| 077651b | andrewjpage | 26 July 2013, 10:46:35 UTC | redundant get opt removed from fastml | 26 July 2013, 10:46:35 UTC |
| 1844cf1 | andrewjpage | 18 July 2013, 15:19:38 UTC | tests for reinserting gaps into sequence | 18 July 2013, 15:19:38 UTC |
| aacddf3 | andrewjpage | 17 July 2013, 09:58:49 UTC | test tree manipulation | 17 July 2013, 09:58:49 UTC |
| ad10510 | andrewjpage | 17 July 2013, 09:07:20 UTC | split tests into separate files | 17 July 2013, 09:07:20 UTC |
| d887a92 | andrewjpage | 16 July 2013, 13:48:26 UTC | tests for generating filenames | 16 July 2013, 13:48:26 UTC |
| 7c0a2b8 | andrewjpage | 16 July 2013, 13:24:31 UTC | class methods | 16 July 2013, 13:24:31 UTC |
| 531428d | andrewjpage | 16 July 2013, 11:25:31 UTC | test which and robinson_foulds_distance | 16 July 2013, 11:25:31 UTC |
| 68054d2 | andrewjpage | 10 July 2013, 12:36:17 UTC | nosetests | 16 July 2013, 09:45:45 UTC |
| bc454f5 | andrewjpage | 10 July 2013, 11:11:31 UTC | basic tests | 16 July 2013, 09:45:44 UTC |
| 78a8bc5 | andrewjpage | 10 July 2013, 10:08:32 UTC | reorganise python scripts into directory | 16 July 2013, 09:45:44 UTC |
| ff9ec07 | andrewjpage | 09 July 2013, 15:39:43 UTC | move python code to external module | 16 July 2013, 09:45:44 UTC |
| 23abbe5 | andrewjpage | 15 July 2013, 15:38:49 UTC | Merge pull request #92 from andrewjpage/master remove duplicate move | 15 July 2013, 15:38:49 UTC |
| 2b165e0 | andrewjpage | 15 July 2013, 15:38:20 UTC | dont move inwards twice | 15 July 2013, 15:38:20 UTC |
| 3b6212d | andrewjpage | 15 July 2013, 15:37:22 UTC | Merge pull request #91 from andrewjpage/master dont move in twice | 15 July 2013, 15:37:22 UTC |
| 06994cc | andrewjpage | 15 July 2013, 15:36:56 UTC | dont move inwards twice | 15 July 2013, 15:36:56 UTC |
| 0faea3e | andrewjpage | 10 July 2013, 15:17:49 UTC | Merge pull request #90 from andrewjpage/master typo in method, too many args | 10 July 2013, 15:17:49 UTC |
| b6a7449 | andrewjpage | 10 July 2013, 15:17:20 UTC | too many args | 10 July 2013, 15:17:20 UTC |
| 530839a | andrewjpage | 10 July 2013, 15:16:39 UTC | Merge pull request #89 from andrewjpage/master move end block in correct number of snps | 10 July 2013, 15:16:39 UTC |
| baf4220 | andrewjpage | 10 July 2013, 15:15:53 UTC | move end of block in correctly | 10 July 2013, 15:15:53 UTC |
| 5dcd091 | andrewjpage | 05 July 2013, 08:35:14 UTC | Merge pull request #88 from andrewjpage/master Span gaps | 05 July 2013, 08:35:14 UTC |
| 5811e55 | andrewjpage | 05 July 2013, 08:24:11 UTC | use child sequence for gaps when generating blocks | 05 July 2013, 08:24:11 UTC |
| 8b50f69 | andrewjpage | 04 July 2013, 15:23:20 UTC | off by one coord when creating blocks | 04 July 2013, 15:23:20 UTC |
| 3acc1d5 | andrewjpage | 04 July 2013, 15:23:07 UTC | print out neg log likelihood for a block | 04 July 2013, 15:23:07 UTC |
| df4ebb5 | andrewjpage | 04 July 2013, 09:25:19 UTC | Merge pull request #87 from andrewjpage/master translate snps and gaps to original genome space coords | 04 July 2013, 09:25:19 UTC |
| b3ff533 | andrewjpage | 03 July 2013, 14:26:20 UTC | translate snp and gaps to original genome space coords | 03 July 2013, 14:26:20 UTC |
