eef3420 | deren | 05 November 2016, 21:31:32 UTC | "Updating ipyrad/__init__.py to version - 0.4.9 | 05 November 2016, 21:31:32 UTC |
edd49c8 | deren | 05 November 2016, 21:25:42 UTC | hotfix for large array size bug introduced in last update | 05 November 2016, 21:25:42 UTC |
ab85da8 | isaacovercast | 05 November 2016, 17:00:10 UTC | "Updating ipyrad/__init__.py to version - 0.4.8 | 05 November 2016, 17:00:10 UTC |
7957906 | deren | 05 November 2016, 16:00:35 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 05 November 2016, 16:00:35 UTC |
28b777c | deren | 05 November 2016, 16:00:30 UTC | fix for geno output | 05 November 2016, 16:00:30 UTC |
e1a1631 | deren | 05 November 2016, 16:00:09 UTC | bug fix to measure array dims from mindepth settings, uses statistical for s4, and majrule for s5 | 05 November 2016, 16:00:09 UTC |
bfa7f0b | isaacovercast | 04 November 2016, 19:50:39 UTC | adding mac bwa binary | 04 November 2016, 19:50:39 UTC |
269d572 | iovercast | 04 November 2016, 19:33:34 UTC | Adding bwa binary for linux. | 04 November 2016, 19:33:34 UTC |
7b02ba8 | deren | 04 November 2016, 19:09:41 UTC | improved N removal from edges of paired reads with variable lengths | 04 November 2016, 19:09:41 UTC |
d26be03 | deren | 03 November 2016, 22:40:53 UTC | new parsing of output formats, and fewer defaults | 03 November 2016, 22:40:53 UTC |
8b457b5 | deren | 03 November 2016, 22:40:08 UTC | only snps in the vcf is new default. Added pair support but still need to decide on spacer default. New cleaner output-formats stored as a tuple | 03 November 2016, 22:40:08 UTC |
973c17b | deren | 03 November 2016, 19:37:00 UTC | small fix for better error catching | 03 November 2016, 19:37:00 UTC |
2016f2a | deren | 03 November 2016, 19:36:34 UTC | new hidepth_min attr to save the mindepth setting at the time when it is used | 03 November 2016, 19:36:34 UTC |
a61fe6c | deren | 03 November 2016, 19:35:38 UTC | mindepth settings are now checked separately from other parameters before 'run' to see if they are incompatible. Avoids race between the two being compared individually in set-params. | 03 November 2016, 19:35:38 UTC |
ea4606a | deren | 03 November 2016, 19:34:07 UTC | new functions in steps 3-5 to accomodate changes to mindepth settings so that clusters-hidepth can be dynamically recalculated | 03 November 2016, 19:34:07 UTC |
9873aca | deren | 03 November 2016, 00:30:06 UTC | fix to tunnel doc | 03 November 2016, 00:30:06 UTC |
7303939 | deren | 02 November 2016, 23:20:10 UTC | "Updating ipyrad/__init__.py to version - 0.4.7 | 02 November 2016, 23:20:10 UTC |
37c3c5a | deren | 02 November 2016, 23:20:00 UTC | hotfix for step5 sample save bug. pushed to soon | 02 November 2016, 23:20:00 UTC |
2f1aec8 | deren | 02 November 2016, 23:06:35 UTC | "Updating ipyrad/__init__.py to version - 0.4.7 | 02 November 2016, 23:06:35 UTC |
ceab488 | deren | 02 November 2016, 23:05:56 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 02 November 2016, 23:05:56 UTC |
096a474 | deren | 02 November 2016, 23:05:48 UTC | make compatible with changes to s6 | 02 November 2016, 23:05:48 UTC |
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 |