(1) Merged DupHMM's old Poisson-fit method and new k-means clustering method into a single program (temporarily named OldDupHMM.py) in which the user chooses the default mode 1 (Poisson) or mode 2 (Clustering). This has not yet been tested for bugs. The latest DupHMM version prior to merging, which only includes k-means clustering, is temporarily saved as DupHMM.py. Once the merged version has been fully debugged, I will delete DupHMM.py and rename OldDupHMM.py to DupHMM.py
(2) Two new scripts have been added. DistantDupSearchWithMatePairs.py looks for reads mapping to within a duplicated region which have mate pairs that are very distant located or on another chromosome in order to determine whether or not these duplications seem like valid DupHMM calls. DistantDupSearch_GenerateRandomRegions.py generates an equally sized list to the duplicated region list containing regions equal in size to the duplicated regions. This list can then be run in DistantDupSearchWithMatePairs.py to determine whether or not the number of distantly mapping mate pairs is unusually high, low, or the same when compared to randomly selected regions.
(3) DupHMM.py, Viterbi.cpp, Viterbi.exe, dist_fir.R, and SAM.py have been packaged into DupHMM.tar.gz. This is the package name that will ultimately be available for download from the GitHub website by anyone wishing to install and use the DupHMM suite. Currently testing the GitHub wiki page and preparing to create Comai/Korf wiki pages for DupHMM.
Merge https://github.com/KorfLab/DupHMM