| 7895d6a | Matthew Hartfield | 11 August 2018, 05:46:52 UTC | Updated README | 11 August 2018, 05:46:52 UTC |
| 5dc1693 | Matthew Hartfield | 11 August 2018, 05:45:46 UTC | Updated README | 11 August 2018, 05:45:46 UTC |
| eeda2a8 | Matthew Hartfield | 09 August 2018, 12:33:39 UTC | Updated citation in manual | 09 August 2018, 12:33:39 UTC |
| d1cd7ed | Matthew Hartfield | 14 June 2018, 11:13:07 UTC | Commit before June upload | 14 June 2018, 11:13:07 UTC |
| d9dbc6f | Matthew Hartfield | 14 June 2018, 11:08:55 UTC | Commit before June upload | 14 June 2018, 11:08:55 UTC |
| 73bea32 | Matthew Hartfield | 11 June 2018, 15:59:06 UTC | Commit before June upload | 11 June 2018, 15:59:06 UTC |
| cebaf68 | Matthew Hartfield | 11 June 2018, 05:40:59 UTC | Altered few comments | 11 June 2018, 05:40:59 UTC |
| 6c198fa | Matthew Hartfield | 07 May 2018, 14:34:39 UTC | Restored old FSC program | 07 May 2018, 14:34:39 UTC |
| eeaeb68 | Matthew Hartfield | 07 May 2018, 11:25:13 UTC | Used non-Q version of complete GC probability for all cases, even NSites > 1 | 07 May 2018, 11:25:13 UTC |
| 94436ba | Matthew Hartfield | 07 May 2018, 09:59:36 UTC | Fixed complete GC calculation for L = 1 | 07 May 2018, 09:59:36 UTC |
| 9bb603a | Matthew Hartfield | 03 May 2018, 09:40:37 UTC | Removed foctor of two in mitotic rec probability | 03 May 2018, 09:40:37 UTC |
| 63ec93a | Matthew Hartfield | 30 April 2018, 11:06:25 UTC | Streamlined reccalx for esex > 1 | 30 April 2018, 11:06:25 UTC |
| 84a4ff9 | Matthew Hartfield | 30 April 2018, 09:50:33 UTC | Fixed reccalx routine after >1 sex events | 30 April 2018, 09:50:33 UTC |
| 877ba54 | Matthew Hartfield | 25 April 2018, 15:50:01 UTC | Fixed issue with accounting for non-anc segment in mitotic rec routine | 25 April 2018, 15:50:01 UTC |
| ab8e00c | Matthew Hartfield | 23 April 2018, 15:57:58 UTC | First attempt at fixing weird mit rec issue | 23 April 2018, 15:57:58 UTC |
| f7107d9 | Matthew Hartfield | 23 April 2018, 15:48:33 UTC | Commit just after finding out that mitotic rec can REMOVE paired samples by placing all extant material on same background. Need to work out best way to account for this particular book-keeping quirk | 23 April 2018, 15:48:33 UTC |
| a40143b | Matthew Hartfield | 23 April 2018, 14:52:16 UTC | First commit of separate FSC with mitotic rec; after fixing reccalx bug | 23 April 2018, 14:52:16 UTC |
| 1ba7e22 | Matthew Hartfield | 20 April 2018, 13:30:01 UTC | Reversion to March version | 20 April 2018, 13:30:01 UTC |
| 8630ff6 | Matthew Hartfield | 05 April 2018, 14:19:09 UTC | Fixed reccalX error due to unsorted sex events | 05 April 2018, 14:19:09 UTC |
| 45b1cc5 | Matthew Hartfield | 05 April 2018, 14:18:55 UTC | Fixed reccalX error due to unsorted sex events | 05 April 2018, 14:18:55 UTC |
| 4ba4942 | Matthew Hartfield | 05 April 2018, 13:12:49 UTC | Removing unused variables from code | 05 April 2018, 13:12:49 UTC |
| 1fbb162 | Matthew Hartfield | 05 April 2018, 11:43:00 UTC | Fixed mis-match between count2 and no. of sex events in reccalx | 05 April 2018, 11:43:00 UTC |
| 763ded8 | Matthew Hartfield | 04 April 2018, 14:08:19 UTC | Fixed bug in adding ghost sample after mitotic recombination event | 04 April 2018, 14:08:19 UTC |
| 73279de | Matthew Hartfield | 04 April 2018, 13:16:01 UTC | Fixed creating ghost sample under mitotic rec | 04 April 2018, 13:16:01 UTC |
| 12970a7 | Matthew Hartfield | 04 April 2018, 11:09:48 UTC | Fixed probability calculation for mitotic rec | 04 April 2018, 11:09:48 UTC |
