| 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 |
| 32d4119 | deren | 07 January 2016, 03:30:54 UTC | fix to broken rejoining of chunks at cleanup | 07 January 2016, 03:30:54 UTC |
| b2cf7e9 | isaacovercast | 07 January 2016, 03:01:30 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 07 January 2016, 03:01:30 UTC |
| 045369a | isaacovercast | 07 January 2016, 03:01:11 UTC | Fixed output formatting on two more parameters. good idea. | 07 January 2016, 03:01:11 UTC |
| 7bd83d7 | deren | 07 January 2016, 02:52:49 UTC | better exception handling in wrapper | 07 January 2016, 02:52:49 UTC |
| fa66134 | isaacovercast | 07 January 2016, 01:33:50 UTC | Adding a sim_popsfile for testing the population assignments. | 07 January 2016, 01:33:50 UTC |
| c174fd2 | isaacovercast | 07 January 2016, 01:09:27 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 07 January 2016, 01:09:27 UTC |
| b814d2f | isaacovercast | 07 January 2016, 01:08:04 UTC | Fixed preview mode for step3. Fixed a nasty bug with PE where reads that map too far apart were making the refmap process bomb. Fixed a stupid bug in util where i forgot to import sys, so merge was a little broken. | 07 January 2016, 01:08:04 UTC |
| 64d85bc | deren | 07 January 2016, 01:04:44 UTC | Merge branch 'supercat' Conflicts: ipyrad/file_conversion/loci2migrate.py | 07 January 2016, 01:04:44 UTC |
| dfb1278 | deren | 07 January 2016, 01:03:03 UTC | supercatg building, still lacks indels | 07 January 2016, 01:03:03 UTC |
| 299f895 | isaacovercast | 06 January 2016, 22:50:52 UTC | updated version to 0.0.8 | 06 January 2016, 22:50:52 UTC |
| 9b605bd | isaacovercast | 06 January 2016, 22:47:20 UTC | Fixed a bug i'd introduced for R2 for paired reads, when i switched from .gz to .fq i forgot to switch R2 as well, very simple stupid fix. | 06 January 2016, 22:47:20 UTC |
| d366e1a | isaacovercast | 06 January 2016, 21:05:37 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 06 January 2016, 21:05:37 UTC |
| 3c26884 | iovercast | 06 January 2016, 21:05:03 UTC | Bug in sending preview to demultiplex | 06 January 2016, 21:05:03 UTC |
| afde10c | isaacovercast | 06 January 2016, 20:30:43 UTC | Merge branch 'master' into refseq Conflicts: ipyrad/assemble/__init__.py | 06 January 2016, 20:30:43 UTC |
| 8cb7791 | isaacovercast | 06 January 2016, 20:28:45 UTC | Some debug code and dropped gzipping the unmapped reads. | 06 January 2016, 20:28:45 UTC |
| 5493bad | iovercast | 06 January 2016, 20:25:51 UTC | Preview of preview mode for steps 1 and 2. Seems to work okay. | 06 January 2016, 20:25:51 UTC |
| 916c017 | iovercast | 06 January 2016, 19:44:15 UTC | Oops fixed formatting bug | 06 January 2016, 19:44:15 UTC |
| 8b92369 | iovercast | 06 January 2016, 19:21:31 UTC | Initial commit of vcf2loci, it doesn't even pretend to work yet, just fleshing out some ideas. | 06 January 2016, 19:21:31 UTC |
| 3c0fc4e | iovercast | 06 January 2016, 18:16:38 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad Conflicts: ipyrad/assemble/write_outfiles.py | 06 January 2016, 18:16:38 UTC |
| eb8d64a | iovercast | 06 January 2016, 18:14:31 UTC | Finished initial cleanup and migration of all loci2*.make() functions. Still needs testing. | 06 January 2016, 18:14:31 UTC |
| 317541c | deren | 06 January 2016, 16:32:36 UTC | commented out ', r' in path string | 06 January 2016, 16:32:36 UTC |
| ca11bf5 | deren | 06 January 2016, 16:31:13 UTC | fix to key/sample selection | 06 January 2016, 16:31:13 UTC |
| 551cd6f | iovercast | 06 January 2016, 14:28:23 UTC | Added new parameter pop_assign_file, and link_populations() function to populate the assembly.populations dict. Fixes tic #42 | 06 January 2016, 14:28:23 UTC |
| cff841d | iovercast | 05 January 2016, 03:41:06 UTC | Continuing revisions on step7, fixed loci2vcf and loci2phynex. Minor changes to loci2treemix and loci2migrate, still needs more work. Updated write_outfiles to do something "smart" with formatting output files, now you can add a new output format by updated the output_formats variable and creating a file in file_conversion called loci2*whatever.py that defines a make() function that takes assembly and samples list as arguments. | 05 January 2016, 03:41:06 UTC |
