqResult;
}