9db5867 | Isaac Overcast | 25 September 2023, 14:59:35 UTC | Update README.md | 25 September 2023, 14:59:35 UTC |
e0f3a5c | Isaac Overcast | 26 May 2023, 11:19:48 UTC | Update README.md | 26 May 2023, 11:19:48 UTC |
18d0de1 | Isaac Overcast | 22 May 2023, 15:24:39 UTC | Fix error in ploidy > 2 | 22 May 2023, 15:24:39 UTC |
1cd19c6 | Isaac Overcast | 20 May 2023, 19:16:15 UTC | Merge branch 'master' of https://github.com/isaacovercast/easySFS | 20 May 2023, 19:16:15 UTC |
e07c7ff | Isaac Overcast | 20 May 2023, 19:15:47 UTC | Add support for ploidy > 2 | 20 May 2023, 19:15:47 UTC |
a69086a | Isaac Overcast | 06 March 2023, 14:20:14 UTC | Update README.md | 06 March 2023, 14:20:14 UTC |
4fa51dd | Isaac Overcast | 29 January 2023, 14:52:03 UTC | Ensure datadict CHROM/POS are unique #55 | 29 January 2023, 14:52:03 UTC |
2f5614e | Isaac Overcast | 28 January 2023, 19:13:02 UTC | cosmetic | 28 January 2023, 19:13:02 UTC |
802e5ca | Isaac Overcast | 28 January 2023, 19:11:46 UTC | Update README | 28 January 2023, 19:11:46 UTC |
e36d80d | Isaac Overcast | 28 January 2023, 18:28:25 UTC | total-length works for multiSFS & fixed an oops with -a (#47) | 28 January 2023, 18:28:25 UTC |
dac10a9 | Isaac Overcast | 28 January 2023, 17:51:54 UTC | total-length now works for 2D SFS (#47) | 28 January 2023, 17:51:54 UTC |
de96207 | Isaac Overcast | 28 January 2023, 17:44:14 UTC | cosmetic | 28 January 2023, 17:44:14 UTC |
213c58f | Isaac Overcast | 28 January 2023, 17:42:54 UTC | add total-length parameter (#47) | 28 January 2023, 17:42:54 UTC |
fa521cd | Isaac Overcast | 28 January 2023, 17:12:26 UTC | Add Spectrum.py modified from dadi codebase, and removed dependency on dadi module. | 28 January 2023, 17:12:26 UTC |
0497b43 | Isaac Overcast | 28 January 2023, 16:23:54 UTC | cosmetic | 28 January 2023, 16:23:54 UTC |
ada6e7e | Isaac Overcast | 28 January 2023, 15:44:16 UTC | Add resample-vcf argument and refactor read_vcf() a bit | 28 January 2023, 15:44:16 UTC |
7365511 | Isaac Overcast | 27 January 2023, 23:00:09 UTC | Add random sampling within windows given windows of size in bp | 27 January 2023, 23:00:09 UTC |
7cc460d | Isaac Overcast | 27 January 2023, 22:04:37 UTC | Add random sampling within windows based on number of snps | 27 January 2023, 22:04:37 UTC |
b331c39 | Isaac Overcast | 27 January 2023, 21:10:02 UTC | Add _thin_windows() function with skel code | 27 January 2023, 21:10:02 UTC |
d896026 | Isaac Overcast | 27 January 2023, 20:50:05 UTC | Add simulated vcf and pops files with well formatted vcf to the examples dir | 27 January 2023, 20:50:05 UTC |
9b43982 | Isaac Overcast | 27 January 2023, 20:30:13 UTC | Merge branch 'master' of https://github.com/isaacovercast/easySFS | 27 January 2023, 20:30:13 UTC |
a8089a9 | Isaac Overcast | 27 January 2023, 20:28:50 UTC | Move some sanity checking for arguments into arg parser function | 27 January 2023, 20:28:50 UTC |
10c92e1 | Isaac Overcast | 30 November 2022, 18:37:13 UTC | Handle blank lines in the popsfile | 30 November 2022, 18:37:13 UTC |
ce51033 | Isaac Overcast | 28 October 2021, 13:59:55 UTC | Add example vcf file | 28 October 2021, 13:59:55 UTC |
e75a00e | Isaac Overcast | 18 September 2021, 12:08:42 UTC | Add simdata notebook | 18 September 2021, 12:08:42 UTC |
7e276c1 | Isaac Overcast | 18 September 2021, 12:06:39 UTC | cleanup notebooks | 18 September 2021, 12:06:39 UTC |
b866269 | Isaac Overcast | 05 February 2021, 17:14:45 UTC | Allow to set population order of output sfs | 05 February 2021, 17:14:45 UTC |
a9bab35 | Isaac Overcast | 28 January 2021, 09:21:01 UTC | Be more careful with overwriting the outdir | 28 January 2021, 09:21:01 UTC |
