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510 check-ins using file LICENSE_1_0.txt version 12bafc460e
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2024-09-22
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| 12:20 | Fix wscript comment Leaf check-in: 78cf9c9636 user: gav tags: trunk | |
| 12:17 | Bump to v1.2.0. Update for C++17 and boost 1.86.0 check-in: 1a41e97844 user: gav tags: trunk | |
| 12:09 | Upgrade to boost 1.86 check-in: c45999b5c7 user: gav tags: trunk | |
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2022-09-10
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| 20:14 | db: require C++11. Add release stub for arm64 (Apple M1) macs. check-in: 703a453117 user: gav tags: trunk | |
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2021-07-02
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| 21:59 | doc updates for bgen check-in: 665dda1221 user: gav tags: trunk | |
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2020-06-29
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| 08:22 | Go back to using 'trunk' instead of 'development', as why fight it? check-in: 40c4c1f54f user: gav tags: trunk | |
| 08:20 | Bump development wscript version to v1.1.8 Leaf check-in: 30361934be user: gav tags: development | |
| 08:19 | Whoops, set VERSION=1.1.7 in wscript Leaf check-in: 6ac2d582f9 user: gav tags: release, v1.1.7 | |
| 08:18 | Pull README.md tweaks from release branch check-in: 99a7b6f7c6 user: gav tags: development | |
| 08:17 | Create new branch named "development" check-in: 15ad974ca0 user: gav tags: development | |
| 08:15 | Release 1.1.7. check-in: a4246e08da user: gav tags: release | |
| 08:03 | README.md updated check-in: 9774e42e05 user: gav tags: trunk | |
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2020-06-27
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| 22:14 | Doc updates for code.enkre.net transition check-in: 2935d98591 user: gav tags: trunk | |
| 21:57 | Create new branch named "release" check-in: 163ec615b8 user: gav tags: release | |
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2020-05-25
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| 21:02 | Remove more unneeded boost files check-in: 976fa37942 user: gav tags: trunk | |
| 21:01 | Remove unneeded boost files as making repo too large/slow check-in: 10036c5a47 user: gav tags: trunk | |
| 20:50 | Test edit README.md check-in: c12407af0b user: gav tags: trunk | |
| 20:48 | Test update bgenix.md check-in: 1803216e99 user: gav tags: trunk | |
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2020-05-22
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| 08:39 | Update bgenix wiki page check-in: a1988afb39 user: gav tags: trunk | |
| 08:32 | wscript: fix bgen_revision_autogenerated.hpp for fossil. Add bgenix.md doc page check-in: 0929325a6c user: gav tags: trunk | |
| 08:29 | bgenix: remove unused variable check-in: 6a82589950 user: gav tags: trunk | |
| 08:16 | Test add of bgenix embedded doc page check-in: 71f6573e56 user: gav tags: trunk | |
| 08:15 | Add PySnpTools to software.html check-in: e6d89657b9 user: gav tags: trunk | |
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2020-03-13
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| 11:54 | Release 1.1.6 check-in: 88c672a1fe user: gavin.band@well.ox.ac.uk tags: trunk, v1.1.6 | |
| 11:43 | Pull PRAGMA synchronous=OFF change from default branch, addressing issue #42. Bump to v1.1.6 Leaf check-in: 1938bde8f1 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 11:40 | wscript: bump to v1.1.6 check-in: 42ba75d8c1 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 11:38 | bgenix: use PRAGMA synchronous=OFF to speed up indexing check-in: 8b016793a3 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
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2020-01-15
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| 21:39 | Merged from master branch check-in: 44ee815dfc user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:26 | Merged from default branch check-in: 1c9cbd1ea7 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 21:08 | Added example/example.8bits.bgen.bgi check-in: 4adbf39684 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 21:07 | Fix Issue #39 and update CHANGELOG. check-in: 39c2a7fd24 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 18:00 | syntax python 2 script was not compatible with python3. updated waf to version 2.0.19 check-in: e4d68bed9e user: maarten@oyat.nl tags: trunk, master | |
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2019-09-12
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| 10:33 | Pull bgenix vcf semicolon fix from master branch check-in: 127fab26b9 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 10:30 | bgenix -vcf: only output unique IDs check-in: 0538a1111d user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 10:27 | Bump to v1.1.5 check-in: 5e59235b8a user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 10:21 | bgenix: use semicolon, not comma to seperate IDs, cf issue check-in: 469a9e0e11 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 10:11 | bgenix: output multiple IDs with semicolon, not comma separator cf issue check-in: 1056f7d900 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
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2019-01-25
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| 09:07 | update docs check-in: e5046f6262 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
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2018-08-07
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| 09:12 | Pull test improvements from master check-in: 6431b0d243 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:05 | pull bitbucket pipeline change from default check-in: c30eb95d7f user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 09:01 | Pull rbgen test changes from master check-in: ff51a97b8b user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 09:00 | bitbucket-pipelines: use my 14.04 build docker image check-in: ccf7f165f8 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 08:44 | Added test for rbgen check-in: 905af42aab user: gavin.band@well.ox.ac.uk tags: trunk, master | |
