[initial version
Ketil Malde <ketil@ii.uib.no>**20060607122009] 
[now reads sequences from file
Ketil Malde <ketil@ii.uib.no>**20060607125104] 
[added Stats
Ketil Malde <ketil@ii.uib.no>**20060607201430] 
[major perf improvement
Ketil Malde <ketil@ii.uib.no>**20060607210648] 
[using Ints
Ketil Malde <ketil@ii.uib.no>**20060609062234] 
[replace filter with dropSpace, 3x perf improvement (from dons)
Ketil Malde <ketil@ii.uib.no>**20060609081842] 
[reorg dir hier
Ketil Malde <ketil@ii.uib.no>**20060609112835] 
[Added Cabal infrastructure
Ketil Malde <ketil@ii.uib.no>**20060609112904] 
[add functionality for RBR
Ketil Malde <ketil@ii.uib.no>**20060611170327] 
[added (naïve) entropy implementation
Ketil Malde <ketil@ii.uib.no>**20060630092315] 
[added Entropy and HashWord modules
Ketil Malde <ketil@ii.uib.no>**20060704113854] 
[changes to fasta module
Ketil Malde <ketil@ii.uib.no>**20060704113933] 
[renamed from 'key' to 'hash'
Ketil Malde <ketil@ii.uib.no>**20060705060546] 
[added simple Makefile
Ketil Malde <ketil@ii.uib.no>**20060705091217] 
[added rcontig for revcompl contigous hashes
Ketil Malde <ketil@ii.uib.no>**20060705094546] 
[better error messages for debugging
Ketil Malde <ketil@ii.uib.no>**20060705101301] 
[bugfix to rcontig
Ketil Malde <ketil@ii.uib.no>**20060705101331] 
[Entropy comment fixes.  Need to get kth-order entropy right.
Ketil Malde <ketil@ii.uib.no>**20060706093840] 
[properly ignore comments
Ketil Malde <ketil@ii.uib.no>**20060706093904] 
[seqlabel returns only first word, seqheader full header
Ketil Malde <ketil@ii.uib.no>**20060706093924] 
[inline fasta/hashwrod accessor function
Ketil Malde <ketil@ii.uib.no>**20060706100048] 
[splitsAt as a toplevel function
Ketil Malde <ketil@ii.uib.no>**20060811063604] 
[output functions
Ketil Malde <ketil@ii.uib.no>**20060811063618] 
[Added types to stop warnings on build
Gord Pollock <gord.pollock@gmail.com>**20060810220121] 
[Changed makefile; doesn't assume Setup.hs executable
Gord Pollock <gord.pollock@gmail.com>**20060810220313] 
[export list for Fasta module
Ketil Malde <ketil@ii.uib.no>**20060811084634] 
[re-export pack/unpack directly
Ketil Malde <ketil@ii.uib.no>**20060811084642] 
[type declaration
Ketil Malde <ketil@ii.uib.no>**20060811084656] 
[fix perf bug - export ! directly from Fasta.hs
Ketil Malde <ketil@ii.uib.no>**20060818073215] 
[added 'clean' target
Ketil Malde <ketil@ii.uib.no>**20060818073744] 
[bumped version
Ketil Malde <ketil@ii.uib.no>**20060818073804] 
[TAG 0.1
Ketil Malde <ketil@ii.uib.no>**20060818073830] 
[reorganized makefile, added haddock step
Ketil Malde <ketil@ii.uib.no>**20060823102523] 
[haddockized comments in Fasta
Ketil Malde <ketil@ii.uib.no>**20060823131759] 
[split up targets in Mf.
