[initial version Ketil Malde **20060607122009] [now reads sequences from file Ketil Malde **20060607125104] [added Stats Ketil Malde **20060607201430] [major perf improvement Ketil Malde **20060607210648] [using Ints Ketil Malde **20060609062234] [replace filter with dropSpace, 3x perf improvement (from dons) Ketil Malde **20060609081842] [reorg dir hier Ketil Malde **20060609112835] [Added Cabal infrastructure Ketil Malde **20060609112904] [add functionality for RBR Ketil Malde **20060611170327] [added (naïve) entropy implementation Ketil Malde **20060630092315] [added Entropy and HashWord modules Ketil Malde **20060704113854] [changes to fasta module Ketil Malde **20060704113933] [renamed from 'key' to 'hash' Ketil Malde **20060705060546] [added simple Makefile Ketil Malde **20060705091217] [added rcontig for revcompl contigous hashes Ketil Malde **20060705094546] [better error messages for debugging Ketil Malde **20060705101301] [bugfix to rcontig Ketil Malde **20060705101331] [Entropy comment fixes. Need to get kth-order entropy right. Ketil Malde **20060706093840] [properly ignore comments Ketil Malde **20060706093904] [seqlabel returns only first word, seqheader full header Ketil Malde **20060706093924] [inline fasta/hashwrod accessor function Ketil Malde **20060706100048] [splitsAt as a toplevel function Ketil Malde **20060811063604] [output functions Ketil Malde **20060811063618] [Added types to stop warnings on build Gord Pollock **20060810220121] [Changed makefile; doesn't assume Setup.hs executable Gord Pollock **20060810220313] [export list for Fasta module Ketil Malde **20060811084634] [re-export pack/unpack directly Ketil Malde **20060811084642] [type declaration Ketil Malde **20060811084656] [fix perf bug - export ! directly from Fasta.hs Ketil Malde **20060818073215] [added 'clean' target Ketil Malde **20060818073744] [bumped version Ketil Malde **20060818073804] [TAG 0.1 Ketil Malde **20060818073830] [reorganized makefile, added haddock step Ketil Malde **20060823102523] [haddockized comments in Fasta Ketil Malde **20060823131759] [split up targets in Mf. Ketil Malde **20060823131849] [comments allowed between sequences Ketil Malde **20060823131908] [multiple changes (keyf uses seqdata, freq uses IntMap, etc) Ketil Malde **20060918115936] [output format fix Ketil Malde **20060918135126] [Fasta exports Offset Ketil Malde **20060919124053] [fix? and added a countSeqs function Ketil Malde **20061003131406] [modify for ghc-6.6 Ketil Malde **20061017130706] [version bumped to 0.2 Ketil Malde **20061017135838] [TAG 0.2 Ketil Malde **20061017135853] [simple N-W impl Ketil Malde **20061129132539] [generalized NW/SW alignment Ketil Malde **20061130111955] [factored out matrix construction Ketil Malde **20061130112023] [showalign function Ketil Malde **20061130112037] [rename backtrack Ketil Malde **20061130112525] [renamed nw-specific backtracking Ketil Malde **20061130142656] [generalized backtracking Ketil Malde **20061130142734] [docs and type sigs Ketil Malde **20061130151614] [generalized backtracking to cover local alignments, too Ketil Malde **20061130155243] [refactor, and add affine scores Ketil Malde **20061201092533] [factored things more finely Ketil Malde **20061204122309] [commented out non-functioning affine scoring Ketil Malde **20061204122333] [almost-working columnwise version Ketil Malde **20061204152643] [fix pesky off-by-one bug Ketil Malde **20061205083625] [qc property Ketil Malde **20061205083641] [no need to be so grumpy about unfoldr Ketil Malde **20061205083739] [Needs glasgow-exts for parallel list comprehension Ketil Malde **20061205124906] [loosen type for mkcolumns (why isn't mkcol's sig accepted?) Ketil Malde **20061205124924] [proper QC properties Ketil Malde **20061205125153] [simpler arbitrary Char, commented-out failing test testing test Ketil Malde **20061205130158] [simplified arb instance for Char Ketil