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Make the formatting of the list of args in the PG tag consistent. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2626 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-19 15:31:37 +00:00
parent a12465b6d5
commit d61cafd19f
1 changed files with 4 additions and 4 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -222,12 +222,12 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
if( !NO_PG_TAG ) { if( !NO_PG_TAG ) {
final SAMProgramRecord programRecord = new SAMProgramRecord( "GATK TableRecalibration" ); final SAMProgramRecord programRecord = new SAMProgramRecord( "GATK TableRecalibration" );
programRecord.setProgramVersion( RecalDataManager.versionString ); programRecord.setProgramVersion( RecalDataManager.versionString );
String commandLineString = "Covariates used = ["; String commandLineString = "Covariates=[";
for( Covariate cov : requestedCovariates ) { for( Covariate cov : requestedCovariates ) {
commandLineString += cov.getClass().getSimpleName() + ", "; commandLineString += cov.getClass().getSimpleName() + ", ";
} }
commandLineString = commandLineString.substring( 0, commandLineString.length() - 2 ); // Trim off the trailing comma commandLineString = commandLineString.substring( 0, commandLineString.length() - 2 ); // Trim off the trailing comma
commandLineString += "] "; commandLineString += "], ";
// Add all of the arguments from the recalibration argument collection to the command line string // Add all of the arguments from the recalibration argument collection to the command line string
final Field[] fields = RAC.getClass().getFields(); final Field[] fields = RAC.getClass().getFields();
for( Field field : fields ) { for( Field field : fields ) {
@ -239,8 +239,8 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
} }
} }
} }
commandLineString += "pQ = " + PRESERVE_QSCORES_LESS_THAN + ", "; commandLineString += "pQ=" + PRESERVE_QSCORES_LESS_THAN + ", ";
commandLineString += "smoothing = " + SMOOTHING; commandLineString += "smoothing=" + SMOOTHING;
programRecord.setCommandLine( commandLineString ); programRecord.setCommandLine( commandLineString );
header.addProgramRecord( programRecord ); header.addProgramRecord( programRecord );