| 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 Also fixed a couple calls to outdated params in write_outfiles.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 |
| 6acef07 | isaacovercast | 11 January 2016, 01:48:21 UTC | "Updating ipyrad/__init__.py toversion - 0.1.8 | 11 January 2016, 01:48:21 UTC |
| 910dd38 | isaacovercast | 11 January 2016, 01:45:44 UTC | Major revisions to write_outfiles, filtering all works and writes to .loci very nicely. | 11 January 2016, 01:45:44 UTC |
| 1a73f9c | deren | 10 January 2016, 23:05:05 UTC | "Updating ipyrad/__init__.py toversion - 0.1.9 | 10 January 2016, 23:05:05 UTC |
| 4320468 | deren | 10 January 2016, 23:01:30 UTC | starting to build statsfiles attributes to Sample | 10 January 2016, 23:01:30 UTC |
| ff4d8e7 | deren | 10 January 2016, 22:52:02 UTC | populations can be linked as a dict. minsamp -> min_samples_locus; ploidy -> max_alleles_consens; max_shared_heterozygosity -> max_shared_Hs_locus. Some improved docstrings. | 10 January 2016, 22:52:02 UTC |
| e1bfa3c | deren | 10 January 2016, 22:50:38 UTC | added some missing modules | 10 January 2016, 22:50:38 UTC |
| e5466c1 | deren | 10 January 2016, 22:50:16 UTC | made AMBIG dict global | 10 January 2016, 22:50:16 UTC |
| d8daf17 | deren | 10 January 2016, 22:49:48 UTC | changed ploidy to max_alleles_consens | 10 January 2016, 22:49:48 UTC |
| 4c260ed | deren | 10 January 2016, 22:49:28 UTC | speed improvement from not gzipping tmps | 10 January 2016, 22:49:28 UTC |
| 97b8460 | deren | 10 January 2016, 22:48:47 UTC | changed ploidy to max_alleles_consens | 10 January 2016, 22:48:47 UTC |
| b2ffaec | deren | 10 January 2016, 22:48:27 UTC | cosmetic code fixes | 10 January 2016, 22:48:27 UTC |
| 1e890c6 | deren | 10 January 2016, 19:01:23 UTC | merge conflict resolved | 10 January 2016, 19:01:23 UTC |
| 82ea254 | deren | 10 January 2016, 18:59:02 UTC | ipython 4.0.1 seems ok | 10 January 2016, 18:59:02 UTC |
| 799e600 | deren | 10 January 2016, 18:58:27 UTC | require state=6 | 10 January 2016, 18:58:27 UTC |
| 8b75d47 | deren | 10 January 2016, 18:58:07 UTC | cleanup code added | 10 January 2016, 18:58:07 UTC |
| 1485c1c | isaacovercast | 10 January 2016, 01:33:27 UTC | Added update to set sample.stats.state to 6 upon completion of clustering | 10 January 2016, 01:33:27 UTC |
| dc14219 | isaacovercast | 10 January 2016, 01:17:07 UTC | Fixed bug in assembly. step7func was testing for data.dirs.outdir, if not exist then it's an attribute doesn't exist error. | 10 January 2016, 01:17:07 UTC |
| 8a22b36 | isaacovercast | 10 January 2016, 00:54:48 UTC | Ooops, missed close perens on the new params | 10 January 2016, 00:54:48 UTC |
| 7a29024 | isaacovercast | 10 January 2016, 00:09:26 UTC | "Updating ipyrad/__init__.py toversion - 0.1.8 | 10 January 2016, 00:09:26 UTC |
| 88d404e | isaacovercast | 10 January 2016, 00:06:42 UTC | Added excludes and outgroups to paramsdict. | 10 January 2016, 00:06:42 UTC |
| cda9c2d | isaacovercast | 09 January 2016, 19:16:56 UTC | Finished filter on excludes/outgroups and filter on minsamp | 09 January 2016, 19:16:56 UTC |
| f190323 | isaacovercast | 09 January 2016, 17:40:48 UTC | Filling in write_output, i'm thinking this module needs a name change. All the moving parts are in place, just needs to be filled in. | 09 January 2016, 17:40:48 UTC |
| 523cb60 | deren | 08 January 2016, 22:31:52 UTC | "Updating ipyrad/__init__.py toversion - 0.1.6 | 08 January 2016, 22:31:52 UTC |
| 38475a7 | deren | 08 January 2016, 22:30:28 UTC | working on reordering, still not right | 08 January 2016, 22:30:28 UTC |
| 009ea24 | deren | 08 January 2016, 22:30:13 UTC | raise error if no samples in link_fastqs | 08 January 2016, 22:30:13 UTC |