| 0a9c845 | andrewjpage | 02 July 2013, 11:24:54 UTC | more efficiently find lower bound of window when close to beginning | 02 July 2013, 11:24:54 UTC |
| 4396e1a | andrewjpage | 02 July 2013, 09:54:59 UTC | Merge pull request #86 from andrewjpage/master extend blocks over gaps | 02 July 2013, 09:54:59 UTC |
| 18f4335 | andrewjpage | 02 July 2013, 09:54:17 UTC | extend blocks over gaps | 02 July 2013, 09:54:17 UTC |
| 7d60f03 | andrewjpage | 01 July 2013, 13:49:55 UTC | Merge pull request #85 from andrewjpage/master dont call methods and variables the same thing | 01 July 2013, 13:49:55 UTC |
| b81cda5 | andrewjpage | 01 July 2013, 13:49:28 UTC | dont call methods and variables the same thing | 01 July 2013, 13:49:28 UTC |
| 58740b7 | andrewjpage | 01 July 2013, 13:28:35 UTC | Merge pull request #84 from andrewjpage/master remove latest tree symlink if it exists, even if its broken | 01 July 2013, 13:28:35 UTC |
| bcd0ec6 | andrewjpage | 01 July 2013, 13:27:18 UTC | remove latest tree symlink if it exists, even if its broken | 01 July 2013, 13:27:18 UTC |
| eb0db7a | andrewjpage | 01 July 2013, 12:43:01 UTC | Merge pull request #83 from andrewjpage/master delete intermediate raxml files | 01 July 2013, 12:43:01 UTC |
| 8c0f4f4 | andrewjpage | 01 July 2013, 12:42:28 UTC | delete intermediate raxml files if they already exist | 01 July 2013, 12:42:28 UTC |
| db49772 | andrewjpage | 01 July 2013, 11:15:05 UTC | Merge pull request #82 from andrewjpage/master Eliminate memory leaks and uninitalised reads/writes | 01 July 2013, 11:15:05 UTC |
| 22a05b9 | andrewjpage | 01 July 2013, 11:14:04 UTC | Merge branch 'memory_copy' | 01 July 2013, 11:14:04 UTC |
| 9916dfe | andrewjpage | 01 July 2013, 11:07:12 UTC | free internal node array | 01 July 2013, 11:07:12 UTC |
| e066246 | andrewjpage | 01 July 2013, 11:01:50 UTC | clean up newick tree in correct order | 01 July 2013, 11:01:50 UTC |
| bfb37b5 | andrewjpage | 01 July 2013, 10:38:44 UTC | free the newick tree | 01 July 2013, 10:38:44 UTC |
| 5eaac09 | andrewjpage | 01 July 2013, 10:27:16 UTC | reenable freeing memory | 01 July 2013, 10:27:16 UTC |
| af88778 | andrewjpage | 01 July 2013, 10:05:29 UTC | use calloc over malloc | 01 July 2013, 10:05:29 UTC |
| 4add250 | andrewjpage | 01 July 2013, 09:54:36 UTC | use calloc instead of memcopy | 01 July 2013, 09:54:36 UTC |
| 9f505f0 | andrewjpage | 01 July 2013, 09:51:10 UTC | use calloc for parsing vcfs | 01 July 2013, 09:51:10 UTC |
| c6355cd | andrewjpage | 01 July 2013, 09:48:31 UTC | use calloc | 01 July 2013, 09:48:31 UTC |
| ebad3fb | andrewjpage | 28 June 2013, 15:06:09 UTC | size of char in mem copy | 28 June 2013, 15:06:09 UTC |
| f2be5a4 | andrewjpage | 28 June 2013, 14:08:13 UTC | remove realloc in wrong scope | 28 June 2013, 14:08:13 UTC |
| 3d708f4 | andrewjpage | 28 June 2013, 13:55:00 UTC | realloc without keeping track of new pointer | 28 June 2013, 13:55:00 UTC |
| 4efbd97 | andrewjpage | 28 June 2013, 13:31:31 UTC | Revert "remove optimasations to find snp index" This reverts commit 8fa4e66b78fb8dc7f0a5d308e1d149365874e5bf. | 28 June 2013, 13:31:31 UTC |
