diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java index 1ccf40a13..dd0047d44 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java @@ -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."); } } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java index 03434be12..efd09bdec 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java @@ -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;