| 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 |
| 3ea0e03 | deren | 19 January 2016, 21:55:32 UTC | changed pair separator from ssss to nnnn | 19 January 2016, 21:55:32 UTC |
| 6e991e6 | deren | 19 January 2016, 17:18:51 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 19 January 2016, 17:18:51 UTC |
| 9c38edc | deren | 19 January 2016, 17:18:48 UTC | cosmetic edits to step7 | 19 January 2016, 17:18:48 UTC |
| bb94bf2 | isaacovercast | 19 January 2016, 01:20:18 UTC | Better user notification for what's going on during reference sequence indexing. | 19 January 2016, 01:20:18 UTC |
| 726ec75 | isaacovercast | 19 January 2016, 01:19:27 UTC | Fixed keyboard interrupt handling for preview demultiplex to clean up preview files. Really fixed preview_truncate so it cleans up if it receives a ctrl+c while it's splitting the file. | 19 January 2016, 01:19:27 UTC |
| 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 |
