pristine:8386f02ed9073aa90fd1c9f1903c3cc3d35a732c92667581beaf964ab27e7637 [skeleton implementation Ketil Malde **20110915103000 Ignore-this: 24f6278a12ef7ed45a903face4de39b3 ] hash: 0000002536-5ea4d43936b8abf0a217a86b97cbeb8b9d7ccb2a21da61a09cfd8c34a45d041c [Simplify a bit, basic merge now works correctly, but is inefficient. Ketil Malde **20110915105908 Ignore-this: 32cd1027193934f6ce94731b4cef178e ] hash: 0000001820-6703f28db77f53cac428c0d0a70dd7f927e46ee013ebf4f1b7bc0103417e55f4 [Call module Cluster Ketil Malde **20110920113423 Ignore-this: 9f22b1e38b28d4699c089aa0aee527c1 ] hash: 0000000176-81b9bd05ff3b277c3fa9f5cf9d17d0984d5fe1bd830519be2e4c4e04b52137ed [Add a main, and make everything compile. Ketil Malde **20110921094546 Ignore-this: 111a2521e5d0d4ae99ce7085c3417fcb ] hash: 0000002701-c63cae33c5fb1dde8695641133201db70ef27fcb50b877e4d81f3320851ef8bc [Working (simplistic) version! Ketil Malde **20110922122409 Ignore-this: 9ff2c634e143a2a1cb13b026355837d2 ] hash: 0000004235-2ddf86bc439c5a7c5f01b901a87f8a09a7ae1932d03179398af11e9b90bc9f9d [Add main for STM Ketil Malde **20110927070147 Ignore-this: f04e08f2c9a4e1c16cef8b21401ef336 ] hash: 0000000996-02680f90a404342496218de284aec192f2ab70646576177288c352761856624e [Add threaded STM main Ketil Malde **20110927120639 Ignore-this: a6426293b0f1d5e9a26a13705725f105 ] hash: 0000001263-776b62136f2fa10cb47129dfda2776ae3a0534692cc2d6d211610b6462df72a6 [rudimentary timing/test skeleton Ketil Malde **20110929081520 Ignore-this: 8879d076175265d1aa7a8df205477162 ] hash: 0000000930-e051e408240e5b27256e3c35c1f83cfa38a08c8992a15fc5fbe312076fa3c77a [Add mainstm and stmt, add script to also run parallel tests Ketil Malde **20110930085124 Ignore-this: 434b46d8a8e0502174e974dd021e7ec6 ] hash: 0000001093-3b8099840b62ceeb87684ef1886a038a0b2f888790fef1d2c790defc46227262 [Add cluster counts Ketil Malde **20111004083316 Ignore-this: c38b2af8bb26b1d27c181225594501b1 ] hash: 0000002115-354d449e78070b1d9e16e4f5cb7220eccbfb06cb4542541065fcbd01559cb68a [Support Nothings (only useful for partial BAM files, I think) Ketil Malde **20111004111319 Ignore-this: 1c1bbe6770cab5d416a6e42103ddc92f ] hash: 0000000528-ec0a003535478dca1dc6f40268bc48659b75a2e5eeb3d3a1323f366f8c4cb3f8 [Slightly more elaborate error message. Ketil Malde **20111004120429 Ignore-this: a349f0b4996a2fc0eace5b6d34d8166a ] hash: 0000000274-c13d339ca827145539c60861b6a30f96b13d12d94e57aab9ec2bcec13cfaac2f [Don't print singletons. Ketil Malde **20111004120438 Ignore-this: 5ee358f79c64967365247a1a6f55c6b ] hash: 0000000261-e54826d0738add9268143f715d8cf76fb514a89e06fff498144fe2acf43f1dac [bugfix - wrong link counts! Ketil Malde **20111004120512 Ignore-this: 3d9959c6acca37a8c4efe04467539762 ] hash: 0000000646-17e2a7c1ef00455a83aa06b8b5e992e09c3497ef7b3754956d0b5dc3d190597a [Don't hide output files. Ketil Malde **20111004120535 Ignore-this: 6d590464480d61992e80f0f0bbc24a56 ] hash: 0000000498-0b3758c14b8d43360a9888ff5d13280e65cefb716b589c39b22a33a6b3407fde [Bugfix: merge works with counts. Ketil Malde **20111004124512 Ignore-this: 24ba3b633fbaf3f4c8c8c9b6fb93a717 ] hash: 0000000595-a74fc45a64c3c5706de6961a4aee179392c09895b7a266271577e89e34928b3f [Ignore it when reads are already clustered Ketil Malde **20111004133458 Ignore-this: d747ff42f6242753f9d4a8bc10555b94 Verified output by comparing it to SSPACE - although the clustering differs, many of the same read pairs are identified. ] hash: 0000001487-0d9f385cead0792fb1d1e53b941c952ffeb5ec0cf962e68ff7668efdd6b0f439 [Avoid the self-links Ketil Malde **20111004224355 Ignore-this: c84b148bea459984c70b3fb72759daa1 ] hash: 0000000784-0a2363e29d778f0bc87b61c62d4fbdbb40d011a91e14c5cb333d4692c047ae78 [Fold InitializeHelper into Cluster. Ketil Malde **20111005113820 Ignore-this: 76b6435f3d50f76413662fe34c143a27 ] hash: 0000001832-861fbb7fca378e31110c284fa2bcd1f21ed4c47749ec861735dc4370a864ed85 [Change data structures, and reorganize. Ketil Malde **20111005130559 