cdc2febbfde50b6460030eaf272d792987e336eb Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/090193e0e6ac48ad2a83ee6eaad47c8fc0ad570a 090193e0e6ac48ad2a83ee6eaad47c8fc0ad570a 2009-12-07T06:59:10-08:00 2009-12-07T06:58:51-08:00 apspm tool: fixed choice options d3fb79beda10d62ab91c66b3d75c5651efe074e4 Giorgio Gonnella ggonnell@yahoo.it 22ab50eee09131cc246ad7fa842bf066bb4f3822 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/cdc2febbfde50b6460030eaf272d792987e336eb cdc2febbfde50b6460030eaf272d792987e336eb 2009-12-07T03:26:43-08:00 2009-12-07T03:26:43-08:00 apspm_esa: proc.specials, read inchar only if really needed 9e013af9258d493d1affe5f0de5d8b0e9971f1e1 Giorgio Gonnella ggonnell@yahoo.it c6babe4e0287443c564d09ea869348f6a12fe205 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/22ab50eee09131cc246ad7fa842bf066bb4f3822 22ab50eee09131cc246ad7fa842bf066bb4f3822 2009-12-07T02:49:06-08:00 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encodedchar access 8032958a3a69239844d76df67873a19c3445c85c Giorgio Gonnella ggonnell@yahoo.it cc245042b5b78d82bbf97bce77500563ef6cae37 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/aec34e6e8b94f100c533391426375e7b56ea14b8 aec34e6e8b94f100c533391426375e7b56ea14b8 2009-12-06T10:06:57-08:00 2009-12-06T10:06:57-08:00 apspm_esa: removed restriction on wildchars 3691033e21514ec94f663b8e09c07fba2eda7342 Giorgio Gonnella ggonnell@yahoo.it 533f74c28ed67599f96c74526049bbb3296e402b Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/cc245042b5b78d82bbf97bce77500563ef6cae37 cc245042b5b78d82bbf97bce77500563ef6cae37 2009-12-06T09:40:57-08:00 2009-12-02T06:39:03-08:00 All pairs suffix-prefix match tool adbf8174024a422632155c072d87c4af0eaadbe3 Giorgio Gonnella ggonnell@yahoo.it 64d161a8bc24484c5dfc2d0f9c7e2e751a144e4f Giorgio Gonnella ggonnell@yahoo.it 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ovl hashtable 4efd51b1602c695a761491235ecdd7961902c557 Giorgio Gonnella ggonnell@yahoo.it 006f697ed77920586f331e9c9e7050302efc1eb1 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/71ce660fb5c01e4a95499e2cbb26e1d4b41069ad 71ce660fb5c01e4a95499e2cbb26e1d4b41069ad 2009-12-06T09:40:54-08:00 2009-12-04T09:29:21-08:00 Functions to use an ovlproc from GtOvl+GtReadspair d700b1aee1b977640beed13e608a1ae85c78d782 Giorgio Gonnella ggonnell@yahoo.it 043d19a12d8e5d44220cf060ee4dbf51a7ec1837 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/006f697ed77920586f331e9c9e7050302efc1eb1 006f697ed77920586f331e9c9e7050302efc1eb1 2009-12-06T09:40:54-08:00 2009-12-04T07:41:36-08:00 ovlproc_a_e: adapter to use GtOvlproc as GtOvlprocA 70a9b779fb7f6395d9a7e8a7c05c8c02b186e889 Giorgio Gonnella ggonnell@yahoo.it e5f882547b231dddc9a88e18dc4c9d4a8136bc8a Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/043d19a12d8e5d44220cf060ee4dbf51a7ec1837 043d19a12d8e5d44220cf060ee4dbf51a7ec1837 2009-12-06T09:40:53-08:00 2009-12-04T05:00:38-08:00 Ovlproc to load overlaps into string graph 4e705d806162e07551338a59ed386af968c20aed Giorgio Gonnella ggonnell@yahoo.it 23f4e82cbcaf2faadee915543df2536e4c92eac3 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/e5f882547b231dddc9a88e18dc4c9d4a8136bc8a e5f882547b231dddc9a88e18dc4c9d4a8136bc8a 2009-12-06T09:40:52-08:00 2009-12-03T09:30:16-08:00 Implementation of the overlaps String graph 3e4a32b8db6a0377a661eb4d5e5787bf773294b1 Giorgio Gonnella ggonnell@yahoo.it 5c7694228df718d2f07e8d4b22bc912f3af842c6 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/23f4e82cbcaf2faadee915543df2536e4c92eac3 23f4e82cbcaf2faadee915543df2536e4c92eac3 2009-12-06T09:40:51-08:00 2009-12-02T14:47:56-08:00 Ovlparse: overlap data from file cf2c9717c2333304a3a6408772bca7b4cc8677c1 Giorgio Gonnella ggonnell@yahoo.it d66d7f9b33d099d6798d1a2a5fbdbb717b205901 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/5c7694228df718d2f07e8d4b22bc912f3af842c6 5c7694228df718d2f07e8d4b22bc912f3af842c6 2009-12-06T09:40:43-08:00 2009-12-02T02:21:33-08:00 APSPM ESA-based solution (top-down trav. of LCP-int. tree) bea34947cc7909e1e6fd3450f8a201f0a86f10fc Giorgio Gonnella ggonnell@yahoo.it 2657ab2ecaedd2a2eea83484890e32107890c009 