| deb41c8 | deren | 08 February 2016, 16:13:17 UTC | "Updating ipyrad/__init__.py to version - 0.1.38 | 08 February 2016, 16:13:17 UTC |
| b324e2c | deren | 08 February 2016, 16:10:12 UTC | cosmetic | 08 February 2016, 16:10:12 UTC |
| ebdd2ea | deren | 08 February 2016, 16:09:47 UTC | s6 and s7 stats are assembly properties, not Sample properties | 08 February 2016, 16:09:47 UTC |
| e51a013 | deren | 08 February 2016, 16:09:19 UTC | can do MPI across nodes easy now with -ip flag | 08 February 2016, 16:09:19 UTC |
| a56f42e | deren | 08 February 2016, 16:08:40 UTC | cleaner launch for ipyparallel 5 | 08 February 2016, 16:08:40 UTC |
| a3a62cf | deren | 08 February 2016, 16:07:36 UTC | writes stats and saves DFs to Assembly | 08 February 2016, 16:07:36 UTC |
| ee6eb83 | deren | 08 February 2016, 16:07:01 UTC | commented out all numba for faster start for now | 08 February 2016, 16:07:01 UTC |
| fc7cc51 | deren | 08 February 2016, 16:06:45 UTC | cosmetic | 08 February 2016, 16:06:45 UTC |
| 50fbe87 | deren | 08 February 2016, 16:06:30 UTC | cleanup to prints from main | 08 February 2016, 16:06:30 UTC |
| 8d390fa | deren | 05 February 2016, 07:09:55 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 05 February 2016, 07:09:55 UTC |
| 0529868 | deren | 05 February 2016, 07:09:50 UTC | cosmetic fixes, and no auto add of * to sorted path | 05 February 2016, 07:09:50 UTC |
| 567e25a | isaacovercast | 05 February 2016, 02:34:13 UTC | added numba to meta.yaml | 05 February 2016, 02:34:13 UTC |
| 999f537 | isaacovercast | 03 February 2016, 16:11:00 UTC | Adding debug code | 03 February 2016, 16:11:00 UTC |
| b795524 | isaacovercast | 31 January 2016, 00:01:16 UTC | Error in ipyrad -n, can't use blank assembly names for tmp assembly anymore. | 31 January 2016, 00:01:16 UTC |
| 4895aa3 | isaacovercast | 30 January 2016, 23:47:24 UTC | Fixed conda recipe so it acually works. | 30 January 2016, 23:47:24 UTC |
| 22dc93e | isaacovercast | 29 January 2016, 00:58:46 UTC | "Updating ipyrad/__init__.py to version - 0.1.37 | 29 January 2016, 00:58:46 UTC |
| f1add56 | isaacovercast | 29 January 2016, 00:57:40 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad Conflicts: ipyrad/__main__.py ipyrad/core/assembly.py | 29 January 2016, 00:57:40 UTC |
| 7007f41 | isaacovercast | 29 January 2016, 00:54:27 UTC | set_params on assembly name now errors out with a helpful message. Assembly name is SET at creation time, and is "unmodifiable". This is through both the CLI and the API, so the behavior is consistent. Also added some error checking at Assembly.__init__, basically making sure the passed in name doesn't have spaces or special characters. | 29 January 2016, 00:54:27 UTC |
| d29090e | deren | 28 January 2016, 17:43:36 UTC | "Updating ipyrad/__init__.py to version - 0.1.36 | 28 January 2016, 17:43:36 UTC |
| a2f04c0 | deren | 28 January 2016, 17:43:20 UTC | pure cosmetic | 28 January 2016, 17:43:20 UTC |
| 511e88d | deren | 28 January 2016, 17:42:56 UTC | 'prefix' was not defined'. some cleanup | 28 January 2016, 17:42:56 UTC |
| f459706 | deren | 28 January 2016, 17:42:25 UTC | added an ip.__interactive__ attribute to know if you are in the CLI or not | 28 January 2016, 17:42:25 UTC |
| 9dcec38 | isaacovercast | 28 January 2016, 06:11:57 UTC | Fixing step1 preview not cleaning up preview files. in fact i fixed all preview mode file fsck not cleaning up. | 28 January 2016, 06:11:57 UTC |
| a12105c | isaacovercast | 28 January 2016, 05:17:08 UTC | "Updating ipyrad/__init__.py to version - 0.1.35 | 28 January 2016, 05:17:08 UTC |
