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Merge pull request #198 from broadinstitute/mc_reduce_reads_ds_doc 

Updates GATKDocs for ReduceReads downsampling
This commit is contained in:
Mark DePristo 2013-04-27 05:49:47 -07:00
parent 651e1f23b1 76e997895e
commit 5dd73ba2d1
1 changed files with 3 additions and 2 deletions
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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.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -229,7 +228,9 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
public double minIndelProportionToTriggerVariant = 0.05; 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. * A value of 0 turns downsampling off.
*/ */
@Argument(fullName = "downsample_coverage", shortName = "ds", doc = "", required = false) @Argument(fullName = "downsample_coverage", shortName = "ds", doc = "", required = false)