| 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 |
| 99e4d5d | deren | 21 January 2016, 22:11:28 UTC | "Updating ipyrad/__init__.py to version - 0.1.26 | 21 January 2016, 22:11:28 UTC |
| f28b969 | deren | 21 January 2016, 22:11:19 UTC | back to raising error on keyboard interr | 21 January 2016, 22:11:19 UTC |
| 7e4abb3 | deren | 21 January 2016, 22:09:51 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 21 January 2016, 22:09:51 UTC |
| 1ea4184 | deren | 21 January 2016, 22:09:47 UTC | ipynb updates | 21 January 2016, 22:09:47 UTC |
| 090f011 | deren | 21 January 2016, 22:09:37 UTC | moved clustdealer here. & added Worker class for now. Being used to test threading on MPI | 21 January 2016, 22:09:37 UTC |
| 89b26ec | deren | 21 January 2016, 21:24:17 UTC | faster array building and counting and execution | 21 January 2016, 21:24:17 UTC |
| 3346761 | deren | 21 January 2016, 21:23:47 UTC | moved clustdealer to util.py | 21 January 2016, 21:23:47 UTC |
| 3672398 | deren | 21 January 2016, 21:22:23 UTC | cosmetic change | 21 January 2016, 21:22:23 UTC |
| 61c566e | isaacovercast | 21 January 2016, 04:31:25 UTC | Fixed tmp file naming issue in cluster across | 21 January 2016, 04:31:25 UTC |
| fb9994f | isaacovercast | 21 January 2016, 02:22:47 UTC | added a conditional to test for preview mode before removing the sample_fastq files, since if we aren't in preview mode these are the real sample fastqs. | 21 January 2016, 02:22:47 UTC |
| 8dbd086 | isaacovercast | 21 January 2016, 02:11:43 UTC | Adjusted the math that was getting optim for splitting files. It was understimating the # of optimal lines by a factor of 8, which would be fine, but if the nlines gets too small then the number of files you're asking split to make inside zcat_make_temps exceeds the # it can make by default. Also added a flag to split to increase the number of files it can make (`-a 4`). | 21 January 2016, 02:11:43 UTC |
| 4f185a1 | isaacovercast | 21 January 2016, 00:25:37 UTC | If not preview mode the finally() block of run() was indexing into an empty list. Put a test for preview mode around it. | 21 January 2016, 00:25:37 UTC |
| d04cb4c | isaacovercast | 21 January 2016, 00:23:50 UTC | Tricky bug with assigning assembly name. I was doing something stupid and it was getting named as the full path to the working directory. Blind bug that showed up in a weird way in step6 | 21 January 2016, 00:23:50 UTC |
| 3057aaf | isaacovercast | 20 January 2016, 23:23:08 UTC | steps 6 and 7 weren't honoring the force flag. | 20 January 2016, 23:23:08 UTC |
| 9855e57 | isaacovercast | 19 January 2016, 23:53:13 UTC | Cosmetic changes to main and load. Fixed the bug for CLI step 5. | 19 January 2016, 23:53:13 UTC |
| ff9eab8 | deren | 19 January 2016, 21:58:04 UTC | "Updating ipyrad/__init__.py to version - 0.1.25 | 19 January 2016, 21:58:04 UTC |
| 0ed4ca0 | deren | 19 January 2016, 21:57:52 UTC | working ipynbs | 19 January 2016, 21:57:52 UTC |
| c3bb0a3 | deren | 19 January 2016, 21:57:36 UTC | warning when _R1. in name instead of _R1_ | 19 January 2016, 21:57:36 UTC |
| db546b1 | deren | 19 January 2016, 21:57:12 UTC | better preview chunking | 19 January 2016, 21:57:12 UTC |
| 2269fe6 | deren | 19 January 2016, 21:56:54 UTC | better chunking for preview | 19 January 2016, 21:56:54 UTC |
| 2728433 | deren | 19 January 2016, 21:56:37 UTC | testing numba speed ups | 19 January 2016, 21:56:37 UTC |
| 26913f3 | deren | 19 January 2016, 21:56:21 UTC | smarter chunking for preview and full | 19 January 2016, 21:56:21 UTC |
| 9b23d1f | deren | 19 January 2016, 21:55:58 UTC | some steps towards working on pairddrad data | 19 January 2016, 21:55:58 UTC |
