https://sourceforge.net/p/sibsim4/activity/Recent activity for SIBsim4enMon, 23 Jul 2018 13:19:07 -0000https://sourceforge.net/p/sibsim4/code/ci/0b24f8f8c481c7ad04535ee9323f2e9d71f31b83/cleanup after cvs2git importChristian IseliMon, 23 Jul 2018 13:19:07 -0000https://sourceforge.net/p/sibsim4/code/ci/0b24f8f8c481c7ad04535ee9323f2e9d71f31b83/https://sourceforge.net/p/sibsim4/code/ci/8c087a5f093aa29a0b96b773622efa923d570ec0/Imported sim4 sourceschris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/8c087a5f093aa29a0b96b773622efa923d570ec0/https://sourceforge.net/p/sibsim4/code/ci/a6f32edf335c47774a22b7a6904dc1e908324863/Added three new options: I, Y, and Z.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/a6f32edf335c47774a22b7a6904dc1e908324863/https://sourceforge.net/p/sibsim4/code/ci/2ef69299c63dc294795e00fda7191dd4c108dea6/changed resolving overlaps for non-canonical splice sitesclottaz <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/2ef69299c63dc294795e00fda7191dd4c108dea6/https://sourceforge.net/p/sibsim4/code/ci/8fba7fe46306669b4a55e4bbe54af705b25f1720/non-canonical splice sites recognitionclottaz <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/8fba7fe46306669b4a55e4bbe54af705b25f1720/https://sourceforge.net/p/sibsim4/code/ci/ae4c49994b54b83737a691b68f0d3ebda5b99bae/Fixed typo in sim4.init.c. Removed dependencies in Makefile.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/ae4c49994b54b83737a691b68f0d3ebda5b99bae/https://sourceforge.net/p/sibsim4/code/ci/326fb3e2a1fef1e5c3a4b9e424352e8ce6b8bf6b/cosmeticsclottaz <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/326fb3e2a1fef1e5c3a4b9e424352e8ce6b8bf6b/https://sourceforge.net/p/sibsim4/code/ci/89e7a518d945d632479c8f167eb33f1996db83f4/fixed the wobble bugclottaz <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/89e7a518d945d632479c8f167eb33f1996db83f4/https://sourceforge.net/p/sibsim4/code/ci/ca9d22516bc8bd83b33e631d9788361bf273dc22/fixed the problem of wrong typesclottaz <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/ca9d22516bc8bd83b33e631d9788361bf273dc22/https://sourceforge.net/p/sibsim4/code/ci/d3f77328b9a5d4ede53fad1461a5f5fb4f8080db/added scoring for splice sitesclottaz <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/d3f77328b9a5d4ede53fad1461a5f5fb4f8080db/https://sourceforge.net/p/sibsim4/code/ci/c44e64bec9556b302bce55bddd6c816822f6b36a/added scoring of splice sitesclottaz <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/c44e64bec9556b302bce55bddd6c816822f6b36a/https://sourceforge.net/p/sibsim4/code/ci/a1ac8a3bffeda5cdc7cd279d97c77cccf36f0f6f/Change format of splice junction quality output.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/a1ac8a3bffeda5cdc7cd279d97c77cccf36f0f6f/https://sourceforge.net/p/sibsim4/code/ci/7635a431de301c01cd20f71e07f74a5c4095510f/Sim4 assumed an upper limit of 200 exons. Hopefully, this is now fixed.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/7635a431de301c01cd20f71e07f74a5c4095510f/https://sourceforge.net/p/sibsim4/code/ci/7ba019dbc48e9fba97ac820e258e887afa5535f7/Reduce intron penalty.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/7ba019dbc48e9fba97ac820e258e887afa5535f7/https://sourceforge.net/p/sibsim4/code/ci/0cb43d2a430899e9b33510a3a84f691eed10de57/Merged changes from sim4 release 2002-03-03cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/0cb43d2a430899e9b33510a3a84f691eed10de57/https://sourceforge.net/p/sibsim4/code/ci/64f2cf45713f381ace5ba842da5064f04600736a/More merging from sim4 release 2002-03-03cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/64f2cf45713f381ace5ba842da5064f04600736a/https://sourceforge.net/p/sibsim4/code/ci/ae9c1fd16a381782854178c4384b4bc08858f444/Start work on sim4b1.c; only cleanups here.