| f98bf4b | deren | 02 November 2016, 23:05:26 UTC | allow sample to fail without crashing | 02 November 2016, 23:05:26 UTC |
| 76a3d13 | deren | 02 November 2016, 23:05:14 UTC | cosmetic | 02 November 2016, 23:05:14 UTC |
| 2703439 | deren | 02 November 2016, 23:04:44 UTC | cleaner progress bar and enforced maxlen trimming of longer reads | 02 November 2016, 23:04:44 UTC |
| f34d935 | deren | 02 November 2016, 23:04:08 UTC | lowered maxlen addon, enforced maxlen trimming in singlecat | 02 November 2016, 23:04:08 UTC |
| a5422ca | isaacovercast | 02 November 2016, 17:39:02 UTC | Cosmetic docs change | 02 November 2016, 17:39:02 UTC |
| 00f3921 | isaacovercast | 02 November 2016, 16:24:22 UTC | cosmetic docs change | 02 November 2016, 16:24:22 UTC |
| 7f4704f | isaacovercast | 02 November 2016, 16:23:50 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 02 November 2016, 16:23:50 UTC |
| 8f78785 | isaacovercast | 02 November 2016, 16:23:42 UTC | cosmetic docs change | 02 November 2016, 16:23:42 UTC |
| 83b308b | deren | 02 November 2016, 14:32:20 UTC | updates to doc | 02 November 2016, 14:32:20 UTC |
| eebfb54 | deren | 02 November 2016, 14:22:08 UTC | updates to doc | 02 November 2016, 14:22:08 UTC |
| b850926 | deren | 02 November 2016, 14:13:37 UTC | updates to doc | 02 November 2016, 14:13:37 UTC |
| df60f6b | deren | 02 November 2016, 14:10:02 UTC | updates to doc | 02 November 2016, 14:10:02 UTC |
| 0993a08 | deren | 02 November 2016, 14:07:34 UTC | updates to doc | 02 November 2016, 14:07:34 UTC |
| caee106 | deren | 02 November 2016, 13:52:54 UTC | testing new maxlen calculation to better acommodate messy variable len paired data sets. | 02 November 2016, 13:52:54 UTC |
| c92eb40 | deren | 02 November 2016, 13:52:17 UTC | update to docs about pre-filtering | 02 November 2016, 13:52:17 UTC |
| ce25469 | deren | 02 November 2016, 13:51:56 UTC | temporary fix for mem limit in step 6 until maxlen is more refined | 02 November 2016, 13:51:56 UTC |
| c405f0a | isaacovercast | 31 October 2016, 21:39:18 UTC | Fix bug in refmap. | 31 October 2016, 21:39:18 UTC |
| 980dd39 | iovercast | 31 October 2016, 18:35:25 UTC | "Updating ipyrad/__init__.py to version - 0.4.6 | 31 October 2016, 18:35:25 UTC |
| c041709 | iovercast | 31 October 2016, 18:34:34 UTC | Nicely clean up temp files if refmap merge fails. | 31 October 2016, 18:34:34 UTC |
| 1ace3f1 | isaacovercast | 31 October 2016, 17:47:23 UTC | "Updating ipyrad/__init__.py to version - 0.4.5 | 31 October 2016, 17:47:23 UTC |
| 1cc6d89 | isaacovercast | 29 October 2016, 19:56:52 UTC | Add docs for running ipcluster by hand w/ MPI enabled. | 29 October 2016, 19:56:52 UTC |
| 0e4f20a | isaacovercast | 28 October 2016, 20:42:58 UTC | Fix PE refmap bug #148 | 28 October 2016, 20:42:58 UTC |
| 8380079 | isaacovercast | 27 October 2016, 01:12:59 UTC | Documenting PYTHONPATH bug that crops up occasionally. | 27 October 2016, 01:12:59 UTC |
| 0044ef9 | isaacovercast | 22 October 2016, 23:50:06 UTC | Adjusted fix to bgzip test. | 22 October 2016, 23:50:06 UTC |
| 57646c9 | isaacovercast | 22 October 2016, 23:34:50 UTC | Fixed a bug w/ testing for bgzip reference sequence. Also add code to fix how PE ref is handled to address #148. | 22 October 2016, 23:34:50 UTC |
| f4d7939 | dereneaton | 14 October 2016, 23:13:06 UTC | fix for last fix | 14 October 2016, 23:13:06 UTC |
