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Merge pull request #198 from broadinstitute/mc_reduce_reads_ds_doc

Updates GATKDocs for ReduceReads downsampling
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2 parents 651e1f2 + 76e9978 commit 5dd73ba2d14cecb93cdbf70aa92531c86796cb78 Mark DePristo committed Apr 27, 2013
@@ -64,7 +64,6 @@
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 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)

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