Starting with tag: [TAG 0.3.1 Ketil Malde **20070524133147] [lazy/streaming fasta+qual output Ketil Malde **20070525125422] [separated out blast data structures Ketil Malde **20070530125448] [Halfway implemented Blast XML format Ketil Malde **20070531203912] [improved xml parsing a bit Ketil Malde **20070531210320] [successful parse of blastn output - yay! Ketil Malde **20070601090936] [FIX: amino table and comment changes Ketil Malde **20070606074854] [Added common matrices Ketil Malde **20070606091428] [Added QAlign - ripped interesting pieces from AlignBase Ketil Malde **20070606125647] [Expose modules, export matrices Ketil Malde **20070606130437] [moved old AlignBase out of the way - retained a bit more for educational purposes :-) Ketil Malde **20070607092140] [no longer reexport matrices Ketil Malde **20070607092321] [add AAlign for affine alignments (global only for now) Ketil Malde **20070607092527] [comment change Ketil Malde **20070607092708] [add simpleMx, comment out readMx Ketil Malde **20070607095030] [moved columns and data strucutres into AlignData Ketil Malde **20070607095205] [add local align/ed with affine gaps, comment mods Ketil Malde **20070607111442] [added local alignments Ketil Malde **20070607112604] [renamed QAlign to SAlign, and started new QAlign Ketil Malde **20070607131509] [more pragma to right file, reformat cabal file Ketil Malde **20070607133706] [generalized score function Ketil Malde **20070608081810] [generic align_select too, rename score to score_select Ketil Malde **20070608083150] [comments added Ketil Malde **20070608083325] [explicit exports list Ketil Malde **20070608083434] [blastn defaults as matrix Ketil Malde **20070608103041] [comment with link to blast defaults Ketil Malde **20070608120506] [inert implementation of q-alignments Ketil Malde **20070608120519] [Affine alignment/scoring with qualities working - yay! Ketil Malde **20070608121835] [factored mkSeqs, implement readQual Ketil Malde **20070611122413] [glasgow exts and import showaling (debugging) Ketil Malde **20070611130101] [updated adjustment function, more theoretically sound, I think. Ketil Malde **20070611130123] [Possibly sensible implementation of "adjust" Ketil Malde **20070611135335] [export readQual Ketil Malde **20070611140644] [alignments return score as well Ketil Malde **20070612121912] [whitespace changes Ketil Malde **20070612121945] [specialized for doubles, broke up 'adjust' for profiling Ketil Malde **20070612133145] [commenting on blast formats Ketil Malde **20070616063907] [don't validate against dtd Ketil Malde **20070616063946] [support both blast xml outputs - part 1 Ketil Malde **20070617184547] [both xml formats, part 2 Ketil Malde **20070619134939] [-fasm necessary for Matrices (ghc/gcc bug) Ketil Malde **20070619134947] [blastn_default polymorphic, ignore case for simpleMx Ketil Malde **20070619135007] [explicit export headers Ketil Malde **20070619135041] [various stuff Ketil Malde **20070619135101] [whitespace fix Ketil Malde **20070619135214] [added test cases and framework Ketil Malde **20070619135224] [qalign passing tests Ketil Malde **20070619184853] [deriving Eq Strand and Aux Ketil Malde **20070620103203] [added recovery test Ketil Malde **20070621094354] [updated options Ketil Malde **20070621094411] [added qc driver script Ketil Malde **20070621095814] [longer output lines Ketil Malde **20070621095841] [mod S/AAlign to align sequences, not seqdata Ketil Malde **20070621112357] [new test + comment change Ketil Malde **20070621112437] [use Word8 as Chr type instead of Char Ketil Malde **20070704140843] [matrices need -fasm to compile with -prof Ketil Malde **20070704141043] [comment changes Ketil Malde **20070704141229] [BUGFIX: incorrect line breaks for qual files Ketil Malde **20070705090750] [Get correct range for qualities Ketil Malde **20070705090917] [new qualMx functionality Ketil Malde **20070705112638] [import AAlign into tests (but don't use yet) Ketil Malde **20070705112803] [differentiate EST and ESTq for testing Ketil Malde **20070705112917] [cleanup interface Ketil Malde **20070705114257] [add serializing tests for Fasta format Ketil Malde **20070705114312] [correct bit scores Ketil Malde **20070709081028] [qualMx just depends on qualities Ketil Malde **20070710200507] [more testing work Ketil Malde **20070710200610] [remove dead code, inline fromQual, move from 5/4 to 4/3 back subst prob Ketil Malde **20070711125155] [default qual is 22 Ketil Malde **20070711132551] [check for nNxX, and score 0.0 Ketil Malde **20070711152845] [added readFastaQual, test, and bugfix Ketil Malde **20070713103407] [error message on illegal qual file Ketil Malde **20070723085602]