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A rogue QualityUtils.MAX_REASONABLE_Q_SCORE managed to get through my previous bug fix. It should instead check the command line -maxQ argument. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2540 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-07 21:17:39 +00:00
parent c7a8dffa89
commit 5f58492401
3 changed files with 4 additions and 5 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -94,7 +94,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
private static final String versionString = "v2.2.4"; // Major version, minor version, and build number
private static final String versionString = "v2.2.5"; // Major version, minor version, and build number
private SAMFileWriter OUTPUT_BAM = null;// The File Writer that will write out the recalibrated bam
private Random coinFlip; // Random number generator is used to remove reference bias in solid bams
private static final long RANDOM_SEED = 1032861495;
@ -393,8 +393,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
}
final double newQuality = qualFromRead + globalDeltaQ + deltaQReported + deltaQCovariates;
return QualityUtils.boundQual( (int)Math.round(newQuality), QualityUtils.MAX_REASONABLE_Q_SCORE );
return QualityUtils.boundQual( (int)Math.round(newQuality), (byte)MAX_QUALITY_SCORE );
// Verbose printouts used to validate with old recalibrator
//if(key.contains(null)) {

2
java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriter.java
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@ -38,7 +38,7 @@ import java.util.List;
* <p/>
* Class ArtificialSAMFileWriter
* <p/>
* generates a fike samwriter, that you can get the output reads
* generates a fake samwriter, that you can get the output reads
* from when you're done.
*/
public class ArtificialSAMFileWriter implements SAMFileWriter {

2
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
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@ -79,7 +79,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorMaxQ70() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "c12b4fd5b4905cc632aa1da19be5c66a" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "bf8d62beda7d3cf38d660d7939901192" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();