| 8f4ba77 | Matthew Hartfield | 04 April 2018, 10:00:28 UTC | Fixed bugs in reccalx book-keeping | 04 April 2018, 10:00:28 UTC |
| 1a50b3a | Matthew Hartfield | 04 April 2018, 09:13:05 UTC | Minor bugfixes before testing mitotic rec coutine | 04 April 2018, 09:13:05 UTC |
| 182d0a0 | Matthew Hartfield | 28 March 2018, 07:58:01 UTC | Added mitotic rec routine to coalesce function | 28 March 2018, 07:58:01 UTC |
| 0980b81 | Matthew Hartfield | 27 March 2018, 15:01:52 UTC | First updates to implement mitotic recombination | 27 March 2018, 15:01:52 UTC |
| abf11cd | Matthew Hartfield | 14 February 2018, 10:18:41 UTC | Updated error reporting functions, more details given (number of samples at exit) | 14 February 2018, 10:18:41 UTC |
| 4bc700d | Matthew Hartfield | 13 December 2017, 09:09:16 UTC | Updated README | 13 December 2017, 09:09:16 UTC |
| e95133b | Matthew Hartfield | 13 December 2017, 09:08:05 UTC | Updated manual | 13 December 2017, 09:08:05 UTC |
| 966e37d | Matthew Hartfield | 12 December 2017, 14:35:00 UTC | Updated Manual | 12 December 2017, 14:35:00 UTC |
| c960eb9 | Matthew Hartfield | 11 December 2017, 15:02:27 UTC | Updated README | 11 December 2017, 15:02:27 UTC |
| 0b24bf3 | Matthew Hartfield | 11 December 2017, 13:15:31 UTC | About to submit online | 11 December 2017, 13:15:31 UTC |
| 23ca857 | Matthew Hartfield | 11 December 2017, 13:07:36 UTC | Modified README | 11 December 2017, 13:07:36 UTC |
| 72c3b58 | Matthew Hartfield | 11 December 2017, 13:07:23 UTC | Modified README | 11 December 2017, 13:07:23 UTC |
| 6bc0d21 | Matthew Hartfield | 11 December 2017, 12:52:51 UTC | Commit before uploading | 11 December 2017, 12:52:51 UTC |
| 40ff3b4 | Matthew Hartfield | 11 December 2017, 12:49:06 UTC | Commit before uploading | 11 December 2017, 12:49:06 UTC |
| df73cef | Matthew Hartfield | 11 December 2017, 12:46:37 UTC | Delete README.md | 11 December 2017, 12:46:37 UTC |
| 2fd000c | Matthew Hartfield | 11 December 2017, 12:40:01 UTC | Last commit before uploading | 11 December 2017, 12:40:01 UTC |
| ef87d76 | Matthew Hartfield | 11 December 2017, 11:30:42 UTC | Updated README; added user documentation | 11 December 2017, 11:30:42 UTC |
| b163e7b | Matthew Hartfield | 11 December 2017, 11:22:20 UTC | Added code header | 11 December 2017, 11:22:20 UTC |
| c2242d3 | Matthew Hartfield | 11 December 2017, 11:17:59 UTC | Initial commit | 11 December 2017, 11:17:59 UTC |
| 05e333a | Matthew Hartfield | 11 December 2017, 11:00:37 UTC | Remove outdated annotations | 11 December 2017, 11:00:37 UTC |
| 931a119 | Matthew Hartfield | 22 June 2017, 13:04:41 UTC | Added option to print out table of coalescent times per segment | 22 June 2017, 13:04:41 UTC |
| 696bd0e | Matthew Hartfield | 17 May 2017, 11:14:19 UTC | Fixed GC bug, 2bp end point MUST be different from start point | 17 May 2017, 11:14:19 UTC |
| b10d9c2 | Matthew Hartfield | 04 May 2017, 15:25:05 UTC | Fixed bug in new 2-bp GC routine | 04 May 2017, 15:25:05 UTC |
| 423892c | Matthew Hartfield | 03 May 2017, 09:43:41 UTC | Rewrote two-part GC, end point conditional on start point | 03 May 2017, 09:43:41 UTC |
| fcb06b6 | Matthew Hartfield | 02 May 2017, 09:07:28 UTC | Implemented Wiuf and Hein 2bp GC calculation | 02 May 2017, 09:07:28 UTC |
| 14c5e50 | Matthew Hartfield | 18 April 2017, 09:43:46 UTC | Included factors of 2 in paired GC routines | 18 April 2017, 09:43:46 UTC |
| 11a8670 | Matthew Hartfield | 22 February 2017, 20:26:19 UTC | Rewrote GC routine to remove reliance on CDFs - still working on low-site simulations | 22 February 2017, 20:26:19 UTC |
