diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java index 82a02ca55..71910e566 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java @@ -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, 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)