| 6ada997 | isaacovercast | 19 January 2016, 00:32:54 UTC | "Updating ipyrad/__init__.py to version - 0.1.24 | 19 January 2016, 00:32:54 UTC |
| ce69720 | isaacovercast | 19 January 2016, 00:31:55 UTC | Significant rewrite of preview mode for step3. Also significant change to how refmap deals with forwarding unmapped reads back into the denovo pipeline. | 19 January 2016, 00:31:55 UTC |
| 77ce635 | isaacovercast | 19 January 2016, 00:20:24 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 19 January 2016, 00:20:24 UTC |
| d4f0ff1 | isaacovercast | 19 January 2016, 00:19:55 UTC | Rewrote preview_truncate to read and write a list of tuples to be more consistent with the format of sample.files.* | 19 January 2016, 00:19:55 UTC |
| 49fd927 | isaacovercast | 19 January 2016, 00:19:10 UTC | Fixed to use the new version of preview_truncate, basically simplified the code a ton. | 19 January 2016, 00:19:10 UTC |
| a7264da | isaacovercast | 18 January 2016, 23:31:05 UTC | Fixed load to actually update the hackersonly dict. Added a 'quiet' flag to Assembly.__init__ | 18 January 2016, 23:31:05 UTC |
| 8fda169 | deren | 18 January 2016, 23:22:38 UTC | "Updating ipyrad/__init__.py to version - 0.1.23 | 18 January 2016, 23:22:38 UTC |
| 6364a62 | deren | 18 January 2016, 23:22:21 UTC | ipynb states | 18 January 2016, 23:22:21 UTC |
| 7463d07 | deren | 18 January 2016, 23:21:51 UTC | little bit smarter build | 18 January 2016, 23:21:51 UTC |
| ad97202 | deren | 18 January 2016, 23:21:40 UTC | alleles building with new splitalleles func | 18 January 2016, 23:21:40 UTC |
| a14363f | deren | 18 January 2016, 23:21:22 UTC | this needs work. Just a small doc edit | 18 January 2016, 23:21:22 UTC |
| 09b629b | deren | 18 January 2016, 23:20:58 UTC | just some doc strings updates | 18 January 2016, 23:20:58 UTC |
| 4bd2635 | deren | 18 January 2016, 23:20:39 UTC | starting on step7 cleanup | 18 January 2016, 23:20:39 UTC |
| 30669de | deren | 18 January 2016, 23:20:23 UTC | working funcs/dicts for storing phase data | 18 January 2016, 23:20:23 UTC |
| ef1ddef | deren | 18 January 2016, 23:20:02 UTC | filters all very cleaned up and working for SE data | 18 January 2016, 23:20:02 UTC |
| 39a8443 | deren | 18 January 2016, 23:19:34 UTC | h5py File needs to stay open until done with array. | 18 January 2016, 23:19:34 UTC |
| 6e6d692 | deren | 18 January 2016, 17:52:00 UTC | mergefix | 18 January 2016, 17:52:00 UTC |
| cc9cdb8 | deren | 18 January 2016, 17:50:08 UTC | cleanup of consens and some format conversions | 18 January 2016, 17:50:08 UTC |
| 778ad0a | isaacovercast | 17 January 2016, 20:23:28 UTC | Wrapped main body of refmap() in a try so we can guarantee cleanup of tmp files | 17 January 2016, 20:23:28 UTC |
| a05cd8f | isaacovercast | 17 January 2016, 19:07:00 UTC | Fixed show results mode | 17 January 2016, 19:07:00 UTC |
| 86e8ace | isaacovercast | 17 January 2016, 18:56:17 UTC | Changes to tuplecheck and how edit_cutsites is handled by set_param to allow for it to be a tuple of either strings or ints. | 17 January 2016, 18:56:17 UTC |
| a007c62 | isaacovercast | 17 January 2016, 02:56:14 UTC | include mpi4py in meta.yaml | 17 January 2016, 02:56:14 UTC |
| 64fa19d | isaacovercast | 17 January 2016, 02:40:54 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 17 January 2016, 02:40:54 UTC |
| f03fbcd | isaacovercast | 17 January 2016, 02:39:32 UTC | Fixed write_params to write out lists and tuples as comma separated values. Also fixed paramschecker for edit_cutsites to test for tuple of ints vs tuple of strings and cast the param value accordingly. | 17 January 2016, 02:39:32 UTC |
| 1267b70 | isaacovercast | 17 January 2016, 02:38:06 UTC | cleaning up cli assembly loading | 17 January 2016, 02:38:06 UTC |
| e766e6a | deren | 17 January 2016, 01:28:02 UTC | "Updating ipyrad/__init__.py to version - 0.1.22 | 17 January 2016, 01:28:02 UTC |
