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Removing used --enable_overlap_filters argument; Eric assures me this won't break the currently broken tests 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3992 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-08-09 22:27:13 +00:00
parent 0f29f2ae3f
commit c2c0c1f57c
1 changed files with 0 additions and 7 deletions
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7
java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -174,10 +174,6 @@ public class GATKArgumentCollection {
@Argument(fullName = "read_group_black_list", shortName="rgbl", doc="Filters out read groups matching <TAG>:<STRING> or a .txt file containing the filter strings one per line.", required = false)
public List<String> readGroupBlackList = null;
@Element(required = false)
@Argument(fullName = "enable_overlap_filters",shortName="eof", doc="Enable automatic removal of bases that overlap adaptor sequence or that overlap their mate pair", required = false)
public boolean enableOverlapFilters = false;
/**
* marshal the data out to a object
*
@ -344,9 +340,6 @@ public class GATKArgumentCollection {
if (other.intervalMerging != this.intervalMerging) {
return false;
}
if (enableOverlapFilters != other.enableOverlapFilters) {
return false;
}
if ((other.RODToInterval == null && RODToInterval != null) ||
(other.RODToInterval != null && !other.RODToInterval.equals(RODToInterval))) {
return false;