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50 most recent check-ins
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2021-02-12
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| 21:54 | Update README to include HPTEST and LDBIRD Leaf check-in: 6d00b396bf user: gav tags: trunk, master | |
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2020-12-13
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| 22:06 | IndependentLogFWeightedPrior: fix prior mode again to compile check-in: 901a3d9966 user: gav tags: trunk, master | |
| 22:01 | bump to v2.1.9. hptest: add -compare-variants-by. Separate results by ID by default as well as position and alleles. check-in: 57135a780c user: gav tags: trunk, master | |
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2020-12-11
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| 17:16 | qcdb::FlatTableDBOutputter: use backtick not double quote for variable/table names in SQL check-in: 3517f8d03e user: gav tags: trunk, master | |
| 17:15 | IndependentLogFWeightedLogLikelihood: get prior mode correct check-in: 9ad662ac01 user: gav tags: trunk, master | |
| 17:14 | ldbirs: add a number_of_haplotypes and frequency column to Frequency table check-in: b8f44058ac user: gav tags: trunk, master | |
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2020-08-22
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| 22:26 | Fix download links for zip and tarball on download page Leaf check-in: beeade86f9 user: gav tags: release | |
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2020-07-24
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| 13:14 | CohortIndividualSource: make sure ID_1 is treated as a column name when searching for it. check-in: ade6dc6afb user: gav tags: trunk, master | |
| 11:44 | Bump to v2.1.8. hptest: add -sample-data option, similar to that in qctool. Also, determine bayesian or frequentist output based on whether there are actually priors applied check-in: 356ce4e502 user: gav tags: trunk, master | |
| 11:30 | hptest: catch case when covariate has no levels check-in: 4d62c8d7f4 user: gav tags: trunk, master | |
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2020-07-21
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| 13:31 | hptest: make prior spec expansion more efficient check-in: 80867ba248 user: gav tags: trunk, master | |
| 13:14 | Bump to v1.1.7. hptest: make default priors apply across strata. check-in: 3578f8631e user: gav tags: trunk, master | |
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2020-07-16
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| 22:03 | hptest: fix issues with -stratify check-in: 2386a58ad3 user: gav tags: trunk, master | |
| 13:48 | hptest: fix -stratify to allow original info and count computation to still work check-in: 180e9e6b06 user: gav tags: trunk, master | |
| 10:14 | hptest: add -stratify option check-in: 8b5c90a411 user: gav tags: trunk, master | |
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2020-07-08
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| 13:02 | selfmap: remove unused variable check-in: 76f8c10c63 user: gav tags: trunk, master | |
| 12:57 | selfmap: fix for output of kmer size check-in: a4b49b4352 user: gav tags: trunk, master | |
| 12:50 | Bump to 2.1.5. selfmap: add -omit-sequence option and output k in the overlap table. check-in: f2a06c1e3f user: gav tags: trunk, master | |
| 12:16 | GenomeSequence: support unprefixed sequences check-in: da828550b0 user: gav tags: trunk, master | |
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2020-06-30
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| 15:47 | Whoops, fix download page again. check-in: b1c78b9a69 user: gav tags: trunk, master | |
| 15:45 | Download page tweak check-in: 63972ea520 user: gav tags: trunk, master | |
| 15:41 | Pull downlaod page change from release branch check-in: 6b12462330 user: gav tags: trunk, master | |
| 15:40 | Fix download page for v2.0.8 check-in: 2a7cc007cf user: gav tags: release, v2.0.8 | |
| 15:13 | Bump to v2.0.8. Implement fixes for [b952a6be] and [4d88dff8cc]. check-in: 2fcd3b2679 user: gav tags: release | |
| 15:03 | qctool: make sure -reorder is rejected if no sample IDs. Add test for -reorder without sample file, and sample filters without sample file Leaf check-in: 69ce5b9cd4 user: gav tags: b952a6be-fix | |
| 14:25 | SampleFilteringSNPDataSOurce: implement get_sample_ids() correctly. check-in: 051b48479e user: gav tags: b952a6be-fix | |
| 14:24 | Improve sample filtering testing for sample IDs fix. check-in: 3326af54c2 user: gav tags: b952a6be-fix | |
| 13:48 | stats_test.R: fix sample identifiers to avoid mismatch issue check-in: 8f58330d92 user: gav tags: b952a6be-fix | |
| 11:20 | Make qctool understand when genotype source contains sample identifiers, to fix issue [b952a6be]. This change should really have been made against trunk but placing here because I have implemented it here. This change requires additional testing; tests fail at present which may be due to incompatible sample IDs in test data sources. check-in: 500cd8c3bd user: gav tags: b952a6be-fix | |
| 09:11 | Import VCF semicolon fix from trunk (0084026f03); fix tests to run again Leaf check-in: 5020f419ab user: gav tags: 4d88dff8cc-fix | |
| 09:08 | Bump to v2.0.8-beta; allow VCF GP field without GT field fixing ticket 4d88dff8cc check-in: 1757d58665 user: gav tags: 4d88dff8cc-fix | |
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2020-06-27
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| 16:15 | Removed .hgignore and .hgrc files check-in: 3d560ec0c8 user: gav tags: trunk, master | |
| 11:23 | Update README and download page again to point to main qctool doc page on well.ox.ac.uk check-in: fdb5c52a05 user: gav tags: trunk, master | |
| 11:16 | Whoops, merge boost files change into release branch check-in: a1361a4ee4 user: gav tags: release | |
| 11:11 | Removed unneeded boost files Leaf check-in: a0360ebe1c user: gav | |
| 11:03 | Create new branch named "release" check-in: cbc5c9afbe user: gav tags: release | |
| 10:58 | README.md: include links to docs and use main doc download page check-in: eb768b84d0 user: gav tags: trunk, master | |
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2020-06-26
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| 23:44 | Fix link to fossil repo home page for acknowledgements check-in: 54c8a80223 user: gav tags: trunk, master | |
| 23:43 | Fix download page link to wiki check-in: eedb65deec user: gav tags: trunk, master | |
| 23:39 | More work linking wiki pages etc. check-in: c0748e5602 user: gav tags: trunk, master | |
| 23:38 | More work linking wiki pages etc. check-in: 14e043d3df user: gav tags: trunk, master | |
| 23:30 | Work on download page. check-in: 349de1f189 user: gav tags: trunk, master | |
| 23:00 | Update README.md check-in: 7955a5f615 user: gav tags: trunk, master | |
| 23:00 | Update README.md check-in: aeaf15ec87 user: gav tags: trunk, master | |
| 22:58 | Work on README and download page for code.enkre.net check-in: 2c0b74be73 user: gav tags: trunk, master | |
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2020-06-02
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| 12:44 | Added boost iostreams, remove more boost files check-in: e1c3e92372 user: gav tags: trunk, master | |
| 12:37 | Remove unneeded boost files check-in: ae70c8b879 user: gav tags: trunk, master | |
| 11:00 | hptest: add -treat-predictor-as-haploid option. Ensure support haploid predictor and outcome. check-in: 0604a16e58 user: gav tags: trunk, master | |
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2020-06-01
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| 23:05 | ldbird: factor out CartesianProduct to genfile::CartesianProductVisitor. hptest: use CartesianProductVisitor check-in: 8907d42d5a user: gav tags: trunk, master | |
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2020-05-28
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| 16:14 | Bump to v2.1.3 check-in: 3d76073841 user: gav tags: trunk, master, v2.1.3 | |