pristine:503cae1f425a152d9c765584e0e1de4ab40d98f4fafef1e5feb1a29458deea44 [skeleton implementation Ketil Malde **20120209172330 Ignore-this: 83820817319df37e3fb21ada5ccebc05 ] hash: 0000007096-4bbdf367a5214b731b2250de8a174f90c2ee499871b4bd80051d26a8b7537226 [Annoying warning removed. Ketil Malde **20120209180955 Ignore-this: 67270eed25a20c8b309816889f73ec1b ] hash: 0000000210-eadaa829a5dde7473a7dce3697aaf0f5de65e7e9c79cf2afabfa4237641220ed [output by printalign and collect_aligns Ketil Malde **20120209181042 Ignore-this: b261430c87518d36662a1f408fc7474e ] hash: 0000001000-0c48d91af9bfde451720bac6833d9243085f3c802301778cdc9288d056df2699 [merge_aligns partial implementation Ketil Malde **20120209181055 Ignore-this: 7a07f4c14428861548e218bbf16a65fe ] hash: 0000000596-9c3472f0f060a12d74d9bcde6275c11e1e9f82444683b99bdd29c50a700af683 [Add scoring, skeleton merging, cleanup Ketil Malde **20120210111041 Ignore-this: adfec1a10475c0cc01fa565e2545a6e1 ] hash: 0000001312-1f23d8be6ac60c180642c9036dbff5ce753ff3b0ca267ad4e4d2145090b8bf18 [Remove unneded AlignAccu Ketil Malde **20120210111507 Ignore-this: 56009096811307c9c6352ac4fac3f737 ] hash: 0000000681-c3ac17ce958337bbfbb762bbcf1ce88df1de0922679e3830726cffa12f3f187b [Use only sequence ids, not full description - and implement invert. Ketil Malde **20120214073853 Ignore-this: 30c0e8cb7f2a88035f710f9b873ac4d6 ] hash: 0000001010-03131615882ba2c3235adc84a4b65126df8c3aec5b5e06f6f8d71fe271b32022 [add BlastExtract Ketil Malde **20120214073909 Ignore-this: 7f913e1ffbfbc1ca8c25277143540663 ] hash: 0000000893-192c0c9b4ae4ba01bc3858bd3ff9991ff7636d0d04c315b480ec80f5bde9a1dd [add main and cabal file Ketil Malde **20120420102932 Ignore-this: 7683f3a638ac3c0237485a404d9bd0db ] hash: 0000001250-e588bd821bb888b61b86849bd4f81b925ae7b5f2b43a7745e7c306fecc54516f [Blastextract outputs to appropriate dirs, cabal updated/fixed. Ketil Malde **20120420104400 Ignore-this: ea2d95744bba6a68207061a710d6e52c ] hash: 0000001381-b8b0131f9d6a4170e3807310dce25496574c1ba14c8813ee66864c3cf1e04e87 [Clarify blastextract, add utility function for reading back. Ketil Malde **20120420105506 Ignore-this: 8d4a1b26713a8c1f40f2dd26164f79f5 ] hash: 0000001632-a954784bac99fa1764dcad5b35f754266f0c16904426ddbabf9de7e818e58cd9 [Make imports specific. Ketil Malde **20120423111005 Ignore-this: 5fd7cf52e3e9e6a0274a1cd69bc7cc13 ] hash: 0000000273-3c89d13182a1042f52e27b6b238ffd9ab39e2b29d43b2cf142c3e9d56789c71f [Cleaned up Blast and BlastCache, modified Annotate accordingly. Ketil Malde **20120423124311 Ignore-this: aca52f2ee81e27ebce89e61d956ff3be ] hash: 0000003962-359c061d2453615f774231a2e54559fe902e4736b18880414ee0eb5b8f52551c [Make collect_aligns use a function instead of an explicit map, import Ketil Malde **20120424101231 Ignore-this: ad1e2779312a58e42275f6a1c5f9b413 tightening, comment/output fixes. ] hash: 0000002054-30d86005a3d3842e7363d440a6009f863a4f8aced4d6a1f2fc99f01abff4629f [remove TransAlign Ketil Malde **20120424101257 Ignore-this: ba1270c35bd70e1d38594baadd984f3f ] hash: 0000000221-d9f847558cdfaeb11603525c95ba7766067a9cea35b261435df27a08f9c5617b [fix cabal, rename to TransAlign