Skip to main content

Browse the archive

https://github.com/dereneaton/ipyrad
22 May 2024, 15:02:59 UTC
sort by:
Revision Author Date Message Commit Date
66bda47 Deren 17 March 2021, 05:37:25 UTC declone flag flipped 17 March 2021, 05:37:25 UTC
c4e228c Deren 17 March 2021, 04:57:09 UTC consens dir fix 17 March 2021, 04:57:09 UTC
e41cc65 Deren 17 March 2021, 04:56:30 UTC error message update 17 March 2021, 04:56:30 UTC
4bd3775 Deren 17 March 2021, 04:56:08 UTC error report fix 17 March 2021, 04:56:08 UTC
8fcb1b1 Deren 17 March 2021, 04:55:51 UTC cosmetic 17 March 2021, 04:55:51 UTC
87ce1e6 Deren 15 March 2021, 16:53:30 UTC Merge commit 'refs/pull/298/head' of https://github.com/dereneaton/ipyrad into trash 15 March 2021, 16:53:30 UTC
5270f46 Deren 06 March 2021, 05:52:03 UTC import order fix 06 March 2021, 05:52:03 UTC
3f3fbd9 Deren 06 March 2021, 05:51:41 UTC simple download func 06 March 2021, 05:51:41 UTC
f8932a4 Deren 06 March 2021, 05:50:26 UTC docstring 06 March 2021, 05:50:26 UTC
15af192 Deren 06 March 2021, 05:50:11 UTC better install instructions 06 March 2021, 05:50:11 UTC
808ab3e Deren 06 March 2021, 05:49:57 UTC new options 06 March 2021, 05:49:57 UTC
019b1e0 Deren 06 March 2021, 05:48:42 UTC update for 2.10 06 March 2021, 05:48:42 UTC
af63d7b Deren 06 March 2021, 05:48:19 UTC tested 06 March 2021, 05:48:19 UTC
7a950cc Deren 06 March 2021, 05:47:38 UTC import order 06 March 2021, 05:47:38 UTC
dae3c94 Deren 06 March 2021, 05:47:10 UTC comment out old hierarch code, and simplify parallel 06 March 2021, 05:47:10 UTC
d248a9b Deren 06 March 2021, 05:46:41 UTC new files loaded 06 March 2021, 05:46:41 UTC
5436d95 Deren 06 March 2021, 05:46:19 UTC write outputs split files 06 March 2021, 05:46:19 UTC
a6db117 Deren 06 March 2021, 05:45:51 UTC save declone stats 06 March 2021, 05:45:51 UTC
3ddb8cb Deren 06 March 2021, 05:45:20 UTC cosmetic 06 March 2021, 05:45:20 UTC
6b24258 Deren 06 March 2021, 05:44:58 UTC ipyraderror works same in cli and api 06 March 2021, 05:44:58 UTC
708f976 Deren 06 March 2021, 05:44:20 UTC enable decloned counts 06 March 2021, 05:44:20 UTC
e16cb1e Deren 06 March 2021, 05:43:51 UTC demux testing 06 March 2021, 05:43:51 UTC
67f9ae3 Deren 06 March 2021, 05:43:32 UTC trim reads with fastp 06 March 2021, 05:43:32 UTC
31f0235 Deren 06 March 2021, 05:43:02 UTC split consens into two files 06 March 2021, 05:43:02 UTC
97887f1 Deren 06 March 2021, 05:42:15 UTC changed trim_reads parameter for fastp style 06 March 2021, 05:42:15 UTC
7c2d13a Deren 06 March 2021, 05:41:41 UTC added new stats to Sample 06 March 2021, 05:41:41 UTC
233090e Deren 05 February 2021, 16:38:43 UTC added logger 05 February 2021, 16:38:43 UTC
6000485 Deren 05 February 2021, 16:37:49 UTC added logger 05 February 2021, 16:37:49 UTC
c08fb9a Deren 05 February 2021, 16:37:33 UTC added loguru logger 05 February 2021, 16:37:33 UTC
fac9061 Deren 05 February 2021, 16:37:13 UTC added main test 05 February 2021, 16:37:13 UTC
c602d8b Deren 05 February 2021, 16:36:55 UTC added main test and used new progressbar 05 February 2021, 16:36:55 UTC
e9ac58a Deren 05 February 2021, 16:36:25 UTC demux and trimreads replacements added 05 February 2021, 16:36:25 UTC
4c8c984 Deren 05 February 2021, 16:36:03 UTC added main test, paralogs check for denovo 05 February 2021, 16:36:03 UTC
8b96c89 Deren 05 February 2021, 16:35:33 UTC added main test 05 February 2021, 16:35:33 UTC
d131239 Deren 05 February 2021, 16:35:12 UTC improved progress bar prints only every 30secs if not tty 05 February 2021, 16:35:12 UTC
4ce9aa3 Deren 05 February 2021, 16:34:43 UTC splitting write_outputs to multiple files 05 February 2021, 16:34:43 UTC
783c45e Deren 05 February 2021, 16:34:13 UTC reformatted demux in new file, assembly calls demux and trimreads now 05 February 2021, 16:34:13 UTC
