[initial idea
Ketil Malde <ketil@ii.uib.no>**20050301153434] 
[extended the notes a lot
Ketil Malde <ketil@ii.uib.no>**20050329143127] 
[Added src dir, parser skeleton and sequence datatype
Ketil Malde <ketil@ii.uib.no>**20050330091915] 
[added potential sdata/nuc parser
Ketil Malde <ketil@ii.uib.no>**20050330102106] 
[provisory metadata and sdata parsers
Ketil Malde <ketil@ii.uib.no>**20050330112740] 
[added test dir and fasta test cases
Ketil Malde <ketil@ii.uib.no>**20050331091254] 
[small fix for label syntax
Ketil Malde <ketil@ii.uib.no>**20050331091404] 
[data format changes (UArrays etc)
Ketil Malde <ketil@ii.uib.no>**20050331091531] 
[added sketch for different parsers
Ketil Malde <ketil@ii.uib.no>**20050331093540] 
[fix to length, and added sketched accessor functions
Ketil Malde <ketil@ii.uib.no>**20050331093603] 
[replaced Seq access with generic seqprop accessor
Ketil Malde <ketil@ii.uib.no>**20050331094354] 
[separate blank and comment parsers
Ketil Malde <ketil@ii.uib.no>**20050331102506] 
[added blanks parser
Ketil Malde <ketil@ii.uib.no>**20050331120122] 
[turned metadata into general header parser
Ketil Malde <ketil@ii.uib.no>**20050331120127] 
[reformatted text
Ketil Malde <ketil@ii.uib.no>**20050331120207] 
[rudimentary NCBI-style parser in place
Ketil Malde <ketil@ii.uib.no>**20050331130709] 
[word parser accepts underscore
Ketil Malde <ketil@ii.uib.no>**20050331133230] 
[ncbi-keys now called annot_keys
Ketil Malde <ketil@ii.uib.no>**20050401095909] 
[stack parser, plus minor fix
Ketil Malde <ketil@ii.uib.no>**20050401100004] 
[formatting change, comment removal
Ketil Malde <ketil@ii.uib.no>**20050401100108] 
[fixes: require at least one blank in many cases, better errors
Ketil Malde <ketil@ii.uib.no>**20050401114847] 
[Added sections and descriptive text for NCBI/Stack
Ketil Malde <ketil@ii.uib.no>**20050401115627] 
[parametrized fasta over data parser as well
Ketil Malde <ketil@ii.uib.no>**20050401122501] 
[minor error reporting improvement
Ketil Malde <ketil@ii.uib.no>**20050401123519] 
[added a test case
Ketil Malde <ketil@ii.uib.no>**20050401134510] 
[some test functions added
Ketil Malde <ketil@ii.uib.no>**20050402190127] 
[lword definition, reformatted indentation
Ketil Malde <ketil@ii.uib.no>**20050402190150] 
[ncbi support for quoted values
Ketil Malde <ketil@ii.uib.no>**20050404071459] 
[renaming of test functions
Ketil Malde <ketil@ii.uib.no>**20050404091524] 
[added F3 main module
Ketil Malde <ketil@ii.uib.no>**20050404094940] 
[changed representation of seqannot
Ketil Malde <ketil@ii.uib.no>**20050404112706
 sequence annotations are now split between known key-value pairs (KKV),
 unknown (UKV), databases (DB db acc) and Annot(ations).
] 
[small parser fixes
Ketil Malde <ketil@ii.uib.no>**20050404142601] 
[explicit list of parsers
Ketil Malde <ketil@ii.uib.no>**20050405080645] 
[rudimentary parser discovery code -- could be more elegant
Ketil Malde <ketil@ii.uib.no>**20050405080705] 
[Dictionary-based implementation of annot decoding
Ketil Malde <ketil@ii.uib.no>**20050406113135] 
[added show_ncbi; not sure if it's the right thing
Ketil Malde <ketil@ii.uib.no>**20050406130442] 
[Ported/rewrote WordMap from xtract, using Data.Map
Ketil Malde <ketil@ii.uib.no>**20050407041808] 
[added nucleotide comments
Ketil Malde <ketil@ii.uib.no>**20050407103256] 
[added names to parsers
Ketil Malde <ketil@ii.uib.no>**20050407103323] 
[added option handling to f3
Ketil Malde <ketil@ii.uib.no>**20050407103346] 
[elaborated option handling, skeleton implementation
Ketil Malde <ketil@ii.uib.no>**20050407114408] 
[added main.tex; small latex fix
Ketil Malde <ketil@ii.uib.no>**20050407115554] 
[added newpages after files
Ketil Malde <ketil@ii.uib.no>**20050414084301] 
[main now prints option summary
Ketil Malde <ketil@ii.uib.no>**20050414084326] 
[f3 now attempts to identify FASTA formats
Ketil Malde <ketil@ii.uib.no>**20050414093048] 
[identify output cleanup
Ketil Malde <ketil@ii.uib.no>**20050414121839] 
[rewrote output code
Ketil Malde <ketil@ii.uib.no>**20050414133617] 
[comment reorg/improvements
Ketil Malde <ketil@ii.uib.no>**20050418110623] 
[added freqcount, sketched mkwordmap
Ketil Malde <ketil@ii.uib.no>**20050418110650] 
[implemented mkwordmap (more testing required)
Ketil Malde <ketil@ii.uib.no>**20050418113642] 
[F3 now counts letter frequencies
Ketil Malde <ketil@ii.uib.no>**20050418120559] 
[specified Fasta exports (to exp. parse)
Ketil Malde <ketil@ii.uib.no>**20050418135400] 
[import fixes
Ketil Malde <ketil@ii.uib.no>**20050419071953] 
[added support for -k
Ketil Malde <ketil@ii.uib.no>**20050419072007] 
[added support for explicit parser selection
Ketil Malde <ketil@ii.uib.no>**20050419072031] 
[slightly better error message on parse failure
Ketil Malde <ketil@ii.uib.no>**20050419072309] 
[freqs are optional, better error reporting
Ketil Malde <ketil@ii.uib.no>**20050419083415] 
[added Parsex (lazyMany from T.Z.)
