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 |