| 1328ea9 | dereneaton | 14 October 2016, 22:41:17 UTC | fix for last push gzip | 14 October 2016, 22:41:17 UTC |
| d9296de | dereneaton | 14 October 2016, 21:03:46 UTC | collate with io.bufferedwriter is faster | 14 October 2016, 21:03:46 UTC |
| ba36274 | dereneaton | 14 October 2016, 19:05:00 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 14 October 2016, 19:05:00 UTC |
| 4e1c9b1 | dereneaton | 14 October 2016, 19:04:48 UTC | faster collating of files | 14 October 2016, 19:04:48 UTC |
| 564d7ea | Isaac | 13 October 2016, 22:49:14 UTC | Continuing work on sim and empirical analysis. | 13 October 2016, 22:49:14 UTC |
| a8ff68a | dereneaton | 13 October 2016, 22:46:28 UTC | rev on barcode in step2 filter pairgbs | 13 October 2016, 22:46:28 UTC |
| 418d08f | dereneaton | 13 October 2016, 22:24:08 UTC | faster readcounter for step1 and fullcomp on gbs filter=2 barcode in step2 | 13 October 2016, 22:24:08 UTC |
| 767d24a | dereneaton | 13 October 2016, 20:46:15 UTC | tunnel docs update | 13 October 2016, 20:46:15 UTC |
| 1274bd3 | dereneaton | 13 October 2016, 20:33:46 UTC | tunnel docs update | 13 October 2016, 20:33:46 UTC |
| c640394 | dereneaton | 13 October 2016, 19:58:53 UTC | tunnel docs update | 13 October 2016, 19:58:53 UTC |
| d9338b0 | dereneaton | 13 October 2016, 19:51:26 UTC | tunnel docs update | 13 October 2016, 19:51:26 UTC |
| cf49285 | dereneaton | 13 October 2016, 19:33:15 UTC | tunnel docs update | 13 October 2016, 19:33:15 UTC |
| f8bdd8b | deren | 13 October 2016, 19:01:12 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 13 October 2016, 19:01:12 UTC |
| 5a89141 | deren | 13 October 2016, 19:01:05 UTC | working on a SSH tunnel doc page | 13 October 2016, 19:01:05 UTC |
| 06552d7 | isaacovercast | 13 October 2016, 18:10:06 UTC | Handle OSError in the case that openpty() fails. | 13 October 2016, 18:10:06 UTC |
| 0545a27 | isaacovercast | 12 October 2016, 20:08:57 UTC | "Updating ipyrad/__init__.py to version - 0.4.4 | 12 October 2016, 20:08:57 UTC |
| 1993399 | isaacovercast | 12 October 2016, 20:08:38 UTC | Handle blank lines at the top of the params file. | 12 October 2016, 20:08:38 UTC |
| 00a95ae | deren | 12 October 2016, 16:33:01 UTC | "Updating ipyrad/__init__.py to version - 0.4.3 | 12 October 2016, 16:33:01 UTC |
| 1bc0cfe | deren | 12 October 2016, 16:27:35 UTC | "Updating ipyrad/__init__.py to version - 0.4.3 | 12 October 2016, 16:27:35 UTC |
| b017b32 | deren | 12 October 2016, 16:26:47 UTC | "Updating ipyrad/__init__.py to version - 0.4.3 | 12 October 2016, 16:26:47 UTC |
| b5e754e | deren | 12 October 2016, 16:24:46 UTC | making smoother progress bar in write vcfs | 12 October 2016, 16:24:46 UTC |
| c21c4f6 | deren | 10 October 2016, 23:52:50 UTC | bugfix for jointestimate | 10 October 2016, 23:52:50 UTC |
| 74e47fe | deren | 10 October 2016, 22:21:30 UTC | testing bugfixes to jointestimate | 10 October 2016, 22:21:30 UTC |
| 81ddce7 | dereneaton | 10 October 2016, 22:20:45 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 10 October 2016, 22:20:45 UTC |
| 46b98a2 | dereneaton | 10 October 2016, 22:20:28 UTC | cosmetic | 10 October 2016, 22:20:28 UTC |
| 945858c | dereneaton | 10 October 2016, 22:20:08 UTC | default to no subsampling in jointestimate call | 10 October 2016, 22:20:08 UTC |
| c8e4b6e | deren | 10 October 2016, 22:19:29 UTC | testing bugfixes to jointestimate | 10 October 2016, 22:19:29 UTC |