Ketil Malde <ketil@ii.uib.no>**20050419120748] 
[correctly modify positions for subsequent seqs (BUGFIX)
Ketil Malde <ketil@ii.uib.no>**20050419125232] 
[modified lazyMany to lazyparse
Ketil Malde <ketil@ii.uib.no>**20050421080854] 
[trivial now ignores all but the label
Ketil Malde <ketil@ii.uib.no>**20050421080956] 
[strictness annotations added
Ketil Malde <ketil@ii.uib.no>**20050421081946
 bm10k.seq: 140Mb -> 80Mb
] 
[added makefile
Ketil Malde <ketil@ii.uib.no>**20050421085614] 
[replaced freqcount by more efficient version
Ketil Malde <ketil@ii.uib.no>**20050426140951] 
[added clean target to Makefile
Ketil Malde <ketil@ii.uib.no>**20050512122148] 
[factored out freqs as a separate function
Ketil Malde <ketil@ii.uib.no>**20050512124757] 
[added a subsection, split out n2i'
Ketil Malde <ketil@ii.uib.no>**20050513074446] 
[Implemented word counting with STMap
Ketil Malde <ketil@ii.uib.no>**20050513074646] 
[removed n2i/i2n, use n2k instead
Ketil Malde <ketil@ii.uib.no>**20050513074726] 
[TAG STMap frequency counting
Ketil Malde <ketil@ii.uib.no>**20050513074824] 
[serious reshuffling and -factoring of code
Ketil Malde <ketil@ii.uib.no>**20050513104225] 
[WordMap -> STMap in main.tex
Ketil Malde <ketil@ii.uib.no>**20050513112058] 
[small fix section header 
Ketil Malde <ketil@ii.uib.no>**20050513112613] 
[Usage textual fix
Ketil Malde <ketil@ii.uib.no>**20050513120652] 
[added RB draft - parsers/prints options
Ketil Malde <ketil@ii.uib.no>**20050513120728] 
[Moved functionality to Fasta
Ketil Malde <ketil@ii.uib.no>**20050513134157] 
[moved frequencies from read to main
Ketil Malde <ketil@ii.uib.no>**20050513143227] 
[sketched RB main
Ketil Malde <ketil@ii.uib.no>**20050513143245] 
[now reads files and calculates freqs
Ketil Malde <ketil@ii.uib.no>**20050513184320] 
[moved read_file to Fasta (needs better name)
Ketil Malde <ketil@ii.uib.no>**20050513195657] 
[implemented coverage, some shuffling of the old stuff
Ketil Malde <ketil@ii.uib.no>**20050515102732] 
[writers implemented
Ketil Malde <ketil@ii.uib.no>**20050519101116] 
[output sequence data with 60-lines
Ketil Malde <ketil@ii.uib.no>**20050519101201] 
[writer option handling and output
Ketil Malde <ketil@ii.uib.no>**20050519101221] 
[changed options (I,O -> p,w)
Ketil Malde <ketil@ii.uib.no>**20050519101246] 
[TAG ready to implement statistics
Ketil Malde <ketil@ii.uib.no>**20050520134913] 
[first masking version, only fixed masking parameters
Ketil Malde <ketil@ii.uib.no>**20050520134944] 
[now accept masking parms on cmdline
Ketil Malde <ketil@ii.uib.no>**20050520140536] 
[coping with various irregularities in the stack format
Ketil Malde <ketil@ii.uib.no>**20050520174329] 
[parameter fix ported to F3 as well
Ketil Malde <ketil@ii.uib.no>**20050520174955] 
[added targets for static and profiling
Ketil Malde <ketil@ii.uib.no>**20050520195315] 
[fixed RB usage output
Ketil Malde <ketil@ii.uib.no>**20050520195339] 
[no masking without -k
Ketil Malde <ketil@ii.uib.no>**20050520195412] 
[local uv_mk, significant speed opt
Ketil Malde <ketil@ii.uib.no>**20050520195437] 
[TAG works for direct lookup table
Ketil Malde <ketil@ii.uib.no>**20050610125152] 
[added infrastructure for constructing the suffix array
Ketil Malde <ketil@ii.uib.no>**20050610125212] 
[fixed suffix array size and nicer type
Ketil Malde <ketil@ii.uib.no>**20050610141030] 
[idiot bugfix
Ketil Malde <ketil@ii.uib.no>**20050613124106] 
[cleanup, introduce sep type for ST arrays
Ketil Malde <ketil@ii.uib.no>**20050614091428] 
[bucket-sorting -- partly tested and working
Ketil Malde <ketil@ii.uib.no>**20050614091451] 
[comment added
Ketil Malde <ketil@ii.uib.no>**20050614105815] 
[changes to use Position = (Seq,Offset)
Ketil Malde <ketil@ii.uib.no>**20050614124416] 
[temporary sketch of bucket sorting
Ketil Malde <ketil@ii.uib.no>**20050615081322] 
[using KeyF, simplistic bucket sort.  Untested.