637d954 Deren 05 February 2021, 16:33:30 UTC update sample stats for new trimreads stats 05 February 2021, 16:33:30 UTC
ecdf2e9 Deren 05 February 2021, 16:32:46 UTC split components of write_outputs for easier reading/testing 05 February 2021, 16:32:46 UTC
6fe2a94 Deren 05 February 2021, 16:32:17 UTC trimreads alternative to cutadapt implemented 05 February 2021, 16:32:17 UTC
9fb5e75 Deren 22 January 2021, 18:39:02 UTC refactored demultiplex into two files 22 January 2021, 18:39:02 UTC
8ed576f Isaac Overcast 17 December 2020, 11:46:05 UTC "Updating ipyrad/__init__.py to version - 0.9.63 17 December 2020, 11:46:05 UTC
1275de9 Isaac Overcast 17 December 2020, 11:45:45 UTC Fix off-by-one error in nexus output 17 December 2020, 11:45:45 UTC
21d0770 deren 15 December 2020, 16:54:24 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 15 December 2020, 16:54:24 UTC
036de34 deren 15 December 2020, 16:54:18 UTC update struct testdocs 15 December 2020, 16:54:18 UTC
a5f7c6c Isaac Overcast 07 December 2020, 16:18:03 UTC cosmetic 07 December 2020, 16:18:03 UTC
8bd0f6f Isaac Overcast 07 December 2020, 16:06:26 UTC Add Tajima's D denominator equation to the popgen analysis tool, because I coded it before and it's a nightmare. 07 December 2020, 16:06:26 UTC
ac66878 Isaac Overcast 05 December 2020, 14:15:20 UTC cosmetic 05 December 2020, 14:15:20 UTC
3819b60 Deren 03 December 2020, 06:01:58 UTC use quiet in lex 03 December 2020, 06:01:58 UTC
e483765 Deren 25 November 2020, 18:28:37 UTC plot posteriors range limits removed 25 November 2020, 18:28:37 UTC
65957a3 Deren 25 November 2020, 18:28:00 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 25 November 2020, 18:28:00 UTC
a0a9040 Isaac Overcast 20 November 2020, 12:10:39 UTC Actually fix pca cookbook 20 November 2020, 12:10:39 UTC
38ca596 Isaac Overcast 20 November 2020, 11:42:23 UTC fix malformatted pca cookbook 20 November 2020, 11:42:23 UTC
41095b9 Isaac Overcast 11 November 2020, 18:22:08 UTC cosmetic 11 November 2020, 18:22:08 UTC
31b052e Deren 09 November 2020, 18:46:38 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 09 November 2020, 18:46:38 UTC
3c229b6 Isaac Overcast 03 November 2020, 15:30:23 UTC "Updating ipyrad/__init__.py to version - 0.9.62 03 November 2020, 15:30:23 UTC
b013ff3 Deren 02 November 2020, 05:27:21 UTC raxml w/ gamma rates 02 November 2020, 05:27:21 UTC
547d2e6 Deren 28 October 2020, 20:26:15 UTC updating mb cookbook 28 October 2020, 20:26:15 UTC
1824c38 Deren 28 October 2020, 17:59:30 UTC bpp transform parser bugfix 28 October 2020, 17:59:30 UTC
6168404 Deren 27 October 2020, 18:30:03 UTC add bpp dev nb 27 October 2020, 18:30:03 UTC
76556d3 Deren 27 October 2020, 18:28:24 UTC allow non-blocking calls again in bpp 27 October 2020, 18:28:24 UTC
e00fcee Deren 27 October 2020, 16:49:18 UTC bpp result split on delimiter 27 October 2020, 16:49:18 UTC
9c86022 Deren 21 October 2020, 19:34:47 UTC allow empty node dist in bpp 21 October 2020, 19:34:47 UTC
2cea712 Deren 21 October 2020, 16:53:35 UTC add option to extract as string/bytes 21 October 2020, 16:53:35 UTC
ed70aae Deren 20 October 2020, 21:26:49 UTC snps_extracter: report maf filter as unique filtered 20 October 2020, 21:26:49 UTC
a4762ed Deren 18 October 2020, 20:02:12 UTC snps extracter reports n unlinked snps 18 October 2020, 20:02:12 UTC
5f4b303 Deren 18 October 2020, 19:43:41 UTC tmp dir for new cookbook docs 18 October 2020, 19:43:41 UTC
ad9d09d Deren 18 October 2020, 04:11:24 UTC allow maf filter in structure 18 October 2020, 04:11:24 UTC
93809eb Deren 18 October 2020, 04:11:10 UTC node_dists check for tips in bpp plot 18 October 2020, 04:11:10 UTC
05a179b Deren 18 October 2020, 02:59:35 UTC new plotting tools for bpp results 18 October 2020, 02:59:35 UTC