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/ae9c1fd16a381782854178c4384b4bc08858f444/https://sourceforge.net/p/sibsim4/code/ci/38fdf9a338c7a35bc49130684652529524447c1d/sim4b1.c: use qsort, remove couple global vars, remove couple functions.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/38fdf9a338c7a35bc49130684652529524447c1d/https://sourceforge.net/p/sibsim4/code/ci/577b3462d5273c8752db161f285ae14ec83de1f8/Use a different (simpler) MSP linking technique.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/577b3462d5273c8752db161f285ae14ec83de1f8/https://sourceforge.net/p/sibsim4/code/ci/71b7f500fffd2255f354834f9b7000d203ecae08/Fix bug in MSP linking...cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/71b7f500fffd2255f354834f9b7000d203ecae08/https://sourceforge.net/p/sibsim4/code/ci/ee39ec14f8bea55ece212a7a2cb6f2a4bf363a87/A bit more overlap tolerance in link_msps.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/ee39ec14f8bea55ece212a7a2cb6f2a4bf363a87/https://sourceforge.net/p/sibsim4/code/ci/d29cd1acc595821002566843107d8a834814bf57/Add combine_msps.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/d29cd1acc595821002566843107d8a834814bf57/https://sourceforge.net/p/sibsim4/code/ci/16b8423c8d71e45c7b080a7f1852e852acf7a11e/Fix bug in combine_msps.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/16b8423c8d71e45c7b080a7f1852e852acf7a11e/https://sourceforge.net/p/sibsim4/code/ci/5432ae6fb866e591da7146087a1138dfe1d4117e/Fix overlap bugs in combine_msps.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/5432ae6fb866e591da7146087a1138dfe1d4117e/https://sourceforge.net/p/sibsim4/code/ci/eda08bd1ec888431be72b975a16a16934b0f5a47/Fix more overlap bugs in combine_msps.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/eda08bd1ec888431be72b975a16a16934b0f5a47/https://sourceforge.net/p/sibsim4/code/ci/bfee252b9ebcc9af2baf3be6056f41895e49f0db/Fix initialization problem in link_msps.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/bfee252b9ebcc9af2baf3be6056f41895e49f0db/https://sourceforge.net/p/sibsim4/code/ci/364ba59ed93dbc7f3e7bbf6b0c5e1253a3cdb9e2/Started cleanup by removing EST_GEN stuff.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/364ba59ed93dbc7f3e7bbf6b0c5e1253a3cdb9e2/https://sourceforge.net/p/sibsim4/code/ci/8f9a5f9f07b52b091b6428228d33b48e9461685a/Remove unused AUXUTILS and STATS stuff.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/8f9a5f9f07b52b091b6428228d33b48e9461685a/https://sourceforge.net/p/sibsim4/code/ci/e29e8e9b25a3eec1a441388cb2bd393fcacfc579/Remove PipMaker stuff.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/e29e8e9b25a3eec1a441388cb2bd393fcacfc579/https://sourceforge.net/p/sibsim4/code/ci/443548e06a8f68f668dd92f940e8b72b699cc079/Removed useless VERSION file.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/443548e06a8f68f668dd92f940e8b72b699cc079/https://sourceforge.net/p/sibsim4/code/ci/f07ccd4ce1a57245f165dd3031ceb04744dedad3/Remove N option and cleanup local variables mess.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/f07ccd4ce1a57245f165dd3031ceb04744dedad3/https://sourceforge.net/p/sibsim4/code/ci/678c223ed32119d678a60355df8400ae7b49e318/Remove a bunch of useless misc functions. Use xmalloc and friends.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/678c223ed32119d678a60355df8400ae7b49e318/https://sourceforge.net/p/sibsim4/code/ci/83d24fc41ebaeb07693d1955505c7c2054c2586a/Dispose of relink.