| 2682729 | deren | 12 February 2016, 01:26:03 UTC | "Updating ipyrad/__init__.py to version - 0.1.42 | 12 February 2016, 01:26:03 UTC |
| 707bf25 | deren | 12 February 2016, 01:25:53 UTC | resolve merge conflict | 12 February 2016, 01:25:53 UTC |
| e77e421 | deren | 12 February 2016, 01:18:54 UTC | doubles count of merged reads | 12 February 2016, 01:18:54 UTC |
| b7b4a9c | deren | 12 February 2016, 01:18:39 UTC | merge pairs parallelized and with suffix | 12 February 2016, 01:18:39 UTC |
| 642b151 | isaacovercast | 12 February 2016, 01:18:05 UTC | CLI branching works now | 12 February 2016, 01:18:05 UTC |
| 441c743 | deren | 12 February 2016, 01:18:00 UTC | rigorous testing and improvements to clustering of pairgbs | 12 February 2016, 01:18:00 UTC |
| 79ca81e | deren | 12 February 2016, 01:17:27 UTC | simple cleanup | 12 February 2016, 01:17:27 UTC |
| ce1db7c | deren | 12 February 2016, 01:15:50 UTC | simplification of logger | 12 February 2016, 01:15:50 UTC |
| b21be9f | isaacovercast | 12 February 2016, 01:08:13 UTC | Refactored preview_truncate_fq so now it actually works for all steps 1,2&3 added a third parameter that defaults to using 10% of the passed in file. Updated demult, rawed, and clust_wi in accordance. Also added try/except around shutil.rmtree calls to protect against the stupid nfs bug i was seeing. | 12 February 2016, 01:08:13 UTC |
| e277fc1 | deren | 12 February 2016, 00:13:04 UTC | need to build tests still, but getting closer.. | 12 February 2016, 00:13:04 UTC |
| be4d379 | deren | 11 February 2016, 23:09:57 UTC | upgrade vsearch. Read merging now parallelized | 11 February 2016, 23:09:57 UTC |
| 2563349 | isaacovercast | 11 February 2016, 22:02:23 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 11 February 2016, 22:02:23 UTC |
| a6fb904 | deren | 11 February 2016, 19:06:53 UTC | "Updating ipyrad/__init__.py to version - 0.1.41 | 11 February 2016, 19:06:53 UTC |
| 34d4c5b | deren | 11 February 2016, 19:06:22 UTC | removed old vsearch | 11 February 2016, 19:06:22 UTC |
| 8f835dd | deren | 11 February 2016, 19:04:51 UTC | upgrade vsearch to v.1.9.10. | 11 February 2016, 19:04:51 UTC |
| 8d23f91 | deren | 11 February 2016, 18:42:12 UTC | some prettier printing for cli and for Errors. Better handling of edit_cutsites tuple | 11 February 2016, 18:42:12 UTC |
| 5597606 | deren | 11 February 2016, 18:41:40 UTC | get sample file names for truncate from sample.name not sample.files.fastqs since fastqs are not necessarily in projdir/name_fastqs/ when step1 links_fastqs instead of demultiplexing | 11 February 2016, 18:41:40 UTC |
| 2753fb5 | deren | 11 February 2016, 18:40:29 UTC | chdir into proj dir when creating new assembly, but stay in cur dir if just loading and load it from the full path to projdir/name | 11 February 2016, 18:40:29 UTC |
| 4a221b2 | isaacovercast | 11 February 2016, 18:17:50 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 11 February 2016, 18:17:50 UTC |
| cf75eba | isaacovercast | 11 February 2016, 18:17:37 UTC | Error handling in assembly, and mostly done on -b for CLI | 11 February 2016, 18:17:37 UTC |
| 0c2b76f | deren | 11 February 2016, 17:50:17 UTC | "Updating ipyrad/__init__.py to version - 0.1.40 | 11 February 2016, 17:50:17 UTC |