| d37576f | deren | 08 January 2016, 22:29:25 UTC | cleanup of zcat_make_temps | 08 January 2016, 22:29:25 UTC |
| afc5fc4 | deren | 08 January 2016, 22:29:03 UTC | big fix for variable length barcodes | 08 January 2016, 22:29:03 UTC |
| f66c24d | deren | 08 January 2016, 03:08:07 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 08 January 2016, 03:08:07 UTC |
| e3a9137 | deren | 08 January 2016, 03:06:50 UTC | removed prefix name, CLI is probably broken at the moment until fixed. | 08 January 2016, 03:06:50 UTC |
| 8fee5b9 | deren | 08 January 2016, 03:06:11 UTC | fixed merge revcomps. Cleanup of zcat_make_temps | 08 January 2016, 03:06:11 UTC |
| 390622b | deren | 08 January 2016, 03:05:29 UTC | improvement of 'cov' parameter for cleaner matching of gbs overlaps | 08 January 2016, 03:05:29 UTC |
| 69b8493 | deren | 08 January 2016, 03:04:50 UTC | lots of code cleanup of early ipyparallel | 08 January 2016, 03:04:50 UTC |
| f2a1974 | deren | 08 January 2016, 03:04:27 UTC | singlecat handles double hits | 08 January 2016, 03:04:27 UTC |
| c28d46b | isaacovercast | 08 January 2016, 02:39:52 UTC | "Updating ipyrad/__init__.py toversion - 0.1.5 | 08 January 2016, 02:39:52 UTC |
| f523075 | isaacovercast | 08 January 2016, 02:18:02 UTC | Fixed tagging in setup.py | 08 January 2016, 02:18:02 UTC |
| e29429b | isaacovercast | 08 January 2016, 02:15:01 UTC | Added code to setup.py to automatically update ipyrad/__init__.py __version__. | 08 January 2016, 02:15:01 UTC |
| 6bf37eb | deren | 08 January 2016, 00:40:05 UTC | Merge branch 'outfiles_start' | 08 January 2016, 00:40:05 UTC |
| 89d844a | deren | 08 January 2016, 00:39:30 UTC | fix to revcomp for read merges | 08 January 2016, 00:39:30 UTC |
| 7b2e49a | deren | 08 January 2016, 00:17:11 UTC | fix to merger with revcomp | 08 January 2016, 00:17:11 UTC |
| 76a1a92 | deren | 07 January 2016, 23:58:33 UTC | starting on step7 | 07 January 2016, 23:58:33 UTC |
| f3382e4 | deren | 07 January 2016, 22:22:34 UTC | raise error and return names for bad samples names in _get_samples() | 07 January 2016, 22:22:34 UTC |
| dc1d5bf | deren | 07 January 2016, 21:42:05 UTC | fix to merge conflict | 07 January 2016, 21:42:05 UTC |
| 74bf439 | deren | 07 January 2016, 21:39:36 UTC | improved Error handling. Doc strings for step funcs | 07 January 2016, 21:39:36 UTC |
| 9590478 | deren | 07 January 2016, 21:38:50 UTC | fix to Sample handling and cleanup | 07 January 2016, 21:38:50 UTC |
| 71618e9 | deren | 07 January 2016, 21:38:16 UTC | better optim | 07 January 2016, 21:38:16 UTC |
| f2c382b | deren | 07 January 2016, 21:37:59 UTC | better optim, close open file. | 07 January 2016, 21:37:59 UTC |
| 9731e1f | isaacovercast | 07 January 2016, 21:25:04 UTC | Set consens_se to read from hackersdict["max_fragment_length"] | 07 January 2016, 21:25:04 UTC |
| 27bcf87 | isaacovercast | 07 January 2016, 20:30:50 UTC | updated to 0.1.0 | 07 January 2016, 20:30:50 UTC |
| d005266 | isaacovercast | 07 January 2016, 20:29:30 UTC | Removed some old global variable crust replaced by hackersonly | 07 January 2016, 20:29:30 UTC |
| 3e5b860 | isaacovercast | 07 January 2016, 20:28:34 UTC | Added hackersonly dict to assembly and also added a data._version stamp. Updated refmap, cluster_accross, and loci2SNP to use the new hackersonly params | 07 January 2016, 20:28:34 UTC |
| 8256059 | isaacovercast | 07 January 2016, 17:30:27 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 07 January 2016, 17:30:27 UTC |
| 776811d | isaacovercast | 07 January 2016, 17:30:04 UTC | Implemented 'denovo_only' assembly method. | 07 January 2016, 17:30:04 UTC |
| 1fbd901 | deren | 07 January 2016, 03:34:02 UTC | cleaning up some exception handling code | 07 January 2016, 03:34:02 UTC |