| df4a7cd | isaacovercast | 28 January 2016, 05:14:10 UTC | Huge refactor of paramsdict. Changed working_directory to project_dir, and also added a paramsdict[0]="assembly_name". | 28 January 2016, 05:14:10 UTC |
| adda989 | isaacovercast | 27 January 2016, 17:53:31 UTC | Disable keyboard interrupt during cluster init. | 27 January 2016, 17:53:31 UTC |
| c58ad47 | isaacovercast | 27 January 2016, 02:09:40 UTC | Fixed merge conflict, added more informative output to an except call Merge branch 'master' of https://github.com/dereneaton/ipyrad Conflicts: ipyrad/assemble/refmap.py | 27 January 2016, 02:09:40 UTC |
| 7d1467e | isaacovercast | 27 January 2016, 02:08:56 UTC | Some cleanup, some debugging code. | 27 January 2016, 02:08:56 UTC |
| a74d8c2 | deren | 27 January 2016, 02:04:37 UTC | "Updating ipyrad/__init__.py to version - 0.1.34 | 27 January 2016, 02:04:37 UTC |
| caccae3 | deren | 27 January 2016, 02:04:10 UTC | fix to pipe call from system bedtools to [...]bin/bedtools | 27 January 2016, 02:04:10 UTC |
| b5feed0 | isaacovercast | 27 January 2016, 01:37:16 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 27 January 2016, 01:37:16 UTC |
| 9869612 | isaacovercast | 27 January 2016, 01:35:27 UTC | This is the mouse mt genome with some a bunch of reads from the SE and PE simulated rad datasets crammed in. | 27 January 2016, 01:35:27 UTC |
| 85c28a8 | deren | 27 January 2016, 00:53:20 UTC | "Updating ipyrad/__init__.py to version - 0.1.33 | 27 January 2016, 00:53:20 UTC |
| d19fab7 | deren | 27 January 2016, 00:52:35 UTC | Merge branch 'h5step7' Conflicts: ipyrad/core/assembly.py | 27 January 2016, 00:52:35 UTC |
| a74dd85 | deren | 27 January 2016, 00:49:30 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 27 January 2016, 00:49:30 UTC |
| eec5402 | deren | 27 January 2016, 00:48:11 UTC | loci file building from super arrays for SE data. | 27 January 2016, 00:48:11 UTC |
| 7021605 | isaacovercast | 26 January 2016, 23:34:58 UTC | Fixed a nasty bug in __main__ that fsck relative paths in working_directory. Now it converts working directory path to abspath before it does anything. Also tested to make sure ./ as working directory works. Added informational output to assembly.py, and fixed a deprecated call to _save in load.py. | 26 January 2016, 23:34:58 UTC |
| d9b965a | isaacovercast | 26 January 2016, 18:46:43 UTC | Fixed all tmpdir creation to prepend data.name to support running multiple assemblies in the same workdir. | 26 January 2016, 18:46:43 UTC |
| 3d1c754 | isaacovercast | 26 January 2016, 16:39:58 UTC | bug in step2 prechecks caused crash on non-denovo methods if no reference sequence provided in params. | 26 January 2016, 16:39:58 UTC |
| 2e7fcfb | deren | 26 January 2016, 08:19:38 UTC | fix to auto looking for sorted path. print on ipp.CompositeError | 26 January 2016, 08:19:38 UTC |
| 9e9bec8 | deren | 26 January 2016, 08:18:31 UTC | chunks save arrays to disk, next step is to save htem in the full array | 26 January 2016, 08:18:31 UTC |
| e7f9ec0 | deren | 26 January 2016, 08:17:56 UTC | removed some loggers | 26 January 2016, 08:17:56 UTC |
| 0e6abb6 | deren | 26 January 2016, 08:17:34 UTC | added snp array to hd5. save names as lists | 26 January 2016, 08:17:34 UTC |
| 311aa72 | deren | 25 January 2016, 20:41:07 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 25 January 2016, 20:41:07 UTC |
| 0c1f32e | deren | 25 January 2016, 20:37:24 UTC | step 7 starting hdf5 overhaul | 25 January 2016, 20:37:24 UTC |
| 08ba474 | deren | 25 January 2016, 20:36:52 UTC | statsfiles building | 25 January 2016, 20:36:52 UTC |
| 53de01f | deren | 25 January 2016, 20:32:48 UTC | more strict 12->20 min overlap | 25 January 2016, 20:32:48 UTC |
