| 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 |
| 118f8cc | Matthew Hartfield | 06 January 2016, 20:06:06 UTC | New paired GC routine; coalescence by parts | 06 January 2016, 20:06:06 UTC |
| 154aee6 | Matthew Hartfield | 05 January 2016, 22:28:07 UTC | Updated GC routine if acting on paired samples | 05 January 2016, 22:28:07 UTC |
| 5dac079 | Matthew Hartfield | 05 January 2016, 19:11:02 UTC | Fixed gc errors where first event started at beginning of sample | 05 January 2016, 19:11:02 UTC |
| a2260ed | Matthew Hartfield | 05 January 2016, 16:05:20 UTC | Fixed further alignment bugs with gene conversion | 05 January 2016, 16:05:20 UTC |
| 46e7041 | Matthew Hartfield | 04 January 2016, 22:30:34 UTC | Fixed some bugs with inserting new GC breakpoints | 04 January 2016, 22:30:34 UTC |
| c084d66 | Matthew Hartfield | 15 December 2015, 16:14:41 UTC | Last commit before Christmas? | 15 December 2015, 16:14:41 UTC |
| fe95f75 | Matthew Hartfield | 15 December 2015, 09:31:21 UTC | Altered gc routine for single-strand breaks | 15 December 2015, 09:31:21 UTC |
| d8c4dc1 | Matthew Hartfield | 14 December 2015, 17:15:49 UTC | End of Mon | 14 December 2015, 17:15:49 UTC |
| b4c9e95 | Matthew Hartfield | 14 December 2015, 16:02:30 UTC | Fixed init error with rec = 0, gc > 0 | 14 December 2015, 16:02:30 UTC |
| f6760d4 | Matthew Hartfield | 14 December 2015, 15:52:07 UTC | Fixed (a) probability of GC; (b) assignment of GC event to WH/BH | 14 December 2015, 15:52:07 UTC |
| 944213d | Matthew Hartfield | 14 December 2015, 13:26:52 UTC | Fixed assignment bugs with gene conversion code | 14 December 2015, 13:26:52 UTC |
| c501de6 | Matthew Hartfield | 11 December 2015, 17:10:26 UTC | Added Gene Conv routine, UNTESTED | 11 December 2015, 17:10:26 UTC |
| 2debb54 | Matthew Hartfield | 04 December 2015, 22:19:01 UTC | No new bp if rec'ing in trapped material - seems to match with MS | 04 December 2015, 22:19:01 UTC |
| 40f426d | Matthew Hartfield | 01 December 2015, 16:30:31 UTC | Fixed tracking bug if only bp at end of tract | 01 December 2015, 16:30:31 UTC |
| d274d94 | Matthew Hartfield | 30 November 2015, 22:20:59 UTC | Fixed small bug in reccal where coalesced/absent areas overlap | 30 November 2015, 22:20:59 UTC |
| 3b6f099 | Matthew Hartfield | 27 November 2015, 22:27:55 UTC | End of Fri commut | 27 November 2015, 22:27:55 UTC |
| c5a1f3b | Matthew Hartfield | 27 November 2015, 15:45:20 UTC | Tweaked calculation of valid sites in reccal routine | 27 November 2015, 15:45:20 UTC |
| d0a6758 | Matthew Hartfield | 26 November 2015, 22:23:04 UTC | Tweaked check of valid breakpoint routine | 26 November 2015, 22:23:04 UTC |
| a3b6925 | Matthew Hartfield | 24 November 2015, 15:53:43 UTC | Fixed bug with space alloc for mut tab. First testable rec program? | 24 November 2015, 15:53:43 UTC |
| e6c6e84 | Matthew Hartfield | 23 November 2015, 22:20:18 UTC | End of Mon commit | 23 November 2015, 22:20:18 UTC |
| e9fb09a | Matthew Hartfield | 23 November 2015, 19:21:09 UTC | Fixed error: bp check at start of genome | 23 November 2015, 19:21:09 UTC |
| 70589d5 | Matthew Hartfield | 23 November 2015, 18:43:55 UTC | Fixed error choosing bp if at end of genome | 23 November 2015, 18:43:55 UTC |
| b2fe849 | Matthew Hartfield | 23 November 2015, 17:03:22 UTC | More bugfix, especially when determining bp with some tracts coalesced | 23 November 2015, 17:03:22 UTC |
| 60da893 | Matthew Hartfield | 20 November 2015, 22:39:02 UTC | Fixed error choosing right bp; checking non-rec regions when splitting by sex | 20 November 2015, 22:39:02 UTC |