Ignore-this: 8ca8707c77e8e722bd5a6ab7fecc895e Change Links to a pair of maps, rather than a map of pairs. Move mklinks etc into ContigEnds ] hash: 0000003465-06711706138dbb6cff65d03af5f6f9cd25913115f38fe85d62f1a23571d21a25 [Add timing support/output Ketil Malde **20111006135257 Ignore-this: c043cd67dc55d57f5cb9c8970abb8e2d ] hash: 0000001912-d42d804e8f719658795afa818f93e9a2a1b914a65cdfd44bb96bbf6c7b9c7795 [Break initializeSTM apart Ketil Malde **20111006135439 Ignore-this: a8ee7d0f692f26ebbf9e32b0160eaaf7 This speeds up initialization significantly ] hash: 0000000649-3397c30e81860048f6db1cf589095a6cff4381105cd728543939498da7f8d469 [Add delta to timestamp output. Ketil Malde **20111010115931 Ignore-this: 4a3941d299edb3efb8597b312c0b739d ] hash: 0000000637-368675ab5e73036b02586480cb99aa4e95f15e21d3565cbee5a06729e7d94b1d [hide groupOn from samtools-unsafe Ketil Malde **20111011113243 Ignore-this: 68ea53085313913032b0f06e97819383 ] hash: 0000000233-80d8cf7da4947122db6be92db5560afd9384df50138b39853a9500744c1c60c2 [Change to use a real 'Link' type, and avoid dummy value (-1,-1) Ketil Malde **20111011114147 Ignore-this: 3560ca7c50a7454c1e60bde94e322ad9 ] hash: 0000003067-ae94984fe27fc5f5360c84a723b63da1681f341d3bc5d21172712a69bfd8714f [Don't read clusters when not necessary. Ketil Malde **20111011120039 Ignore-this: e608884ba2e6817bc55498b72aba21ef ] hash: 0000000424-42fd935b6544d33d11cc971852ebb146cd62eabbc2b9a63df44f8eff69e4dfe2 [Delete commented-out code. Ketil Malde **20111011120052 Ignore-this: 3f4e8a119c1e2623c8653ae3751ae521 ] hash: 0000000546-76982278434390db5d921a0b6e2fe5d399bf6fdf9f61664ce5a8c1e1669cf287 [Move groupOn to Base, remove mklink. Ketil Malde **20111011135927 Ignore-this: 7078923d9fe858530696f7d2dd61a5cc ] hash: 0000002993-b2c45f69d5852ee8ff434a54bcaf2879589158e32fe3cb2eab3a0d69b3e67d79 [Get links in the correct direction only. Ketil Malde **20111011140042 Ignore-this: 11c30ea87635f322edf17e3ae838bfa8 Tested and - apparently - working. ] hash: 0000001225-e87efd06b59193d027aeacb35e1218b8d335ccda939e80336cd17c3927cb7b79 [removed/reformat comments Ketil Malde **20111013110155 Ignore-this: eb9ed55f1e21198b440ae5d03c25ef8b ] hash: 0000001090-70481ea435a78e547d7f7ab003f62e4ca144886c1be251ab940db2ff8d114c1d [Add type sigs Ketil Malde **20111013110303 Ignore-this: 72eb3f6f614c20fca709b91f51404e17 ] hash: 0000000343-e5bcd8add748b6daf1bb91917205385dd9b5e37fc1d5f28efb7cba68d2fa8c82 [Make specialized printing functions. Ketil Malde **20111014153750 Ignore-this: 1ba687fa5936b6665eb07b2c975cb1d9 Zog caveman. Zog not grok STM. Zog just print whole array. Thog say Zog go make wheel instead of STM program. ] hash: 0000000834-65d0c642fdf3be9bb917f6a7304833f403e8b052daeee65eb58e8ee176a06393 [Add classifications (but don't use them just yet) Ketil Malde **20111021140330 Ignore-this: 3be557f76607114889db44455478cd49 ] hash: 0000001251-4ab2a94b5841197c0d6a3398055f25c240429b5a5d8299a835f214ed270d5f53 [Update for use with new samtools and the bamstats library. Ketil Malde **20111021140403 Ignore-this: df33f3a0dc3a3a91c1d47731c09087e0 ] hash: 0000000955-c9089ce4834da9a1908825fcfbe7071658f9a91fbc2faa9a425a97d891973c80 [Use the appropriate number of threads. Ketil Malde **20111021140444 Ignore-this: 2640d20b954b616f9ea724f68abfc004 ] hash: 0000000343-01bdc07a8139ff256d96521a534115dc59aab3c9074d74a7a93a871bb541abc7 [Add support for reads map. Ketil Malde **20111024095506 Ignore-this: 54bceb2e4004453672b5d6287722b07d ] hash: 0000002943-190ea521d6c5198195147d08b427ad8c7806d9e2688547f77d986be7366d16ae [Also collect which ends are connected. Ketil Malde **20111024095526 Ignore-this: 9e5c6501da7bb743aa97308fe159979 ] hash: 0000001410-5d810f61e94746d05b1d4ca661dab59cafe71184fb386616caea6191f21bf0c7 [Filter duplicates, merge intmap constructing functions. Ketil Malde **20111025071610 Ignore-this: e16bb5de59c6c2a525a36aec6ba2530 ] hash: 0000002132-35213b2af7b85d06974414672bc7feb3cbc8cbb181671dd72b62d1fd4a6ab9f8