| 79dcd7c | deren | 25 January 2016, 20:32:24 UTC | just some comments while re-checking the code | 25 January 2016, 20:32:24 UTC |
| 8169b8e | deren | 25 January 2016, 20:31:48 UTC | more rigorous checks on allele finding | 25 January 2016, 20:31:48 UTC |
| a72911e | deren | 25 January 2016, 20:31:01 UTC | clean up to clust building, and merge counting | 25 January 2016, 20:31:01 UTC |
| 5c8d071 | deren | 25 January 2016, 20:30:18 UTC | added more data sets in hdf5 | 25 January 2016, 20:30:18 UTC |
| f6a4819 | isaacovercast | 25 January 2016, 17:51:41 UTC | Fixed bug in main that was fscking relative paths in params.txt file | 25 January 2016, 17:51:41 UTC |
| 3031bf0 | isaacovercast | 25 January 2016, 17:38:22 UTC | moved precheck inside the try to handle cleanup of tmp files if keyboard interrupt during precheck | 25 January 2016, 17:38:22 UTC |
| d1e17b1 | isaacovercast | 25 January 2016, 15:35:56 UTC | Add error handling for too few hi depth clusters. It's possible for a sample to be in state 3 and have zero high depth clusters in which case you have problems. Test for this and prevent it. | 25 January 2016, 15:35:56 UTC |
| e4ec1c3 | isaacovercast | 24 January 2016, 19:15:29 UTC | Fixed bug with empty path to sorted_fastq path crashing. | 24 January 2016, 19:15:29 UTC |
| 9f2a096 | isaacovercast | 24 January 2016, 18:21:17 UTC | Cosmetic changes | 24 January 2016, 18:21:17 UTC |
| c850c98 | isaacovercast | 24 January 2016, 18:16:30 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 24 January 2016, 18:16:30 UTC |
| c5c40b4 | isaacovercast | 24 January 2016, 18:15:53 UTC | Fixed access before assignment for fwdseq | 24 January 2016, 18:15:53 UTC |
| 3415689 | deren | 24 January 2016, 08:00:04 UTC | "Updating ipyrad/__init__.py to version - 0.1.32 | 24 January 2016, 08:00:04 UTC |
| 98673bb | deren | 24 January 2016, 07:59:30 UTC | step7 checks step6 database for all samples | 24 January 2016, 07:59:30 UTC |
| 568e3e7 | deren | 24 January 2016, 07:56:50 UTC | ipynb updates | 24 January 2016, 07:56:50 UTC |
| 361ab21 | deren | 24 January 2016, 07:28:42 UTC | ipynb updates | 24 January 2016, 07:28:42 UTC |
| c3f9539 | deren | 24 January 2016, 07:26:30 UTC | cosmetic changes | 24 January 2016, 07:26:30 UTC |
| 7857cf5 | deren | 24 January 2016, 07:25:17 UTC | building statsfiles | 24 January 2016, 07:25:17 UTC |
| 3804378 | deren | 24 January 2016, 07:24:48 UTC | step7 checks database for samples. .save is no longer hidden. | 24 January 2016, 07:24:48 UTC |
| a2c3e51 | deren | 24 January 2016, 07:22:37 UTC | statsfiles.s2 builds | 24 January 2016, 07:22:37 UTC |
| a374261 | deren | 24 January 2016, 07:21:11 UTC | build func for statsfiles | 24 January 2016, 07:21:11 UTC |
| c1507cb | deren | 24 January 2016, 07:20:50 UTC | fixed bug for indels breaking allele counting | 24 January 2016, 07:20:50 UTC |
| 70063ea | deren | 24 January 2016, 07:19:46 UTC | data.statsfiles.s3 builds | 24 January 2016, 07:19:46 UTC |
| a5ad620 | isaacovercast | 24 January 2016, 00:49:04 UTC | fixed expander to handle more than one ../ in paths. | 24 January 2016, 00:49:04 UTC |
| f6ff88d | isaacovercast | 23 January 2016, 23:10:04 UTC | Cosmetic changes | 23 January 2016, 23:10:04 UTC |
| 56763b0 | isaacovercast | 23 January 2016, 22:17:23 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 23 January 2016, 22:17:23 UTC |
| b459560 | isaacovercast | 23 January 2016, 22:16:29 UTC | Fixed behavior of step7 to align with other steps on dealing with no samples reading for writing. | 23 January 2016, 22:16:29 UTC |