| 69d9bc1 | deren | 17 January 2016, 01:27:47 UTC | catgs are now hdf5, much less disk overhead. cluster_wihtin raises error if all clusters fail align. | 17 January 2016, 01:27:47 UTC |
| c9d3129 | deren | 17 January 2016, 00:12:33 UTC | "Updating ipyrad/__init__.py to version - 0.1.21 | 17 January 2016, 00:12:33 UTC |
| 99fd28e | deren | 17 January 2016, 00:11:56 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 17 January 2016, 00:11:56 UTC |
| 2ee8007 | deren | 17 January 2016, 00:11:33 UTC | added mpi4py, and ipyparallel update. | 17 January 2016, 00:11:33 UTC |
| 5273dce | deren | 17 January 2016, 00:10:30 UTC | set data.dirs.working to working default if not changed | 17 January 2016, 00:10:30 UTC |
| 7b84378 | isaacovercast | 16 January 2016, 22:12:15 UTC | Added more error handling to paramschecker. Fixed a bug during keyboard interrupt handling of _clientwrapper | 16 January 2016, 22:12:15 UTC |
| 2be7bc2 | isaacovercast | 16 January 2016, 19:33:28 UTC | Fixed test_assembly to test the hackersonly dict as well. | 16 January 2016, 19:33:28 UTC |
| 2f406b8 | isaacovercast | 16 January 2016, 19:25:33 UTC | Added a \n to output of cathaps to handle variable length clusters. Bug fixes to consens_se. | 16 January 2016, 19:25:33 UTC |
| 9319416 | deren | 15 January 2016, 22:08:04 UTC | "Updating ipyrad/__init__.py to version - 0.1.20 | 15 January 2016, 22:08:04 UTC |
| 47d9f87 | deren | 15 January 2016, 22:07:25 UTC | handling exits in step3 | 15 January 2016, 22:07:25 UTC |
| 57ccb49 | deren | 14 January 2016, 20:10:23 UTC | "Updating ipyrad/__init__.py to version - 0.1.19 | 14 January 2016, 20:10:23 UTC |
| af8ee87 | deren | 14 January 2016, 20:10:17 UTC | exceptions bypass missing utemp fail of individual samples in step3 for denovo | 14 January 2016, 20:10:17 UTC |
| 1f7c160 | deren | 14 January 2016, 19:35:24 UTC | raise error to exit build_clusters when no utemp file | 14 January 2016, 19:35:24 UTC |
| 9b36b21 | deren | 14 January 2016, 19:28:27 UTC | "Updating ipyrad/__init__.py to version - 0.1.19 | 14 January 2016, 19:28:27 UTC |
| e47a0ce | deren | 14 January 2016, 19:27:32 UTC | cosmetic cleanup | 14 January 2016, 19:27:32 UTC |
| 4fe4d36 | deren | 14 January 2016, 19:27:05 UTC | kill leftover engines in step3 | 14 January 2016, 19:27:05 UTC |
| c4f0811 | deren | 14 January 2016, 19:16:38 UTC | added pseudo-code for node-balanced threading | 14 January 2016, 19:16:38 UTC |
| 0a82339 | deren | 14 January 2016, 18:53:19 UTC | cosmetic changes + Exceptions moved to util | 14 January 2016, 18:53:19 UTC |
| b21dd00 | isaacovercast | 14 January 2016, 02:59:22 UTC | Added code to fetch the key as specified in the params.txt file rather than using range. CLI is still busted but i'm working on it. | 14 January 2016, 02:59:22 UTC |
| dfa6d09 | isaacovercast | 14 January 2016, 02:54:16 UTC | Removed a couple print statements. Oops! | 14 January 2016, 02:54:16 UTC |
| 64c16b8 | isaacovercast | 14 January 2016, 02:37:53 UTC | Removed newparamsfile.py and references to it in __main__ and assembly. | 14 January 2016, 02:37:53 UTC |
| b7daba1 | isaacovercast | 14 January 2016, 02:30:03 UTC | Significant modification to the new params.txt creation process. Added a function to assembly called write_params(). It writes out the current assembly config in params.txt format to whatever location you specify. Updated __main__ to take advantage of this, so new params.txt file is created automatically from a clean current Assembly object. write_params() pulls in short descriptions from paramsinfo. | 14 January 2016, 02:30:03 UTC |
| 37cd68d | isaacovercast | 13 January 2016, 21:30:30 UTC | Fixed order of all the params, fixed naming and indices. Did not fix all descriptions yet. | 13 January 2016, 21:30:30 UTC |
