| 23fe92f | Alex Rubinsteyn | 19 August 2020, 19:40:48 UTC | Merge pull request #191 from openvax/use-isovar-for-all-variant-counts Use Isovar for all variant counts, change Python versions in tests to 3.6 and 3.7 | 19 August 2020, 19:40:48 UTC |
| 7e808ce | Alex Rubinsteyn | 19 August 2020, 19:23:57 UTC | don't shadow name of run_isovar_from_args | 19 August 2020, 19:23:57 UTC |
| c13f790 | Alex Rubinsteyn | 19 August 2020, 18:56:22 UTC | moved some of the logic about gene names to Isovar | 19 August 2020, 18:56:22 UTC |
| e8f1be5 | Alex Rubinsteyn | 18 August 2020, 21:27:17 UTC | added test for isovar output | 18 August 2020, 21:27:17 UTC |
| d008f49 | Alex Rubinsteyn | 18 August 2020, 20:48:17 UTC | smarter use of gene_names | 18 August 2020, 20:48:17 UTC |
| 66fa687 | Alex Rubinsteyn | 18 August 2020, 15:11:36 UTC | make sure has_vaccine_peptide is always present | 18 August 2020, 15:11:36 UTC |
| 7258edb | Alex Rubinsteyn | 18 August 2020, 14:47:11 UTC | using 3.6+ | 18 August 2020, 14:47:11 UTC |
| f4983d6 | Alex Rubinsteyn | 18 August 2020, 14:21:52 UTC | removed Python 2.7 from tests, added Python 3.6 | 18 August 2020, 14:21:52 UTC |
| 5982599 | Alex Rubinsteyn | 17 August 2020, 22:12:53 UTC | update | 17 August 2020, 22:12:53 UTC |
| a64e173 | Alex Rubinsteyn | 17 August 2020, 21:54:14 UTC | changed how numbers get generated | 17 August 2020, 21:54:14 UTC |
| 653febf | Alex Rubinsteyn | 22 February 2020, 02:58:19 UTC | Merge pull request #186 from openvax/use-new-isovar-api-but-old-effects-logic use new Isovar API but keep old logic for determining variant effects | 22 February 2020, 02:58:19 UTC |
| 3b0be11 | Alex Rubinsteyn | 22 February 2020, 01:53:05 UTC | remove outdated comment | 22 February 2020, 01:53:05 UTC |
| dc20fc0 | Alex Rubinsteyn | 22 February 2020, 01:49:32 UTC | use --count-mismatches-after-variant | 22 February 2020, 01:49:32 UTC |
| 98069f4 | Alex Rubinsteyn | 21 February 2020, 19:42:41 UTC | use newer pysam | 21 February 2020, 19:42:41 UTC |
| ba817c6 | Alex Rubinsteyn | 21 February 2020, 19:41:16 UTC | removed redundant constructor arg | 21 February 2020, 19:41:16 UTC |
| 3bcd458 | Alex Rubinsteyn | 21 February 2020, 18:43:57 UTC | moved variant_to_protein_sequences onto VaxrankResults | 21 February 2020, 18:43:57 UTC |
| c2407f5 | Alex Rubinsteyn | 21 February 2020, 18:41:35 UTC | boolean not int | 21 February 2020, 18:41:35 UTC |
| 45fb901 | Alex Rubinsteyn | 21 February 2020, 18:39:57 UTC | making VaxrankResults work with isovar results | 21 February 2020, 18:39:57 UTC |
| 20da1ee | Alex Rubinsteyn | 20 February 2020, 20:35:04 UTC | added CLI defaults to help | 20 February 2020, 20:35:04 UTC |
| 6ca3e6e | Alex Rubinsteyn | 19 February 2020, 05:22:12 UTC | added serialization unit test | 19 February 2020, 05:22:12 UTC |
| ab4673e | Alex Rubinsteyn | 19 February 2020, 01:27:04 UTC | using netmhc instead of random predictor | 19 February 2020, 01:27:04 UTC |
| 4a61ae4 | Alex Rubinsteyn | 19 February 2020, 01:24:20 UTC | got most unit tests working | 19 February 2020, 01:24:20 UTC |
| 08abc7c | Alex Rubinsteyn | 18 February 2020, 23:07:03 UTC | figuring out MutantProteinFragment | 18 February 2020, 23:07:03 UTC |
| 0b98400 | Alex Rubinsteyn | 18 February 2020, 22:10:07 UTC | unit tests at least failing in main logic | 18 February 2020, 22:10:07 UTC |
| 75025af | Alex Rubinsteyn | 18 February 2020, 22:07:34 UTC | fixing up commandline tests | 18 February 2020, 22:07:34 UTC |
| 3bb712b | Alex Rubinsteyn | 18 February 2020, 19:43:44 UTC | got new CLI working | 18 February 2020, 19:43:44 UTC |