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/d66d7f9b33d099d6798d1a2a5fbdbb717b205901 d66d7f9b33d099d6798d1a2a5fbdbb717b205901 2009-12-04T07:44:49-08:00 2009-12-01T03:39:39-08:00 Overlap processor hashtable for results maximization 25c69ca1c8baf0a957c09d6ca3c3168a8cd6c798 Giorgio Gonnella ggonnell@yahoo.it bde2d72c842614b9917af2fff2d6040274fed867 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/2657ab2ecaedd2a2eea83484890e32107890c009 2657ab2ecaedd2a2eea83484890e32107890c009 2009-12-04T07:44:48-08:00 2009-11-30T15:14:19-08:00 All pairs suffix-prefix match: ovlfind_bf/ovlfind_dp solution 330127cd783cfd2a990414f258f153e7d0ba9cb9 Giorgio Gonnella ggonnell@yahoo.it 8b7be1967da3b93804d6faa310cac1942c163462 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/bde2d72c842614b9917af2fff2d6040274fed867 bde2d72c842614b9917af2fff2d6040274fed867 2009-12-04T07:44:46-08:00 2009-11-30T08:28:53-08:00 Module to find exact and approximate overlaps by dyn.prog. 295592179077368893e0e5b76aa5ee5b3b81d28c Giorgio Gonnella ggonnell@yahoo.it bcdf39f2356d2985898aca42c29dcd6a48a529ff Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/8b7be1967da3b93804d6faa310cac1942c163462 8b7be1967da3b93804d6faa310cac1942c163462 2009-12-04T07:44:45-08:00 2009-11-30T07:30:09-08:00 Module to find overlaps by naive memcmp bc13398c2aa3ad1cdcf7afa8d271e0fd65044016 Giorgio Gonnella ggonnell@yahoo.it 0dd54c5c8afb678f0042164749119b0edd231c12 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/bcdf39f2356d2985898aca42c29dcd6a48a529ff bcdf39f2356d2985898aca42c29dcd6a48a529ff 2009-12-04T07:44:44-08:00 2009-11-30T06:00:47-08:00 hashtable for overlaps, with a show function 8670f2a9a5e06bb953c57be9dfe00fd5522c9819 Giorgio Gonnella ggonnell@yahoo.it 3a67cef57e01e5bf892e11d84af783806c79d275 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/0dd54c5c8afb678f0042164749119b0edd231c12 0dd54c5c8afb678f0042164749119b0edd231c12 2009-12-04T07:44:43-08:00 2009-11-30T05:24:15-08:00 ensure_output applied in ovlshow.c unit test 891106947c06ac1e3100c78774a8eaf0a1fdb658 Giorgio Gonnella ggonnell@yahoo.it d9d408571df0346ebf63ae0a249368105fd45a95 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/3a67cef57e01e5bf892e11d84af783806c79d275 3a67cef57e01e5bf892e11d84af783806c79d275 2009-12-04T07:44:07-08:00 2009-11-30T05:23:44-08:00 ensure_output: macros to simplify test of output to tmpfile 327b494315efd9e5ede5a8222f6c879aadc9d675 Giorgio Gonnella ggonnell@yahoo.it 680378ca00c34756daad991a74f2b5a62f2034ae Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/d9d408571df0346ebf63ae0a249368105fd45a95 d9d408571df0346ebf63ae0a249368105fd45a95 2009-11-29T16:00:18-08:00 2009-11-29T16:00:18-08:00 Ovlnorm: enforce 'only seq mit higher seqnum may be revcompl' 748390366a8d8522ce4a53b06886e0ef1f350340 Giorgio Gonnella ggonnell@yahoo.it cfb272615ac6a7146684bc7bb680ebc74adea1a5 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/680378ca00c34756daad991a74f2b5a62f2034ae 680378ca00c34756daad991a74f2b5a62f2034ae 2009-11-29T15:07:00-08:00 2009-11-29T15:07:00-08:00 Ovlshow: functions to output overlap information - defines implicitely an output format for overlaps (exact / approx) - output from component variables or from GtReadpair+GtOvl[A] d070b52a363dd90096d7d2048d8276c8f69e1fbf Giorgio Gonnella ggonnell@yahoo.it 1ddf6b489aef89fa9e5c8765b26b780f08996f37 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/cfb272615ac6a7146684bc7bb680ebc74adea1a5 cfb272615ac6a7146684bc7bb680ebc74adea1a5 2009-11-29T14:03:33-08:00 2009-11-29T14:03:33-08:00 GtOvl/GtOvlA: data structure for overlaps (exact / approx) 251994c7e4e3c87bc9358689a35ae550c69e4eeb Giorgio Gonnella ggonnell@yahoo.it c239ee96865a5fdba72c8941979aca3043069627 Giorgio Gonnella ggonnell@yahoo.it http://github.com/ggonnella/genometools/commit/1ddf6b489aef89fa9e5c8765b26b780f08996f37 1ddf6b489aef89fa9e5c8765b26b780f08996f37 2009-11-29T09:12:36-08:00 2009-11-29T09:12:36-08:00 GtReadspair (pair of uint32_t, hashkey for overlaps hash table) pair of integers to be used as hash table key, with a defined sorting order a837252acaf10a3f6540b40159000f999bcfce44 Giorgio Gonnella ggonnell@yahoo.it