7b33767 Deren 18 October 2020, 02:59:10 UTC added download util 18 October 2020, 02:59:10 UTC
999d034 Deren 18 October 2020, 02:58:40 UTC add minmaf filter to snps_extracter, pca 18 October 2020, 02:58:40 UTC
a90c21d Deren 15 October 2020, 17:24:00 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 15 October 2020, 17:24:00 UTC
c0067e1 Deren 15 October 2020, 17:23:58 UTC additionall bpp summary tools 15 October 2020, 17:23:58 UTC
93ebe75 Isaac Overcast 15 October 2020, 14:42:43 UTC cosmetic 15 October 2020, 14:42:43 UTC
f9b2da3 Isaac Overcast 15 October 2020, 10:11:02 UTC "Updating ipyrad/__init__.py to version - 0.9.61 15 October 2020, 10:11:02 UTC
ef9ee14 Isaac Overcast 15 October 2020, 10:10:14 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 15 October 2020, 10:10:14 UTC
516ed3c Isaac Overcast 15 October 2020, 10:10:11 UTC Fix nasty nasty bug in step 7 for issue #422 15 October 2020, 10:10:11 UTC
d607692 Isaac Overcast 13 October 2020, 08:49:24 UTC "Updating ipyrad/__init__.py to version - 0.9.60 13 October 2020, 08:49:24 UTC
ecec2cb Isaac Overcast 13 October 2020, 08:49:05 UTC Fix mapping minus reads bug step 3 13 October 2020, 08:49:05 UTC
1e189ab Isaac Overcast 20 September 2020, 19:24:49 UTC "Updating ipyrad/__init__.py to version - 0.9.59 20 September 2020, 19:24:49 UTC
c3f6b4a Isaac Overcast 20 September 2020, 19:24:21 UTC In structure._call_structure() self is not in scope, so now we pass in the full path to the structure binary. 20 September 2020, 19:24:21 UTC
1d35b2e Isaac Overcast 10 September 2020, 16:05:52 UTC "Updating ipyrad/__init__.py to version - 0.9.58 10 September 2020, 16:05:52 UTC
ce790fe Isaac Overcast 10 September 2020, 16:05:44 UTC fix oops in window_extracter 10 September 2020, 16:05:44 UTC
f0057d5 Isaac Overcast 10 September 2020, 16:02:40 UTC Allow scaffold idxs to be int 10 September 2020, 16:02:40 UTC
5b22c8c eaton-lab 31 August 2020, 15:45:44 UTC bugfix to skip scaffs with no hits even when end=None 31 August 2020, 15:45:44 UTC
3186f56 eaton-lab 31 August 2020, 15:33:42 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 31 August 2020, 15:33:42 UTC
b2e7e0a eaton-lab 31 August 2020, 15:33:29 UTC end arg offset bugfix, may have affected size of windows in treeslider 31 August 2020, 15:33:29 UTC
4fad04b Isaac Overcast 31 August 2020, 07:55:06 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 31 August 2020, 07:55:06 UTC
75b6fb9 Isaac Overcast 31 August 2020, 07:53:48 UTC Add handler for malformed loci in baba.py 31 August 2020, 07:53:48 UTC
5edbbef eaton-lab 30 August 2020, 16:16:17 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 30 August 2020, 16:16:17 UTC
f81602d eaton-lab 30 August 2020, 16:16:15 UTC fix to allow digest of single end RAD 30 August 2020, 16:16:15 UTC
a12aa6d Carlos Alonso Maya Lastra 26 August 2020, 14:47:34 UTC Changed astral annotation to default (#417) Changed current default (-t 1) to Astral default (-t 3) 26 August 2020, 14:47:34 UTC
ff94022 Isaac Overcast 21 August 2020, 20:47:16 UTC Update dependency documentation 21 August 2020, 20:47:16 UTC
3d6b653 eaton-lab 17 August 2020, 18:10:03 UTC baba2 draw fix 17 August 2020, 18:10:03 UTC
cad93e6 eaton-lab 17 August 2020, 16:42:31 UTC return canvas in draw 17 August 2020, 16:42:31 UTC
4d5b467 Isaac Overcast 15 August 2020, 13:19:36 UTC Fix an oops iff hackersonly.declone_PCR_duplicates && reference assembly 15 August 2020, 13:19:36 UTC
3585f93 Deren Eaton 12 August 2020, 16:02:36 UTC Merge pull request #409 from camayal/master Changes in Drawing class 12 August 2020, 16:02:36 UTC
b4962c0 eaton-lab 12 August 2020, 15:51:04 UTC path fix for conda envs 12 August 2020, 15:51:04 UTC
bed3259 eaton-lab 12 August 2020, 15:50:02 UTC path fix for conda envs 12 August 2020, 15:50:02 UTC
back to top