| af7469f | Matthew Hartfield | 20 November 2015, 20:51:50 UTC | Fixed further rec errors and issue with table realloc | 20 November 2015, 20:51:50 UTC |
| c380019 | Matthew Hartfield | 20 November 2015, 19:03:02 UTC | More misc fixing of rec issues | 20 November 2015, 19:03:02 UTC |
| 69c7b0d | Matthew Hartfield | 20 November 2015, 17:19:22 UTC | Fixed misc bugs in rec routine | 20 November 2015, 17:19:22 UTC |
| aff88f9 | Matthew Hartfield | 19 November 2015, 22:49:40 UTC | Fixed bugs with rec routine, updating tracts following coalescence. | 19 November 2015, 22:49:40 UTC |
| 30544f1 | Matthew Hartfield | 19 November 2015, 22:49:30 UTC | Fixed bugs with rec routine, updating tracts following coalescence. | 19 November 2015, 22:49:30 UTC |
| 89deab0 | Matthew Hartfield | 18 November 2015, 20:03:28 UTC | First testing, fixed misc bugs. Need to redo rec checking and bp adding | 18 November 2015, 20:03:28 UTC |
| 1598b55 | Matthew Hartfield | 18 November 2015, 16:55:49 UTC | Altered code to account for varying number of samples (due to recombination) | 18 November 2015, 16:55:49 UTC |
| 8e98878 | Matthew Hartfield | 17 November 2015, 22:27:05 UTC | Added Printout for Trees | 17 November 2015, 22:27:05 UTC |
| 1a0c28e | Matthew Hartfield | 17 November 2015, 20:43:42 UTC | Added reccal routine and dynamic allocation of tables. Need to adjust adding mutants for multiple sites | 17 November 2015, 20:43:42 UTC |
| ec7c34d | Matthew Hartfield | 17 November 2015, 15:42:05 UTC | Added first go of rec part of coalescent routine | 17 November 2015, 15:42:05 UTC |
| ba19c22 | Matthew Hartfield | 16 November 2015, 16:52:33 UTC | Started introducting rec into coalescent routine. Fixing of small errors (isall functions) | 16 November 2015, 16:52:33 UTC |
| 6c4d51d | Matthew Hartfield | 13 November 2015, 21:02:47 UTC | Working version of 1-site program! Corrected bug in filename assignments for large no. reps | 13 November 2015, 21:02:47 UTC |
| 8d7bb25 | Matthew Hartfield | 13 November 2015, 18:09:53 UTC | Implemented dynamic mutation tables; fixed bug in case 3 resolution II | 13 November 2015, 18:09:53 UTC |
| d0d57d8 | Matthew Hartfield | 13 November 2015, 18:08:46 UTC | Implemented dynamic mutation tables; fixed bug in case 3 resolution | 13 November 2015, 18:08:46 UTC |
| 10e1b43 | Matthew Hartfield | 12 November 2015, 22:57:43 UTC | Created dynamic strings for trees; tried re-implementing dynamic mutation table | 12 November 2015, 22:57:43 UTC |
| c073eb7 | Matthew Hartfield | 12 November 2015, 22:55:19 UTC | Created dynamic strings for trees; tried re-implementing dynamic mutation table | 12 November 2015, 22:55:19 UTC |
| 01b2d69 | Matthew Hartfield | 06 November 2015, 22:29:25 UTC | End of Fri commit | 06 November 2015, 22:29:25 UTC |
| 87c40d9 | Matthew Hartfield | 06 November 2015, 20:18:27 UTC | Fixed bug with case 1 reassigning indv numbers | 06 November 2015, 20:18:27 UTC |
| 6679cc8 | Matthew Hartfield | 06 November 2015, 17:01:02 UTC | Fixed issue with sampling split indvs (event 3) | 06 November 2015, 17:01:02 UTC |
| 2cc17cb | Matthew Hartfield | 05 November 2015, 22:12:52 UTC | Fixed probelem with choosing samples from pairs | 05 November 2015, 22:12:52 UTC |
| 7163ac8 | Matthew Hartfield | 03 November 2015, 21:57:59 UTC | Made small correction in coalesce routine with two pairs | 03 November 2015, 21:57:59 UTC |
