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Updating docs to include output

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Eric Banks 2011-09-15 16:10:34 -04:00
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public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -56,6 +56,22 @@ import java.util.*;
* <h2>Output</h2>
* <p>
* Evaluation tables detailing the results of the eval modules which were applied.
* For example:
* <pre>
* output.eval.gatkreport:
* ##:GATKReport.v0.1 CountVariants : Counts different classes of variants in the sample
* CountVariants CompRod CpG EvalRod JexlExpression Novelty nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate ...
* CountVariants dbsnp CpG eval none all 65900028 135770 0 135770 0.00206024 ...
* CountVariants dbsnp CpG eval none known 65900028 47068 0 47068 0.00071423 ...
* CountVariants dbsnp CpG eval none novel 65900028 88702 0 88702 0.00134601 ...
* CountVariants dbsnp all eval none all 65900028 330818 0 330818 0.00502000 ...
* CountVariants dbsnp all eval none known 65900028 120685 0 120685 0.00183133 ...
* CountVariants dbsnp all eval none novel 65900028 210133 0 210133 0.00318866 ...
* CountVariants dbsnp non_CpG eval none all 65900028 195048 0 195048 0.00295976 ...
* CountVariants dbsnp non_CpG eval none known 65900028 73617 0 73617 0.00111710 ...
* CountVariants dbsnp non_CpG eval none novel 65900028 121431 0 121431 0.00184265 ...
* ...
* </pre>
* </p>
*
* <h2>Examples</h2>