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Reverting the previous solid change. We now refuse to recalibrate if the solid read doesn't contain proper color space information. The exception message has been updated to say this. Also, Tile has been downgraded to an ExperimentalCovariate due to performance issues. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2662 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-22 20:55:28 +00:00
parent 7732f98e56
commit fd223e955c
2 changed files with 4 additions and 11 deletions
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13
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
View File

@ -259,10 +259,6 @@ public class RecalDataManager {
if( attr != null ) {
char[] colorSpace;
if( attr instanceof String ) {
if( ((String)attr).contains(".") ) { // empty color space, abort
read.getReadGroup().setPlatform("illumina");
return;
}
colorSpace = ((String)attr).toCharArray();
} else {
throw new StingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));
@ -308,16 +304,12 @@ public class RecalDataManager {
if( attr != null ) {
char[] colorSpace;
if( attr instanceof String ) {
if( ((String)attr).contains(".") ) { // empty color space, abort
read.getReadGroup().setPlatform("illumina");
return originalQualScores;
}
colorSpace = ((String)attr).toCharArray();
} else {
throw new StingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));
}
// Loop over the read and calculate first the infered bases from the color and then check if it is consistent with the read
// Loop over the read and calculate first the inferred bases from the color and then check if it is consistent with the read
byte[] readBases = read.getReadBases();
final byte[] colorImpliedBases = readBases.clone();
char[] refBasesDirRead = AlignmentUtils.alignmentToCharArray( read.getCigar(), read.getReadString().toCharArray(), refBases ); //BUGBUG: This needs to change when read walkers are changed to give the aligned refBases
@ -475,7 +467,8 @@ public class RecalDataManager {
case '3': // simple complement
return BaseUtils.simpleComplement( prevBase );
default:
throw new StingException( "Unrecognized color space in SOLID read, color = " + color );
throw new StingException( "Unrecognized color space in SOLID read, color = " + color +
" Unfortunately this bam file can not be recalibrated without full color space information because of potential reference bias.");
}
}

2
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java
View File

@ -32,7 +32,7 @@ import edu.mit.broad.picard.illumina.parser.IlluminaUtil;
* @author alecw@broadinstitute.org
*/
public class TileCovariate implements StandardCovariate {
public class TileCovariate implements ExperimentalCovariate {
private static boolean exceptionWhenNoTile = false;