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Adding expected output doc to CountCovariates

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Ryan Poplin 2011-09-15 16:26:11 -04:00
parent 6d02a34bfb
commit 2f58fdb369
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public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
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@ -76,6 +76,42 @@ import java.util.Map;
* <h2>Output</h2>
* <p>
* A recalibration table file in CSV format that is used by the TableRecalibration walker.
* It is a comma-separated text file relating the desired covariates to the number of such bases and their rate of mismatch in the genome, and its implied empirical quality score.
*
* The first 20 lines of such a file is shown below.
* * The file begins with a series of comment lines describing:
* ** The number of counted loci
* ** The number of counted bases
* ** The number of skipped loci and the fraction skipped, due to presence in dbSNP or bad reference bases
*
* * After the comments appears a header line indicating which covariates were used as well as the ordering of elements in the subsequent records.
*
* * After the header, data records occur one per line until the end of the file. The first several items on a line are the values of the individual covariates and will change
* depending on which covariates were specified at runtime. The last three items are the data- that is, number of observations for this combination of covariates, number of
* reference mismatches, and the raw empirical quality score calculated by phred-scaling the mismatch rate.
*
* <pre>
* # Counted Sites 19451059
* # Counted Bases 56582018
* # Skipped Sites 82666
* # Fraction Skipped 1 / 235 bp
* ReadGroup,QualityScore,Cycle,Dinuc,nObservations,nMismatches,Qempirical
* SRR006446,11,65,CA,9,1,10
* SRR006446,11,48,TA,10,0,40
* SRR006446,11,67,AA,27,0,40
* SRR006446,11,61,GA,11,1,10
* SRR006446,12,34,CA,47,1,17
* SRR006446,12,30,GA,52,1,17
* SRR006446,12,36,AA,352,1,25
* SRR006446,12,17,TA,182,11,12
* SRR006446,11,48,TG,2,0,40
* SRR006446,11,67,AG,1,0,40
* SRR006446,12,34,CG,9,0,40
* SRR006446,12,30,GG,43,0,40
* ERR001876,4,31,AG,1,0,40
* ERR001876,4,31,AT,2,2,1
* ERR001876,4,31,CA,1,0,40
* </pre>
* </p>
*
* <h2>Examples</h2>