July 10th, 2009
· Officially added the GUI.
· Added a new application for merging two microarray designs (FilterIntersectingRegions). Modified Alleler output for generating bed files from INDELS.
June 26th, 2009
· Modified the FilterDuplicateAlignments app to enable unique sequence selection.
· Added a new app for rapid intersection of two microarray designs.
June 19th, 2009
· Added several applications to assist in the design of capture/ release -> sequencing microarrays.
· Added instructions for such to the user guide.
June 17th, 2009
· Fixed an error in the ReadCoverage application, negative stranded reads were being shifted 1/2 the read length in the wrong direction.
June 12th, 2009
· Added several apps needed for generating cap-seq arrays, made many additions to the OligoTiler application to speed array design through Agilent eArray.
May 12th, 2009
· Fixed reporting bug in DefinedRegionScanSeqs when using bed files.
May 11th, 2009
· Added a catch for cases when the R qvalue estimation returns infinity.
May 8th, 2009
· Bug fix for qValueFDR estimation in ScanSeqs, inadvertently disabled this feature in prior release. Updated documentation.
May 4th, 2009
· Upgrade of the q-value FDR estimation in ScanSeqs and DefinedRegionScanSeqs. Much better accuracy through the use of fuzzy p-values for trials with < 20 observations.