Ketil Malde <ketil@ii.uib.no>**20050615094318] 
[sketched KeyF factories
Ketil Malde <ketil@ii.uib.no>**20050615112145] 
[naive impl. of contigous (non-optimized)
Ketil Malde <ketil@ii.uib.no>**20050615131132] 
[type modifications of dubious nature
Ketil Malde <ketil@ii.uib.no>**20050615131207] 
[implemented genkeys
Ketil Malde <ketil@ii.uib.no>**20050616093304] 
[parametrized KeyF type
Ketil Malde <ketil@ii.uib.no>**20050616093658] 
[updated main modules to account for new KeyF
Ketil Malde <ketil@ii.uib.no>**20050616111520] 
[bugfix in contigous (indexing problem)
Ketil Malde <ketil@ii.uib.no>**20050616111556] 
[yet another small bug in contigous
Ketil Malde <ketil@ii.uib.no>**20050616131758] 
[added RB to printout
Ketil Malde <ketil@ii.uib.no>**20050616143141] 
[makefile options update (little if any difference)
Ketil Malde <ketil@ii.uib.no>**20050617123430] 
[minor fix, plus comments
Ketil Malde <ketil@ii.uib.no>**20050617123456] 
[added a gapped keys function (todo: abstract it?)
Ketil Malde <ketil@ii.uib.no>**20050617123512] 
[f3 calculates and outputs suffix arrays
Ketil Malde <ketil@ii.uib.no>**20050617124811] 
[implemented k2-keys, works with test case in f3
Ketil Malde <ketil@ii.uib.no>**20050622041321] 
[warning eliminations, formatting
Ketil Malde <ketil@ii.uib.no>**20050622041502] 
[bugfix: incorrect invocation of cont_offs in f3
Ketil Malde <ketil@ii.uib.no>**20050622044558] 
[generalized offset function
Ketil Malde <ketil@ii.uib.no>**20050622044906] 
[implement and use "simple" -- faster but doesn't check for N!
Ketil Malde <ketil@ii.uib.no>**20050622060840] 
[stateful KeyFs, dummy implementation only (for now)
Ketil Malde <ketil@ii.uib.no>**20050622073646] 
[warning fixes in Fasta.lhs
Ketil Malde <ketil@ii.uib.no>**20050622110601] 
[added state-passing to genkeys
Ketil Malde <ketil@ii.uib.no>**20050622110617] 
[added implementation with state for N-skipping contigous
Ketil Malde <ketil@ii.uib.no>**20050622110649] 
[implemented right-shifting speedup
Ketil Malde <ketil@ii.uib.no>**20050622114557] 
[k param now accepts a k1,k2 tuple
Ketil Malde <ketil@ii.uib.no>**20050623124712] 
[Bugfix: forgot a hard-coded "6" in F3
Ketil Malde <ketil@ii.uib.no>**20050624104352] 
[check for N in simple
Ketil Malde <ketil@ii.uib.no>**20050628085227] 
[implemented simple with state (tested briefly)
Ketil Malde <ketil@ii.uib.no>**20050630110444] 
[Moved stuff to Keys module
Ketil Malde**20050701140314] 
[small import clarification
Ketil Malde <ketil@ii.uib.no>**20050701141254] 
[forgot to add Keys to main.tex
Ketil Malde <ketil@ii.uib.no>**20050704111320] 
[added printing target to Makefile
Ketil Malde <ketil@ii.uib.no>**20050704143420] 
[added MaskCount sources
Ketil Malde <ketil@ii.uib.no>**20050704143432] 
[RB compiles
Ketil Malde <ketil@ii.uib.no>**20050707080545] 
[freqtab and contig work - UNDER CONSTRUCTION
Ketil Malde <ketil@ii.uib.no>**20050707125337] 
[U.C.: RB also compiles
Ketil Malde <ketil@ii.uib.no>**20050707125716] 
[added error msg instead of undefined
Ketil Malde <ketil@ii.uib.no>**20050708094610] 
[removed old contigous definition
Ketil Malde <ketil@ii.uib.no>**20050708094631] 
[Added MC.lhs
Ketil Malde <ketil@ii.uib.no>**20050726131909] 
[bug fix: incorrect counting
Ketil Malde <ketil@ii.uib.no>**20050726133020] 
[todo list for MC
Ketil Malde <ketil@ii.uib.no>**20050726144146] 