Malde **20061205141329] [substitution matrices supported (and checked) Ketil Malde **20061205141341] [doc additions Ketil Malde **20061205141538] [type decl fix (thanks, dons) Ketil Malde **20061206091417] [proper hierarchical module name Ketil Malde **20061206132305] [big reorganization of everything in AlignBase Ketil Malde **20061206144540] [latex preamble/end Ketil Malde **20061206145413] [reorganized the scoring function stuff Ketil Malde **20061207134203] [quickcheck stuff Ketil Malde **20061207134316] [direct recursion for illustration purposes only Ketil Malde **20061207134344] [linear space score calculation Ketil Malde **20061207134400] [minor doc/comment/latex fixes Ketil Malde **20061207134415] [moved QC defs earlier in the file Ketil Malde **20061208125429] [parametrize columns by hd/tl Ketil Malde **20061208125451] [added parametrized reversal of sequences Ketil Malde **20061208125514] [rephrasing and cabal resolution Ketil Malde **20061211085624] [comment added Ketil Malde **20061211135442] [generalized qc_align and bug fix Ketil Malde **20061211135550] [added iterative linear space algorithm Ketil Malde **20061211135611] [separate tabulate - simpler, but uses more memory(?) Ketil Malde **20061214110240] [mod to qc prop Ketil Malde **20070208092628] [reorg seqdata, added 2bit format (read only for now) Ketil Malde **20070208092659] [read2bit works - yay! Ketil Malde **20070208195554] [factored out decoding function Ketil Malde **20070212102131] [comment fix, reshuffling Ketil Malde **20070221090749] [fix: negative numbers didn't work out so well, be positive instead Ketil Malde **20070221090840] [partially implemented parser for BLAST output Ketil Malde **20070307153445] [QC and a property ketil@malde.org**20070308094303] [put impl for SRLE ketil@malde.org**20070308094331] [set glasgow-exts for Fasta.hs Ketil Malde **20070308094609] [added sequence metamodule Ketil Malde **20070308095036] [moved alignment stuff to separate directory Ketil Malde **20070308121608] [blast working - but chunk parsing missing Ketil Malde **20070308122422] [moved to ByteStrings Ketil Malde **20070309090113] [modified data structures, debugging reads Ketil Malde **20070309224316] [remove commented-out code Ketil Malde **20070314112724] [section header for gapped (unfinished) Ketil Malde **20070314112736] [added (untested) rcpacked for 454 sequences Ketil Malde **20070315123430] [protect against older formats (blast ver. 2.2.13 puts db inside each record) Ketil Malde **20070315143733] [Added some QC tests Ketil Malde **20070316123714] [QC for rcontig Ketil Malde **20070319103212] [added debian infrastructure Ketil Malde **20070320124823] [export most stuff through Sequence.hs (cf. bio-0.3 patch for RBR) Ketil Malde **20070323101126] [updates to compile against ghc-6.4.2 Ketil Malde **20070323125330] [(had)doc(k) fixes and additions Ketil Malde **20070323143725] [added amino translation stuff Ketil Malde **20070420200114] [Add Xxx amino, trans1 no longer maybe Ketil Malde **20070422194429] [added IUPAC stuff for proteins Ketil Malde **20070423205814] [fix for RNA, commments Ketil Malde **20070423210511] [Xaa not Xxx, added Xle Ketil Malde **20070423211511] [export IUPAC funcs, comment typo fix Ketil Malde **20070510133626] [warn fix Ketil Malde **20070511132558] [added phd support Ketil Malde **20070511132631] [support quality info for Sequences Ketil Malde **20070511132714] [output qual files Ketil Malde **20070518083104] [strictness fix(?) Ketil Malde **20070522220824] [Simple README added Ketil Malde **20070522220837] [major documentation overhaul - some export mods Ketil Malde **20070524130759] [export hashword stuff Ketil Malde **20070524133131] [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] [TAG qualign:xref Ketil Malde **20070723090857] [bugfix: old blast format doesn't have hit-frame, only query Ketil Malde **20070809190309] [update error - todo: fix blastx/p Ketil Malde **20070810193321] [handle both formats (again!) Ketil Malde **20070810195614] [deprecate Blast text format Ketil Malde **20070831145812] [fix pragma Ketil Malde **20070831145915] [add location info for blast hits Ketil Malde **20070831145922] [warning elim Ketil Malde **20070831150015] [added prelim. blastflat module Ketil Malde **20070831151602] [implement Ketil Malde **20070903080536] [add test Makefile target Ketil Malde **20070903081444] [bugfix! (How the hell did that happen?) Ketil Malde **20070903084629] [auto make qc before test Ketil Malde **20070903084647] [extend blastflat exports Ketil Malde **20070905124449] [simpler recover check Ketil Malde **20070905124716] [add indirect alignments, first implementation Ketil Malde **20070905124737] [simplified indirect Ketil Malde **20070905125648] [add 1/13 N's to arbitrary nucleotide data Ketil Malde **20070906065523] [rename Indirect to Multiple Ketil Malde **20070906111111] [add type sig for progressive clustering Ketil Malde **20070906111226] [added Clustering, with rudimentary single link impl Ketil Malde **20070906131633] [added clustering test Ketil Malde **20070906133736] [add triangle test to cluster Ketil Malde **20070906193740] [add update target to makefile Ketil Malde **20070906193753] [README update, removed regex dep. Ketil Malde **20070906194905] [haddock fixes Ketil Malde **20070906201429] [small warning fixes, removed superflous cmd line param Ketil Malde **20070906201500] [haddock updates Ketil Malde **20070907091552] [added initial ACE Ketil Malde **20070909073244] [added tokenizer and sketched (non-working) ACE parser Ketil Malde **20070917074035] [added show functionality to unused test (for interactive use at this point) Ketil Malde **20070917113716] [incorrect 'test' target fixed Ketil Malde **20070917114837] [test aalign vs qualign Ketil Malde **20070917125859] [refactored columns Ketil Malde **20070918084819] [added AS to tokenizer Ketil Malde **20070918084927] [workaround BS bug Ketil Malde **20070918094624] [test reorg/fixes, util added Ketil Malde **20070918201029] [added EditGraph data structure Ketil Malde **20070919090520] [added separate internal test Ketil Malde **20070919091754] [added benchmarking Ketil Malde **20071002205837] [compile test module directly Ketil Malde **20071002205926] [moved TestBase to Util dir Ketil Malde **20071002211556] [actually run long test, fix precision bug, reduce size of EST_long Ketil Malde **20071003065107] [better time reporting Ketil Malde **20071003065214] [moved splitWhen to Util Ketil Malde **20071003102445] [remove unused function Ketil Malde **20071003102550] [general 'time' function, moved to TestBase Ketil Malde **20071003102613] [added empty bench case for Sequence Ketil Malde **20071003102646] [workaround for non-lazy XML parser - ugly, ugly Ketil Malde **20071004081041] [partially implemented ACE parser, based on Parsec Ketil Malde **20071004105108] [more parsec/ACE stuff Ketil Malde **20071011081827] [log benchmarks Ketil Malde **20071011081838] [do fast benchmarks first Ketil Malde **20071012083713] [added sequence benchmarks Ketil Malde **20071012083728] [quiet benchmarking Ketil Malde **20071012083806] [specialize rcontig (but no effect yet) Ketil Malde **20071012090011] [factor out making of test/bench progs Ketil Malde **20071012124630] [refactored a separate Test.QuickBench Ketil Malde **20071012143756] [Use Interlude for better error reporting Ketil Malde **20071016153145] [derive Show instances Ketil Malde **20071016153229] [AF has three fields Ketil Malde **20071016153301] [fix source (position updating) Ketil Malde **20071016153359] [added blank parser Ketil Malde **20071016153501] [working (but not complete) parser Ketil Malde **20071016153618] [add local alignments to benchmarks Ketil Malde **20071016153624] [many AS'es in an ACE file Ketil Malde **20071016162233] [fix for CAP3 