| e9b822c | Bjarni J. Vilhjalmsson | 17 October 2019, 10:31:28 UTC | Merge pull request #119 from bvilhjal/develop Develop | 17 October 2019, 10:31:28 UTC |
| 710baf0 | Bjarni J. Vilhjalmsson | 17 October 2019, 10:30:50 UTC | Merge pull request #118 from bvilhjal/master update develop | 17 October 2019, 10:30:50 UTC |
| 93c06ac | Bjarni Vilhjalmsson | 17 October 2019, 10:10:37 UTC | updated readme | 17 October 2019, 10:10:37 UTC |
| 00b76e7 | Bjarni Vilhjalmsson | 17 October 2019, 10:04:51 UTC | updated readme | 17 October 2019, 10:04:51 UTC |
| 5d99231 | Bjarni Vilhjalmsson | 17 October 2019, 10:04:40 UTC | removed test files that were too large for pip | 17 October 2019, 10:04:40 UTC |
| 244a2ca | Bjarni J. Vilhjalmsson | 17 October 2019, 09:46:32 UTC | Merge pull request #117 from bvilhjal/master updating develop | 17 October 2019, 09:46:32 UTC |
| 283c2a0 | Bjarni Vilhjalmsson | 17 October 2019, 09:45:31 UTC | deleted an uneeded file | 17 October 2019, 09:45:31 UTC |
| 281c218 | Bjarni J. Vilhjalmsson | 17 October 2019, 09:44:11 UTC | Merge pull request #116 from bvilhjal/master updating develop to latest | 17 October 2019, 09:44:11 UTC |
| 1c5d266 | Bjarni Vilhjalmsson | 17 October 2019, 09:41:23 UTC | Merge branch 'bigmerge' | 17 October 2019, 09:41:23 UTC |
| e6b9a7f | Bjarni Vilhjalmsson | 17 October 2019, 09:40:56 UTC | Merge branch 'master' into bigmerge | 17 October 2019, 09:40:56 UTC |
| 9f1bfcb | Bjarni Vilhjalmsson | 17 October 2019, 09:34:03 UTC | Fixed CI issue? | 17 October 2019, 09:34:03 UTC |
| 44efb97 | Bjarni Vilhjalmsson | 17 October 2019, 09:31:04 UTC | Fixing CI issue? | 17 October 2019, 09:31:04 UTC |
| 705c956 | Bjarni Vilhjalmsson | 17 October 2019, 09:23:28 UTC | Try integreation tests | 17 October 2019, 09:23:28 UTC |
| 587d70a | Bjarni Vilhjalmsson | 17 October 2019, 09:15:30 UTC | updated CI file | 17 October 2019, 09:15:30 UTC |
| d1ab0c7 | Bjarni Vilhjalmsson | 17 October 2019, 09:13:06 UTC | updated circleCI | 17 October 2019, 09:13:06 UTC |
| 8faefe3 | Bjarni Vilhjalmsson | 17 October 2019, 09:07:08 UTC | updated README and CHANGES file, and other files added | 17 October 2019, 09:07:08 UTC |
| 0d7d5a1 | Bjarni Vilhjalmsson | 17 October 2019, 09:01:03 UTC | updated test results | 17 October 2019, 09:01:03 UTC |
| f10d9e0 | Bjarni Vilhjalmsson | 17 October 2019, 09:00:46 UTC | Fixed tests, so that they now work when ldpred is installed via pip | 17 October 2019, 09:00:46 UTC |
| 0799d21 | Bjarni Vilhjalmsson | 17 October 2019, 05:47:48 UTC | Improved setup and re-structured LDpred | 17 October 2019, 05:47:48 UTC |
| 97bd208 | Bjarni Vilhjalmsson | 16 October 2019, 15:05:30 UTC | removed a couple of testfiles | 16 October 2019, 15:05:30 UTC |
| eb42732 | Bjarni Vilhjalmsson | 16 October 2019, 15:02:03 UTC | Fixed a testing bug | 16 October 2019, 15:02:03 UTC |
| 45bae3a | Bjarni Vilhjalmsson | 16 October 2019, 14:56:21 UTC | restructured package | 16 October 2019, 14:56:21 UTC |