[better usage for MC
Ketil Malde <ketil@ii.uib.no>**20050726144208] 
[two-way coverage function
Ketil Malde <ketil@ii.uib.no>**20050726144229] 
[text formatting added
Ketil Malde <ketil@ii.uib.no>**20050727083129] 
[added skeleton option handling for K/T/F output modes
Ketil Malde <ketil@ii.uib.no>**20050729115145] 
[Param fixes/error handling for F3
Ketil Malde <ketil@ii.uib.no>**20050729135024] 
[comment/whitespace changes, extraneous import removed
Ketil Malde <ketil@ii.uib.no>**20050811092144] 
[added implementations of verify and half offset
Ketil Malde <ketil@ii.uib.no>**20050811092257] 
[added freqtable
Ketil Malde <ketil@ii.uib.no>**20050811104638] 
[reshuffled F3 with separate main per output option
Ketil Malde <ketil@ii.uib.no>**20050811112024] 
[more compact output for f3 -K
Ketil Malde <ketil@ii.uib.no>**20050812124614] 
[explicit export declarations
Ketil Malde <ketil@ii.uib.no>**20050812124706] 
[Single-sequence keys func, part 1: Keys.lhs
Ketil Malde <ketil@ii.uib.no>**20050815093114] 
[Single-sequence keys func, part 2: FreqTable
Ketil Malde <ketil@ii.uib.no>**20050815103053] 
[STMap -> IndexMap
Ketil Malde <ketil@ii.uib.no>**20050815103338] 
[Single-sequence keys func, part 3: IndexArray
Ketil Malde <ketil@ii.uib.no>**20050815111557] 
[(unoptimized) offset implemented
Ketil Malde <ketil@ii.uib.no>**20050815140436] 
[F3 fix
Ketil Malde <ketil@ii.uib.no>**20050815140527] 
[cleaned up FreqTable, skeleton accessors
Ketil Malde <ketil@ii.uib.no>**20050815140558] 
[cleaned up F3 (warnings/formatting)
Ketil Malde <ketil@ii.uib.no>**20050816101246] 
[cleaner interface to FT, F3 updated acc.
Ketil Malde <ketil@ii.uib.no>**20050816101323] 
[Suffix->IndexArray, skeleton interface as well
Ketil Malde <ketil@ii.uib.no>**20050816101359] 
[naive implementation of "simple" keyf
Ketil Malde <ketil@ii.uib.no>**20050816110911] 
[updated RB to "work" (only fwd coverage)
Ketil Malde <ketil@ii.uib.no>**20050816110940] 
[impl. curve output for RB
Ketil Malde <ketil@ii.uib.no>**20050816120156] 
[skeleton for bsearch
Ketil Malde <ketil@ii.uib.no>**20050818084954] 
[Replaced SuffixIndex -> PreIndex
Ketil Malde <ketil@ii.uib.no>**20050818085100] 
[(fwd)coverage now returns correct number of values
Ketil Malde <ketil@ii.uib.no>**20050818115120] 
[added all-* targets in makefile
Ketil Malde <ketil@ii.uib.no>**20050818115307] 
[added TODO-list
Ketil Malde <ketil@ii.uib.no>**20050819122021] 
[cleanup of idea.txt - current status added
Ketil Malde <ketil@ii.uib.no>**20050819122510] 
[account for revcompl sequences
Ketil Malde <ketil@ii.uib.no>**20050819122540] 
[TAG works for contigous keys and freqtables
Ketil Malde <ketil@ii.uib.no>**20050819122637] 
[renamed mc to mct, added static target
Ketil Malde <ketil@ii.uib.no>**20050822113704] 
[export isN, needed for mct
Ketil Malde <ketil@ii.uib.no>**20050822113726] 
[(untested) improved error handling in mct
Ketil Malde <ketil@ii.uib.no>**20050823101554] 
[more thoughts, fixes to todos
Ketil Malde <ketil@ii.uib.no>**20050829115111] 
[named Key type for clarity, signatures to count etc
Ketil Malde <ketil@ii.uib.no>**20050829115142] 
[added (completely untested) bsearch function
Ketil Malde <ketil@ii.uib.no>**20050829115225] 
[type checking fixes
Ketil Malde <ketil@ii.uib.no>**20050906065353] 
[working bsearch and count
Ketil Malde <ketil@ii.uib.no>**20050916080804] 