Ketil Malde **20120424104446 Ignore-this: 342dc9a8147b9f2f6eb97c4caea6b5d9 ] hash: 0000000643-5ae1e92c4ee2a2ee14ad7780bb08dab0086356197832f6ab0663b0ab62c767b0 [Make blast prog a parameter to many functions. Ketil Malde **20120426125757 Ignore-this: dd5458034a8ae25c0a5287a5a03ef815 ] hash: 0000003135-7237c296c92fc383dc762d13f4bd0b64e26f4de2ad7b850373b02ea5b2207d4e [Add locking for cache dir. Ketil Malde **20120426192017 Ignore-this: 4acd24626ac593402bb2cfeead64f64c ] hash: 0000001230-50602720e42392ceece3db0eac40dbc95666b24f35a0237d409d28791479ca29 [Move merge_align to Align.hs, and implement it (untested) Ketil Malde **20120430122005 Ignore-this: b484dd5a69fae2f588cf103bce219e9 ] hash: 0000003027-b77ae3ffb12132056a2eca397a2ec5ae6fd1073a73060168371876ffad4ba7af [Add error patterns Ketil Malde **20120430123407 Ignore-this: 808b28a931470afa907f97dfbcf5a2cc ] hash: 0000000291-97c83d3eec21bb55993a296f13c95163038ad29a29091c129ae2dfc03fd749ca [Lots of work fixing merge, tested on test data in file. Ketil Malde **20120430134629 Ignore-this: 3ebc5a43327d3e04633a60fde3b354a1 ] hash: 0000002197-03ba2e71fdf8b14dc3d151fe9cf046516d8ae2cb98086a3606711bea0c5f6a49 [Debug output. Ketil Malde **20120430142224 Ignore-this: 2664852d9a39a549626e4e19ab4d46c4 ] hash: 0000000581-0a573371282d950a346c1d56eef6305fb1ff20a062e9d8e916dc55a13311c949 [Filter out empty alignments Ketil Malde **20120430144715 Ignore-this: ff51ce5625cbd2383f894c3a6cfd5731 ] hash: 0000000485-5fecf8b8403700014c1a8bc0189abcc497003849f7c6937aa0a93a37c4682fb0 [print one target alignment per line Ketil Malde **20120430190814 Ignore-this: e6b7487d5e1e2e82476e304cb7e403c3 ] hash: 0000000305-8fc886fa37f5ab0470ac012a0cea1407d6f04a5dd8372b85e837303184a2af9b [Move collect_aligns to Align.hs Ketil Malde **20120430190824 Ignore-this: 3ad8dceff0132c80d3e52e125e5b379b ] hash: 0000001250-6d6665ca5a459bd858991c9e278d21e9988f649d3d850144cad2e882b6999f49 [Stricter readAlignmentCache Ketil Malde **20120430192648 Ignore-this: e580d014a83513e2e014a3268f66cfe4 ] hash: 0000000577-c148d1261a33f8d01e7c2ee4e596e28e974e6c2123dc48ebb1b0b870c0fa034c [Refactor, and simplify output. Ketil Malde **20120501101219 Ignore-this: 53804d34b7e21a82016f23d7aad8c300 ] hash: 0000001266-676b89b5c6fdb88648387dcc0003b2214e842ebe11d887ef93318ce132e21664 [add a couple of comments Ketil Malde **20120509124747 Ignore-this: 616016b3721a956f990d954641eac48f ] hash: 0000000791-808cc253031ceb6df457b30d356809ac21e6652571bf3665a72151758c6cad48 [Faster group_al. Ketil Malde **20120509140058 Ignore-this: 8232627b71f5ede882ee1bec1ca81b4b ] hash: 0000000657-d5f656839190a84522c36c394891ed04d25452cb750c104cfb9a03aac7733f89 [Add new linear-time group_al. Keep old versions to compare correctness. Ketil Malde **20120510134420 Ignore-this: cf4684f0661ee9428c2476029c326d6c ] hash: 0000001189-cba8ac3c50cbf4b325cb8603cfbde7b6c16e1fa815957067283e07a89dff897b [Type sig fix and assumption check in collect. Ketil Malde **20120511080328 Ignore-this: 5dafbd4b445dd51149e1d2351a1590af ] hash: 0000000589-5f888bd0805f013c27754520815053f871d9fc4d80cd59c19ce83d5dd0182361 [Fix group_al to output sorted qs, as required