[initial sketch, using Data.Set Ketil Malde **20080814133815] [add test module Ketil Malde **20080815075711] [fix matches and swords to pass test Ketil Malde **20080815080147] [use Test data type, add more tests Ketil Malde **20080815081804] [fix, passing more tests Ketil Malde **20080815081841] [fix regression: pass test Ketil Malde **20080815082037] [stricter test Ketil Malde **20080815082429] [add test with multiple target sequences Ketil Malde **20080815082436] [output cleanup/fixes Ketil Malde **20080815094115] [use aliases (but don't define them yet) Ketil Malde **20080815094459] [use bloom filters instead of sets Ketil Malde **20080815094722] [comment out failing test Ketil Malde **20080815101448] [separate matches/matchcount Ketil Malde **20080819131842] [output indices Ketil Malde **20080819132150] [revert to using match count Ketil Malde **20080820075645] [remove 'copy' from swords Ketil Malde **20080820081654 This is not needed with a correct hashable instance for lazy BS. ] [update tests to use matchcount Ketil Malde **20080820084626] [resolve test conflict Ketil Malde **20080820084827] [higher FP rate, but filter lone hits Ketil Malde **20080821085135] [cabalized it Ketil Malde **20080821085743] [remove warnings (add types) Ketil Malde **20080821095223] [add skips, define constants Ketil Malde **20080821102310] [remove FP removal - doesn't work with skips Ketil Malde **20080821102344] [attempt to adjust output score for expected number of false positives Ketil Malde **20080821102404] [FP adjustment improvements, report stdev, correct for overlaps due to low complexity Ketil Malde **20080821132209] [warning fixes Ketil Malde **20080821141916] [scale by file size, not number of calculated swords Ketil Malde **20080821150450] [output sizes (debug only) Ketil Malde **20080821150836] [add type sig for genfilter Ketil Malde **20080821163841] [output every sequence; show stat details Ketil Malde **20080822104508] [ensure all input is upper case Ketil Malde **20080822104538] [print generated filters to stderr Ketil Malde **20080822134447] [remove extra LF at end of output Ketil Malde **20080822134528] [let 'classify' handle output Ketil Malde **20080824210156] [moved genfilter to BloomFilter Ketil Malde **20080825070958] [type annot for member (warning fix) Ketil Malde **20080825071025] [output processing counts, parametric classifier (by IO action) Ketil Malde **20080825072041] [add 'separately' action Ketil Malde **20080825115304] [output coverage for match Ketil Malde **20080825121038] [more structured choice of main function Ketil Malde **20080826105025] [added partial impl of masking function Ketil Malde **20080826113812] [fix(?) statistics Ketil Malde **20080828124741] [warning and output fixes Ketil Malde **20080829075707] [factor out statistics calculations Ketil Malde **20080829075757] [adj_score deals with 0 base score Ketil Malde **20080829080740] [actually output non-significant hits to 'unknown' file Ketil Malde **20080829080808] [comment on significance Ketil Malde **20080829081201] [bugfix - 0 matches -> unknown classification Ketil Malde **20080829125320] [Inline toUpper, giving a 7.4% speedup Bryan O'Sullivan **20080831150129] [Export nothing, giving GHC more opportunities to inline. Bryan O'Sullivan **20080831150522] [statistics fixes Ketil Malde **20080902113057] [coverage is zero when no matches are found Ketil Malde **20080902114617] [added simple pval calc, but it seems to strict. (bug?) Ketil Malde **20080903124023] [add various statistics, use exact binomial based Ketil Malde **20080905091805] [slightly faster by limiting the number of hits to check - also avoid -0.0 as result Ketil Malde **20080905092427]