| 66bb559 | Bjarni Vilhjalmsson | 16 October 2019, 14:55:48 UTC | fixed minor things | 16 October 2019, 14:55:48 UTC |
| 0a0bc65 | Bjarni Vilhjalmsson | 16 October 2019, 14:55:34 UTC | Updated readme | 16 October 2019, 14:55:34 UTC |
| c2a6fe3 | Bjarni Vilhjalmsson | 16 October 2019, 14:43:20 UTC | Updated structure | 16 October 2019, 14:43:20 UTC |
| 022c6c6 | Bjarni Vilhjalmsson | 16 October 2019, 14:43:03 UTC | Updated version.. | 16 October 2019, 14:43:03 UTC |
| d475617 | Bjarni Vilhjalmsson | 16 October 2019, 10:51:32 UTC | updated tests | 16 October 2019, 10:51:32 UTC |
| 7ca66b8 | Bjarni Vilhjalmsson | 16 October 2019, 10:51:08 UTC | updated tests | 16 October 2019, 10:51:08 UTC |
| 467bab8 | Bjarni Vilhjalmsson | 16 October 2019, 10:34:06 UTC | updated test results | 16 October 2019, 10:34:06 UTC |
| 222c881 | Bjarni Vilhjalmsson | 16 October 2019, 10:25:30 UTC | Added tiny LD shrink... | 16 October 2019, 10:25:30 UTC |
| c2961d8 | Bjarni Vilhjalmsson | 16 October 2019, 10:18:15 UTC | A tiny LD shrink... | 16 October 2019, 10:18:15 UTC |
| aba50cf | Bjarni Vilhjalmsson | 16 October 2019, 07:55:41 UTC | Fixed a bug pointed out by @rickyota | 16 October 2019, 07:55:41 UTC |
| f0f71b0 | Bjarni Vilhjalmsson | 16 October 2019, 07:54:39 UTC | Small refactoring of validate.py | 16 October 2019, 07:54:39 UTC |
| a397622 | Bjarni Vilhjalmsson | 16 October 2019, 07:54:03 UTC | Updated tests | 16 October 2019, 07:54:03 UTC |
| ab6e2e2 | Bjarni Vilhjalmsson | 16 October 2019, 07:53:33 UTC | Updated test data | 16 October 2019, 07:53:33 UTC |
| 07edd1d | Bjarni Vilhjalmsson | 16 October 2019, 07:52:28 UTC | Updated test data | 16 October 2019, 07:52:28 UTC |
| dfdb898 | Bjarni Vilhjalmsson | 16 October 2019, 07:51:42 UTC | Updated test results | 16 October 2019, 07:51:42 UTC |
| 4cd56f9 | Bjarni Vilhjalmsson | 16 October 2019, 07:51:04 UTC | Updated test results | 16 October 2019, 07:51:04 UTC |
| 5e4a5e1 | Bjarni Vilhjalmsson | 15 October 2019, 13:30:56 UTC | Fixed a minor bug that may or may not improve convergence.. | 15 October 2019, 13:30:56 UTC |
| 2dbf530 | Bjarni Vilhjalmsson | 15 October 2019, 10:16:00 UTC | added golden files | 15 October 2019, 10:16:00 UTC |
| fe4eb50 | Bjarni Vilhjalmsson | 15 October 2019, 10:15:15 UTC | Merged large google pull request Also improved testing and other minor improvements | 15 October 2019, 10:15:15 UTC |
| 94b87d7 | Bjarni Vilhjalmsson | 15 October 2019, 09:08:39 UTC | Fixed a bug that prevented PRS files with multiple LD r2 threshold to be written.. | 15 October 2019, 09:08:39 UTC |
| 0c484fb | Bjarni J. Vilhjalmsson | 14 October 2019, 09:45:18 UTC | Merge branch 'develop' into bigmerge | 14 October 2019, 09:45:18 UTC |
| 2bc2ec2 | Bjarni J. Vilhjalmsson | 14 October 2019, 09:39:15 UTC | Merge pull request #88 from jdijamco/master Bug fixes and refactoring of tests. | 14 October 2019, 09:39:15 UTC |
| 95d0d38 | Bjarni J. Vilhjalmsson | 11 October 2019, 12:58:51 UTC | Merge pull request #94 from borisevichdi/master Fixing output of progress bars | 11 October 2019, 12:58:51 UTC |
