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Updates GATKDocs for ReduceReads downsampling 

[fixes #48258295]
This commit is contained in:
Mauricio Carneiro 2013-04-26 23:33:09 -04:00
parent 759c531d1b
commit 76e997895e
1 changed files with 3 additions and 2 deletions
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5
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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@ -64,7 +64,6 @@ import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -229,7 +228,9 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
public double minIndelProportionToTriggerVariant = 0.05;
/**
* Downsamples the coverage of a variable region approximately (guarantees the minimum to be equal to this).
* The number of reads emitted per sample in a variant region can be downsampled for better compression.
* This level of downsampling only happens after the region has been evaluated, therefore it can
* be combined with the engine level downsampling.
* A value of 0 turns downsampling off.
*/
@Argument(fullName = "downsample_coverage", shortName = "ds", doc = "", required = false)