| b0bda2d | iovercast | 05 January 2016, 00:37:02 UTC | Step 7 - Added an 'output_files' parameter to assembly. Added the write_outfiles module to do the heavy lifting. Included the list of possible output files as a global at the top of write_outfiles, for convenience. Also imported all the old loci2* file conversion code, though none of it works yet. | 05 January 2016, 00:37:02 UTC |
| 733782e | iovercast | 04 January 2016, 21:55:24 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 04 January 2016, 21:55:24 UTC |
| cf8ccb4 | iovercast | 04 January 2016, 21:54:20 UTC | Added code to run step7(), also added a function to read convert sample names list to list of sample objects so all step*() functions now handle this identically. | 04 January 2016, 21:54:20 UTC |
| 89e239c | deren | 04 January 2016, 20:30:57 UTC | cleanup of test files | 04 January 2016, 20:30:57 UTC |
| 30dccac | deren | 04 January 2016, 20:30:12 UTC | test_rad 1-6 | 04 January 2016, 20:30:12 UTC |
| 22793b5 | deren | 04 January 2016, 20:29:43 UTC | fix for defaults in step5 when step4 is skipped | 04 January 2016, 20:29:43 UTC |
| 848355d | deren | 04 January 2016, 19:02:39 UTC | fixed merge conflicts in cluster_within, consens_se and rawedit | 04 January 2016, 19:02:39 UTC |
| 2f4c4c5 | deren | 04 January 2016, 18:49:01 UTC | new order of params. New set_params. New catching for IPClusterError | 04 January 2016, 18:49:01 UTC |
| af1e53b | isaacovercast | 28 December 2015, 22:14:17 UTC | Merge branch 'master' into refseq | 28 December 2015, 22:14:17 UTC |
| 7296a37 | iovercast | 28 December 2015, 22:10:22 UTC | Fix rawedit to _not_ gzip tmp files, and also not to gzip the edits file Seems to work ok, through step3 | 28 December 2015, 22:10:22 UTC |
| 8b39d1a | isaacovercast | 28 December 2015, 21:04:25 UTC | Fixed a stupid mistake that made PE work but broke SE. Works again | 28 December 2015, 21:04:25 UTC |
| be40668 | isaacovercast | 27 December 2015, 02:48:28 UTC | Fixed all PE merging. Moved reference sequence indexing to refmap.py | 27 December 2015, 02:48:28 UTC |
| 167897f | isaacovercast | 26 December 2015, 23:24:38 UTC | fixed refmap to work with new assembly.bins.* format | 26 December 2015, 23:24:38 UTC |
| dba79c6 | isaacovercast | 26 December 2015, 21:23:57 UTC | Big merge of master into refseq to incorporate refactoring changes Merge branch 'master' of https://github.com/dereneaton/ipyrad into tmpref Conflicts: ipyrad/assemble/__init__.py ipyrad/assemble/cluster_across.py ipyrad/assemble/cluster_within.py ipyrad/assemble/util.py ipyrad/core/assembly.py | 26 December 2015, 21:23:57 UTC |
| 2b61418 | isaacovercast | 26 December 2015, 21:15:27 UTC | wat | 26 December 2015, 21:15:27 UTC |
| 2a43ec7 | iovercast | 26 December 2015, 20:56:41 UTC | Created a new function in util.py called merge_pairs, it takes data, sample, and a tuple of files to merge as args and returns the merged file path, and the number of reads successfully merged. Refactored cluster_within to use the new format. | 26 December 2015, 20:56:41 UTC |
| b27cedb | isaacovercast | 25 December 2015, 20:51:24 UTC | got refmapping working for PE, finalize() still doesn't work. | 25 December 2015, 20:51:24 UTC |
| 21fdd4c | isaacovercast | 25 December 2015, 03:15:08 UTC | Finished mod'ing refmap to handle PE. | 25 December 2015, 03:15:08 UTC |
| 7cc6a3a | iovercast | 25 December 2015, 02:30:16 UTC | Cherry-picked the commit introducing util.py Refactored a bunch of code to move common functions into ipyrad/assemble/util.py Moved functions include ambigcutters() comp() getoptim() getsplits() revcomp() unhetero() uplow() and zcat_make_temps(). Conflicts: ipyrad/assemble/__init__.py ipyrad/assemble/cluster_across.py ipyrad/assemble/cluster_within.py ipyrad/assemble/rawedit.py | 25 December 2015, 02:44:10 UTC |
| 1c8bf13 | iovercast | 25 December 2015, 02:30:16 UTC | Refactored a bunch of code to move common functions into ipyrad/assemble/util.py Moved functions include ambigcutters() comp() getoptim() getsplits() revcomp() unhetero() uplow() and zcat_make_temps(). | 25 December 2015, 02:30:16 UTC |