Ketil Malde <ketil@ii.uib.no>**20060823131849] 
[comments allowed between sequences
Ketil Malde <ketil@ii.uib.no>**20060823131908] 
[multiple changes (keyf uses seqdata, freq uses IntMap, etc)
Ketil Malde <ketil@ii.uib.no>**20060918115936] 
[output format fix
Ketil Malde <ketil@ii.uib.no>**20060918135126] 
[Fasta exports Offset
Ketil Malde <ketil@ii.uib.no>**20060919124053] 
[fix? and added a countSeqs function
Ketil Malde <ketil@ii.uib.no>**20061003131406] 
[modify for ghc-6.6
Ketil Malde <ketil@ii.uib.no>**20061017130706] 
[version bumped to 0.2
Ketil Malde <ketil@ii.uib.no>**20061017135838] 
[TAG 0.2
Ketil Malde <ketil@ii.uib.no>**20061017135853] 
[simple N-W impl
Ketil Malde <ketil@ii.uib.no>**20061129132539] 
[generalized NW/SW alignment
Ketil Malde <ketil@ii.uib.no>**20061130111955] 
[factored out matrix construction
Ketil Malde <ketil@ii.uib.no>**20061130112023] 
[showalign function
Ketil Malde <ketil@ii.uib.no>**20061130112037] 
[rename backtrack
Ketil Malde <ketil@ii.uib.no>**20061130112525] 
[renamed nw-specific backtracking
Ketil Malde <ketil@ii.uib.no>**20061130142656] 
[generalized backtracking
Ketil Malde <ketil@ii.uib.no>**20061130142734] 
[docs and type sigs
Ketil Malde <ketil@ii.uib.no>**20061130151614] 
[generalized backtracking to cover local alignments, too
Ketil Malde <ketil@ii.uib.no>**20061130155243] 
[refactor, and add affine scores
Ketil Malde <ketil@ii.uib.no>**20061201092533] 
[factored things more finely
Ketil Malde <ketil@ii.uib.no>**20061204122309] 
[commented out non-functioning affine scoring
Ketil Malde <ketil@ii.uib.no>**20061204122333] 
[almost-working columnwise version
Ketil Malde <ketil@ii.uib.no>**20061204152643] 
[fix pesky off-by-one bug
Ketil Malde <ketil@ii.uib.no>**20061205083625] 
[qc property
Ketil Malde <ketil@ii.uib.no>**20061205083641] 
[no need to be so grumpy about unfoldr
Ketil Malde <ketil@ii.uib.no>**20061205083739] 
[Needs glasgow-exts for parallel list comprehension
Ketil Malde <ketil@ii.uib.no>**20061205124906] 
[loosen type for mkcolumns (why isn't mkcol's sig accepted?)
Ketil Malde <ketil@ii.uib.no>**20061205124924] 
[proper QC properties
Ketil Malde <ketil@ii.uib.no>**20061205125153] 
[simpler arbitrary Char, commented-out failing test testing test
Ketil Malde <ketil@ii.uib.no>**20061205130158] 
[simplified arb instance for Char
Ketil Malde <ketil@ii.uib.no>**20061205141329] 
[substitution matrices supported (and checked)
Ketil Malde <ketil@ii.uib.no>**20061205141341] 
[doc additions
Ketil Malde <ketil@ii.uib.no>**20061205141538] 
[type decl fix (thanks, dons)
Ketil Malde <ketil@ii.uib.no>**20061206091417] 
[proper hierarchical module name
Ketil Malde <ketil@ii.uib.no>**20061206132305] 
[big reorganization of everything in AlignBase
Ketil Malde <ketil@ii.uib.no>**20061206144540] 
[latex preamble/end
Ketil Malde <ketil@ii.uib.no>**20061206145413] 
[reorganized the scoring function stuff
Ketil Malde <ketil@ii.uib.no>**20061207134203] 
[quickcheck stuff
Ketil Malde <ketil@ii.uib.no>**20061207134316] 
[direct recursion for illustration purposes only
Ketil Malde <ketil@ii.uib.no>**20061207134344] 
[linear space score calculation
Ketil Malde <ketil@ii.uib.no>**20061207134400] 
[minor doc/comment/latex fixes
Ketil Malde <ketil@ii.uib.no>**20061207134415] 
[moved QC defs earlier in the file
Ketil Malde <ketil@ii.uib.no>**20061208125429] 
[parametrize columns by hd/tl
Ketil Malde <ketil@ii.uib.no>**20061208125451] 
[added parametrized reversal of sequences
Ketil Malde <ketil@ii.uib.no>**20061208125514] 
[rephrasing and cabal resolution
Ketil Malde <ketil@ii.uib.no>**20061211085624] 
[comment added
Ketil Malde <ketil@ii.uib.no>**20061211135442] 
[generalized qc_align and bug fix
Ketil Malde <ketil@ii.uib.no>**20061211135550] 
[added iterative linear space algorithm
Ketil Malde <ketil@ii.uib.no>**20061211135611]