zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Updating excessive coverage default parameter 

most people don't care about excessive coverage (unless you're very
particular about your analysis). Therefore the best possible default
value for this is Integer.maxValue so it doesn't get in the way.

Itemized Changes:
   * change maximumCoverage threshold to Integer.maxValue

[delivers #57353620]
This commit is contained in:
Mauricio Carneiro 2013-09-19 23:07:20 -04:00
parent add17dc463
commit 74639463b9
1 changed files with 1 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
View File

@ -77,7 +77,7 @@ final class ThresHolder {
* If at any locus, a sample has more coverage than this, it will be reported as EXCESSIVE_COVERAGE
*/
@Argument(fullName = "maximum_coverage", shortName = "max", doc = "The maximum allowable coverage, used for calling EXCESSIVE_COVERAGE", required = false)
public int maximumCoverage = 700;
public int maximumCoverage = Integer.MAX_VALUE;
/**
* If any sample has a paired read whose distance between alignment starts (between the pairs) is greater than this, it will be reported as BAD_MATE