[implemented positions
Ketil Malde <ketil@ii.uib.no>**20050916094620] 
[Temp checkin: compiles, but incorrect
Ketil Malde <ketil@ii.uib.no>**20050921115925] 
[added multi-T words to F3
Ketil Malde <ketil@ii.uib.no>**20050923184031] 
[bug fixes to RB and IA
Ketil Malde <ketil@ii.uib.no>**20050923184111] 
[mods to commented trace stmts
Ketil Malde <ketil@ii.uib.no>**20050923210852] 
[check for out of bounds in IA
Ketil Malde <ketil@ii.uib.no>**20050923220017] 
[guard against out-of-bounds in bsearch(1,2)
Ketil Malde <ketil@ii.uib.no>**20050927124331] 
[main_coverage impl
Ketil Malde <ketil@ii.uib.no>**20050927124458] 
[fix coverage offset bug (would look for incorrect keys)
Ketil Malde <ketil@ii.uib.no>**20050927124525] 
[type decl, comment removal
Ketil Malde <ketil@ii.uib.no>**20050927124601] 
[fixed coverage functions
Ketil Malde <ketil@ii.uib.no>**20050927124623] 
[Mods for tracing
Ketil Malde <ketil@ii.uib.no>**20050927125726] 
[bug fix - now correctly aligns fwd and rev coverage
Ketil Malde <ketil@ii.uib.no>**20050927201109
 Also: define rev coverage as a mod to fwd coverage
] 
[new masked function - symmetric masking
Ketil Malde <ketil@ii.uib.no>**20050928101432] 
[TAG to øystein for testing
Ketil Malde <ketil@ii.uib.no>**20050928114649] 
[bugfix: mct would always fail
Ketil Malde <ketil@ii.uib.no>**20051003130144] 
[makefile fix: install target
Ketil Malde <ketil@ii.uib.no>**20051003130218] 
[EOL at end
Ketil Malde <ketil@ii.uib.no>**20051003135225] 
[fix for install target
Ketil Malde <ketil@ii.uib.no>**20051003140015] 
[ignore zero count words for statistics purposes
Ketil Malde <ketil@ii.uib.no>**20051003140024] 
[added FASTA thresh annot, and bugfix for all-N sequences
Ketil Malde <ketil@ii.uib.no>**20051003150442] 
[type decl and cleanup
Ketil Malde <ketil@ii.uib.no>**20051004130113] 
[experimental: use simple_unsafe to speed things up a bit
Ketil Malde <ketil@ii.uib.no>**20051004205905] 
[small offset/keys optimization
Ketil Malde <ketil@ii.uib.no>**20051004212420] 
[commented-out code removal
Ketil Malde <ketil@ii.uib.no>**20051004212516] 
[added -v (verbose) switch, with some output
Ketil Malde <ketil@ii.uib.no>**20051005084324] 
[eliminated extra checks (no noticable perf benefit)
Ketil Malde <ketil@ii.uib.no>**20051005132922] 
[more robust option parsing
Ketil Malde <ketil@ii.uib.no>**20051006121942] 
[updated TODO list
Ketil Malde <ketil@ii.uib.no>**20051021124157] 
[Updated F3 to work with contigous keys
Ketil Malde <ketil@ii.uib.no>**20051021124210] 
[frequency counting working
Ketil Malde <ketil@ii.uib.no>**20051021125640
 at least apparently.  It also accounts for (ignores) positions with N in the k2 part
] 
[Intermediate checkin: freqarray compiles
Ketil Malde <ketil@ii.uib.no>**20051025104931] 
[complete, but buggy
Ketil Malde <ketil@ii.uib.no>**20051025135818] 
[switch to least sign first, fix returning correct pi(?)
Ketil Malde <ketil@ii.uib.no>**20051025201150] 
[fix: mod is the other k
Ketil Malde <ketil@ii.uib.no>**20051025201505] 
[implemented F3 using Data.Map
Ketil Malde <ketil@ii.uib.no>**20051028194414] 
[freqtable takes only one k-param
Ketil Malde <ketil@ii.uib.no>**20051028195135] 
[updated RB to use FT maps
Ketil Malde <ketil@ii.uib.no>**20051028200651] 
[keys cleanup, typo, new TODO
Ketil Malde <ketil@ii.uib.no>**20051031142754] 
[Added progress meters - yay!