| 04c50f3 | Matthew Hartfield | 20 February 2017, 16:58:21 UTC | Updated code to scale GC by number of breakpoints, NOT number of sites. Removed junk code | 20 February 2017, 16:58:21 UTC |
| e30b579 | Matthew Hartfield | 09 November 2016, 19:11:50 UTC | Updated MS style printout to include command line input | 09 November 2016, 19:11:50 UTC |
| 151f61f | Matthew Hartfield | 25 July 2016, 13:36:48 UTC | Fixed code to account for ob sex properly | 25 July 2016, 13:36:48 UTC |
| f1d39c2 | Matthew Hartfield | 13 July 2016, 14:09:42 UTC | Rewrote rec routine, streamlined choosing samples/sites | 13 July 2016, 14:09:42 UTC |
| 749ad8c | Matthew Hartfield | 10 June 2016, 19:44:19 UTC | Increased memory allocated to tree printout | 10 June 2016, 19:44:19 UTC |
| ec1b7d4 | Matthew Hartfield | 08 June 2016, 20:44:11 UTC | Then tidied up code. Again | 08 June 2016, 20:44:11 UTC |
| 7bfc3e4 | Matthew Hartfield | 08 June 2016, 20:36:37 UTC | Then tidied up code | 08 June 2016, 20:36:37 UTC |
| 5d49f15 | Matthew Hartfield | 08 June 2016, 20:34:39 UTC | Updated pruning of old samps routine for WH case | 08 June 2016, 20:34:39 UTC |
| 3ff8e89 | Matthew Hartfield | 08 June 2016, 20:34:10 UTC | Updated pruning of old samps routine for WH case | 08 June 2016, 20:34:10 UTC |
| ca49028 | Matthew Hartfield | 07 June 2016, 17:19:27 UTC | Major rewrite: made coal'ed material ancestral, tidied code | 07 June 2016, 17:19:27 UTC |
| 7caa6e5 | Matthew Hartfield | 01 June 2016, 14:01:45 UTC | Fixed issue with mitotic GC only occurring over 1 site | 01 June 2016, 14:01:45 UTC |
| e691953 | Matthew Hartfield | 31 May 2016, 16:00:10 UTC | Fixed minor bug, printing out trees with no rec | 31 May 2016, 16:00:10 UTC |
| 0422201 | Matthew Hartfield | 27 May 2016, 20:33:37 UTC | Added 'burst' of mutations, clustering of SNPs | 27 May 2016, 20:33:37 UTC |
| a0d8655 | Matthew Hartfield | 17 May 2016, 14:45:22 UTC | Rewrote rec routine to implement weighted sampling due to extant breakpoints | 17 May 2016, 14:45:22 UTC |
| 98b9cce | Matthew Hartfield | 08 May 2016, 13:46:04 UTC | Major rewrite of GC routine, accurately account for edge effects | 08 May 2016, 13:46:04 UTC |
| 4170c9f | Matthew Hartfield | 28 April 2016, 17:37:41 UTC | Fixed GC bug, going right-to-left and new BPs created | 28 April 2016, 17:37:41 UTC |
| 4ca60a8 | Matthew Hartfield | 19 April 2016, 22:50:21 UTC | Added extra error printout when sum of probs exceeds 1 | 19 April 2016, 22:50:21 UTC |
| 0adaad3 | Matthew Hartfield | 21 March 2016, 13:44:28 UTC | New error reporting if excessively high rec rates 2 | 21 March 2016, 13:44:28 UTC |
| d84dbc4 | Matthew Hartfield | 21 March 2016, 13:44:08 UTC | New error reporting if excessively high rec rates | 21 March 2016, 13:44:08 UTC |
| f5706b2 | Matthew Hartfield | 14 March 2016, 19:17:20 UTC | Tidied up some command inits | 14 March 2016, 19:17:20 UTC |
| 9e5d74d | Matthew Hartfield | 14 March 2016, 15:34:41 UTC | Made mutation rate optional | 14 March 2016, 15:34:41 UTC |
| f640263 | Matthew Hartfield | 11 March 2016, 20:41:24 UTC | Cleaned up inputs with heterogeneous sex | 11 March 2016, 20:41:24 UTC |
| 181eeee | Matthew Hartfield | 11 March 2016, 15:33:58 UTC | Cleaned up file output (deletes files from old runs) | 11 March 2016, 15:33:58 UTC |
| 7570316 | Matthew Hartfield | 10 March 2016, 20:59:21 UTC | Added option to print out data, MS style | 10 March 2016, 20:59:21 UTC |
| 47a2f0d | Matthew Hartfield | 03 March 2016, 18:07:07 UTC | Implemented new GC calculations | 03 March 2016, 18:07:07 UTC |
