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https://github.com/dereneaton/ipyrad
22 March 2024, 03:55:05 UTC
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Revision Author Date Message Commit Date
5a78cd0 Isaac Overcast 07 May 2021, 15:35:03 UTC "Updating ipyrad/__init__.py to version - 0.9.73 07 May 2021, 15:35:03 UTC
fb87679 Isaac Overcast 07 May 2021, 15:34:45 UTC cosmetic 07 May 2021, 15:34:45 UTC
2d4f63a Isaac Overcast 07 May 2021, 15:21:50 UTC "Updating ipyrad/__init__.py to version - 0.9.72 07 May 2021, 15:21:50 UTC
b16f665 Isaac Overcast 07 May 2021, 15:21:36 UTC cosmetic 07 May 2021, 15:21:36 UTC
cfc70ee Isaac Overcast 07 May 2021, 15:17:31 UTC Docs: add some assembly guidelines 07 May 2021, 15:17:31 UTC
c9a8e6a Isaac Overcast 07 May 2021, 14:38:14 UTC cosmetic 07 May 2021, 14:38:14 UTC
0f27083 Isaac Overcast 07 May 2021, 14:23:43 UTC Docs: update sharing and popgen sumstats 07 May 2021, 14:23:43 UTC
4731e8f Isaac Overcast 05 May 2021, 15:06:54 UTC Step1.FileLinker fix oops with trapping bz2 formatted input files. 05 May 2021, 15:06:54 UTC
fd39d7c Isaac Overcast 16 April 2021, 14:39:56 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 16 April 2021, 14:39:56 UTC
5eb3f27 Isaac Overcast 16 April 2021, 14:39:51 UTC cosmetic 16 April 2021, 14:39:51 UTC
3b6dbea Isaac Overcast 15 April 2021, 19:50:41 UTC "Updating ipyrad/__init__.py to version - 0.9.71 15 April 2021, 19:50:41 UTC
65783d4 Isaac Overcast 15 April 2021, 18:31:06 UTC demultiplex: Properly handle 3rad barcodes of different length 15 April 2021, 18:31:06 UTC
4456d08 Isaac Overcast 01 April 2021, 19:22:37 UTC "Updating ipyrad/__init__.py to version - 0.9.70 01 April 2021, 19:22:37 UTC
9ff02e3 Isaac Overcast 01 April 2021, 19:22:14 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 01 April 2021, 19:22:14 UTC
0c13134 Isaac Overcast 01 April 2021, 19:22:09 UTC Allow snps_extractor to handle snps.hdf5 files with names not encoded as bytes 01 April 2021, 19:22:09 UTC
ebe1c91 Mike Renfro 01 April 2021, 10:17:23 UTC Fixing mismatch of #SBATCH and command parameters (#440) 01 April 2021, 10:17:23 UTC
8a566f1 Isaac Overcast 19 March 2021, 17:16:32 UTC "Updating ipyrad/__init__.py to version - 0.9.69 19 March 2021, 17:16:32 UTC
c61e27a Isaac Overcast 19 March 2021, 17:16:02 UTC ipa.structure: handle edge case with running more jobs with different K values 19 March 2021, 17:16:02 UTC
955de66 Isaac Overcast 23 February 2021, 11:04:23 UTC "Updating ipyrad/__init__.py to version - 0.9.68 23 February 2021, 11:04:23 UTC
8f45ab9 Isaac Overcast 23 February 2021, 11:04:00 UTC Handle i7 demux to strip trailing newline from barcode 23 February 2021, 11:04:00 UTC
e414641 Isaac Overcast 23 February 2021, 10:43:12 UTC demultiplex.py: Allow very short input fq files. 23 February 2021, 10:43:12 UTC
1c0e095 Isaac Overcast 22 February 2021, 19:06:12 UTC Fix project_dir inconsistency in merged assemblies. 22 February 2021, 19:06:12 UTC
d314684 Isaac Overcast 22 February 2021, 17:26:31 UTC Raise an error if setting a bad parameter in API mode #354 22 February 2021, 17:26:31 UTC
ce7d76c Isaac Overcast 21 February 2021, 10:40:14 UTC "Updating ipyrad/__init__.py to version - 0.9.67 21 February 2021, 10:40:14 UTC
86d0805 Isaac Overcast 21 February 2021, 10:37:53 UTC Don't blank extra p3/p5 adapters in step2.check_adapters if filter_adapters != 3. 21 February 2021, 10:37:53 UTC
4c5bce4 Isaac Overcast 21 February 2021, 10:19:17 UTC cosmetic 21 February 2021, 10:19:17 UTC
00c5b49 Isaac Overcast 18 February 2021, 11:09:29 UTC "Updating ipyrad/__init__.py to version - 0.9.66 18 February 2021, 11:09:29 UTC
d9d8698 Isaac Overcast 11 February 2021, 21:33:50 UTC cosmetic 11 February 2021, 21:33:50 UTC