Ketil Malde <ketil@ii.uib.no>**20051101102405] 
[added long term goals
Ketil Malde <ketil@ii.uib.no>**20051124130831] 
[made -k take a single number in RB
Ketil Malde <ketil@ii.uib.no>**20051124140012] 
[added progress while masking as well as coverage
Ketil Malde <ketil@ii.uib.no>**20051130103815] 
[cleaned up countIO usage (progress reporting)
Ketil Malde <ketil@ii.uib.no>**20051130113233] 
[sketched new parameters (gap, sparse, shaped)
Ketil Malde <ketil@ii.uib.no>**20051130114647] 
[make MC output more detailed response
Ketil Malde <ketil@ii.uib.no>**20051220112108] 
[diff output for each sequence
Ketil Malde <ketil@ii.uib.no>**20051222105622] 
[small formatting change
Ketil Malde <ketil@ii.uib.no>**20060104125637] 
[gap closing, first attempt
Ketil Malde <ketil@ii.uib.no>**20060104125730] 
[comment changes
Ketil Malde <ketil@ii.uib.no>**20060104125807] 
[connected to rest of code - buggy corner cases
Ketil Malde <ketil@ii.uib.no>**20060104131008] 
[rewrote closegaps more elegantly
Ketil Malde <ketil@ii.uib.no>**20060104133504] 
[removed commented-out, old closegap code
Ketil Malde <ketil@ii.uib.no>**20060104133540] 
[support for -l and -s parameters
Ketil Malde <ketil@ii.uib.no>**20060106115704] 
[TAG 0.1 mask with mean and stdev
Ketil Malde <ketil@ii.uib.no>**20060124090353] 
[new treshold code
Ketil Malde <ketil@ii.uib.no>**20060124090811] 
[added pearson's phi to mct
Ketil Malde <ketil@ii.uib.no>**20060124090848] 
[added median calc to rb
Ketil Malde <ketil@ii.uib.no>**20060124090902] 
[cleanups to output code, added header
Ketil Malde <ketil@ii.uib.no>**20060124115940] 
[output limit, not highest remaining
Ketil Malde <ketil@ii.uib.no>**20060124120159] 
[changed the trivial parser (andersl request)
Ketil Malde <ketil@ii.uib.no>**20060124154854] 
[new defaults
Ketil Malde <ketil@ii.uib.no>**20060124154933] 
[usage w/o lineshift
Ketil Malde <ketil@ii.uib.no>**20060124154950] 
[threhsold now returns more values
Ketil Malde <ketil@ii.uib.no>**20060124155000] 
[added 3-pass 2do
Ketil Malde <ketil@ii.uib.no>**20060127125821] 
[added median to output
Ketil Malde <ketil@ii.uib.no>**20060127125900] 
[renamed/moved around RB and MC
Ketil Malde <ketil@ii.uib.no>**20060127130426] 
[parametrized FreqTable, support k>15
Ketil Malde <ketil@ii.uib.no>**20060130125412] 
[updated TODO
Ketil Malde <ketil@ii.uib.no>**20060131131531] 
[added server mode
Ketil Malde <ketil@ii.uib.no>**20060131131553] 
[exporting showdata directly from Fasta.lhs
Ketil Malde <ketil@ii.uib.no>**20060131132850] 
[ouput done only in batch mode
Ketil Malde <ketil@ii.uib.no>**20060131132926] 
[output masked sequences first (to get info header)
Ketil Malde <ketil@ii.uib.no>**20060131132941] 
[name change: RB -> RBR
Ketil Malde <ketil@ii.uib.no>**20060202192855] 
[added 'score' to ouput
Ketil Malde <ketil@ii.uib.no>**20060203103831] 
[bump RBR version
Ketil Malde <ketil@ii.uib.no>**20060203103901] 
[TAG 0.2 server mode, k>15
Ketil Malde <ketil@ii.uib.no>**20060203104544] 
[added "READY" prompt to server mode
Ketil Malde <ketil@ii.uib.no>**20060206133359] 
[added line-oriented interact
Ketil Malde <ketil@ii.uib.no>**20060206143824] 
[support multiple sequence requests (server)
Ketil Malde <ketil@ii.uib.no>**20060206144047] 
[support three MPars (stdevs,mincov, and maxscore)
Ketil Malde <ketil@ii.uib.no>**20060207093042] 
["TODO" addition
Ketil Malde <ketil@ii.uib.no>**20060207093054] 
[fixed main.tex
Ketil Malde <ketil@ii.uib.no>**20060207093122] 
[actually remove unique words as well (i.e. read errors)
Ketil Malde <ketil@ii.uib.no>**20060217212130] 
[added TODO in comment
Ketil Malde <ketil@ii.uib.no>**20060220093043] 
[fix for glasgow-exts (now autodetects in GHCi)
Ketil Malde <ketil@ii.uib.no>**20060221105125] 
[debugging code, ready for testing
Ketil Malde <ketil@ii.uib.no>**20060221105153] 
[calc thresh from mode (rbr6)
Ketil Malde <ketil@ii.uib.no>**20060222142356] 
[comment update: fix probs with rbr6
Ketil Malde <ketil@ii.uib.no>**20060222142445] 
[Use sqrt(n) window
Ketil Malde <ketil@ii.uib.no>**20060223084306] 
[added blunt'ing (improves scores - rbr8)
Ketil Malde <ketil@ii.uib.no>**20060223125948] 
[mincov is relative to mean (again)
Ketil Malde <ketil@ii.uib.no>**20060223131036] 
[try all (more?) windows