| 949b73d | Alex Rubinsteyn | 18 February 2020, 19:34:35 UTC | version bump | 18 February 2020, 19:34:35 UTC |
| 7139a27 | Alex Rubinsteyn | 18 February 2020, 19:34:11 UTC | making CLI more usable externally | 18 February 2020, 19:34:11 UTC |
| b102bad | Alex Rubinsteyn | 18 February 2020, 14:10:12 UTC | smallest possible change to use new Isovar | 18 February 2020, 14:10:12 UTC |
| d0e74d9 | Alex Rubinsteyn | 17 February 2020, 23:33:40 UTC | Merge pull request #185 from openvax/deconstruct-VaxrankCoreLogic Split VaxrankCoreLogic into smaller stateless functions | 17 February 2020, 23:33:40 UTC |
| 40ebc4e | Alex Rubinsteyn | 17 February 2020, 18:15:49 UTC | version bump | 17 February 2020, 18:15:49 UTC |
| 7cf225b | Alex Rubinsteyn | 17 February 2020, 16:49:59 UTC | patched test involving VaxrankCoreLogic | 17 February 2020, 16:49:59 UTC |
| 933ab19 | Alex Rubinsteyn | 16 February 2020, 23:30:40 UTC | updated, lets see if tests pass | 16 February 2020, 23:30:40 UTC |
| 9c66220 | Alex Rubinsteyn | 16 February 2020, 03:55:58 UTC | deleted empty file | 16 February 2020, 03:55:58 UTC |
| 9655d70 | Alex Rubinsteyn | 16 February 2020, 03:55:16 UTC | moved variant_properties to results object | 16 February 2020, 03:55:16 UTC |
| c43e1a0 | Alex Rubinsteyn | 16 February 2020, 03:49:04 UTC | replacing VaxrankCoreLogic class with module full of plain functions with explicit signatures | 16 February 2020, 03:49:04 UTC |
| cadc4d8 | Alex Rubinsteyn | 15 February 2020, 20:51:53 UTC | almost done pulling apart VaxrankCoreLogic | 15 February 2020, 20:51:53 UTC |
| a21df35 | Alex Rubinsteyn | 15 February 2020, 20:43:38 UTC | pulling apart VaxrankCoreLogic into stateless functions | 15 February 2020, 20:43:38 UTC |
| f129952 | Alex Rubinsteyn | 14 February 2020, 16:20:23 UTC | Merge pull request #184 from openvax/small-fixes Removed namedtuple, other small changes in preparation for rewrite | 14 February 2020, 16:20:23 UTC |
| ab5bf39 | Alex Rubinsteyn | 14 February 2020, 01:17:57 UTC | fixed nits | 14 February 2020, 01:17:57 UTC |
| 9955288 | Alex Rubinsteyn | 13 February 2020, 14:49:16 UTC | set PyPI version back to 2.7 | 13 February 2020, 14:49:16 UTC |
| ee26bb5 | Alex Rubinsteyn | 13 February 2020, 14:48:53 UTC | re-enable testing on Py2.7 | 13 February 2020, 14:48:53 UTC |
| 4fceafe | Alex Rubinsteyn | 13 February 2020, 14:47:42 UTC | disable pylint for ExcelWriter | 13 February 2020, 14:47:42 UTC |
| 381ac62 | Alex Rubinsteyn | 13 February 2020, 14:30:09 UTC | tried to move dependency to conda env | 13 February 2020, 14:30:09 UTC |
| 78a5970 | Alex Rubinsteyn | 13 February 2020, 04:07:05 UTC | only setuptools in conda env? | 13 February 2020, 04:07:05 UTC |
| 691fd10 | Alex Rubinsteyn | 13 February 2020, 02:51:08 UTC | what if we put wrapt in the conda env | 13 February 2020, 02:51:08 UTC |
| 1e97bea | Alex Rubinsteyn | 13 February 2020, 02:24:18 UTC | moved upgrade of setuptools into conda environment | 13 February 2020, 02:24:18 UTC |
| a0b93e8 | Alex Rubinsteyn | 13 February 2020, 02:02:19 UTC | push to PyPI for 3.x instead of 2.7 | 13 February 2020, 02:02:19 UTC |
| 4aac8ad | Alex Rubinsteyn | 13 February 2020, 02:01:33 UTC | got rid of py2.7 on Travis -- who needs it anymore? | 13 February 2020, 02:01:33 UTC |
| cc77c6f | Alex Rubinsteyn | 13 February 2020, 01:27:46 UTC | try installing newer wrapt for py3.5 | 13 February 2020, 01:27:46 UTC |
| d713b62 | Alex Rubinsteyn | 13 February 2020, 01:18:03 UTC | try fixing via setup tools | 13 February 2020, 01:18:03 UTC |
| a8e16b1 | Alex Rubinsteyn | 13 February 2020, 01:13:29 UTC | changed requirements to specify wrapt version that will work with python 3.5 on travis | 13 February 2020, 01:13:29 UTC |