weirdness Ketil Malde **20071016162258] [dead code removal Ketil Malde **20071016162310] [add Parsex/lazyMany from T.Z. Ketil Malde **20071016163109] [strictness in blast data structs Ketil Malde **20071024133616] [modified the aux structure Ketil Malde **20071024133804] [big rewrite to use tagsoup and parallelism Ketil Malde **20071024133846] [sketch for GOA data Ketil Malde **20071024142133] [parsing GOA now works, at least for the uniprot assocs Ketil Malde **20071025090356] [now reads GO.terms_and_ids Ketil Malde **20071025094646] [blast comments Ketil Malde **20071030141301] [GOA additions Ketil Malde **20071030141412] [added 6.8-style dependencies Ketil Malde **20071030141428] [interlude deps for tests Ketil Malde **20071030141524] [added countIO Ketil Malde **20071031091638] [stricter data structures Ketil Malde **20071031142634] [fixed blastn parsing Ketil Malde **20071103235944] ['break' description from GO annot (retain less of the file) Ketil Malde **20071105085222] [better error in case of parse failure for go defs Ketil Malde **20071107084357] [necessary export for Reps Ketil Malde **20071123115953] [version bump Ketil Malde **20071123120008] [TAG 0.3.3 Ketil Malde **20071123120037] [tblastn adaption Ketil Malde **20080117121906] [haddock fixes Ketil Malde **20080117121931] [README updates Ketil Malde **20080117121950] [explicit copy to avoid holding chunks of the input file in mem Ketil Malde **20080117135127] [update for TagSoup v0.5 Ketil Malde **20080126231841] [gratuitious copy function Ketil Malde **20080126231916] [add version dep for tagsoup, URL to GPL Ketil Malde **20080128140446] [repair borked cabal fields Ketil Malde **20080205102103] [limit error reporting to five tags Ketil Malde **20080205102433] [add bs parser - needed for (recent) CAP3 Ketil Malde **20080206091628] [warning fixes Ketil Malde **20080206091656] [export and dependency fixes Ketil Malde **20080206091713] [add functions for inserting/extracting gaps Ketil Malde **20080207224157] [support gaps in contigs Ketil Malde **20080207224216] [clarify signature Ketil Malde **20080207224324] [explicit exports from ACE Ketil Malde **20080228135635] [explicit imports for ACE Ketil Malde **20080228135645] [warning cleanup Ketil Malde **20080228135704] [move test to Test.hs Ketil Malde **20080228135736] [export Gaps from ACE Ketil Malde **20080228140121] [+LICENSE gwern0@gmail.com**20080302052438] [+metadata to cabal, fix up dependencies gwern0@gmail.com**20080302052447] [ch build-options - hackage really dislikes -fasm, and for good reason gwern0@gmail.com**20080302052507] [named EditList, reserving Alignment for gap-lists which allow multiple alingments Ketil Malde **20080309131521] [improve README gwern0@gmail.com**20080304195144] [improve cabal metadata gwern0@gmail.com**20080304195207] [switch some OPTIONS to LANGUAGE pragmas gwern0@gmail.com**20080304200200] [conflict resolution Ketil Malde **20080310090321] [naming fixes - urgh. Ketil Malde **20080311102725] [warning fix Ketil Malde **20080311143251] [move stuff to AlignData Ketil Malde **20080311143329] [use maybe monad for better error handling Ketil Malde **20080311143343] [micro-bump version Ketil Malde **20080311143405] [reduce tagsoup dep (for hackage) Ketil Malde **20080311145743] [TAG 0.3.3.1 Ketil Malde **20080311145753] [update darcs link Ketil Malde **20080311150102] [remove interlude dependency Ketil Malde **20080312080426] [explicit export, warning removal Ketil Malde **20080312080524] [explicit entroypy export from sequence Ketil Malde **20080312091424] [warning fixes Ketil Malde **20080312091454] [version 0.3.3.2 Ketil Malde **20080312091522] [TAG 0.3.3.2 Ketil Malde **20080312091531] [comment/haddock fixes Ketil Malde **20080313143554] [overlap-alignments implemented - perhaps even correctly Ketil Malde **20080314130604] [comment fix, test function improvements, typo Ketil Malde **20080316123817] [more