Ketil Malde <ketil@ii.uib.no>**20060227105915] 
[lower case masking option
Ketil Malde <ketil@ii.uib.no>**20060308184555] 
[todo update
Ketil Malde <ketil@ii.uib.no>**20060328083539] 
[changed parameters -M -> -s, -t
Ketil Malde <ketil@ii.uib.no>**20060328083558] 
[new blunting code
Ketil Malde <ketil@ii.uib.no>**20060328083646] 
[TAG 0.3 revised statistics model, param changes
Ketil Malde <ketil@ii.uib.no>**20060328084001] 
[mct now uses printf
Ketil Malde <ketil@ii.uib.no>**20060329101223] 
[bugfix: don't fail on short sequences
Ketil Malde <ketil@ii.uib.no>**20060404092339] 
[added hooks for 80% heap limit
Ketil Malde <ketil@ii.uib.no>**20060418113936] 
[amend to short seq
Ketil Malde <ketil@ii.uib.no>**20060419113529] 
[TAG 0.4b release (for review)
Ketil Malde <ketil@ii.uib.no>**20060419113723] 
[all-0 freqs caused rbr to abort
Ketil Malde <ketil@ii.uib.no>**20060601084442] 
[added README
Ketil Malde <ketil@ii.uib.no>**20060624134615] 
[minor README update
Ketil Malde <ketil@ii.uib.no>**20060625111928] 
[bumped version to 0.4
Ketil Malde <ketil@ii.uib.no>**20060627144629] 
[cleanup: remove unnecessary files
Ketil Malde <ketil@ii.uib.no>**20060609133240] 
[using Bio to read Fasta seqs
Ketil Malde <ketil@ii.uib.no>**20060609133436] 
[Actually link hooks.o
Ketil Malde <ketil@ii.uib.no>**20060624134551] 
[conflict resolution
Ketil Malde <ketil@ii.uib.no>**20060627144713] 
[more TODOs
Ketil Malde <ketil@ii.uib.no>**20060629222130] 
[Reworked to use 'bio' functionality, cleaned up
Ketil Malde <ketil@ii.uib.no>**20060706092351] 
[Plugging compile-time warnings
Ketil Malde <ketil@ii.uib.no>**20060706093746] 
[version bumped to 0.5
Ketil Malde <ketil@ii.uib.no>**20060706100105] 
[TAG 0.5 using the bio package
Ketil Malde <ketil@ii.uib.no>**20060706100140] 
[modified to use rcontig keys (slightly faster)
Ketil Malde <ketil@ii.uib.no>**20060707122028] 
[changed output option, ready for library
Ketil Malde <ketil@ii.uib.no>**20060710115741] 
[cleanup and remove mask'
Ketil Malde <ketil@ii.uib.no>**20060710120527] 
[data type for lower case/Ns
Ketil Malde <ketil@ii.uib.no>**20060710121750] 
[moved Options to separate module
Ketil Malde <ketil@ii.uib.no>**20060711121521] 
[replaced threshold with distrib
Ketil Malde <ketil@ii.uib.no>**20060711132713] 
[united masked_lc and masked_n (defactored?)
Ketil Malde <ketil@ii.uib.no>**20060810102655] 
[todo updates
Ketil Malde <ketil@ii.uib.no>**20060810104302] 
[renamed mask to mask_stat
Ketil Malde <ketil@ii.uib.no>**20060810114744] 
[perror fixlet
Ketil Malde <ketil@ii.uib.no>**20060810114805] 
[comment fixes
Ketil Malde <ketil@ii.uib.no>**20060810115223] 
[masked takes [Bool]
Ketil Malde <ketil@ii.uib.no>**20060810131049] 
[added ps target for lhs files
Ketil Malde <ketil@ii.uib.no>**20060811084609] 
[removed old, unused tests
Ketil Malde <ketil@ii.uib.no>**20060811090537] 
[added (simple) test case
Ketil Malde <ketil@ii.uib.no>**20060811095137] 
[RBR dependency for generating test file
Ketil Malde <ketil@ii.uib.no>**20060811115327] 
[perror macro fix
Ketil Malde <ketil@ii.uib.no>**20060811122038] 
[more refactoring work
Ketil Malde <ketil@ii.uib.no>**20060811122453] 
[comment fix
Ketil Malde <ketil@ii.uib.no>**20060811122943] 
[define mask_stat in terms of mask_generic
Ketil Malde <ketil@ii.uib.no>**20060814100819] 
[cleanup comments, reshuffle
Ketil Malde <ketil@ii.uib.no>**20060814112723] 
[gap closing/lower case masking combo fix
Ketil Malde <ketil@ii.uib.no>**20060814114849] 
[simplified gap-closing
Ketil Malde <ketil@ii.uib.no>**20060814120925] 
[moved gap-closing out of mask_generic
Ketil Malde <ketil@ii.uib.no>**20060814132201] 
[added mask_table (rudimentary and untested)
Ketil Malde <ketil@ii.uib.no>**20060814145557] 
[simplified and extracted mask_func building
Ketil Malde <ketil@ii.uib.no>**20060814145709] 
[added automatic tests for more functionality
Ketil Malde <ketil@ii.uib.no>**20060815094930] 
[bigtest target based on test
Ketil Malde <ketil@ii.uib.no>**20060815103723] 
[version bump to 0.6
Ketil Malde <ketil@ii.uib.no>**20060815104524] 
[test tgt to top-lev Makefile
Ketil Malde <ketil@ii.uib.no>**20060815112634] 
[integrated pre/post msgs into countIO
Ketil Malde <ketil@ii.uib.no>**20060815125742] 
[added tests for -D (coverage)