| c82822e | isaacovercast | 13 January 2016, 19:28:07 UTC | updated default size of preview_truncate_length to help ensure preview mode samples have enough reads to cluster properly (#72). Added a little error message to help in the event utemp is empty. | 13 January 2016, 19:28:07 UTC |
| 4eb8de1 | isaacovercast | 13 January 2016, 18:23:36 UTC | Added code to test for empty utemp file in build_clusters(). It just does a sys.exit for now, but at least it catches this bug. | 13 January 2016, 18:23:36 UTC |
| b441076 | isaacovercast | 13 January 2016, 16:47:17 UTC | Moved cleanup of tmp sample tmpcat and tmpcons files to a finally block in cleanup(). | 13 January 2016, 16:47:17 UTC |
| 791362f | isaacovercast | 13 January 2016, 15:56:10 UTC | Fixed bug in build_clusters, was crashing step3 | 13 January 2016, 15:56:10 UTC |
| 07a9cb1 | isaacovercast | 13 January 2016, 15:05:11 UTC | "Updating ipyrad/__init__.py to version - 0.1.18 | 13 January 2016, 15:05:11 UTC |
| 282a9c8 | isaacovercast | 13 January 2016, 15:03:59 UTC | Changed the naming convention of temp files for preview | 13 January 2016, 15:03:59 UTC |
| 4f278cf | isaacovercast | 13 January 2016, 14:45:00 UTC | Added code to test and update assemblies on load. Also fixed a couple calls to outdated params in write_outfiles. | 13 January 2016, 14:45:00 UTC |
| 94408ab | isaacovercast | 12 January 2016, 21:23:45 UTC | Fixed merge conflict. Also added -f flags to the calls to gzip so it wouldn't prompt if the fastq files already exist, which they do if you run it with the force flag. Merge branch 'master' of https://github.com/dereneaton/ipyrad Conflicts: ipyrad/assemble/demultiplex.py | 12 January 2016, 21:23:45 UTC |
| c34d023 | isaacovercast | 12 January 2016, 20:50:11 UTC | Added preview to the steps | 12 January 2016, 20:50:11 UTC |
| 8f5beb8 | isaacovercast | 12 January 2016, 20:43:02 UTC | Moved preview_truncate_file to util.py. Updated the tmp directory it writes temp files to (now writes to data.dirs.working). and changed the location of preview data truncation so it comes before parallel chunking, runs much faster now. | 12 January 2016, 20:43:02 UTC |
| d83d203 | deren | 12 January 2016, 01:46:06 UTC | "Updating ipyrad/__init__.py to version - 0.1.17 | 12 January 2016, 01:46:06 UTC |
| 269c56a | deren | 12 January 2016, 01:45:50 UTC | debugger | 12 January 2016, 01:45:50 UTC |
| 463e05a | deren | 12 January 2016, 01:45:27 UTC | still working on indels | 12 January 2016, 01:45:27 UTC |
| 7157751 | deren | 12 January 2016, 01:45:10 UTC | fix to leftlimit trim filter for gbs | 12 January 2016, 01:45:10 UTC |
| 3947c5e | deren | 12 January 2016, 01:14:23 UTC | "Updating ipyrad/__init__.py to version - 0.1.16 | 12 January 2016, 01:14:23 UTC |
| 03dcec8 | deren | 12 January 2016, 01:14:13 UTC | "Updating ipyrad/__init__.py to version - 0.1.6 | 12 January 2016, 01:14:13 UTC |
| 7607831 | deren | 12 January 2016, 01:13:22 UTC | "Updating ipyrad/__init__.py to version - 0.1.14 | 12 January 2016, 01:13:22 UTC |
| 2ed92b5 | deren | 12 January 2016, 01:13:08 UTC | cutoff at maxdepth if use_maxdepth | 12 January 2016, 01:13:08 UTC |
| a72501b | deren | 12 January 2016, 01:12:41 UTC | no longer needed worker.py | 12 January 2016, 01:12:41 UTC |
| fa15b34 | deren | 12 January 2016, 01:12:20 UTC | better optim handling | 12 January 2016, 01:12:20 UTC |
| 2e13f25 | deren | 12 January 2016, 01:12:02 UTC | indel filters added and trimming of merged pairgbs after alignment | 12 January 2016, 01:12:02 UTC |
| 051fdc6 | deren | 12 January 2016, 00:32:37 UTC | started on statsfiles property. | 12 January 2016, 00:32:37 UTC |
| 4b1a97b | deren | 12 January 2016, 00:31:49 UTC | moved ObjDict to util | 12 January 2016, 00:31:49 UTC |
| 0ce28ba | deren | 12 January 2016, 00:31:38 UTC | rawedit now uses chunk tmpdir | 12 January 2016, 00:31:38 UTC |