| 52ad551 | Bjarni J. Vilhjalmsson | 11 October 2019, 12:58:20 UTC | Merge branch 'master' into master | 11 October 2019, 12:58:20 UTC |
| f46ddc4 | Bjarni Vilhjalmsson | 11 October 2019, 12:25:51 UTC | #101 | 11 October 2019, 12:25:51 UTC |
| 5b72db0 | Bjarni Vilhjalmsson | 11 October 2019, 12:23:56 UTC | #103 | 11 October 2019, 12:23:56 UTC |
| a120b0b | Bjarni Vilhjalmsson | 11 October 2019, 11:55:23 UTC | #106 Added BASIC format. It had been left out by mistake. | 11 October 2019, 11:55:23 UTC |
| 3db18bb | Bjarni J. Vilhjalmsson | 11 October 2019, 11:49:29 UTC | Merge pull request #109 from bvilhjal/develop Develop | 11 October 2019, 11:49:29 UTC |
| 69a7631 | Bjarni Vilhjalmsson | 11 October 2019, 11:24:39 UTC | Small bug in progression percentage | 11 October 2019, 11:24:39 UTC |
| 1875995 | Bjarni Vilhjalmsson | 11 October 2019, 11:19:41 UTC | Small improvements in reporting | 11 October 2019, 11:19:41 UTC |
| 6fdfe28 | Bjarni Vilhjalmsson | 11 October 2019, 10:37:06 UTC | Replaced these simulations with more elaborate ones... | 11 October 2019, 10:37:06 UTC |
| b2dad8f | Bjarni Vilhjalmsson | 11 October 2019, 10:36:27 UTC | tested on python 2.7 | 11 October 2019, 10:36:27 UTC |
| 2f23d04 | Bjarni Vilhjalmsson | 11 October 2019, 10:23:12 UTC | Updated version and pip setup files | 11 October 2019, 10:23:12 UTC |
| 6117a77 | Bjarni Vilhjalmsson | 11 October 2019, 08:45:41 UTC | Minor improvements | 11 October 2019, 08:45:41 UTC |
| 0bcc72c | Bjarni Vilhjalmsson | 11 October 2019, 08:31:02 UTC | Several minor improvements - Improved reporting for P+T and LDpred-inf - Added an option --use-gw-h2 for LDpred-gibbs and LDpred-inf, which forces LDpred to estimate h2 genome-wide and partition it proportional to the number of SNPs on each chromosome (this is what LDpred used to do by default). - Improved tests | 11 October 2019, 08:31:02 UTC |
| 2bc5bf5 | Bjarni Vilhjalmsson | 10 October 2019, 14:34:53 UTC | Simulated datasets | 10 October 2019, 14:34:53 UTC |
| d15463f | Bjarni Vilhjalmsson | 10 October 2019, 14:33:13 UTC | A lot of small improvements. - Fixed an issue that caused SNPs w p-values rounded to 0 to be excluded from analysis. If the p-value is 0, LDpred now attempts to use the SE together with the effect size instead. - Added an option that enables the user to always use SE together with the effect size instead of p-value. - The gibbs sampler now accounts for differing sample sizes per SNP, if those are provided in the summary stats. This seems to improve robustness of the gibbs samler, and leads to better predictions in simulations. However, this option slows the Gibbs sampler a lot. - It now estimates the LD score heritability per chromosome by default (instead of partitioning it proportional to the number of SNPs.) - Improved testing | 10 October 2019, 14:33:13 UTC |
| ab39376 | Bjarni Vilhjalmsson | 07 October 2019, 11:59:48 UTC | Added the option of deriving Z-scores from effect estimates and SEs, instead of p-values. Also, fixed a bug that prevented the use of N in summary stats to work. | 07 October 2019, 11:59:48 UTC |