| 507bca5 | deren | 11 February 2016, 17:49:58 UTC | not in curdir, so don't collapse curdir path. print full path to assembly object | 11 February 2016, 17:49:58 UTC |
| e8ecfe8 | deren | 11 February 2016, 17:49:31 UTC | bug fix for too many open files, was loading multiple ip clients | 11 February 2016, 17:49:31 UTC |
| 6b786d0 | deren | 11 February 2016, 17:49:00 UTC | correct orientation for unmerged pairs | 11 February 2016, 17:49:00 UTC |
| 5e68f2a | deren | 11 February 2016, 17:48:41 UTC | loads assembly object from project_dir | 11 February 2016, 17:48:41 UTC |
| 16091d2 | deren | 11 February 2016, 17:19:27 UTC | step2 does not do link_fastqs, but instead raises warning that step1 should be run | 11 February 2016, 17:19:27 UTC |
| 290a917 | deren | 11 February 2016, 17:19:02 UTC | correct orientation of non-merged pairs | 11 February 2016, 17:19:02 UTC |
| ecadfae | deren | 11 February 2016, 17:18:20 UTC | -n flag takes a name argument | 11 February 2016, 17:18:20 UTC |
| 1fde58e | deren | 11 February 2016, 15:52:28 UTC | merge fix | 11 February 2016, 15:52:28 UTC |
| b49a125 | isaacovercast | 11 February 2016, 02:26:09 UTC | oops. bad syntax fixed in cluster_within. | 11 February 2016, 02:26:09 UTC |
| 6df9bfe | isaacovercast | 11 February 2016, 02:23:16 UTC | Cosmetic merge fixes to documentation/print statements Merge branch 'master' of https://github.com/dereneaton/ipyrad Conflicts: ipyrad/__main__.py ipyrad/core/assembly.py | 11 February 2016, 02:23:16 UTC |
| e372b4e | isaacovercast | 11 February 2016, 02:17:14 UTC | 2/3 done with -b branching for cli | 11 February 2016, 02:17:14 UTC |
| cb8432b | isaacovercast | 11 February 2016, 02:16:00 UTC | Fixed #108 (handle all-indel reverse gbs reads) | 11 February 2016, 02:16:00 UTC |
| 9bebc62 | deren | 11 February 2016, 02:00:13 UTC | "Updating ipyrad/__init__.py to version - 0.1.39 | 11 February 2016, 02:00:13 UTC |
| 943f3a8 | deren | 11 February 2016, 01:59:39 UTC | never need to launch during load. Old idea. | 11 February 2016, 01:59:39 UTC |
| 2492d42 | deren | 11 February 2016, 01:59:11 UTC | faster connection to known number of cores. Cleaner interface to data._ipcluster dict. | 11 February 2016, 01:59:11 UTC |
| 562878d | deren | 11 February 2016, 01:58:38 UTC | new launch command. Better handling for bad params args. Empty defaults for paths params. | 11 February 2016, 01:58:38 UTC |
| a17e3af | deren | 11 February 2016, 01:57:53 UTC | IPyradWarningExit acts like sys.exit | 11 February 2016, 01:57:53 UTC |
| 9a2d839 | deren | 11 February 2016, 01:57:30 UTC | better handling for finding input files | 11 February 2016, 01:57:30 UTC |
| 554ef1d | deren | 11 February 2016, 01:56:58 UTC | no longer launch during load. ipcluster args are in a dict attribute of data. | 11 February 2016, 01:56:58 UTC |
| 5c6176d | Isaac | 09 February 2016, 22:50:50 UTC | Fixed call to stats() to output all samples instead of just a subset. | 09 February 2016, 22:50:50 UTC |
| dadc19a | deren | 09 February 2016, 00:17:33 UTC | cosmetic | 09 February 2016, 00:17:33 UTC |
| deb41c8 | deren | 08 February 2016, 16:13:17 UTC | "Updating ipyrad/__init__.py to version - 0.1.38 | 08 February 2016, 16:13:17 UTC |
| b324e2c | deren | 08 February 2016, 16:10:12 UTC | cosmetic | 08 February 2016, 16:10:12 UTC |