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/83d24fc41ebaeb07693d1955505c7c2054c2586a/https://sourceforge.net/p/sibsim4/code/ci/1a1d606394c4737fdc08c168d9846f625d3cd5eb/Fix usage message.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/1a1d606394c4737fdc08c168d9846f625d3cd5eb/https://sourceforge.net/p/sibsim4/code/ci/9b4cdb4a70b5b5dd066a4fea3dc6f9b674832ebf/Remove Xtend1.c Xtend1.h, and update fatal().cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/9b4cdb4a70b5b5dd066a4fea3dc6f9b674832ebf/https://sourceforge.net/p/sibsim4/code/ci/12fb0912a7be8627cf425f7009dc8db26f658002/Cleanup bld_table +1 mess. Harmonize encoding. Add debug output.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/12fb0912a7be8627cf425f7009dc8db26f658002/https://sourceforge.net/p/sibsim4/code/ci/5ec1547336b235f330328f8fa9058ae985c9e21e/Cleanup search() function.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/5ec1547336b235f330328f8fa9058ae985c9e21e/https://sourceforge.net/p/sibsim4/code/ci/ef197bd1d29a2b3b2c3abdbb7433df3506c82f65/Cleanup exon_cores() function.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/ef197bd1d29a2b3b2c3abdbb7433df3506c82f65/https://sourceforge.net/p/sibsim4/code/ci/06b9873c9f4c6e38e6e37ed3fb3f51344b3367f3/Cleanup DEBUG printout.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/06b9873c9f4c6e38e6e37ed3fb3f51344b3367f3/https://sourceforge.net/p/sibsim4/code/ci/373fa69f35aedb99a7982c42f7dbb8221751445b/Remove (seemingly) useless stats stuff.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/373fa69f35aedb99a7982c42f7dbb8221751445b/https://sourceforge.net/p/sibsim4/code/ci/3494b3eec7a98c9a65bf80e8c8d883d3ebcb818b/Fix exon merging.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/3494b3eec7a98c9a65bf80e8c8d883d3ebcb818b/https://sourceforge.net/p/sibsim4/code/ci/894e9d66bc88e088e83270fee81abbccbe237b7b/Kill is_DNA. Move add_word() to inline.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/894e9d66bc88e088e83270fee81abbccbe237b7b/https://sourceforge.net/p/sibsim4/code/ci/a307067e0d4289caecf63449d11920aca60068b8/Use new file reading stuff, and clean up junk.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/a307067e0d4289caecf63449d11920aca60068b8/https://sourceforge.net/p/sibsim4/code/ci/6fc8f8f8e2ab2dd47b439b947210cc39049f281e/Forgot to remove seq_read.c.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/6fc8f8f8e2ab2dd47b439b947210cc39049f281e/https://sourceforge.net/p/sibsim4/code/ci/249fd6addbbeaf35722aac014dff98d5b70ed177/Use tsearch and friends instead of lists in hash table.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/249fd6addbbeaf35722aac014dff98d5b70ed177/https://sourceforge.net/p/sibsim4/code/ci/dabb3183506e274a7d80cde16d67f7d80783217b/Fix a few leaks.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/dabb3183506e274a7d80cde16d67f7d80783217b/https://sourceforge.net/p/sibsim4/code/ci/47553ad4cfaa7a18c87fe9b4a1a056f57032fb5b/Cleanup, and localize some variables.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/47553ad4cfaa7a18c87fe9b4a1a056f57032fb5b/https://sourceforge.net/p/sibsim4/code/ci/341649cdcd4b3e0c3a4afe36ecb066cb53ded2d9/Remove unused dist parameter.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/341649cdcd4b3e0c3a4afe36ecb066cb53ded2d9/https://sourceforge.net/p/sibsim4/code/ci/dc5b4a19b001d8f879a2ee8c0e9322e807310fe4/Add debugging stuff.