| bebe5ef | Matthew Hartfield | 03 November 2015, 20:56:44 UTC | First complete non-rec program; issues with low rates of sex? Need to resort indv table properly? | 03 November 2015, 20:56:44 UTC |
| 75bb0bd | Matthew Hartfield | 02 November 2015, 22:27:39 UTC | End of Mon, fixed mutation rate input, tested | 02 November 2015, 22:27:39 UTC |
| 7138391 | Matthew Hartfield | 02 November 2015, 20:50:52 UTC | First draft of treemaker; need to add dynamic mem allocation for MTree | 02 November 2015, 20:50:52 UTC |
| 9585162 | Matthew Hartfield | 02 November 2015, 18:34:13 UTC | Halfway through new Treemaker routine | 02 November 2015, 18:34:13 UTC |
| 618109d | Matthew Hartfield | 30 October 2015, 20:55:36 UTC | End of Fri, slight work on Treemaker | 30 October 2015, 20:55:36 UTC |
| 4a51217 | Matthew Hartfield | 29 October 2015, 21:50:14 UTC | End of Thur: created ancestry table and started treemaker routine | 29 October 2015, 21:50:14 UTC |
| d9771bf | Matthew Hartfield | 29 October 2015, 18:41:01 UTC | Tested two-sample coalescent times. About to add treemaker routine. | 29 October 2015, 18:41:01 UTC |
| 52f6e25 | Matthew Hartfield | 28 October 2015, 22:29:33 UTC | End of day: implemented sort, tested sampling procedures | 28 October 2015, 22:29:33 UTC |
| f53f88f | Matthew Hartfield | 28 October 2015, 18:43:56 UTC | Finished 'coalesced' routine and sex sampling - what about table sorting? | 28 October 2015, 18:43:56 UTC |
| 81a7664 | Matthew Hartfield | 28 October 2015, 16:05:27 UTC | Coded up to event 7 | 28 October 2015, 16:05:27 UTC |
| b2cabaa | Matthew Hartfield | 28 October 2015, 15:02:44 UTC | More updates on Coalescent events (up to ev 5) | 28 October 2015, 15:02:44 UTC |
| 50bbd20 | Matthew Hartfield | 27 October 2015, 21:24:46 UTC | End of Tue commit | 27 October 2015, 21:24:46 UTC |
| 2887ad7 | Matthew Hartfield | 27 October 2015, 20:51:33 UTC | Added event 2 code: added coalescent update routines | 27 October 2015, 20:51:33 UTC |
| ff33e0d | Matthew Hartfield | 27 October 2015, 19:02:21 UTC | Fixed bug when calculating prob no sex events | 27 October 2015, 19:02:21 UTC |
| e07106c | Matthew Hartfield | 27 October 2015, 16:05:33 UTC | Slow updates to coalescent routine; added events 0,1 | 27 October 2015, 16:05:33 UTC |
| ccf6f90 | Matthew Hartfield | 26 October 2015, 19:52:50 UTC | Started to implement coalescent code; functions for creating subtables | 26 October 2015, 19:52:50 UTC |
| 3c59c95 | Matthew Hartfield | 26 October 2015, 18:54:44 UTC | Added event choosing; changing of sample numbers depending on state | 26 October 2015, 18:54:44 UTC |
| ad0d259 | Matthew Hartfield | 26 October 2015, 14:49:54 UTC | Added first event selection; fixed prob calculation routine | 26 October 2015, 14:49:54 UTC |
| 9bbeecf | Matthew Hartfield | 23 October 2015, 20:19:30 UTC | Added more init code | 23 October 2015, 20:19:30 UTC |
| 13415ba | Matthew Hartfield | 23 October 2015, 15:55:43 UTC | Added tables setup (to be tested) | 23 October 2015, 15:55:43 UTC |
| ce5d825 | Matthew Hartfield | 22 October 2015, 21:42:09 UTC | Added HUGE_VALF - need to double-check if works? | 22 October 2015, 21:42:09 UTC |
| 4b71a38 | Matthew Hartfield | 22 October 2015, 21:39:22 UTC | Added more code, up to rate change definition | 22 October 2015, 21:39:22 UTC |
| b3db6e0 | Matthew Hartfield | 22 October 2015, 18:56:44 UTC | Program initialisation in place, tested | 22 October 2015, 18:56:44 UTC |
| 3b1a54a | Matthew Hartfield | 22 October 2015, 17:51:14 UTC | My first commit | 22 October 2015, 17:51:14 UTC |