844e833 | Isaac Overcast | 21 January 2021, 16:13:18 UTC | Fix raw_input reference | 21 January 2021, 16:13:18 UTC |
8b991eb | Isaac Overcast | 29 August 2020, 13:39:06 UTC | fix a bug in fsc joint sfs files where the pop data was transposed | 29 August 2020, 13:39:06 UTC |
c2b26c5 | Isaac Overcast | 08 April 2020, 18:31:33 UTC | Update README.md | 08 April 2020, 18:31:33 UTC |
e655987 | Isaac Overcast | 08 April 2020, 18:28:50 UTC | Update README.md | 08 April 2020, 18:28:50 UTC |
0a9bc74 | Isaac Overcast | 19 March 2020, 15:49:44 UTC | Update README.md | 19 March 2020, 15:49:44 UTC |
bdcd9c0 | Isaac Overcast | 19 February 2020, 16:12:50 UTC | Fix a bug in opening gzip vcf files (open in 'rt' mode to fix). | 19 February 2020, 16:12:50 UTC |
a258885 | Isaac Overcast | 15 February 2020, 17:08:33 UTC | fix open rU mode deprecation warning | 15 February 2020, 17:08:33 UTC |
66a594a | Isaac Overcast | 15 February 2020, 17:08:07 UTC | Update README.md | 15 February 2020, 17:08:07 UTC |
aaf80ea | Isaac Overcast | 12 September 2019, 18:00:57 UTC | remove xrange | 12 September 2019, 18:00:57 UTC |
128d82b | Isaac Overcast | 18 July 2019, 16:07:03 UTC | Fix 2d sfs for fsc2 | 18 July 2019, 16:07:03 UTC |
4e5b9a5 | Isaac Overcast | 14 July 2019, 08:52:57 UTC | Transpose the pop0/pop1 ids in the fsc2 joint SFS | 14 July 2019, 08:52:57 UTC |
1132100 | Isaac Overcast | 06 December 2018, 23:31:20 UTC | Fix removing samples in list not in vcf - Thanks to Annabel Beichman | 06 December 2018, 23:31:20 UTC |
c7261e6 | Isaac Overcast | 15 October 2018, 21:38:03 UTC | Update README.md | 15 October 2018, 21:38:03 UTC |
02f2082 | Isaac Overcast | 08 October 2018, 17:24:27 UTC | update the usage | 08 October 2018, 17:24:27 UTC |
5e84efd | Isaac Overcast | 13 September 2018, 22:52:16 UTC | ignore .gz files | 13 September 2018, 22:52:16 UTC |
a051ec6 | Isaac Overcast | 13 September 2018, 22:51:55 UTC | Merge branch 'master' of https://github.com/isaacovercast/easySFS | 13 September 2018, 22:51:55 UTC |
6ccf754 | iovercast | 13 September 2018, 22:53:47 UTC | Adding momi sfs export code even though it doesn't work right now. | 13 September 2018, 22:53:47 UTC |
75991e2 | Isaac Overcast | 13 September 2018, 22:51:52 UTC | Show possible preview keeping all samples. | 13 September 2018, 22:51:52 UTC |
c7b9e8e | Isaac Overcast | 13 September 2018, 22:47:47 UTC | Updating notebooks | 13 September 2018, 22:47:47 UTC |
8cf6d05 | Isaac Overcast | 09 September 2018, 22:27:12 UTC | Fix a hideous bug counting heterozygotes | 09 September 2018, 22:27:12 UTC |
420e6cb | Isaac Overcast | 09 September 2018, 22:26:04 UTC | fix momi nb | 09 September 2018, 22:26:04 UTC |
9ac5761 | Isaac Overcast | 09 September 2018, 22:24:56 UTC | updates to momi analysis nb | 09 September 2018, 22:24:56 UTC |
03b9f36 | Isaac Overcast | 04 September 2018, 00:56:40 UTC | update momi nb | 04 September 2018, 00:56:40 UTC |
8b5e016 | Isaac Overcast | 04 September 2018, 00:56:19 UTC | Merge branch 'master' of https://github.com/isaacovercast/easySFS | 04 September 2018, 00:56:19 UTC |
3443059 | Isaac Overcast | 04 September 2018, 00:56:17 UTC | add simdata nb | 04 September 2018, 00:56:17 UTC |
910c9b3 | Isaac Overcast | 04 September 2018, 00:55:00 UTC | add momi analysis nb | 04 September 2018, 00:55:00 UTC |
cc20f4c | Isaac Overcast | 03 September 2018, 21:53:28 UTC | adding notebook | 03 September 2018, 21:53:28 UTC |
e1ed1a5 | Isaac Overcast | 31 August 2018, 21:29:01 UTC | Naming fix for MAF/DAF fsc files | 31 August 2018, 21:29:01 UTC |
727ace9 | Isaac Overcast | 05 April 2018, 14:45:23 UTC | Add a more informative error message if the input vcf is malformed. | 05 April 2018, 14:45:23 UTC |