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/dc5b4a19b001d8f879a2ee8c0e9322e807310fe4/https://sourceforge.net/p/sibsim4/code/ci/dd1f28fea02627295a5ed71593159dfe7a13f3c4/Some work on call to extend_bw().cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/dd1f28fea02627295a5ed71593159dfe7a13f3c4/https://sourceforge.net/p/sibsim4/code/ci/6b3da1c05d8d370aeadf806f8ce1d965674d65d7/Handle case of extend_fw().cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/6b3da1c05d8d370aeadf806f8ce1d965674d65d7/https://sourceforge.net/p/sibsim4/code/ci/76e6b00d81460da2d9da40f44d13fb80c68e0c12/Remove unused stuff in sim4.h.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/76e6b00d81460da2d9da40f44d13fb80c68e0c12/https://sourceforge.net/p/sibsim4/code/ci/47d0867e558285026db6df66e69768c6e512333b/Msp_ptr -> msp_p_t.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/47d0867e558285026db6df66e69768c6e512333b/https://sourceforge.net/p/sibsim4/code/ci/a32594ec687cb0d03752d3fe51178f1a939a0183/Generalized collection type.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/a32594ec687cb0d03752d3fe51178f1a939a0183/https://sourceforge.net/p/sibsim4/code/ci/76e6b00d81460da2d9da40f44d13fb80c68e0c12/Remove unused stuff in sim4.h.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/76e6b00d81460da2d9da40f44d13fb80c68e0c12/https://sourceforge.net/p/sibsim4/code/ci/71f4a638a7eabbd8a0a7fe8645329b4f4cae5511/Fix exon freeing problem.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/71f4a638a7eabbd8a0a7fe8645329b4f4cae5511/https://sourceforge.net/p/sibsim4/code/ci/f8e45872068478939af4acc0cfe1573aa9d6fab5/Use exon collection instead of list. Misc cleanups.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/f8e45872068478939af4acc0cfe1573aa9d6fab5/https://sourceforge.net/p/sibsim4/code/ci/94cea0f96a77c0aed6ffbc6c33f7659e7881030d/A bit more debug output.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/94cea0f96a77c0aed6ffbc6c33f7659e7881030d/https://sourceforge.net/p/sibsim4/code/ci/fe09e133e082ddd1c5efb39913cf553766b5daaf/Fix stupid missing sizeof(type) multiplier in some memmove.cvs <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/fe09e133e082ddd1c5efb39913cf553766b5daaf/https://sourceforge.net/p/sibsim4/code/ci/05e2de817a4e1a8515f8fd074c1e43ee756da4e5/Use getopt to parse args. Add locale setting.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/05e2de817a4e1a8515f8fd074c1e43ee756da4e5/https://sourceforge.net/p/sibsim4/code/ci/9fdef768be371826964f49bf443166efda0748f7/Kill argv.[ch].chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/9fdef768be371826964f49bf443166efda0748f7/https://sourceforge.net/p/sibsim4/code/ci/d029404174211f78d578b2a309b195c91d2b6df7/Fix remaining fixed argv usage.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/d029404174211f78d578b2a309b195c91d2b6df7/https://sourceforge.net/p/sibsim4/code/ci/c75f6a167cc303b51062197ffa29cbe7307ce625/Change handling of polyA tails. No polyA report printed yet.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/c75f6a167cc303b51062197ffa29cbe7307ce625/https://sourceforge.net/p/sibsim4/code/ci/fdc98a5ec33da124226c8b9f9aa8a3842fd310b8/Minor cleanup on IA64.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/fdc98a5ec33da124226c8b9f9aa8a3842fd310b8/https://sourceforge.net/p/sibsim4/code/ci/847551ec29aaa50444689bb4dfb497cfbc537222/Remove exit(1) on some input.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/847551ec29aaa50444689bb4dfb497cfbc537222/https://sourceforge.net/p/sibsim4/code/ci/1a9e116c5d0079c10a82e227a39876af915fe9b2/Provide dummy tdestroy when there is no glibc.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/1a9e116c5d0079c10a82e227a39876af915fe9b2/https://sourceforge.net/p/sibsim4/code/ci/c8b20f037ddceaa35790d998022dd4e9eff31405/Better exon merging. Fix output for large DNA. Unsigned nitpicking. Trailing spaces nitpicking.