1ae1075 Isaac Overcast 08 February 2021, 20:55:29 UTC cosmetic 08 February 2021, 20:55:29 UTC
88697ea Isaac Overcast 03 February 2021, 10:02:03 UTC analysis.popgen: _collect_results() function to compile and organize results from the engines. It's a little ugly. 03 February 2021, 10:02:03 UTC
6e7b6bd Isaac Overcast 02 February 2021, 19:21:26 UTC analysis.popgen Change default minmap value to 4 02 February 2021, 19:21:26 UTC
ff280eb Isaac Overcast 02 February 2021, 19:18:56 UTC analysis.popgen Chunking of loci and parallelization of analysis working. 02 February 2021, 19:18:56 UTC
5a1e53d Isaac Overcast 02 February 2021, 17:49:05 UTC cosmetic 02 February 2021, 17:49:05 UTC
129326c Isaac Overcast 02 February 2021, 17:47:37 UTC analysis.popgen._fst_full() implemented. Had to slightly tweak the code that was there, and it works a bit different than the other sumstats, but whatever for now it works. 02 February 2021, 17:47:37 UTC
69f3844 Isaac Overcast 02 February 2021, 17:02:16 UTC analysis.popgen implemented Dxy 02 February 2021, 17:02:16 UTC
0cf053d Isaac Overcast 02 February 2021, 14:46:56 UTC analysis.popgen._process_locus_pops() to prepare data for pairwise summary statistics 02 February 2021, 14:46:56 UTC
54e05be Isaac Overcast 02 February 2021, 13:57:50 UTC analysis.popgen: Stats returned as dict instead of tuple, and remote processes dump full stats to pickle files. 02 February 2021, 13:57:50 UTC
cd8495e Isaac Overcast 02 February 2021, 12:28:12 UTC Add a _process_locus function to remove a bunch of redundancy, and split consens bases to account for diploidy in all the calcs 02 February 2021, 12:28:12 UTC
d9315fe Isaac Overcast 01 February 2021, 21:55:27 UTC analysis.popgen: If no imap then all samples are considered from the same population. 01 February 2021, 21:55:27 UTC
d4dbd16 Isaac Overcast 01 February 2021, 21:36:44 UTC analysis.popgen: refactor _Watterson to accept sequence length and return raw and per base theta values. 01 February 2021, 21:36:44 UTC
9e90457 Isaac Overcast 01 February 2021, 21:24:40 UTC analysis.popgen: Refactor into 'public' sumstat methods which can be called on array-like locus data, and 'semi-private' methods (e.g. _pi, or _Watterson) that are much more efficient but accept very specific information. The Processor.run() function will do some housekeeping per locus and call the 'semi-private' methods, for efficiency. Public methods are for testing. 01 February 2021, 21:24:40 UTC
514b739 Isaac Overcast 01 February 2021, 20:49:24 UTC analysis.popgen Tajima's D function 01 February 2021, 20:49:24 UTC
d9ae6cf Isaac Overcast 01 February 2021, 18:42:04 UTC analysis.popgen Watterson's theta function 01 February 2021, 18:42:04 UTC
259dc27 Isaac Overcast 01 February 2021, 17:53:30 UTC cosmetic 01 February 2021, 17:53:30 UTC
3a95140 Isaac Overcast 01 February 2021, 17:44:59 UTC clustmap: Handle bam files with very large chromosomes (#435) 01 February 2021, 17:44:59 UTC
79187dc Isaac Overcast 01 February 2021, 17:40:58 UTC clustmap_across: Catch samtools indexing failure for large bam files and try again with .csi indexing with the flag. 01 February 2021, 17:40:58 UTC
10cf441 Isaac Overcast 01 February 2021, 16:05:46 UTC Adopting the Processor() structure to enable parallelization. Also implemented nucleotide diversity. 01 February 2021, 16:05:46 UTC
df32338 Isaac Overcast 31 January 2021, 22:16:19 UTC cosmetic 31 January 2021, 22:16:19 UTC
3150dc4 Isaac Overcast 31 January 2021, 22:12:31 UTC analysis.popgen add parallelization support for calculating all sumstats per locus. 31 January 2021, 22:12:31 UTC
f06e8fc Isaac Overcast 31 January 2021, 22:11:15 UTC cosmetic 31 January 2021, 22:11:15 UTC
