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Updating doc text 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4732 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin 2010-11-24 21:34:14 +00:00
parent ed08899abc
commit 0dd40c3684
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
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@ -66,7 +66,7 @@ class AnalyzeCovariatesCLP extends CommandLineProgram {
private int IGNORE_QSCORES_LESS_THAN = 5;
@Argument(fullName = "numRG", shortName = "numRG", doc = "Only process N read groups. Default value: -1 (process all read groups)", required = false)
private int NUM_READ_GROUPS_TO_PROCESS = -1; // -1 means process all read groups
@Argument(fullName="max_quality_score", shortName="maxQ", required = false, doc="The integer value at which to cap the quality scores, default is 40")
@Argument(fullName="max_quality_score", shortName="maxQ", required = false, doc="The integer value at which to cap the quality scores, default is 50")
private int MAX_QUALITY_SCORE = 50;
@Argument(fullName="max_histogram_value", shortName="maxHist", required = false, doc="If supplied, this value will be the max value of the histogram plots")
private int MAX_HISTOGRAM_VALUE = 0;

2
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -96,7 +96,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
private int PRESERVE_QSCORES_LESS_THAN = 5;
@Argument(fullName="smoothing", shortName="sm", required = false, doc="Number of imaginary counts to add to each bin in order to smooth out bins with few data points, default=1")
private int SMOOTHING = 1;
@Argument(fullName="max_quality_score", shortName="maxQ", required = false, doc="The integer value at which to cap the quality scores, default=40")
@Argument(fullName="max_quality_score", shortName="maxQ", required = false, doc="The integer value at which to cap the quality scores, default=50")
private int MAX_QUALITY_SCORE = 50;
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