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/c8b20f037ddceaa35790d998022dd4e9eff31405/https://sourceforge.net/p/sibsim4/code/ci/4638ee10c4cb614d1131e951a6c380601891fdfe/Do not create exons longer than the sequences.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/4638ee10c4cb614d1131e951a6c380601891fdfe/https://sourceforge.net/p/sibsim4/code/ci/df4a1c1a2893ed974f87f08ef8fe971f17ccc49e/Fix bug introduced in revision 1.56 of sim4b1.c.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/df4a1c1a2893ed974f87f08ef8fe971f17ccc49e/https://sourceforge.net/p/sibsim4/code/ci/2fd99822cbe2391bcf50aa9f3c20f023310549db/Output polyA info.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/2fd99822cbe2391bcf50aa9f3c20f023310549db/https://sourceforge.net/p/sibsim4/code/ci/b284e5961fc74fd6b610a6def55535ed01b4b01d/Add mcheck() and mtrace() in DEBUG mode.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/b284e5961fc74fd6b610a6def55535ed01b4b01d/https://sourceforge.net/p/sibsim4/code/ci/fffe3ae38c0042cc65419469f9749eb6d10ae7f4/Fix exon number bug in sim4b1.c. Fix error messages.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/fffe3ae38c0042cc65419469f9749eb6d10ae7f4/https://sourceforge.net/p/sibsim4/code/ci/48d9bf203969f173ed630df2182501c1663029f4/Changed sort order in msp_compare, to prepare for multi-hits.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/48d9bf203969f173ed630df2182501c1663029f4/https://sourceforge.net/p/sibsim4/code/ci/86fdb44a5ff4416429d0618b9fcb7a869a7523a7/Start changes to allow duplicated genes resolution. Fix edit_script types...chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/86fdb44a5ff4416429d0618b9fcb7a869a7523a7/https://sourceforge.net/p/sibsim4/code/ci/15d77404a1985b75ede514680d6c9156480ade4a/Fix uninitialized variable.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/15d77404a1985b75ede514680d6c9156480ade4a/https://sourceforge.net/p/sibsim4/code/ci/6d0077f5905186f4a4ff9baece2b7a26b596eae6/Fix decrement typo (bug).chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/6d0077f5905186f4a4ff9baece2b7a26b596eae6/https://sourceforge.net/p/sibsim4/code/ci/52a72dbfa526d67a353b684fb52806108d57a678/Prepare SIBsim4 package.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/52a72dbfa526d67a353b684fb52806108d57a678/https://sourceforge.net/p/sibsim4/code/ci/cfdb736a6d729db11b4ee9422af363c71779fb11/initial checkinroot <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/cfdb736a6d729db11b4ee9422af363c71779fb11/https://sourceforge.net/p/sibsim4/code/ci/3583d069c2018bf962b4612994e150407e1dc90b/Remove unused enum is sim4.h.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/3583d069c2018bf962b4612994e150407e1dc90b/https://sourceforge.net/p/sibsim4/code/ci/8e799ff22f0cdf1ad1e383d98ff013204ce1931c/Completed duplicated genes detection.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/8e799ff22f0cdf1ad1e383d98ff013204ce1931c/https://sourceforge.net/p/sibsim4/code/ci/3f1a0a269c68f613ac7c3d02969f98f69ed47481/Started duplicated gene detection.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/3f1a0a269c68f613ac7c3d02969f98f69ed47481/https://sourceforge.net/p/sibsim4/code/ci/abe9854229570a6186892a003d63e30e9b53725d/Fix thinko in length calculation.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/abe9854229570a6186892a003d63e30e9b53725d/https://sourceforge.net/p/sibsim4/code/ci/4168c66e3baf41ca5cfdad108a75687bdc4ead12/Fix stupid variable name overlap.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/4168c66e3baf41ca5cfdad108a75687bdc4ead12/https://sourceforge.net/p/sibsim4/code/ci/8195c0b6a097bd32f17284c0968917590f1a7822/Fix off by 1 in seq header setup.