| b213523 | Alex Rubinsteyn | 13 February 2020, 00:23:38 UTC | fixed manufacturability import | 13 February 2020, 00:23:38 UTC |
| 261324f | Alex Rubinsteyn | 12 February 2020, 21:00:02 UTC | added manufacturability_scores back to vaccine_peptide | 12 February 2020, 21:00:02 UTC |
| 8dc13da | Alex Rubinsteyn | 12 February 2020, 20:32:54 UTC | run tests in py3.5 | 12 February 2020, 20:32:54 UTC |
| da863b8 | Alex Rubinsteyn | 12 February 2020, 20:14:19 UTC | added missing patient_info module | 12 February 2020, 20:14:19 UTC |
| d7173eb | Alex Rubinsteyn | 12 February 2020, 19:56:14 UTC | correct import path for PatientInfo | 12 February 2020, 19:56:14 UTC |
| bb498ae | Alex Rubinsteyn | 12 February 2020, 19:41:54 UTC | removed namedtuple, other small changes in preparation for a much larger rewrite | 12 February 2020, 19:41:54 UTC |
| ba9d719 | Alex Rubinsteyn | 11 June 2019, 15:17:11 UTC | Merge pull request #177 from openvax/limit-isovar-versions broader version range for isovar, still excluding newest isovar PR | 11 June 2019, 15:17:11 UTC |
| aad6822 | Alex Rubinsteyn | 11 June 2019, 15:16:33 UTC | version bump | 11 June 2019, 15:16:33 UTC |
| 56b706e | Alex Rubinsteyn | 11 June 2019, 15:15:51 UTC | broader version range for isovar, still excluding newest isovar PR | 11 June 2019, 15:15:51 UTC |
| 57f0033 | Alex Rubinsteyn | 10 June 2019, 19:12:55 UTC | Merge pull request #176 from openvax/limit-isovar-versions Don't use the new Isovar version when it's merged | 10 June 2019, 19:12:55 UTC |
| ab762c0 | Alex Rubinsteyn | 10 June 2019, 18:48:10 UTC | version update | 10 June 2019, 18:48:10 UTC |
| ece560e | Alex Rubinsteyn | 10 June 2019, 17:43:22 UTC | don't use the new isovar version when it's merged | 10 June 2019, 17:43:22 UTC |
| 69100b7 | Julia Kodysh | 27 March 2019, 17:59:30 UTC | Merge pull request #175 from openvax/use-auto-genome-install-in-test-script Add --download-reference-genome-data arg to Vaxrank test run script. | 27 March 2019, 17:59:30 UTC |
| f45f0a6 | Julia K | 27 March 2019, 15:52:01 UTC | Add --download-reference-genome-data arg to Vaxrank test run script. Also update a CSS param | 27 March 2019, 15:52:01 UTC |
| fa368b6 | Alex Rubinsteyn | 21 October 2018, 02:23:37 UTC | creating range of desirable GRAVY scores | 21 October 2018, 02:23:37 UTC |
| bd9ecda | Alex Rubinsteyn | 18 October 2018, 20:13:13 UTC | added --version to Vaxrank CLI | 18 October 2018, 20:13:13 UTC |
| 7b75ae7 | Alex Rubinsteyn | 18 October 2018, 20:03:04 UTC | new manufacturability criteria which minimizes cysteines and keeps overall hydrophobicity under 2.5 and C-term hydrophobicity under 1.5, also added rounding to epitope scores to minimize impact of small floating point errors | 18 October 2018, 20:03:04 UTC |
| 446fd1f | Alex Rubinsteyn | 18 October 2018, 19:45:22 UTC | Version bump to 0.8.11 | 18 October 2018, 19:45:22 UTC |
| 4d61ac2 | Alex Rubinsteyn | 18 October 2018, 19:08:26 UTC | removed papers | 18 October 2018, 19:08:26 UTC |
| 47fab7b | Alex Rubinsteyn | 18 October 2018, 19:07:39 UTC | moved paper to own repo, removed pypandoc dependency | 18 October 2018, 19:07:39 UTC |
| 18ba006 | Alex Rubinsteyn | 12 October 2018, 04:36:57 UTC | Update __init__.py | 12 October 2018, 04:36:57 UTC |
| 68a5661 | Alex Rubinsteyn | 12 October 2018, 01:42:06 UTC | Merge pull request #173 from openvax/update-paper Update paper | 12 October 2018, 01:42:06 UTC |
| 76381ea | Alex Rubinsteyn | 11 October 2018, 21:18:47 UTC | Merge pull request #172 from openvax/formatting-cleanup Superficial cleanup | 11 October 2018, 21:18:47 UTC |