| 5b8e88f | andrewjpage | 28 June 2013, 13:31:21 UTC | Revert "missing round bracket" This reverts commit dcac69c400b3b4d9bdc6444a635969431fae4fb4. | 28 June 2013, 13:31:21 UTC |
| dcac69c | andrewjpage | 28 June 2013, 13:29:41 UTC | missing round bracket | 28 June 2013, 13:29:41 UTC |
| 8fa4e66 | andrewjpage | 28 June 2013, 13:28:36 UTC | remove optimasations to find snp index | 28 June 2013, 13:28:36 UTC |
| 8b49229 | andrewjpage | 28 June 2013, 13:21:50 UTC | using index for snp sites instead of overall snp locations | 28 June 2013, 13:21:50 UTC |
| 74df0e2 | andrewjpage | 28 June 2013, 13:00:17 UTC | out of bounds by 1 in find index | 28 June 2013, 13:00:17 UTC |
| c01bd8c | andrewjpage | 28 June 2013, 09:33:50 UTC | intialise sequence and sample names from phylip | 28 June 2013, 09:33:50 UTC |
| 6f77c7e | andrewjpage | 28 June 2013, 09:08:45 UTC | dont redeclare memory | 28 June 2013, 09:08:45 UTC |
| 84b3b3c | andrewjpage | 28 June 2013, 09:01:02 UTC | get size of string without using str len | 28 June 2013, 09:01:02 UTC |
| f2fded8 | andrewjpage | 28 June 2013, 08:55:08 UTC | use mem copy in alignement file and in reads | 28 June 2013, 08:55:08 UTC |
| fb4d0af | andrewjpage | 28 June 2013, 08:49:11 UTC | add extensions with null character at end | 28 June 2013, 08:49:11 UTC |
| ebe68cd | andrewjpage | 28 June 2013, 08:35:07 UTC | mem copy input parameters | 28 June 2013, 08:35:07 UTC |
| 47ed02c | andrewjpage | 28 June 2013, 08:26:42 UTC | fix failing multi recombination test | 28 June 2013, 08:26:42 UTC |
| d6f3d0a | andrewjpage | 28 June 2013, 08:21:57 UTC | snp searching extend block | 28 June 2013, 08:21:57 UTC |
| 6af4912 | andrewjpage | 28 June 2013, 08:11:31 UTC | declare empty and delimiter strs within curly brackets | 28 June 2013, 08:11:31 UTC |
| 0dd0f2d | andrewjpage | 27 June 2013, 15:53:12 UTC | calc size of strings before mem copy | 27 June 2013, 15:53:12 UTC |
| af61acc | andrewjpage | 27 June 2013, 15:48:32 UTC | parse strings in phylip to get size before concat | 27 June 2013, 15:48:32 UTC |
| 6a6a3ac | andrewjpage | 27 June 2013, 15:41:05 UTC | merging in stashed changes | 27 June 2013, 15:41:05 UTC |
| b80a95f | andrewjpage | 27 June 2013, 15:01:51 UTC | limit taxon name copy | 27 June 2013, 15:01:51 UTC |
| e72436f | andrewjpage | 27 June 2013, 14:56:00 UTC | use size of mem copy | 27 June 2013, 14:56:00 UTC |
| 9f30004 | andrewjpage | 27 June 2013, 14:20:46 UTC | use mem copy | 27 June 2013, 14:20:46 UTC |
| 2c9868a | andrewjpage | 27 June 2013, 13:15:51 UTC | remove fasttree binary | 27 June 2013, 13:15:51 UTC |
| 7612869 | andrewjpage | 27 June 2013, 13:08:02 UTC | use bundled executables if system ones are not available | 27 June 2013, 13:08:02 UTC |
| 5f1d842 | andrewjpage | 27 June 2013, 12:33:58 UTC | fastml lib makefile | 27 June 2013, 12:33:58 UTC |
| 141e21e | andrewjpage | 27 June 2013, 11:25:58 UTC | add fasttree | 27 June 2013, 11:25:58 UTC |
| 3fbfaed | andrewjpage | 27 June 2013, 11:14:29 UTC | bundled execs | 27 June 2013, 11:14:29 UTC |
| c9ff37a | andrewjpage | 27 June 2013, 11:14:11 UTC | cleanup files | 27 June 2013, 11:14:11 UTC |
| 25f9a19 | andrewjpage | 27 June 2013, 10:31:04 UTC | add external dependancies | 27 June 2013, 10:31:04 UTC |