by 'collect'. Ketil Malde **20120511080357 Ignore-this: bceb8296b4695c9ed1ed0a032f7bea5f ] hash: 0000001163-e7c7f48d029080f666a1892afd8d2e87a9f9208b8629a1404c4393b39f36604c [Fix group_al' sorting output. Ketil Malde **20120511081800 Ignore-this: 24e9df1e7130d20b29cd307742b44c9e ] hash: 0000000658-99cd288ae8aff44ae9814dbd3ab912eb598fcf35a04927275dfbc9adf0bc6940 [Strict maps and group_al''' - best so far. Ketil Malde **20120511085630 Ignore-this: 7cf90578db713c670223c4f2e0f103ab ] hash: 0000001634-a0e6a36078d611f7b78f1fdbacb13a7689a999501b674f1e4e7b5e35d057e7bd [group_al''' does collect internally Ketil Malde **20120511085727 Ignore-this: 9c3954aad0045d344d6cdc548e9a4123 ] hash: 0000000333-865e804743b37e08989d6e86ed8175baa10f9382c1c4f73795d8957037fde9f0 [Improved output format. Ketil Malde **20120511131602 Ignore-this: 6fbb64c4a23dedcbd2c8eadd1b405589 ] hash: 0000001194-0a2246e31d0c8877c8c3cbd9397273ae844bf0a23e1de534530ef19e6eaa4865 [temp fix: read cache also for first hits Ketil Malde **20120513200925 Ignore-this: 7da1f46a2a45a82dcd297064d8bb0f9c ] hash: 0000000490-68d0ccab883c275700657407cad0de48134d8903c36aebbee02d42f9c248dea7 [Separate out showcache and blastextract. Ketil Malde **20120518120331 Ignore-this: 89621bd1551fb865397b8f772f0486f1 ] hash: 0000001187-cf5e9fc42f1c7860fa1965f2c776b9c65efbfa2e01821f1f61b395b9692fd97e [Use max not (+) to calculate score. Also, fold in toMap/toList in merge function Ketil Malde **20120518120410 Ignore-this: 1fe05feda4c44b60b812d753f840b35 ] hash: 0000000793-ebf003d40000a93e3579203fb3a3c422435a46f9b4b61e11474f3580caa6ab62 [Add print_alignment function (but comment it out in Main) Ketil Malde **20120518120519 Ignore-this: b897b62a18541b99169526b0c64a44b7 ] hash: 0000000910-5a8ad0e03a2d2423db7c9ec94a4011955707dd26e8383f50fa8f943c01f011cb [Calculate lenght as number of aligned positions, not coordinates of ends. Ketil Malde **20120518120539 Ignore-this: 7b19c045dc6c21fec49ab54414bb0e99 ] hash: 0000000387-e8084a5b6a69645951cc6e33cbf76d0a06701dcc6a2966813d50703906118eb6 [Simplify readAlignmentCache to use only String Ketil Malde **20120530134153 Ignore-this: 25b6daa8c41746fe57dbc15205f068fb ] hash: 0000001128-a6f64f102e0b391e1d93ba6db9c5c98bce97a86c3acd4b504e90f218246e5058 [Remove unused function (commented). Ketil Malde **20120613083412 Ignore-this: ef1a709975c68fcc6ecb1cc5bca97ea1 ] hash: 0000000482-fe352cc36b2477e923ee4ca858700fe9622f93c2848058003520a6c39d4f724c [Use type alias for BlastAlignments. Ketil Malde **20120613085131 Ignore-this: 833644cebb369778a7d1792ac669fcac ] hash: 0000000445-68b2dd2b5c49fa353862918e2e6f6596b095e5596f8ce16498350498510bb4d2 [specialize p and q to Int and use IntMap Ketil Malde **20120718090352 Ignore-this: 1caa41eb146f787c3a61881521839d74 ] hash: 0000001643-28f457b7ab063496042b6b76e7be8bb7c47e833b76d82c7cabc8e1009fefa8fa [remove unused definitions Ketil Malde **20120719084506 Ignore-this: 22cd2583c8855eb94e7b6835275b13b ] hash: 0000000167-a672ab117cf399ebadc61fadb6372bcadc5093098f643d17fa7fa1e717803791 [Use 32bit data types for blast alignment caches Ketil Malde **20120719084536 Ignore-this: 122e5cc47621505170b6e83a221e2c27 ] hash: 0000002595-e25be80cadc9eaad5a97f386c331d90b6cf5913e7778370243020d83212234b8 [Store even more compactly by factoring out 's' Ketil Malde **20120719095442 Ignore-this: ee3c6a3dcec41687fe7bfa98221f12d3 ('s' is constant for blast alignments) ] hash: 0000000654-245623603e588a0dd903de47780261b17985b49a7aa1eac187639c7f66c6ad38 [comment cleanup Ketil Malde **20120719162512 Ignore-this: c5ddf7ae2c3e4afbf299a5062cd5ab68 ] hash: 0000000297-d9122474c54752fb300298f00f2d5fcf35d0c467aa70d00d7455db11d9631e47 [more robust showcache, absolute paths Ketil Malde **20120719163807 Ignore-this: d33ec309f1c14f156b91654fe0527a8d ] hash: 0000000721-8c9f329a8f19c995258b7ed0628165728ae920d6b490ebce482addb7a5439207 [strictness in unconvert Ketil Malde **20120721065954 Ignore-this: c6f703ac326471ff8039ac95d5504454 ] hash: 0000000300-5cb68ddcd9a1018f047f39d9bf4bc1f45e5d9294d2b68f268367595f680ada73 [more unconvert strictness Ketil Malde **20120721071538 Ignore-this: 95983cd136150388c2748cbe94c40e38 ] hash: 0000000337-558b7a0a79e570c755f38fc42a431d4f5b81541d0a2543ccbdfd94c3fafe90ad [switch to strict triples (but still parametric and boxed) Ketil Malde **20120721084155 Ignore-this: e3b14323d8fea06756175de0d9ed9e56 ] hash: 0000005259-2154419ee58f80888b8ddb0ec0da2f3a4fc477b1f4027e6892030a8a15681e90 [hack types to allow unboxing Ketil Malde **20120721103314 Ignore-this: a217bb3485f2e4ca82aeed855af64080 ] hash: 0000002091-6a4970c123974f615bc063864786a487f0bdab09040c35c43cbea7cd401a82d5 [simplify (de-parametrize) the A type Ketil Malde **20120721104858 Ignore-this: bd9eddc40002ad991bdbdb455a2dc2c5 ] hash: 0000001660-a918d3889da920386c50d17d344dc1830be581bbe2fff8dda456327cebc67193 [Deepseq the binary output. Ketil Malde **20120721154844 Ignore-this: b81b115bfb7380bae451b763b86fe3d6 ] hash: 0000001116-2768033e84b5d17a3091e812695589fbd49112e54cfccf4296f24f768935018c [Simplify (more specific) types, cleanup type signatures. Ketil Malde **20120806082321 Ignore-this: 74b3feb7051db876c88c6cc780a3da0c ] hash: 0000002772-7e342390e057e03196bf02874852161a85ee851f70b4e8b98ee9e3f07aa78f10 [use strict map for caches Ketil Malde **20120806101729 Ignore-this: 890d24aa2ad96a9e4ce3f4b20a5c1af0 ] hash: 0000000224-9cd8b5c2e65eed1ee6487ffba9d16292a5afbdb32a1613589a7790644be7459c [Uniquify hitnames Ketil Malde **20120806110739 Ignore-this: 85f175dccfee83ac0104832a062cda6a ] hash: 0000000495-d3244c4afe9766abd2f043a738c9f6ceed1723a274072f172cf49c3354274898 [typo in comment Ketil Malde **20120816111217 Ignore-this: 5dce254fa5e578a03f0551d4459b8aa5 ] hash: 0000000303-a9cc2e4f0e8434e27067fa3d3025c04f2061bcd245e09b7c353aaed697711d4d [Add cmdargs option handling (incomplete) Ketil Malde **20120816111234 Ignore-this: d589ff214c8d970eb7dfed281408399 ] hash: 0000004319-39326505ac8a3f9c77a4eeefaa140ae6c623f628bac04701f98c2b2231c68405 [Use log/warn functions Ketil Malde **20120816120600 Ignore-this: e6b87362bdb241d775b3a1a7fb5b1aed ] hash: 0000001658-029aacc86c4319daaba313a938664c99842c33e47c810877f50fe1d4261dc7b1 [Oops. Process list if supplied Ketil Malde **20120817063713 Ignore-this: d2eba96b4353e5749b85ceaf8c096564 ] hash: 