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Minor clarifications & formatting tweaks for dcov docs

This commit is contained in:
Geraldine Van der Auwera 2013-09-26 14:28:22 -04:00
parent a9fa5206ee
commit 66d0235efc
1 changed files with 17 additions and 9 deletions
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26
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -119,21 +119,29 @@ public class GATKArgumentCollection {
// Downsampling Arguments
//
// --------------------------------------------------------------------------------------------------------------
@Argument(fullName = "downsampling_type", shortName="dt", doc="Type of reads downsampling to employ at a given locus. Reads will be selected randomly to be removed from the pile based on the method described here", required = false)
/**
* Reads will be selected randomly to be removed from the pile based on the method described here.
*/
@Argument(fullName = "downsampling_type", shortName="dt", doc="Type of reads downsampling to employ at a given locus", required = false)
public DownsampleType downsamplingType = null;
@Argument(fullName = "downsample_to_fraction", shortName = "dfrac", doc = "Fraction [0.0-1.0] of reads to downsample to", required = false)
public Double downsampleFraction = null;
/**
* For locus-based traversals (eg., LocusWalkers and ActiveRegionWalkers), downsample_to_coverage controls the
* maximum depth of coverage at each locus. For non-locus-based traversals (eg., ReadWalkers), this controls the
* maximum number of reads sharing the same alignment start position. Note that for ReadWalkers, since -dcov controls
* the maximum number of reads sharing the same alignment start position, you will typically need to use much lower
* dcov values than you would with LocusWalkers to see an effect. Note also that this downsampling option does NOT
* produce an unbiased random sampling from all available reads at each locus: instead, the primary goal of the
* to-coverage downsampler is to maintain an even representation of reads from all alignment start positions when
* removing excess coverage. For a true across-the-board unbiased random sampling of reads, use -dfrac instead. Also
* note that the coverage target is an approximate goal that is not guaranteed to be met exactly: the downsampling
* algorithm will under some circumstances retain slightly more coverage than requested.
*/
@Argument(fullName = "downsample_to_coverage", shortName = "dcov",
doc = "Coverage [integer] to downsample to. For locus-based traversals (eg., LocusWalkers and ActiveRegionWalkers)," +
"this controls the maximum depth of coverage at each locus. For non-locus-based traversals (eg., ReadWalkers), " +
"this controls the maximum number of reads sharing the same alignment start position. Note that this downsampling " +
"option does NOT produce an unbiased random sampling from all available reads at each locus: instead, the primary goal of " +
"the to-coverage downsampler is to maintain an even representation of reads from all alignment start positions " +
"when removing excess coverage. For a true across-the-board unbiased random sampling of reads, use -dfrac instead. " +
"Also note that the coverage target is an approximate goal that is not guaranteed to be met exactly: the downsampling " +
"algorithm will under some circumstances retain slightly more coverage than requested.",
doc = "Coverage [integer] to downsample to",
required = false)
public Integer downsampleCoverage = null;