[initial (slow) version Ketil Malde **20081106092142] [replace printf, and improve speed Ketil Malde **20081106092431] [switch to lazy bytestring output, and bytestring construction Ketil Malde **20081106100143] [enable Fasta output Ketil Malde **20081106135914] [add fastq format, and better error message Ketil Malde **20081106143126] [fix for runs > 9 bases Ketil Malde **20081107145012] [fix some warnings, even faster output, small, constant, mem footprint Ketil Malde **20081107152906] [temp record: histogram accumulation using ST Ketil Malde **20081110155157] [output histogram for all chars to stdout Ketil Malde **20081110203150] [add usage for -h Ketil Malde **20081110203534] [fix output format Ketil Malde **20081111082429] [rename tab Ketil Malde **20081111083412] [remove a parameter speeds things up 10x Ketil Malde **20081111083424] [use unsafeFreeze (another 10%) Ketil Malde **20081111083643] [cleanup errors/dead code Ketil Malde **20081114092343] [cabalized it Ketil Malde **20081114114743] [use zipWith3 - suggestion from SF Ketil Malde **20081121114144] [add stuff to statistics Ketil Malde **20081126131658] [add invcumnorm (iterative search) Ketil Malde **20081126135358] [working version of invcumnorm Ketil Malde **20081127082626] [export Sys.Rand, add normals Ketil Malde **20081127114051] [sim454 partial impl Ketil Malde **20081127114115] [could have sworn this worked previously? Fix parallel list comp Ketil Malde **20081209130639] [separate flows in generation and permutations Ketil Malde **20081209130702] [changes to sim454 Ketil Malde **20090121195809] [add quality value output to -f Ketil Malde **20090121201347] [really working quality info for flower Ketil Malde **20090122013206] [add type sig Ketil Malde **20090122013440] [comments added Ketil Malde **20090122190625] [ExtractQuals working with strictness annotations Ketil Malde **20090122190645] [use better types from SFF module Ketil Malde **20090126141938] [version bump Ketil Malde **20090130191208] [TAG 0.1 Ketil Malde **20090130195851] [update flower to match new data structures in biolib Ketil Malde **20090207211050] [rudimentary -s output Ketil Malde **20090209095537] [update ExtractQuals to new SFF interface Ketil Malde **20090209112016] [typo - newline missing Ketil Malde **20090209112052] [remove gratuitous dependency Ketil Malde **20090209134845] [use builder for -s output, slightly faster Ketil Malde **20090209142911] [moved printer-builder to separate file Ketil Malde **20090210125649] [add simple quality metric Ketil Malde **20090210130931] [add summary header Ketil Malde **20090210132646] [align summary header with data Ketil Malde **20090210144349] [add quality measure (is it correct?) Ketil Malde **20090210144410] [add -R output (fasta+qual, to files) Ketil Malde **20090223130049] [update bio dep Ketil Malde **20090302205431] [TAG 0.1.1 Ketil Malde **20090302205439] [branched from flower to sim454, add QT stuff Ketil Malde **20090414164248] [add test seq Ketil Malde **20090415082651] [split up makeFlows to accomodate N's in input sequence Ketil Malde **20090415082840] [export gs20lookup from the qualtable Ketil Malde **20090416094002] [working call function for base and quality Ketil Malde **20090416094040] [use gs20lookup to build quals Ketil Malde **20090416094135] [integrate postions into the call function Ketil Malde **20090416094959] [generic Distribution data type Ketil Malde **20090416185311] [sketch test cases, comment changes Ketil Malde **20090428073755] [fix? for call Ketil Malde **20090428073849] [restructure generations as a struct Ketil Malde **20090428075223] [move more stuff out to Generation, now produces correct header Ketil Malde **20090429134234] [trap unitialized fields, elim warnings Ketil Malde **20090502110245] [sample now works in the Rand monad Ketil Malde **20090502110422] [update to use Rand monad throughout Ketil Malde **20090502110507] [comment/whitespace fixes Ketil Malde **20090502110527] [mock-up various output values, produce credible SFF output Ketil Malde **20090502194528] [add random permutations from model Ketil Malde **20090504101114] [pick random dir/pos too Ketil Malde **20090504101147] [use a real lognormal noise distrib Ketil Malde **20090504115324] [random direction, prepend key sequence Ketil Malde **20090504115349] [count bases in output Ketil Malde **20090504115412] [implement a primitive mkQualTable Ketil Malde **20090504135559] [rename to pyrosim, update cabal file Ketil Malde **20090508091501] [bugfix: limit flowgram lenght to flow_lenght ch Ketil Malde **20090508094712] [model is now a function from hpoly lenght and sequence (i.e. flow) position Ketil Malde **20090509105217] [dead code chop chop Ketil Malde **20090509105451] [set clip_qual limits to whole sequence Ketil Malde **20090511094537] [slightly improved arg handling Ketil Malde **20090629084344 Ignore-this: 335e826228d71908b0e3e3260f4aac22 ] [num_reads is a property of the header Ketil Malde **20090703114343 Ignore-this: dabc91e9c79b567c4cf2fc7fdbdb482 ] [commented-out test for flows revcomps s = reverse flows s Ketil Malde **20090703114427 Ignore-this: 11d5254077111ec659d2e7df6c61e9d3 ] [define sampling in terms of the cumulative distribution and its inverse Ketil Malde **20090707112529 Ignore-this: 66cc8314d87f9cbc9d132c1b54137103 ] [update sampling functions Ketil Malde **20090709124656 Ignore-this: 2ae2d4cf8dc9ac1d5396a12d8d41247b ] [add real option handling Ketil Malde **20090709124832 Ignore-this: 3425dbda36d91ca1edd0e66c4dc13634 ] [comment fixes and updates Ketil Malde **20090709124916 Ignore-this: 6d8c6b3f35af1c0ff6c2c76cb77178a9 ] [added README file Ketil Malde **20090710093723 Ignore-this: 982156c7be73286e5c9650c8e8f9c825 ] [allow reading from stdin, small mod to generated read names Ketil Malde **20090710093942 Ignore-this: 3a5704c5ca44825a0660420f3be05afd ] [use number of reads from generation or cmd line Ketil Malde **20090710094032 Ignore-this: e5f29aa63f6e3fbef5ba0833e3a65268 ] [support selection of flow lengths Ketil Malde **20090710102253 Ignore-this: 3b8ac8932bc35e72b162c95dd97d78df ] [massive speedup - fac lookup table, use int indexing Ketil Malde **20090713093206 Ignore-this: 9f8a64ae2d0fd52b2f47437270794264 ]