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Updating outdated comments. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2595 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-15 19:17:52 +00:00
parent ba2acda406
commit 7078219b89
1 changed files with 4 additions and 4 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
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@ -52,9 +52,9 @@ import net.sf.samtools.SAMRecord;
* Since there is a large amount of data one can then calculate an empirical probability of error
* given the particular covariates seen at this site, where p(error) = num mismatches / num observations
* The output file is a CSV list of (the several covariate values, num observations, num mismatches, empirical quality score)
* The first lines of the output file give the name of the covariate classes that were used for this calculation.
* The first non-comment line of the output file gives the name of the covariates that were used for this calculation.
*
* Note: ReadGroupCovariate and QualityScoreCovariate are required covariates and must be at the start of the list.
* Note: ReadGroupCovariate and QualityScoreCovariate are required covariates and will be added for the user regardless of whether or not they were specified
* Note: This walker is designed to be used in conjunction with TableRecalibrationWalker.
*
* @author rpoplin
@ -472,7 +472,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
// Output the RecalDatum entry
recalTableStream.println( ((RecalDatumOptimized)val).outputToCSV() );
} else { // Another layer in the nested hash map
printMappingsSorted( recalTableStream, curPos + 1, key, (Map) val);
printMappingsSorted( recalTableStream, curPos + 1, key, (Map) val );
}
}
}
@ -490,7 +490,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
// Output the RecalDatum entry
recalTableStream.println( ((RecalDatumOptimized)val).outputToCSV() );
} else { // Another layer in the nested hash map
printMappings( recalTableStream, curPos + 1, key, (Map) val);
printMappings( recalTableStream, curPos + 1, key, (Map) val );
}
}
}