| 0a94a14 | deren | 10 October 2016, 22:19:10 UTC | added hackersonly option for additional adapters to be filtered | 10 October 2016, 22:19:10 UTC |
| ee33965 | dereneaton | 10 October 2016, 16:38:19 UTC | bug fix to joint H,E estimate for large data sets introduced in v.0.3.14 that was yielding inflated rates. | 10 October 2016, 16:38:19 UTC |
| f9b9b14 | deren | 09 October 2016, 22:43:12 UTC | fix for core count when using API | 09 October 2016, 22:43:12 UTC |
| d8428e0 | Isaac | 09 October 2016, 17:50:38 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 09 October 2016, 17:50:38 UTC |
| 45171d7 | Isaac | 09 October 2016, 17:50:32 UTC | Added plots of snp depth across loci, as well as loci counts per sample to results notebook. | 09 October 2016, 17:50:32 UTC |
| 3f09edf | dereneaton | 07 October 2016, 17:53:25 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 07 October 2016, 17:53:25 UTC |
| e2451ea | dereneaton | 07 October 2016, 16:10:22 UTC | phylogenetic_invariants notebook up | 07 October 2016, 16:10:22 UTC |
| a3bed11 | dereneaton | 07 October 2016, 16:10:01 UTC | some notes on output formats plans | 07 October 2016, 16:10:01 UTC |
| 464bc54 | dereneaton | 07 October 2016, 16:09:40 UTC | removed leftjust arg b/c unnecessary and doesn't work well with left trimmed data | 07 October 2016, 16:09:40 UTC |
| 77f9dae | deren | 06 October 2016, 19:44:59 UTC | "Updating ipyrad/__init__.py to version - 0.4.2 | 06 October 2016, 19:44:59 UTC |
| ff0fba2 | deren | 06 October 2016, 19:44:41 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 06 October 2016, 19:44:41 UTC |
| 75a1fd4 | deren | 06 October 2016, 19:44:34 UTC | Merging for Samples at any state, with warning for higher level states. Prettier printing for API. Fix to default cores setting on API. | 06 October 2016, 19:44:34 UTC |
| 913131f | deren | 06 October 2016, 19:42:07 UTC | fix for merged Assemblies/Samples for s2 | 06 October 2016, 19:42:07 UTC |
| 61b2356 | deren | 06 October 2016, 19:41:47 UTC | fix for merged Assemblies&Samples in s3 | 06 October 2016, 19:41:47 UTC |
| 21a5b25 | deren | 06 October 2016, 19:40:58 UTC | removed limit on number of engines used during indexing | 06 October 2016, 19:40:58 UTC |
| 31061ce | Isaac | 05 October 2016, 23:29:44 UTC | Added ddocent to manuscript analysis. | 05 October 2016, 23:29:44 UTC |
| 8eaad21 | dereneaton | 04 October 2016, 23:18:34 UTC | tutorial update | 04 October 2016, 23:18:34 UTC |
| 9e828b9 | dereneaton | 04 October 2016, 22:54:20 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 04 October 2016, 22:54:20 UTC |
| c6af53d | dereneaton | 04 October 2016, 22:54:14 UTC | in progress doc notebook | 04 October 2016, 22:54:14 UTC |
| 04f421d | dereneaton | 04 October 2016, 22:53:53 UTC | parallel waits for all engines when engines are designated, up until timeout limit | 04 October 2016, 22:53:53 UTC |
| cef81a6 | dereneaton | 04 October 2016, 22:53:29 UTC | parallelized loading demux files, added threads to _ipcluster dict, removed print statement from save | 04 October 2016, 22:53:29 UTC |
| efff36e | dereneaton | 04 October 2016, 22:52:17 UTC | vcf header was missing | 04 October 2016, 22:52:17 UTC |
| 77b6430 | dereneaton | 04 October 2016, 22:52:04 UTC | added step number to progress bar when in interactive mode | 04 October 2016, 22:52:04 UTC |
