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Added help.description to the recalibration walkers. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2331 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin 2009-12-11 19:02:29 +00:00
parent 2ea7632b76
commit 60c3eb4b60
2 changed files with 4 additions and 0 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
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@ -61,6 +61,8 @@ import net.sf.samtools.SAMRecord;
*
* Note: ReadGroupCovariate and QualityScoreCovariate are required covariates and must be at the start of the list.
* Note: This walker is designed to be used in conjunction with TableRecalibrationWalker.
*
* @help.description First pass of the recalibration. Generates recalibration table based on various user-specified covariates (such as reported quality score, cycle, and dinucleotide).
*/
@By( DataSource.READS ) // Only look at covered loci, not every loci of the reference file

2
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -55,6 +55,8 @@ import java.io.FileNotFoundException;
*
* Note: This walker expects as input the recalibration table file generated previously by CovariateCounterWalker.
* Note: This walker is designed to be used in conjunction with CovariateCounterWalker.
*
* @help.description Second pass of the recalibration. Uses the table generated by CountCovariates to update the base quality scores of the input bam file using a sequential table calculation making the base quality scores more accurately reflect the actual quality of the bases as mesaured by reference mismatch rate.
*/
@WalkerName("TableRecalibration")