| 49c1289 | deren | 12 January 2016, 00:30:03 UTC | unparallelized disk limited funcs | 12 January 2016, 00:30:03 UTC |
| 2bf6a1d | deren | 12 January 2016, 00:29:17 UTC | debug back | 12 January 2016, 00:29:17 UTC |
| 78ff2bc | deren | 11 January 2016, 23:13:02 UTC | commenting out indel array for now | 11 January 2016, 23:13:02 UTC |
| e0d7c10 | deren | 11 January 2016, 23:12:28 UTC | starting on statsfiles storage | 11 January 2016, 23:12:28 UTC |
| 925ec0a | isaacovercast | 11 January 2016, 22:24:51 UTC | "Updating ipyrad/__init__.py to version - 0.1.15 | 11 January 2016, 22:24:51 UTC |
| 8062388 | isaacovercast | 11 January 2016, 22:24:29 UTC | Fixed it for real this time. Also i made it smarter. | 11 January 2016, 22:24:29 UTC |
| 2d4e6d3 | isaacovercast | 11 January 2016, 22:08:32 UTC | oops! | 11 January 2016, 22:08:32 UTC |
| 9f7c33f | isaacovercast | 11 January 2016, 22:05:57 UTC | "Updating ipyrad/__init__.py to version - 0.1.14 | 11 January 2016, 22:05:57 UTC |
| 930942f | isaacovercast | 11 January 2016, 22:05:33 UTC | Another stupid control flow bug. | 11 January 2016, 22:05:33 UTC |
| 09bb219 | isaacovercast | 11 January 2016, 22:03:16 UTC | Fixed a dumb bug in versioner.py | 11 January 2016, 22:03:16 UTC |
| 07f2e1a | deren | 11 January 2016, 22:03:03 UTC | hide debugging | 11 January 2016, 22:03:03 UTC |
| c8d2b98 | isaacovercast | 11 January 2016, 22:02:03 UTC | Moved git tag script to versioner.py and updated so it hax the default log level too. | 11 January 2016, 22:02:03 UTC |
| c574c92 | isaacovercast | 11 January 2016, 18:21:52 UTC | loci2migrate is still broken. I added an early return and a debug message just so it won't prevent step7 from finishing. | 11 January 2016, 18:21:52 UTC |
| d0d8190 | isaacovercast | 11 January 2016, 17:59:21 UTC | Removed a bunch of debug code | 11 January 2016, 17:59:21 UTC |
| b5421b8 | isaacovercast | 11 January 2016, 17:53:45 UTC | step 7 now finishes and writes out most output files. | 11 January 2016, 17:53:45 UTC |
| 8587111 | deren | 11 January 2016, 17:17:40 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 11 January 2016, 17:17:40 UTC |
| 2646a37 | deren | 11 January 2016, 17:17:37 UTC | moving chunks to a tmp folder. Using global dicts in util. | 11 January 2016, 17:17:37 UTC |
| afb22d8 | deren | 11 January 2016, 17:16:51 UTC | nloci is counted and used in cluster_across | 11 January 2016, 17:16:51 UTC |
| 2aa075c | isaacovercast | 11 January 2016, 14:15:04 UTC | Fixed loci2phynex. Both phylip and nexus files write to outdir. Lookin good. Also fixed a bug in info output during file conversion in write_outfiles. | 11 January 2016, 14:15:04 UTC |
| b0a87ad | isaacovercast | 11 January 2016, 13:48:33 UTC | "Updating ipyrad/__init__.py to version - 0.1.13 | 11 January 2016, 13:48:33 UTC |
| 152c3c1 | isaacovercast | 11 January 2016, 13:47:26 UTC | Moved breakalleles() to from cluster_across to util. Added loci2alleles, tested and it work good. | 11 January 2016, 13:47:26 UTC |
| 0208815 | isaacovercast | 11 January 2016, 02:34:30 UTC | "Updating ipyrad/__init__.py to version - 0.1.12 | 11 January 2016, 02:34:30 UTC |
| 4c3a161 | isaacovercast | 11 January 2016, 02:33:49 UTC | Moved version munging code out of setup.py | 11 January 2016, 02:33:49 UTC |
| ed8118d | isaacovercast | 11 January 2016, 02:33:01 UTC | "Updating ipyrad/__init__.py to version - 0.1.11 | 11 January 2016, 02:33:01 UTC |
| d010250 | isaacovercast | 11 January 2016, 02:29:38 UTC | "Updating ipyrad/__init__.py to version - 0.1.10 | 11 January 2016, 02:29:38 UTC |
| 76bb777 | isaacovercast | 11 January 2016, 02:29:17 UTC | "Updating ipyrad/__init__.py to version - 0.1.9 | 11 January 2016, 02:29:17 UTC |
| 117fde5 | isaacovercast | 11 January 2016, 01:48:26 UTC | "Updating ipyrad/__init__.py toversion - 0.1.9 | 11 January 2016, 01:48:26 UTC |