0000000238-ee82f3e198ec51a1f148c7c91241717a5b1fae7dc702cb09d3c2920618e43a51 [oops: filter out . and .. from dir contents Ketil Malde **20120817064135 Ignore-this: da5176d1202b55cb2d402835cc4b4433 ] hash: 0000000311-7173dbe7c2f384fcaa87eb877d3fa0255444892417ca9b8bf0f191ce4641614b [output more BLAST-like (prefix query) Ketil Malde **20120817081550 Ignore-this: cc331547348722f912c34377d080c044 ] hash: 0000001832-c3a268e1e6544178217b91c3e291bebe484d3551db7cea99d8cfbeee811ed7da [minor change to long output Ketil Malde **20120817082755 Ignore-this: 88011c81c7f2cd8b5ce7bcb4c7148826 ] hash: 0000000870-fc40d5d96cb1432830f1a5712cf1d3d5b62f7ebf1c3d5555f311a2aaf03f48e8 [Tab not space in tabular output. Ketil Malde **20120817100429 Ignore-this: abfb045660354a9d41f8680daf541158 ] hash: 0000000288-70b9b2b54d273dfcb7a748b3d3866e88eb7ef4582b5c30ce5f3a55ddc1084dfb [TAG Submitted to Wabi 2012 Ketil Malde **20120530124405 Ignore-this: df31590d135d40c46fa59a99898b6e22 ] hash: 0000005793-4aa60f3082136e8f62f2d43b263b8b2f1216383dabe440a2f6c13129752ed01f [specify short option names Ketil Malde **20120817104425 Ignore-this: e6c61b464b1d7dbcca304211dfdda7a8 ] hash: 0000000463-8d169db14cbed88ed4bbad3b4ab1cbea9cc5aa888b7e61dfcc3f73d28d50b6e0 [Factor out output functions, and use them for showcache Ketil Malde **20120817114213 Ignore-this: 18eaf7d25c6eb5c396f13ecb50a3828f ] hash: 0000003360-4712e6a0c7244e2ef83db391c2e9db3260861eb40776cad5b2d0553e5bc1df00 [Better help messages. Ketil Malde **20120904130432 Ignore-this: 95a0740ba20bdeb94a6308b61d6c05ff ] hash: 0000000447-be72e7e46b86e20ace6b9f3f2d39a26b6914df7fc7479f0af5d00e38fe402f3d [Use stderr for logging/warnings. Ketil Malde **20120904131101 Ignore-this: 1577587e8840d314a189b7906983ba3 ] hash: 0000000606-5373f3a919e8e83a37caf3f92ea864e775125470dff1517128b8a6fe5950e277 [Add README file Ketil Malde **20121106130237 Ignore-this: 9d2ae2eb03e1e287abb0cd327925cad1 ] hash: 0000004246-9bbe1a7c008db1a09759d6a4ae854f17704ddba06936e571dc46fa0e8199ed79 [attempt to control caching with -c option Ketil Malde **20130301150207 Ignore-this: 2c8ab47640e28395419791dfb42ed068 ] hash: 0000002160-be428bf006993bc2229a5d0be8490ec6e8222b3a244121c37f9861dbac388dfc [Update README. Ketil Malde **20130301150916 Ignore-this: 76edd877d31234a80f8e8c6941f91844 ] hash: 0000001264-dfef94a491e3fd52ef6fdf2dbff9c3c84e6ac0b9b50d4e4a36f9842906c4721d [update to use blastxml 0.3 and new biocore Ketil Malde **20130304074028 Ignore-this: 841183012175269d5fc5e811cdf996fc ] hash: 0000001281-837e1eb0c373fbbe50d6f9c59f3700076d4992d91a81b4e2119c11739eec0bf3 [Add --cite option. Ketil Malde **20130304093935 Ignore-this: 67f154e4d68b7148f992bba2c2bdcfa5 ] hash: 0000000631-c061a90291e5896cd6e440f981721326d687bfcc16e7d41dd511d536a6e9426d [Cap bytestring dep, it breaks with 0.10. Ketil Malde **20130305122536 Ignore-this: c39605f0e04914f2d241c277734a4d40 ] hash: 0000000972-5bbc347bb7ef2daba5d45ff217b06eebe07a8c000987f8b7a9d7f3a6470f0b1d [Comment updates for Align. Ketil Malde **20140529121822 Ignore-this: fb98c4976ef53c8d929c12e265f3f68d ] hash: 0000003397-f7747755ab7dde8f7b34b8b41972b23d2f3a4c0ba3d3fe00a5347515543cbc34