ac7e411 | Isaac Overcast | 03 April 2018, 12:43:42 UTC | typo | 03 April 2018, 12:43:42 UTC |
9c238bd | Isaac Overcast | 07 March 2018, 15:50:24 UTC | Set default mask corners to true. | 07 March 2018, 15:50:24 UTC |
ef57f46 | Isaac Overcast | 27 October 2017, 15:55:26 UTC | Delete leuco_pops.txt | 27 October 2017, 15:55:26 UTC |
b223517 | Isaac Overcast | 27 October 2017, 15:55:15 UTC | Delete leuco_1200.vcf | 27 October 2017, 15:55:15 UTC |
1206be3 | Isaac Overcast | 04 August 2017, 15:44:30 UTC | Add support for true haploid calls. | 04 August 2017, 15:44:30 UTC |
81c66aa | Isaac Overcast | 19 April 2017, 13:21:01 UTC | Populations are written out to SFS in the order they occur in the pops file. | 19 April 2017, 13:21:01 UTC |
b427d0e | Isaac Overcast | 19 April 2017, 11:00:00 UTC | Fix readme errors. | 19 April 2017, 11:00:00 UTC |
ddf6f88 | isaacovercast | 30 November 2016, 19:06:33 UTC | oops fixed broken jointMAF format. | 30 November 2016, 19:06:33 UTC |
3babf8c | isaacovercast | 18 November 2016, 04:11:08 UTC | Added dtype flag to write out int bins instead of float. | 18 November 2016, 04:11:08 UTC |
94f9f19 | isaacovercast | 18 November 2016, 00:30:25 UTC | Adding support for gzipped vcf files. | 18 November 2016, 00:30:25 UTC |
87753f6 | isaacovercast | 21 October 2016, 18:25:16 UTC | Add the --unfolded flag to support polarized vcf. | 21 October 2016, 18:25:16 UTC |
50d24c1 | isaacovercast | 21 October 2016, 18:07:09 UTC | Clarified some of the docs. | 21 October 2016, 18:07:09 UTC |
9f8162a | isaacovercast | 11 October 2016, 16:04:24 UTC | Merge branch 'master' of https://github.com/isaacovercast/easySFS | 11 October 2016, 16:04:24 UTC |
12b8d4a | isaacovercast | 11 October 2016, 16:04:13 UTC | Fixed a ploidy bug in preview, and added support for vcf files w/ genotype info. | 11 October 2016, 16:04:13 UTC |
ee71643 | isaacovercast | 16 September 2016, 20:49:52 UTC | Better handling for removing diffs btwn populations file and inds in the vcf | 16 September 2016, 20:49:52 UTC |
aa2acfd | Isaac Overcast | 15 August 2016, 21:16:58 UTC | Update README.md | 15 August 2016, 21:16:58 UTC |
6d2c61a | isaacovercast | 15 August 2016, 21:05:22 UTC | Merge branch 'master' of https://github.com/isaacovercast/easySFS | 15 August 2016, 21:05:22 UTC |
7447413 | isaacovercast | 15 August 2016, 21:05:11 UTC | cosmetic change to usage for -a | 15 August 2016, 21:05:11 UTC |
9e01b3c | Isaac Overcast | 15 August 2016, 21:02:01 UTC | Update README.md | 15 August 2016, 21:02:01 UTC |
cd30577 | Isaac Overcast | 15 August 2016, 20:57:23 UTC | Update README.md | 15 August 2016, 20:57:23 UTC |
d2a5fc7 | isaacovercast | 15 August 2016, 20:16:12 UTC | More info about output files | 15 August 2016, 20:16:12 UTC |
b789116 | isaacovercast | 15 August 2016, 19:33:42 UTC | Fixed --preview output, and made --preview not try to write the datadict file | 15 August 2016, 19:33:42 UTC |
cbf684a | isaacovercast | 15 August 2016, 19:25:20 UTC | More info on input file formats | 15 August 2016, 19:25:20 UTC |
c52c4e0 | isaacovercast | 15 August 2016, 19:19:19 UTC | cosmetic change | 15 August 2016, 19:19:19 UTC |
ccda059 | isaacovercast | 15 August 2016, 19:18:14 UTC | Updating example run docs | 15 August 2016, 19:18:14 UTC |
5781620 | isaacovercast | 15 August 2016, 19:01:36 UTC | More docs | 15 August 2016, 19:01:36 UTC |
4fe4c7e | isaacovercast | 15 August 2016, 18:55:24 UTC | Adding some meager docs | 15 August 2016, 18:55:24 UTC |
1ebf38a | isaacovercast | 15 August 2016, 18:08:56 UTC | Initial commit of easySFS script and example files | 15 August 2016, 18:08:56 UTC |
cd7045f | Isaac Overcast | 15 August 2016, 18:07:25 UTC | Initial commit | 15 August 2016, 18:07:25 UTC |