| a928562 | Bjarni Vilhjalmsson | 07 October 2019, 09:22:08 UTC | Organised and improved testing.. | 07 October 2019, 09:22:08 UTC |
| 5f81b0f | Bjarni Vilhjalmsson | 07 October 2019, 08:53:19 UTC | Fixed an issue in weights file naming when running LDpred-inf only.. | 07 October 2019, 08:53:19 UTC |
| dae2d77 | Bjarni Vilhjalmsson | 04 October 2019, 07:09:21 UTC | Fixed percentage when parsing zipped sum stats | 04 October 2019, 07:09:21 UTC |
| 4b5be46 | borisevichdi | 18 June 2019, 17:34:19 UTC | Fixing output of progress bars | 18 June 2019, 17:34:19 UTC |
| 97c5d1d | Jojo Dijamco | 22 May 2019, 22:30:15 UTC | Fix (#2) for https://github.com/bvilhjal/ldpred/issues/83 | 22 May 2019, 22:30:15 UTC |
| 1976b27 | Jojo Dijamco | 22 May 2019, 21:50:31 UTC | Fix for https://github.com/bvilhjal/ldpred/issues/81 | 22 May 2019, 21:50:31 UTC |
| 4dd4a29 | Jojo Dijamco | 22 May 2019, 17:10:06 UTC | Merge from upstream | 22 May 2019, 17:10:06 UTC |
| 737d69c | Bjarni J. Vilhjalmsson | 16 May 2019, 12:35:50 UTC | Merge pull request #76 from choishingwan/patch-2 [Update] Allow LSTANDARD in parameter list | 16 May 2019, 12:35:50 UTC |
| 8b333eb | Bjarni Vilhjalmsson | 15 May 2019, 10:06:35 UTC | #79 | 15 May 2019, 10:06:35 UTC |
| 90ba409 | Bjarni Vilhjalmsson | 15 May 2019, 09:45:10 UTC | #75 | 15 May 2019, 09:45:10 UTC |
| 71bb050 | Jojo Dijamco | 02 May 2019, 21:58:12 UTC | Exclude test.py and setup.py from code coverage metrics. | 02 May 2019, 21:58:12 UTC |
| b698f2f | Jojo Dijamco | 02 May 2019, 21:24:07 UTC | Fix case inconsistency: change "LDPred" to "LDpred" | 02 May 2019, 21:24:07 UTC |
| b6f8778 | Jojo Dijamco | 02 May 2019, 21:20:28 UTC | Move the np.random.seed(42) call to the gibbs unit test, since it's the only test golden that relies on a fixed random seed. | 02 May 2019, 21:20:28 UTC |
| f7079ee | Jojo Dijamco | 02 May 2019, 21:14:38 UTC | Pass explicit "r" or "w" mode to h5py.File(), to prevent file changes when the intended context is read-only. | 02 May 2019, 21:14:38 UTC |
| 40d1baa | Jojo Dijamco | 02 May 2019, 21:03:51 UTC | Forward the `debug` flag from coord_genotypes.py to plinkfiles.get_chrom_dict(). | 02 May 2019, 21:03:51 UTC |
| bf52cc4 | Jojo Dijamco | 02 May 2019, 20:43:01 UTC | Add unit test for ld.get_chromosome_herits() | 02 May 2019, 20:43:01 UTC |
| 836713f | Jojo Dijamco | 02 May 2019, 20:20:43 UTC | Factor out a get_ld_dict_from_p_dict() function, to reduce code duplication. | 02 May 2019, 20:20:43 UTC |
| ccfbf7b | Jojo Dijamco | 02 May 2019, 20:03:23 UTC | Add a coverage.sh script, which will run code coverage analysis of tests and write all temporary files to a directory outside the source tree. | 02 May 2019, 20:03:23 UTC |
| 7a15007 | Jojo Dijamco | 02 May 2019, 20:00:52 UTC | In test.py, fully qualify all paths to files under test_data. This sets up the ability to run tests and write temp files outside the source tree. | 02 May 2019, 20:00:52 UTC |