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/8195c0b6a097bd32f17284c0968917590f1a7822/https://sourceforge.net/p/sibsim4/code/ci/d5294a64e0384f1e4ed4bdbe9ef7ac8b5d523067/Add missing check when looking for more tail exons.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/d5294a64e0384f1e4ed4bdbe9ef7ac8b5d523067/https://sourceforge.net/p/sibsim4/code/ci/229ea92de3802808f078076bf1be35ced6c37cb6/Fix parameter swap in call to exon_cores().chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/229ea92de3802808f078076bf1be35ced6c37cb6/https://sourceforge.net/p/sibsim4/code/ci/b379c3735084109670257c6e3d98d4c813906258/Add missing check when looking for more head exons.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/b379c3735084109670257c6e3d98d4c813906258/https://sourceforge.net/p/sibsim4/code/ci/a445dc56b0247474bbe2a07774a025279fff8ab1/Remove useless error message.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/a445dc56b0247474bbe2a07774a025279fff8ab1/https://sourceforge.net/p/sibsim4/code/ci/7b7351ed86ba6f03feef6ccb00f0dcb7138fa6f5/Print only the better matches.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/7b7351ed86ba6f03feef6ccb00f0dcb7138fa6f5/https://sourceforge.net/p/sibsim4/code/ci/ab507002266598ea14dc39fa5ddb4f764743d0d5/Properly handle unsigned comparison.chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/ab507002266598ea14dc39fa5ddb4f764743d0d5/https://sourceforge.net/p/sibsim4/code/ci/90ffdd6e9c89844e02525b00071a3b506773323c/Add man page. Fix usage info.c4chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/90ffdd6e9c89844e02525b00071a3b506773323c/https://sourceforge.net/p/sibsim4/code/ci/c40b95d4e747769c6f03e42aea27456edfbc6fad/This commit was manufactured by cvs2svn to create tag 'SIBsim4_0_5'.c4chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/c40b95d4e747769c6f03e42aea27456edfbc6fad/https://sourceforge.net/p/sibsim4/code/ci/e2ebb0098a409467c3c2c5bee7943cc183dcc530/Create htdocs module.c4chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/e2ebb0098a409467c3c2c5bee7943cc183dcc530/https://sourceforge.net/p/sibsim4/code/ci/0d5561cbdd11a1dbdd974d846729248eb24c511b/This commit was manufactured by cvs2svn to create tag 'start'.c4chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/0d5561cbdd11a1dbdd974d846729248eb24c511b/https://sourceforge.net/p/sibsim4/code/ci/bb6b6e24e82de74cd559458cdd36483608dad11d/Add links to manpage and changes.c4chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/bb6b6e24e82de74cd559458cdd36483608dad11d/https://sourceforge.net/p/sibsim4/code/ci/251ed3077a4507795dbd7d4394554fd8896d7744/Add initial release info.c4chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/251ed3077a4507795dbd7d4394554fd8896d7744/https://sourceforge.net/p/sibsim4/code/ci/4cdc9a997197ad2b057d82d46d29373dbb2fc179/Replace col_t with collec_t, as col_t is used in AIX.c4chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/4cdc9a997197ad2b057d82d46d29373dbb2fc179/https://sourceforge.net/p/sibsim4/code/ci/6e86bd332dd3a7ac188e7b665e6ce1ab023b2b5b/Cleanup leftover memory alloc stuff.c4chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/6e86bd332dd3a7ac188e7b665e6ce1ab023b2b5b/https://sourceforge.net/p/sibsim4/code/ci/3da0af22936d39ee573ffa2a99bb7c3f4e00adbe/Instrument for a bit more debugging output.c4chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/3da0af22936d39ee573ffa2a99bb7c3f4e00adbe/https://sourceforge.net/p/sibsim4/code/ci/3299d1b810f52389c9dc732e36b55317a628f7df/Cleanup.c4chris <>Mon, 23 Jul 2018 13:15:34 -0000https://sourceforge.net/p/sibsim4/code/ci/3299d1b810f52389c9dc732e36b55317a628f7df/