[initial version, prints all forward ORFs Ketil Malde **20070420195838] [added cabal file and Setup.hs Ketil Malde **20070420200825] [display orfs (pipe to less -S) Ketil Malde **20070420201552] [added rfs Ketil Malde **20070421065844] [show reverse too, boldface ORFs Ketil Malde **20070422194403] [simple option handling, correct indent -a Ketil Malde **20070508100440] [added rrfs for reverse frames Ketil Malde **20070508101826] [bold ORFs didn't quite work, red/green aug/stp Ketil Malde **20070508102922] [added fasta output Ketil Malde **20071002140057] [added README Ketil Malde **20071002142955] [sketched code for orf from blast hits Ketil Malde **20080330163140] [keep indices, local optimum (partly) Ketil Malde **20080330170942] [generate local alignment, terminate at maximum Ketil Malde **20080330173456] [todo note in readme Ketil Malde **20080330173526] [cleanups, comments Ketil Malde **20080330180403] [more cleanups, plan patterns Ketil Malde **20080330224935] [comment fixes Ketil Malde **20080331082337] [simple impl of redirection tool Ketil Malde **20080331085547] [fix termination Ketil Malde **20080331133147] [print CDS prediction Ketil Malde **20080331133707] [small negative default to discourage non-matches Ketil Malde **20080331134427] [label CDS prediction in header Ketil Malde **20080331134722] [add type sig Ketil Malde **20080402075754] [penalty parameter for opt_score Ketil Malde **20080402080233] [info on competition Ketil Malde **20080402080313] [correct order in CDS, weak is 2* Ketil Malde **20080402080413] [moved main to separate module Ketil Malde **20080402080855] [merge redirect into blastx Ketil Malde **20080402082029] [cleanups Ketil Malde **20080402082601] [bits per nuc, not amino, parametric sumW Ketil Malde **20080402084134] [formatting and warning fixes Ketil Malde **20080402084203] [type Frame Ketil Malde **20080402104006] [skeleton genFasta/CDS Ketil Malde **20080402104238] [move process to main, use frames directly Ketil Malde **20080402115936] [frames generate groupings using joins Ketil Malde **20080402122354] [simplify a bit Ketil Malde **20080402122453] [use handles for IO Ketil Malde **20080402122519] [separate out select_dir from formatting Ketil Malde **20080402133257] [add CDS output support Ketil Malde **20080402135457] [comment note added Ketil Malde **20080409113129] [patterns impl (only STP for now) Ketil Malde **20080409113145] [sumW separate function Ketil Malde **20080409113219] [high scores are suspicious, even in the presence of even higher scores Ketil Malde **20080409113234] [incorporate patterns Ketil Malde **20080409114020] [added poly-A detection code (not integrated yet) Ketil Malde **20080415142253] [fixes to poly-A scoring Ketil Malde **20080416093202 Add negative score to opposite strand as well when a poly-A is detected. Negative score is lower than the positive score given to sequence preceeding poly-A, so in the case of both both poly-A and poly-T (reverse dir poly-A), this will give a smaller positive is added to both preceeding sequences. ] [move source to src/ subdir, fix cabal Ketil Malde **20080416093924] [switch to real option handling Ketil Malde **20080416114206] [output lengths as well (along with CDS) Ketil Malde **20080416114912] [usage formatting fixes Ketil Malde **20080416115856] [README updates Ketil Malde **20080725102543] [cleanups Ketil Malde **20080725102557] [removed 'Vague'/indet, refactored a bit Ketil Malde **20080806101026] [warning removal Ketil Malde **20080806101117] [added --all option (no impl yet) Ketil Malde **20080806101125] [check for non-options too Ketil Malde **20080806102018] [separate out error message for incompatible options Ketil Malde **20080806102031] [add case in main for --all Ketil Malde **20080806102049] [support --all to file and stdout Ketil Malde **20080806103650] [update desc in .cabal Ketil Malde **20080806111900] [redefined Weights to be one dir at a time Ketil Malde **20080807122753] [fix patterns to be uni-directional Ketil Malde **20080807125501] [debug patch - adds tracing Ketil Malde **20080807121620] [conflict res with tracing Ketil Malde **20080807125607] [reverse CDS works (at least for one example) Ketil Malde **20080807132026] [debug output numbering Ketil Malde **20080807132456] [commented out debugging output Ketil Malde **20080808112542] [type annotations (remove warnings) Ketil Malde **20080811105320] [modify seqheader with frame in all-frames output Ketil Malde **20080811105335]