| 9147369 | Jojo Dijamco | 02 May 2019, 00:28:16 UTC | Make each step separately testable, by reading inputs from the goldens directory. Added an example command on how to run an individual test. Also make cleanup code more consistent. | 02 May 2019, 00:28:16 UTC |
| 33f251f | Jojo Dijamco | 01 May 2019, 00:36:11 UTC | Fix for issue https://github.com/bvilhjal/ldpred/issues/83 and updated test goldens. | 01 May 2019, 00:36:11 UTC |
| f299a7d | Jojo Dijamco | 30 April 2019, 23:45:20 UTC | Fix error message reporting when diffing text files in test. | 30 April 2019, 23:45:20 UTC |
| 60b9135 | Jojo Dijamco | 29 April 2019, 23:44:04 UTC | Add setUp() and tearDown() to test.py and update test_ldpred() to use them. | 29 April 2019, 23:44:04 UTC |
| fb9b6f4 | babak-ra | 29 April 2019, 22:36:46 UTC | fixed LD golden file | 29 April 2019, 22:36:46 UTC |
| e707ecc | Jojo Dijamco | 29 April 2019, 18:56:08 UTC | Factor out helper functions. | 29 April 2019, 18:56:08 UTC |
| c2c9066 | Jojo Dijamco | 24 April 2019, 18:11:39 UTC | Extract a make_p_dict() function in test.py | 24 April 2019, 18:11:39 UTC |
| fe67494 | Babak Alipanahi | 23 April 2019, 22:42:03 UTC | added plink test files for LD calculation | 23 April 2019, 22:42:03 UTC |
| a389578 | Jojo Dijamco | 23 April 2019, 07:41:26 UTC | Fix bug in coord_genotypes.py and add unit test to cover the fix. | 23 April 2019, 07:41:26 UTC |
| 991921f | Jojo Dijamco | 22 April 2019, 21:50:22 UTC | Add unit test for sum_stats_parsers | 22 April 2019, 21:50:22 UTC |
| 4d40cf8 | Jojo Dijamco | 22 April 2019, 21:30:58 UTC | Use Python unittest module in test.py | 22 April 2019, 21:30:58 UTC |
| f41af00 | Jojo Dijamco | 18 April 2019, 22:59:52 UTC | Update to test.py to use test goldens. | 18 April 2019, 22:59:52 UTC |
| 5578f87 | Jojo Dijamco | 18 April 2019, 22:57:52 UTC | Added golden files to test_data and assert that test results match them. | 18 April 2019, 22:57:52 UTC |
| 83c6a6a | Shing Wan Choi | 18 April 2019, 17:35:33 UTC | [Update] Allow LSTANDARD in parameter list | 18 April 2019, 17:35:33 UTC |
| 3e587bc | Jojo Dijamco | 17 April 2019, 00:49:11 UTC | Update tests to work better with code coverage analysis tools. | 17 April 2019, 00:49:11 UTC |
| aab1190 | Jojo Dijamco | 16 April 2019, 23:21:36 UTC | Internal refactoring of test.py | 16 April 2019, 23:21:36 UTC |
| 6fba2c8 | Bjarni Vilhjalmsson | 29 March 2019, 10:01:19 UTC | Fixed validation step bug which failed if P+T had no SNPs | 29 March 2019, 10:01:19 UTC |
| ade8008 | Bjarni Vilhjalmsson | 29 March 2019, 09:54:25 UTC | Fixed a bug... | 29 March 2019, 09:54:25 UTC |
| 23896f1 | Bjarni J. Vilhjalmsson | 19 March 2019, 06:56:50 UTC | Merge pull request #69 from bvilhjal/develop Develop | 19 March 2019, 06:56:50 UTC |
| 92cddb9 | Bjarni Vilhjalmsson | 18 March 2019, 15:17:11 UTC | Version 1.0.6 | 18 March 2019, 15:17:11 UTC |
| 228dff5 | Bjarni Vilhjalmsson | 18 March 2019, 15:13:45 UTC | Improved error messaging | 18 March 2019, 15:13:45 UTC |