| 788f959 | deren | 23 January 2016, 22:16:05 UTC | cli output messages update | 23 January 2016, 22:16:05 UTC |
| 02163c0 | deren | 23 January 2016, 22:14:17 UTC | "Updating ipyrad/__init__.py to version - 0.1.31 | 23 January 2016, 22:14:17 UTC |
| 51d9dbf | deren | 23 January 2016, 22:08:39 UTC | removed all _stamps. Made superseqs into array (nloci, ntax, maxlen) | 23 January 2016, 22:08:39 UTC |
| 00ca014 | deren | 23 January 2016, 20:29:43 UTC | "Updating ipyrad/__init__.py to version - 0.1.30 | 23 January 2016, 20:29:43 UTC |
| 9d2f17d | deren | 23 January 2016, 20:29:30 UTC | ipynb updates | 23 January 2016, 20:29:30 UTC |
| 50b5820 | deren | 23 January 2016, 20:29:17 UTC | was missing the last chunk of consens when building catgs! | 23 January 2016, 20:29:17 UTC |
| ed108cc | deren | 23 January 2016, 20:28:46 UTC | super seqs array now building in h5. Still need to optimize chunking. | 23 January 2016, 20:28:46 UTC |
| ae8d93c | deren | 23 January 2016, 20:28:19 UTC | remove redundant 'loading' message | 23 January 2016, 20:28:19 UTC |
| 20d0429 | deren | 23 January 2016, 07:06:16 UTC | "Updating ipyrad/__init__.py to version - 0.1.29 | 23 January 2016, 07:06:16 UTC |
| 20325be | deren | 23 January 2016, 07:05:33 UTC | ipynb updates | 23 January 2016, 07:05:33 UTC |
| 1a81640 | deren | 23 January 2016, 07:05:13 UTC | need better warning when no barcodes file | 23 January 2016, 07:05:13 UTC |
| e6cf3d8 | deren | 23 January 2016, 07:04:47 UTC | removed print statement | 23 January 2016, 07:04:47 UTC |
| 95739b0 | deren | 23 January 2016, 06:39:37 UTC | "Updating ipyrad/__init__.py to version - 0.1.28 | 23 January 2016, 06:39:37 UTC |
| db21f1f | deren | 23 January 2016, 06:38:46 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 23 January 2016, 06:38:46 UTC |
| 563315f | deren | 23 January 2016, 06:38:25 UTC | ipynb updates | 23 January 2016, 06:38:25 UTC |
| 89e0ad9 | deren | 23 January 2016, 06:38:02 UTC | moved fullcomp here | 23 January 2016, 06:38:02 UTC |
| 4015334 | deren | 23 January 2016, 06:37:42 UTC | handles pair splits | 23 January 2016, 06:37:42 UTC |
| 4a064f4 | deren | 23 January 2016, 06:37:11 UTC | datatypes all consistent, maybe can lower size later | 23 January 2016, 06:37:11 UTC |
| bc32660 | deren | 23 January 2016, 06:35:42 UTC | cosmetic change | 23 January 2016, 06:35:42 UTC |
| 4f3df53 | deren | 23 January 2016, 06:35:17 UTC | supercatg building. Not seqs yet. | 23 January 2016, 06:35:17 UTC |
| a0159f2 | isaacovercast | 22 January 2016, 22:59:47 UTC | "Updating ipyrad/__init__.py to version - 0.1.27 | 22 January 2016, 22:59:47 UTC |
| 2f814e7 | isaacovercast | 22 January 2016, 22:58:27 UTC | Added psutil as a requirement | 22 January 2016, 22:58:27 UTC |
| a6b5b9d | isaacovercast | 22 January 2016, 21:38:13 UTC | Normalizing behavior of all steps in the face of samples in unexpected states. | 22 January 2016, 21:38:13 UTC |
| e2c5948 | isaacovercast | 22 January 2016, 19:06:56 UTC | Added smalt_index_wordlen flag to hackers only dict so it's possible to tune indexing. Added the force command to index_reference to make it reindex if you pass in force=true. Still on the fence about this change. | 22 January 2016, 19:06:56 UTC |
| a418ca4 | isaacovercast | 22 January 2016, 19:02:00 UTC | Stupid bug prevented hackersonly from triggering an update | 22 January 2016, 19:02:00 UTC |
| 8a2834e | isaacovercast | 22 January 2016, 17:29:58 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 22 January 2016, 17:29:58 UTC |
| ca727e9 | isaacovercast | 22 January 2016, 17:29:38 UTC | Fixed new assembly creation to make it not use full path for the name | 22 January 2016, 17:29:38 UTC |