211acc2 Isaac Overcast 31 January 2021, 20:15:44 UTC analysis.popgen _fst() is working for snp data 31 January 2021, 20:15:44 UTC
a11a992 Isaac Overcast 31 January 2021, 20:13:27 UTC Add an option to LocusExtracter.get_locus to return a pd.DataFrame indexed by sample names 31 January 2021, 20:13:27 UTC
5de7ca7 Isaac Overcast 31 January 2021, 17:32:49 UTC analysis.popgen getting it into current analysis tools format and starting to flesh it out. 31 January 2021, 17:32:49 UTC
1113775 Isaac Overcast 31 January 2021, 16:27:23 UTC CLI honors the -q flag now 31 January 2021, 16:27:23 UTC
61fdf33 Isaac Overcast 31 January 2021, 16:25:25 UTC cosmetic 31 January 2021, 16:25:25 UTC
dabd25a Isaac Overcast 31 January 2021, 14:23:29 UTC analysis.sharing allow subsampling inside draw() to prevent recalculating data 31 January 2021, 14:23:29 UTC
bd66785 Isaac Overcast 31 January 2021, 14:04:49 UTC analysis.shared allow sorting by mean pairwise sharing or missing 31 January 2021, 14:04:49 UTC
a07a9a6 Isaac Overcast 31 January 2021, 13:43:42 UTC Allow analysis.sharing to reorder samples, and add a progress bar 31 January 2021, 13:43:42 UTC
3ca048e Isaac Overcast 30 January 2021, 21:11:59 UTC Add new pairwise snp/missingness sharing analysis tool. 30 January 2021, 21:11:59 UTC
e0df412 Isaac Overcast 30 January 2021, 18:24:16 UTC cosmetic 30 January 2021, 18:24:16 UTC
d9928b5 Isaac Overcast 30 January 2021, 18:18:47 UTC add locus sharing/missingness sharing analysis tool skel 30 January 2021, 18:18:47 UTC
ac295df Isaac Overcast 30 January 2021, 16:38:34 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 30 January 2021, 16:38:34 UTC
99b3349 Isaac Overcast 30 January 2021, 16:37:55 UTC cosmetic 30 January 2021, 16:37:55 UTC
07bef22 Isaac Overcast 24 January 2021, 17:07:19 UTC cosmetic 24 January 2021, 17:07:19 UTC
4286271 Isaac Overcast 22 January 2021, 18:53:47 UTC pin numpy >=1.15, a known working version to address #429 22 January 2021, 18:53:47 UTC
d472271 Isaac Overcast 22 January 2021, 18:42:21 UTC Fix weird race condition with branching and pop_assign_files. See #430. 22 January 2021, 18:42:21 UTC
49fb7ec Isaac Overcast 22 January 2021, 16:59:15 UTC cosmetic 22 January 2021, 16:59:15 UTC
f4f341f Isaac Overcast 22 January 2021, 12:00:32 UTC "Updating ipyrad/__init__.py to version - 0.9.65 22 January 2021, 12:00:32 UTC
82e338d Isaac Overcast 22 January 2021, 11:53:30 UTC Fix #429 weird masking bug in older versions of numpy. 22 January 2021, 11:53:30 UTC
eaa68d3 Isaac Overcast 20 January 2021, 12:27:56 UTC Add refs to the analysis.popgen tool. 20 January 2021, 12:27:56 UTC
12d4f0e Isaac Overcast 16 January 2021, 11:44:41 UTC cosmetic 16 January 2021, 11:44:41 UTC
098d9be Isaac Overcast 16 January 2021, 11:42:04 UTC "Updating ipyrad/__init__.py to version - 0.9.64 16 January 2021, 11:42:04 UTC
95bc407 Isaac Overcast 16 January 2021, 11:41:46 UTC replaced core.Assembly.database which actually wasn't doing anything with snps_database and seqs_database to retain info about the hdf5 files in the assembly object 16 January 2021, 11:41:46 UTC
efe2178 Isaac Overcast 16 January 2021, 11:13:22 UTC fix empirical api structure params format 16 January 2021, 11:13:22 UTC
d994f69 Isaac Overcast 16 January 2021, 10:46:15 UTC Allow structure to accept vcf files and auto-convert to hdf5 16 January 2021, 10:46:15 UTC
c9a5fdb Isaac Overcast 16 January 2021, 09:57:01 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 16 January 2021, 09:57:01 UTC
e4b6b0d Isaac Overcast 16 January 2021, 09:56:52 UTC fix oops in i7 demux cookbook 16 January 2021, 09:56:52 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
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