contiBAIT v0.99.4
==============

- Added some core R dependencies to make things happy with the new devel version of R
- Shortened some lines of code


contiBAIT v0.99.3
==============

Bug fixes:
- fixed error where strandTable removal in preprocessStrandTable was resulting in empty matrix
- fixed error where combineZeroDistances was creating an empty matrix that was too small for some data
- fixed bugs in contiBAIT:
a) bug where error would occur if verbose=FALSE but saveFiles=TRUE (because this.message only produced if verbose is TRUE)
b) changed linkage.groups to linkage.merged the second time reorientLinkageGroups is called

contiBAIT v0.99.2
==============
(In response to first round of Bioconductor review).

CLUSTERCONTIGS:
-Now pre-creates the LinkageGroupList; more efficient than copy and replace

MAKECHRTABLE:
-Now returns GRanges object
-All subsequent programs edited to take chrTable call as a GRanges
-Divided chromosome table now included in makeChrTable, so dividedChrTable function removed
-Ability to include additional split locations

MERGELINKAGEGROUPS:
-Now if clusNum is NULL, parallel clustering is not performed

PLOTTING FUNCTIONS WITH GGPLOTS:
-No longer return false positive issues with R CMD check

MAPGAPFROMOVERLAP:
-Retains data in GRanges, speeding up function

GENERAL:
-Simplified some longer one-liners.
-Imported methods
-All classes now have constructor functions


contiBAIT v0.99.1
==============

IDEOGRAMPLOT:
-fixed orientation issue. Now accepts OrientationTable to flip Watson and Crick reads

MERGELINKAGEGROUPS:
-fixed intermediate issue in mergeLinkageGroups where rownames were sometimes maintained and sometimes not after computeconsensus resulting in melt error.

PREPROCESSSTRANDTABLE:
- no longer looks for sex chromosomes. Was mostly pointless and didn't work well. Better method is to look for linkage groups with computeConsensus where consensus is mostly homozygous.

REORIENTLINKAGEGROUPS
-fixed bug where second iteration after mergeLinkageGroups was overwriting the OrientationTable.  Now accepts a previousOrient argument if performing second reorientation.


contiBAIT v0.99.0 (Submitted for BioC review 2016-01-20)
==============