specific Ketil Malde **20080316123903] [export overlap_align and test Ketil Malde **20080317142803] [fixes for overlap alignmnet Ketil Malde **20080317142902] [bench/test additions Ketil Malde **20080317142946] [add reverse overlap output to test function Ketil Malde **20080317143035] [export readXML directly from BlastFlat Ketil Malde **20080331091609] [benchmark fixes Ketil Malde **20080331091732] [improve error reporting (and remove warnings) Ketil Malde **20080415103321] [mods to qalign Ketil Malde **20080513084416] [better output in case of errors Ketil Malde **20080513084446] [header modification functions for fasta Ketil Malde **20080513084504] [lower opt, version bump Ketil Malde **20080513084531] [TAG 0.3.3.3 Ketil Malde **20080513084553] [attempt at improved read for EvidenceCode Ketil Malde **20080517094925] [error reporting for evidence codes Ketil Malde **20080517101902] [fix bug in getEC Ketil Malde **20080517105204] [more elaborate error reporting, warning fixes Ketil Malde **20080518134143] [bytestring go parser Ketil Malde **20080518134221] [Vector NTI is weird. Support the parts I grok. Ketil Malde **20080521132741] [robustify - treat lines with only \r as empty Ketil Malde **20080521132811] [rename GOA to GeneOnthology Ketil Malde **20080711135328] [add skeleton KEGG module Ketil Malde **20080711135341] [bump version Ketil Malde **20080725102718 Version incremented. Includes some interface changes, but mostly the increment signifies that my disk crashed. ] [added OBO support (untested) Ketil Malde **20080729065407] [fix typo Ketil Malde **20080729072521] [add GOA (depr) for backwards compat Ketil Malde **20080729072614] [readObo now tested on current obo file, and appears to work Ketil Malde **20080729074314] [comments and reshuffling Ketil Malde **20080729084532] [haddock fixes, explicit exports Ketil Malde **20080729090433] [typo, comment added Ketil Malde **20080730193127] [TAG 0.3.3.4 Ketil Malde **20080730193158] [added hpc support to tests/bench Ketil Malde **20080731081723] [update description and homepage in .cabal Ketil Malde **20080731100717] [add rudimentary KEGG support Ketil Malde **20080731111847] [check for correct XML prefix and bail early Ketil Malde **20080804092829] [bump version Ketil Malde **20080804093131] [export TestBase (Arbitrary instances for sequence data) Ketil Malde **20080815075737] [Fix big memory leak in readFasta Bryan O'Sullivan **20080908042050] [bump bytestring requirement Ketil Malde **20080909090530 bytestring 0.9.0.1 made a relatively simple function quadratic in time (and then blow the stack), where using bytestring 0.9.1 made it linear. While everything should work with older bytestrings, I feel this is a safer choice. ] [version bump Ketil Malde **20080909114509] [support FastQ format, add tests (that pass) Ketil Malde **20080909121516] [fix for haddock Ketil Malde **20080909121530] [fix for test case: force end of qual and seq f Ketil Malde **20080909190407] [warning removals for TestBase Ketil Malde **20081024084659] [first draft, reading works (but stack overflows) Ketil Malde **20081105123849] [fix space leak - decodeFile checks for complete consumptions Ketil Malde **20081105145842] [better name for 'read_name' Ketil Malde **20081106133412] [add sffToSequence function Ketil Malde **20081106133425] [comment fixes Ketil Malde **20081107072654] [add put implementations, remove dead code Ketil Malde **20081107072913] [add test function Ketil Malde **20081107085247] [add improved (human-readable) show instance Ketil Malde **20081107091332] [small formatting fix for show instance Ketil Malde **20081107095726] [format show fix Ketil Malde **20081107124056] [set index_offset to zero when enconding Ketil Malde **20081107130410] [comment fixes, cleanups, warning removal Ketil Malde **20081107130904] [comments extended Ketil Malde **20081108214037] [add explicit exports to SFF Ketil Malde **20081114113109] [doc fix Ketil Malde **20081114211533] [eliminate magic, version, cheader length from SFF format Ketil Malde **20081127102109] [remove rhl from read header Ketil Malde **20081127102850] [check and trim key sequence when converting Ketil Malde **20081209094152] [add (and export) flow type Ketil Malde **20081217153220] [Expose FastQ parsing interface as a good producer nick@ingolia.org**20081217022449] [Added location data types nick@ingolia.org**20081213221309] [Map to allow efficient location searching nick@ingolia.org**20081213223243] [Functorial addition of sequence names to locations nick@ingolia.org**20081215043024] [Functorial lifting of efficient location searching to named sequence locations nick@ingolia.org**20081215043718] [Clean up warnings and unneeded uses of extensions, actually build Location nick@ingolia.org**20081215050937] [Tests of sequence data extraction, fixed edge case bug nick@ingolia.org**20081215191642] [Added GFF features and parsing nick@ingolia.org**20081215233801] [Generally useful utilities to global testing module nick@ingolia.org**20081217221239] [Read and write Soap format alignments nick@ingolia.org**20081217221407] [Restore test lists nick@ingolia.org**20081217221659] [warning fixes Ketil Malde **20081219130846] [Fix SoapAlign use of ContigLoc, verify with end-to-end test nick@ingolia.org**20081219071128] [resolve refCLoc conflict Ketil Malde **20081219131306] [More accurate function name nick@ingolia.org**20090110175834] [Use standard library for group nick@ingolia.org**20090110175905] [Build ContigLoc from Pos nick@ingolia.org**20090110175926] [New signature for Data.Map.lookup nick@ingolia.org**20090114211006] [Drop back to Prelude.catch for consisten interface on 6.8 and 6.10 nick@ingolia.org**20090114212428] [export Qual from more modules Ketil Malde **20090126121207] [better type names and exports Ketil Malde **20090126141917] [TAG 0.3.5 Ketil Malde **20090130192615] [Improved show-instance for Sequences michael.lesniak@gmail.com**20090131182854] [added SFF_name.hs Ketil Malde **20090207205442] [change sff data structure to match rest of biolib Ketil Malde **20090207211035] [Rework TwoBit support vigalchin@gmail.com**20090208203323] [add SFF_name, reexport it from SFF Ketil Malde **20090209095151] [Extensive documentation and minor interface improvements nick@ingolia.org**20090307065353] [Tutorial for location and position stuff nick@ingolia.org**20090315065855] [Change tutorial to markdown and pandoc-compile html nick@ingolia.org**20090315190044] [Parser for Bowtie alignments nick@ingolia.org**20090316000308] [Improvements to Bowtie parsing nick@ingolia.org**20090316010741] [Abstracted Display typeclass nick@ingolia.org**20090321222149] [Fixed bug in integer parsing and added double parsing nick@ingolia.org**20090331065816] [Useful utility to optimize memory usage of Sequence nick@ingolia.org**20090331065858] [Reader-like monad to look up sequences by name nick@ingolia.org**20090331065931] [Utility functions to take advantage of SequenceReader nick@ingolia.org**20090331070005] [Build new SequenceReader nick@ingolia.org**20090331070113] [Use new Bio.Util.Parsing to read in Bowtie output nick@ingolia.org**20090331070210] [Properly parse skipping reserved field nick@ingolia.org**20090409053519] [Documented and organized Bio.GFF3.Feature nick@ingolia.org**20090410012420] [Added reader-like monad for FeatureHier context, reorganized, documented nick@ingolia.org**20090410012505] [Renamed module, converted to a concrete ReaderT-like transformer providing SequenceReader and FeatureHierReader functionality nick@ingolia.org**20090410012548] [Changed to use the new SequenceReader and FeatureHierReader classes nick@ingolia.org**20090410012642] [Interface improvements, deal with multiple annotation lines per ID nick@ingolia.org**20090412174619] [Tutorial for using GFF modules nick@ingolia.org**20090414185929]