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No reason to warn the user anymore because it's no longer possible for them to specify a dbsnp file on the command-line.

This commit is contained in:
Eric Banks 2011-08-11 13:44:07 -04:00
parent e93538cdf7
commit 200f73b008
1 changed files with 0 additions and 13 deletions
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13
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -29,10 +29,8 @@ import net.sf.samtools.*;
import net.sf.samtools.util.SequenceUtil; import net.sf.samtools.util.SequenceUtil;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
@ -155,17 +153,6 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
int lineNumber = 0; int lineNumber = 0;
boolean foundAllCovariates = false; boolean foundAllCovariates = false;
// Warn the user if a dbSNP file was specified since it isn't being used here
boolean foundDBSNP = false;
for( ReferenceOrderedDataSource rod : this.getToolkit().getRodDataSources() ) {
if( rod.getName().equalsIgnoreCase(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
foundDBSNP = true;
}
}
if( foundDBSNP ) {
Utils.warnUser("A dbSNP rod file was specified but TableRecalibrationWalker doesn't make use of it.");
}
// Read in the data from the csv file and populate the data map and covariates list // Read in the data from the csv file and populate the data map and covariates list
logger.info( "Reading in the data from input csv file..." ); logger.info( "Reading in the data from input csv file..." );