Ketil Malde <ketil@ii.uib.no>**20060815131427] 
[add .SECONDARY tgts for d/l files
Ketil Malde <ketil@ii.uib.no>**20060815131445] 
[test k>16
Ketil Malde <ketil@ii.uib.no>**20060816071640] 
[added user string identifier to wget cmd
Ketil Malde <ketil@ii.uib.no>**20060816082014] 
[added *test_kl to default test cases
Ketil Malde <ketil@ii.uib.no>**20060816082117] 
[factored out FT building
Ketil Malde <ketil@ii.uib.no>**20060816082143] 
[fix library option to use Maybe FilePath
Ketil Malde <ketil@ii.uib.no>**20060816104927] 
[added support for library masking
Ketil Malde <ketil@ii.uib.no>**20060816105003] 
[rewrote countIO for more accurate counts
Ketil Malde <ketil@ii.uib.no>**20060816111303] 
[updated README
Ketil Malde <ketil@ii.uib.no>**20060821114325] 
[mct measures lower case, not n
Ketil Malde <ketil@ii.uib.no>**20060822112056] 
[support -N options (no stats masking)
Ketil Malde <ketil@ii.uib.no>**20060822112120] 
[countIO blanks the line before producing output
Ketil Malde <ketil@ii.uib.no>**20060822115656] 
[make_ft parametrized by message
Ketil Malde <ketil@ii.uib.no>**20060822115710] 
[multiple changes (keyf uses seqdata, freq uses IntMap, etc)
Ketil Malde <ketil@ii.uib.no>**20060918115924] 
[version bump
Ketil Malde <ketil@ii.uib.no>**20060918135105] 
[Framework for k>16 in place
Ketil Malde <ketil@ii.uib.no>**20060919104512] 
[print test results at the end
Ketil Malde <ketil@ii.uib.no>**20060919115638] 
[implement freqtable_integer
Ketil Malde <ketil@ii.uib.no>**20060919115653] 
[remove unnecessary parm to freqtable*
Ketil Malde <ketil@ii.uib.no>**20060919120434] 
[warning removal
Ketil Malde <ketil@ii.uib.no>**20060919124040] 
[todo update
Ketil Malde <ketil@ii.uib.no>**20060919131445] 
[cleaned up freqtable
Ketil Malde <ketil@ii.uib.no>**20060926085728] 
[pass around IO action (for large files).  Test case for stdin.
Ketil Malde <ketil@ii.uib.no>**20060926085801] 
[infrastructure for sparse/skip
Ketil Malde <ketil@ii.uib.no>**20061004150607] 
[added sparsetab_int
Ketil Malde <ketil@ii.uib.no>**20061006105324] 
[implement sparse indices (for Int, anyway)
Ketil Malde <ketil@ii.uib.no>**20061010091751] 
[comment removal/cleanups
Ketil Malde <ketil@ii.uib.no>**20061010091853] 
[sliding_average
Ketil Malde <ketil@ii.uib.no>**20061010093623] 
[fix for sparsetable
Ketil Malde <ketil@ii.uib.no>**20061010104455
 Repeated keys in the same sequence were only entered into
 the sparse table once.
] 
[support sparse indices
Ketil Malde <ketil@ii.uib.no>**20061010104654] 
[RBR needs -cpp
Ketil Malde <ketil@ii.uib.no>**20061012073349] 
[added skip handling to masking, add tests for eq when skip=1
Ketil Malde <ketil@ii.uib.no>**20061012073359] 
[TODO cleanup
Ketil Malde <ketil@ii.uib.no>**20061017130829] 
[-D outputs distrib as well (deliberate test breakage alert)
Ketil Malde <ketil@ii.uib.no>**20061017131506] 
[small naming changes
Ketil Malde <ketil@ii.uib.no>**20061017131536] 
[experimental (and inefficient) sparse mask compensation
Ketil Malde <ketil@ii.uib.no>**20061017131617] 
[notice failure, and continue
Ketil Malde <ketil@ii.uib.no>**20061017132319] 
[version bump, README update
Ketil Malde <ketil@ii.uib.no>**20061017135608] 
[TAG 0.7
Ketil Malde <ketil@ii.uib.no>**20061017135643] 
[cabalized rbr
Ketil Malde <ketil@ii.uib.no>**20061031113510] 
[cabal ghc opts
Ketil Malde <ketil@ii.uib.no>**20061107133704] 
[implement sparsetable_integer (copy/paste)
Ketil Malde <ketil@ii.uib.no>**20061107133732] 
[comments added
Ketil Malde <ketil@ii.uib.no>**20070205102154] 
[simplified (Tomas Zielonka-style) option handling
Ketil Malde <ketil@ii.uib.no>**20070205110154] 
[cleaning up option handling
Ketil Malde <ketil@ii.uib.no>**20070205112018] 
[extended -v header
Ketil Malde <ketil@ii.uib.no>**20070205114512] 
[better default options, and readme updates
Ketil Malde <ketil@ii.uib.no>**20070205131938] 
[warning elimination/type signature cleanup
Ketil Malde <ketil@ii.uib.no>**20070205132202] 
[simplified modal interval calculation
Ketil Malde <ketil@ii.uib.no>**20070205132602] 
[updated README for v0.8
Ketil Malde <ketil@ii.uib.no>**20070205133633] 
[TAG 0.8
Ketil Malde <ketil@ii.uib.no>**20070205150053] 
[use hooks when building via cabal, too
Ketil Malde <ketil@ii.uib.no>**20070314091831]