| ebdd2ea | deren | 08 February 2016, 16:09:47 UTC | s6 and s7 stats are assembly properties, not Sample properties | 08 February 2016, 16:09:47 UTC |
| e51a013 | deren | 08 February 2016, 16:09:19 UTC | can do MPI across nodes easy now with -ip flag | 08 February 2016, 16:09:19 UTC |
| a56f42e | deren | 08 February 2016, 16:08:40 UTC | cleaner launch for ipyparallel 5 | 08 February 2016, 16:08:40 UTC |
| a3a62cf | deren | 08 February 2016, 16:07:36 UTC | writes stats and saves DFs to Assembly | 08 February 2016, 16:07:36 UTC |
| ee6eb83 | deren | 08 February 2016, 16:07:01 UTC | commented out all numba for faster start for now | 08 February 2016, 16:07:01 UTC |
| fc7cc51 | deren | 08 February 2016, 16:06:45 UTC | cosmetic | 08 February 2016, 16:06:45 UTC |
| 50fbe87 | deren | 08 February 2016, 16:06:30 UTC | cleanup to prints from main | 08 February 2016, 16:06:30 UTC |
| 8d390fa | deren | 05 February 2016, 07:09:55 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 05 February 2016, 07:09:55 UTC |
| 0529868 | deren | 05 February 2016, 07:09:50 UTC | cosmetic fixes, and no auto add of * to sorted path | 05 February 2016, 07:09:50 UTC |
| 567e25a | isaacovercast | 05 February 2016, 02:34:13 UTC | added numba to meta.yaml | 05 February 2016, 02:34:13 UTC |
| 999f537 | isaacovercast | 03 February 2016, 16:11:00 UTC | Adding debug code | 03 February 2016, 16:11:00 UTC |
| b795524 | isaacovercast | 31 January 2016, 00:01:16 UTC | Error in ipyrad -n, can't use blank assembly names for tmp assembly anymore. | 31 January 2016, 00:01:16 UTC |
| 4895aa3 | isaacovercast | 30 January 2016, 23:47:24 UTC | Fixed conda recipe so it acually works. | 30 January 2016, 23:47:24 UTC |
| 22dc93e | isaacovercast | 29 January 2016, 00:58:46 UTC | "Updating ipyrad/__init__.py to version - 0.1.37 | 29 January 2016, 00:58:46 UTC |
| f1add56 | isaacovercast | 29 January 2016, 00:57:40 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad Conflicts: ipyrad/__main__.py ipyrad/core/assembly.py | 29 January 2016, 00:57:40 UTC |
| 7007f41 | isaacovercast | 29 January 2016, 00:54:27 UTC | set_params on assembly name now errors out with a helpful message. Assembly name is SET at creation time, and is "unmodifiable". This is through both the CLI and the API, so the behavior is consistent. Also added some error checking at Assembly.__init__, basically making sure the passed in name doesn't have spaces or special characters. | 29 January 2016, 00:54:27 UTC |
| d29090e | deren | 28 January 2016, 17:43:36 UTC | "Updating ipyrad/__init__.py to version - 0.1.36 | 28 January 2016, 17:43:36 UTC |
| a2f04c0 | deren | 28 January 2016, 17:43:20 UTC | pure cosmetic | 28 January 2016, 17:43:20 UTC |
| 511e88d | deren | 28 January 2016, 17:42:56 UTC | 'prefix' was not defined'. some cleanup | 28 January 2016, 17:42:56 UTC |
| f459706 | deren | 28 January 2016, 17:42:25 UTC | added an ip.__interactive__ attribute to know if you are in the CLI or not | 28 January 2016, 17:42:25 UTC |
| 9dcec38 | isaacovercast | 28 January 2016, 06:11:57 UTC | Fixing step1 preview not cleaning up preview files. in fact i fixed all preview mode file fsck not cleaning up. | 28 January 2016, 06:11:57 UTC |
| 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 |