| 4731cc0 | Alex Rubinsteyn | 11 October 2018, 20:16:01 UTC | don't use container based infra to get more disk space | 11 October 2018, 20:16:01 UTC |
| 1ceecd6 | Alex Rubinsteyn | 11 October 2018, 20:14:15 UTC | changed travis config | 11 October 2018, 20:14:15 UTC |
| 13dce00 | Alex Rubinsteyn | 11 October 2018, 19:02:00 UTC | moved FM index code to its own file to hide implementation details | 11 October 2018, 19:02:00 UTC |
| 0fb8015 | Alex Rubinsteyn | 11 October 2018, 15:17:54 UTC | added second test of driver variant | 11 October 2018, 15:17:54 UTC |
| f780770 | Alex Rubinsteyn | 11 October 2018, 15:15:38 UTC | added Ensembl 75 for unit test | 11 October 2018, 15:15:38 UTC |
| b59b47d | Alex Rubinsteyn | 10 October 2018, 21:18:24 UTC | fixed small bug and added unit test for GenePathwayCheck | 10 October 2018, 21:18:24 UTC |
| a2f080a | Alex Rubinsteyn | 10 October 2018, 19:43:44 UTC | version bump | 10 October 2018, 19:46:13 UTC |
| d469b04 | Alex Rubinsteyn | 10 October 2018, 19:39:55 UTC | PEP8 and style changes, made GenePathwayCheck easier to read | 10 October 2018, 19:45:31 UTC |
| 64dc542 | Julia Kodysh | 24 September 2018, 22:20:11 UTC | Merge pull request #170 from openvax/fix-float-display Showing 5 significant figures for floats in Vaxrank reports. | 24 September 2018, 22:20:11 UTC |
| 4225b7d | Julia K | 24 September 2018, 20:36:45 UTC | Showing 5 significant figures for floats in Vaxrank reports. | 24 September 2018, 20:36:45 UTC |
| 733913c | Alex Rubinsteyn | 20 September 2018, 18:11:31 UTC | Update README.md | 20 September 2018, 18:11:31 UTC |
| 21ddf24 | Alex Rubinsteyn | 20 September 2018, 18:11:09 UTC | Update README.md | 20 September 2018, 18:11:09 UTC |
| b29bb57 | Julia Kodysh | 07 September 2018, 19:08:19 UTC | Merge pull request #169 from openvax/fix-data-packaging Fixing how we package data/* files. | 07 September 2018, 19:08:19 UTC |
| 2499e5a | Julia K | 07 September 2018, 16:12:17 UTC | Fixing how we package data/* files - right now they're not making it into the build | 07 September 2018, 16:12:17 UTC |
| 47decce | Julia Kodysh | 06 September 2018, 19:59:55 UTC | Merge pull request #168 from openvax/keep-all-variants Keep all variants, add gene set membership check | 06 September 2018, 19:59:55 UTC |
| 43f90cc | Julia K | 06 September 2018, 15:42:42 UTC | iskander cr | 06 September 2018, 15:42:42 UTC |
| 86973af | Julia K | 22 August 2018, 18:57:13 UTC | Adding gene name to all-variants CSV output | 22 August 2018, 18:57:13 UTC |
| 1dc9416 | Julia K | 17 August 2018, 20:50:31 UTC | Fixing DataFrame constructor issue for Python 3 | 17 August 2018, 20:50:31 UTC |
| 5943ebe | Julia K | 17 August 2018, 16:04:13 UTC | Inheriting from object | 17 August 2018, 16:04:13 UTC |
| 89de7b5 | Julia K | 17 August 2018, 16:02:50 UTC | Adding a small test | 17 August 2018, 16:02:50 UTC |
| c684914 | Julia K | 17 August 2018, 15:55:35 UTC | Upping Vaxrank version | 17 August 2018, 15:55:35 UTC |
| ef631dc | Julia K | 16 August 2018, 22:27:03 UTC | Slight refactor of the keep-all-variants change: including gene list data in this package | 16 August 2018, 22:27:03 UTC |
| ac87c9b | Julia K | 08 August 2018, 18:24:59 UTC | A couple more changes | 08 August 2018, 18:24:59 UTC |
| b236f54 | Julia K | 05 August 2018, 22:06:13 UTC | Factored out gene_pathway_check into its own class | 07 August 2018, 18:45:02 UTC |
| 03b05ea | Julia K | 24 July 2018, 17:06:22 UTC | Start of refactor to get some info for all passing variants and check against known gene lists | 07 August 2018, 18:43:41 UTC |