| caf1ddc | dereneaton | 04 October 2016, 22:51:21 UTC | added warning message when filter=2 and no barcodes are present | 04 October 2016, 22:51:21 UTC |
| 432dc91 | dereneaton | 04 October 2016, 22:50:53 UTC | improved kill switch in step 1 | 04 October 2016, 22:50:53 UTC |
| 68faa65 | dereneaton | 04 October 2016, 22:50:05 UTC | cosmetic changes | 04 October 2016, 22:50:05 UTC |
| 73b7ea1 | dereneaton | 04 October 2016, 22:49:46 UTC | cosmetic changes | 04 October 2016, 22:49:46 UTC |
| 09c2763 | dereneaton | 04 October 2016, 22:49:22 UTC | use select to improve cluster progress bar | 04 October 2016, 22:49:22 UTC |
| 726b81b | dereneaton | 04 October 2016, 20:57:01 UTC | added a CLI option to fine-tune threading | 04 October 2016, 20:57:01 UTC |
| 20ec999 | deren | 04 October 2016, 00:54:47 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 04 October 2016, 00:54:47 UTC |
| 816c817 | deren | 04 October 2016, 00:54:26 UTC | added dstat storage by default | 04 October 2016, 00:54:26 UTC |
| 4482190 | deren | 04 October 2016, 00:54:10 UTC | new default trim_overhang setting and function (0,0,0,0) | 04 October 2016, 00:54:10 UTC |
| b58c88f | deren | 04 October 2016, 00:53:45 UTC | fix for overzealous warning message on demultiplexing when allowing differences | 04 October 2016, 00:53:45 UTC |
| 586c060 | isaacovercast | 01 October 2016, 16:58:17 UTC | "Updating ipyrad/__init__.py to version - 0.4.1 | 01 October 2016, 16:58:17 UTC |
| 74e8564 | isaacovercast | 01 October 2016, 16:57:55 UTC | Fixed reference before assignment error in step 2. | 01 October 2016, 16:57:55 UTC |
| 4358e70 | isaacovercast | 30 September 2016, 16:46:55 UTC | "Updating ipyrad/__init__.py to version - 0.4.0 | 30 September 2016, 16:46:55 UTC |
| a3c3f6a | isaacovercast | 30 September 2016, 16:46:20 UTC | Cosmetic change | 30 September 2016, 16:46:20 UTC |
| 9c74c78 | dereneaton | 29 September 2016, 22:49:07 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 29 September 2016, 22:49:07 UTC |
| 34cf4aa | dereneaton | 29 September 2016, 22:44:32 UTC | new sim data and notebook up | 29 September 2016, 22:44:32 UTC |
| aeaa17d | Isaac | 29 September 2016, 18:47:21 UTC | Added aftrRAD to the manuscript analysis horserace | 29 September 2016, 18:47:21 UTC |
| 29a15f9 | dereneaton | 29 September 2016, 15:44:28 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 29 September 2016, 15:44:28 UTC |
| 5f87669 | dereneaton | 29 September 2016, 15:44:17 UTC | made merging reads compatible with gzipped files from step2 | 29 September 2016, 15:44:17 UTC |
| a1b2ef6 | dereneaton | 29 September 2016, 15:43:49 UTC | modify help message | 29 September 2016, 15:43:49 UTC |
| ed3d6e8 | dereneaton | 29 September 2016, 15:43:16 UTC | made TESTS global var, made maparr bug fix to work with no map info | 29 September 2016, 15:43:16 UTC |
| 5f8f9e2 | isaacovercast | 28 September 2016, 23:43:31 UTC | More carefully save state after completion of each step. | 28 September 2016, 23:43:31 UTC |
| 10888ad | dereneaton | 28 September 2016, 07:57:48 UTC | limit vsearch merging to 2 threads to improve parallel, but should eventually make match to cluster threading. Added removal of temp ungzipped files. | 28 September 2016, 07:57:48 UTC |
| d811615 | dereneaton | 28 September 2016, 07:38:49 UTC | more detailed Sample stats_df.s2 categories for paired data | 28 September 2016, 07:38:49 UTC |