| f581d12 | Matthew Hartfield | 01 March 2016, 22:34:13 UTC | Altered GC routine, less picky over choosing breakpoints | 01 March 2016, 22:34:13 UTC |
| 42f414a | Matthew Hartfield | 26 February 2016, 19:36:18 UTC | Further refining and fixing of parameter input | 26 February 2016, 19:36:18 UTC |
| acef496 | Matthew Hartfield | 26 February 2016, 18:39:36 UTC | Added usage table when error occurs | 26 February 2016, 18:39:36 UTC |
| edc2228 | Matthew Hartfield | 26 February 2016, 17:04:07 UTC | Implemented new command-line interface; need to test | 26 February 2016, 17:04:07 UTC |
| a702bd8 | Matthew Hartfield | 25 February 2016, 20:14:19 UTC | Introduced different GC types (mitotic, meiotic) | 25 February 2016, 20:14:19 UTC |
| 1a56328 | Matthew Hartfield | 24 February 2016, 21:05:37 UTC | Fixed errors with rescaling small GC events in non-anc material | 24 February 2016, 21:05:37 UTC |
| 4653949 | Matthew Hartfield | 24 February 2016, 19:57:49 UTC | Further refining, fixed rescaling of GC parameter with multiple demes | 24 February 2016, 19:57:49 UTC |
| f512dfe | Matthew Hartfield | 23 February 2016, 22:15:10 UTC | Added modifications to rec/GC, created paired samples after event | 23 February 2016, 22:15:10 UTC |
| 605c679 | Matthew Hartfield | 21 January 2016, 22:08:15 UTC | Re-added Complete GC event, changed GC/nsites scaling to fit | 21 January 2016, 22:08:15 UTC |
| 2b56070 | Matthew Hartfield | 18 January 2016, 20:12:11 UTC | Fixed errors with partial GC coal and truncating up to coaled segments | 18 January 2016, 20:12:11 UTC |
| 7bc29e4 | Matthew Hartfield | 15 January 2016, 20:09:14 UTC | Altered rate of GC to account for events starting outside tract | 15 January 2016, 20:09:14 UTC |
| 6f77915 | Matthew Hartfield | 12 January 2016, 16:56:30 UTC | Further check of end GC in coalesced material | 12 January 2016, 16:59:46 UTC |
| 3943d20 | Matthew Hartfield | 11 January 2016, 22:20:08 UTC | Refining previous change | 11 January 2016, 22:20:08 UTC |
| 2967332 | Matthew Hartfield | 11 January 2016, 22:04:39 UTC | Added check so that end of gc does not occur in coalesced material | 11 January 2016, 22:04:39 UTC |
| d8b2973 | Matthew Hartfield | 11 January 2016, 20:07:49 UTC | Commiting now because I think it is close to done | 11 January 2016, 20:07:49 UTC |
| c232a59 | Matthew Hartfield | 11 January 2016, 15:57:22 UTC | Updated memory assignment, fixed errors with multiple bps added | 11 January 2016, 15:57:22 UTC |
| a5a127a | Matthew Hartfield | 11 January 2016, 15:26:26 UTC | New reassignment of coalesced material - easier to account for partial coalescence | 11 January 2016, 15:26:26 UTC |
| ee65f1d | Matthew Hartfield | 08 January 2016, 22:33:28 UTC | End of Friday 8th jan commit | 08 January 2016, 22:33:28 UTC |
| 0de292b | Matthew Hartfield | 08 January 2016, 20:11:26 UTC | New implementation of GC coal routine; coal'ed samples become non-anc | 08 January 2016, 20:11:26 UTC |
| 4edc16c | Matthew Hartfield | 08 January 2016, 20:06:04 UTC | New implementation of GC coal routine; coal'ed samples become non-anc | 08 January 2016, 20:06:04 UTC |
| e76c4eb | Matthew Hartfield | 07 January 2016, 21:38:54 UTC | Fixed cases where coalesced material swapped within individuals | 07 January 2016, 21:38:54 UTC |
| f5a6d0d | Matthew Hartfield | 07 January 2016, 16:40:50 UTC | Fixed GC bugs (1) inserting new max bp (2) swapping material in partially-coalesced regions | 07 January 2016, 16:40:50 UTC |
| 4576339 | Matthew Hartfield | 06 January 2016, 22:35:56 UTC | Testing of new routine to consider part coalescence with GC | 06 January 2016, 22:35:56 UTC |
