| 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 |
| 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 |