| 3560093 | andrewjpage | 26 June 2013, 14:44:18 UTC | Merge pull request #81 from andrewjpage/master GPL | 26 June 2013, 14:44:18 UTC |
| 0c86f59 | andrewjpage | 26 June 2013, 14:41:28 UTC | gpl 2 | 26 June 2013, 14:41:28 UTC |
| d6ca62c | andrewjpage | 26 June 2013, 14:01:56 UTC | Merge pull request #80 from andrewjpage/master reduce memory usage and fix seg fault | 26 June 2013, 14:01:56 UTC |
| acc1166 | andrewjpage | 26 June 2013, 14:00:31 UTC | reduce memory usage | 26 June 2013, 14:00:31 UTC |
| e7c9354 | andrewjpage | 26 June 2013, 12:45:06 UTC | realloc the recombintation array after use | 26 June 2013, 12:45:06 UTC |
| cb0d93d | andrewjpage | 26 June 2013, 12:22:43 UTC | don't reallocate memory causes an error | 26 June 2013, 12:22:43 UTC |
| 4f82f58 | andrewjpage | 26 June 2013, 12:03:43 UTC | reduce the recombination memory and don't free at the end because theres a seg fault that needs attention | 26 June 2013, 12:03:43 UTC |
| 992b2a9 | andrewjpage | 25 June 2013, 12:50:51 UTC | close files and free small memory | 25 June 2013, 12:50:51 UTC |
| e53731f | andrewjpage | 25 June 2013, 11:22:54 UTC | free up the root sequence which isn't used for anything | 25 June 2013, 11:22:54 UTC |
| e901534 | andrewjpage | 25 June 2013, 10:59:35 UTC | stats sample name free | 25 June 2013, 10:59:35 UTC |
| 8c47587 | andrewjpage | 25 June 2013, 10:56:00 UTC | free up sample names and tree stats | 25 June 2013, 10:56:00 UTC |
| dbd7596 | andrewjpage | 25 June 2013, 10:43:55 UTC | free column names from vcf | 25 June 2013, 10:43:55 UTC |
| 481b8e3 | andrewjpage | 25 June 2013, 10:30:42 UTC | cleanup tree nodes | 25 June 2013, 10:30:42 UTC |
| 45b2761 | andrewjpage | 25 June 2013, 10:11:30 UTC | recombinations | 25 June 2013, 10:11:30 UTC |
| 7965c94 | andrewjpage | 25 June 2013, 09:51:31 UTC | free memory | 25 June 2013, 09:53:13 UTC |
| 79fea56 | andrewjpage | 25 June 2013, 09:42:29 UTC | method itself passed in instead of array | 25 June 2013, 09:42:29 UTC |
| 43a4e50 | andrewjpage | 03 June 2013, 11:16:52 UTC | Merge pull request #79 from andrewjpage/master move math lib linking to end | 03 June 2013, 11:16:52 UTC |
| 0477c1a | andrewjpage | 03 June 2013, 11:16:30 UTC | move math lib linking to end | 03 June 2013, 11:16:30 UTC |
| e11e30a | andrewjpage | 03 June 2013, 11:04:43 UTC | Merge pull request #78 from andrewjpage/master move zlib linking to end | 03 June 2013, 11:04:43 UTC |
| 3862ec1 | andrewjpage | 03 June 2013, 11:04:04 UTC | move zlib linking to end | 03 June 2013, 11:04:04 UTC |
| 24354fe | andrewjpage | 21 May 2013, 15:37:06 UTC | Merge pull request #77 from andrewjpage/master swap output suppression | 21 May 2013, 15:37:06 UTC |
| 518baee | andrewjpage | 21 May 2013, 15:36:45 UTC | swap output suppression | 21 May 2013, 15:36:45 UTC |
| 0a9b595 | andrewjpage | 21 May 2013, 15:35:01 UTC | Merge pull request #76 from andrewjpage/master memory leaks | 21 May 2013, 15:35:01 UTC |
| 134ce5c | andrewjpage | 21 May 2013, 15:33:08 UTC | suppress raxml output | 21 May 2013, 15:33:08 UTC |
| 685e33d | andrewjpage | 21 May 2013, 14:44:52 UTC | freeing memory thats already been freed | 21 May 2013, 14:44:52 UTC |
