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Making nContigs parameter hidden in ReduceReads 

For now, the het reduction should only be performed for diploids (n=2). We haven't really tested it for other ploidy so it should remain hidden until someone braves it out.
This commit is contained in:
Mauricio Carneiro 2012-10-10 15:00:17 -04:00
parent d7308646e9
commit a234bacb02
1 changed files with 8 additions and 9 deletions
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17
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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@ -181,15 +181,6 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
@Argument(fullName = "minimum_del_proportion_to_trigger_variant", shortName = "mindel", doc = "", required = false)
private double minIndelProportionToTriggerVariant = 0.05;
/**
* Minimum proportion of indels in a site to trigger a variant region. Anything below this will be
* considered consensus.
*/
@Argument(fullName = "contigs", shortName = "ctg", doc = "", required = false)
private int nContigs = 2;
/**
* Downsamples the coverage of a variable region approximately (guarantees the minimum to be equal to this).
* A value of 0 turns downsampling off.
@ -197,6 +188,14 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
@Argument(fullName = "downsample_coverage", shortName = "ds", doc = "", required = false)
private int downsampleCoverage = 250;
/**
* Number of chromossomes in the sample (this is used for the polyploid consensus compression). Only
* tested for humans (or organisms with n=2). Use at your own risk!
*/
@Hidden
@Argument(fullName = "contigs", shortName = "ctg", doc = "", required = false)
private int nContigs = 2;
@Hidden
@Argument(fullName = "", shortName = "dl", doc = "", required = false)
private int debugLevel = 0;