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2018-08-04
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| 14:08 | Merge pipeline change from master branch check-in: 632628bd28 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:07 | Pull bitbucket pipelines change from default branch check-in: 769c966627 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 13:51 | Move qctool version to 2.0.1 check-in: 56f5982b89 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
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2018-08-03
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| 12:13 | Added tag v1.1.4 for changeset 8404a6f8186c check-in: 1c50841623 user: gavin.band@well.ox.ac.uk tags: trunk, v1.1.4, master | |
| 12:12 | Merged doc changes from master branch Leaf check-in: 97afbc805b user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 12:11 | Merged doc changes from default branch check-in: 2bb5c0e4d1 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 11:23 | Merge fix with online doc change check-in: ba1eb1638b user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 11:22 | Merged fixes from master check-in: 91e7b8aa5f user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 11:21 | Pull bgen fix from master branch check-in: 6368824c43 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 11:20 | bgen: fix issue with incorrect filtering of samples from BGEN v1.1 file. Bump to v1.1.4 check-in: 160878394d user: gavin.band@well.ox.ac.uk tags: trunk, master | |
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2018-05-16
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| 09:02 | README.md edited online with Bitbucket check-in: e5ffb19a1a user: gavin.band@well.ox.ac.uk tags: trunk, master | |
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2018-05-09
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| 11:05 | Close branch fixvcf. Leaf check-in: 495387d753 user: gavin.band@well.ox.ac.uk tags: trunk, fixvcf | |
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2018-05-02
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| 12:03 | Added tag v1.1.3 for changeset 1afa2d270596 Leaf check-in: e060cd9c08 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:03 | release: merge changes from master for v1.1.3 check-in: 082c198cbb user: gavin.band@well.ox.ac.uk tags: trunk, v1.1.3 | |
| 12:02 | Added tag v1.1.2 for changeset 5473ffdf1278 check-in: 513c0ca5d3 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:02 | release: merge changes from v1.1.2 check-in: b31e73e294 user: gavin.band@well.ox.ac.uk tags: trunk, v1.1.2 | |
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2018-04-30
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| 15:11 | merge bibucket pipelines changes from default, make CI tests pass again check-in: b989d2bace user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 15:03 | bitbucket-pipelines.yml edited online with Bitbucket check-in: 70dfcaf5bd user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 15:00 | bitbucket-pipelines.yml edited online with Bitbucket check-in: 8662898212 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 14:13 | bitbucket-pipelines.yml edited online with Bitbucket check-in: a2a8b8f92e user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 14:07 | bitbucket-pipelines.yml edited online with Bitbucket check-in: 3dce3aff55 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 13:59 | bitbucket-pipelines.yml edited online with Bitbucket check-in: d39c243e9d user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 13:50 | Pipielines: see if we can get qctool check-in: 4e75b4e150 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 13:29 | Whoops, really merge bgenix -vcf changes from default branch check-in: 75b00401ba user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 13:12 | Merge bgenix -vcf performance improvements from default branch. Bump to v1.1.3 check-in: e8b5cb169b user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 13:09 | Merged with doc changed from bitbucket.org check-in: 84178c6eaa user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 13:09 | bgenix -vcf: tests.txt: use qctool to test for correct vcf conversion. check-in: c81aa024a1 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 12:44 | bgenix -vcf: use a buffer and std::cout.write, not ostream_iterator, as it's about a billion times faster check-in: 2505d8f468 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 09:44 | README.md edited online with Bitbucket check-in: a965606c38 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 09:44 | README.md edited online with Bitbucket check-in: c4f539c839 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 08:40 | README.md edited online with Bitbucket check-in: 4ca5b18422 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
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2018-04-26
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| 10:53 | merge rbgen change from default check-in: 14838a252e user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 10:50 | rbgen: add SQLITE_USE_URI=1 check-in: edd10874e4 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 10:43 | Merge test improvements from default to master check-in: fc31c70b82 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 10:40 | tests.txt: improve test setup/teardown check-in: ab8f252276 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 10:13 | Merge test changes from master check-in: 19c8c83614 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 10:12 | merge from default branch. Add test for 8 bit -> vcf conversion. Bump to v1.1.2. Leaf check-in: 66d430b905 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:27 | Merged changes to fix bgenix -vcf into default check-in: 91bd2dfd58 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
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2018-04-25
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| 14:03 | wscript: move to v1.1.2-dev check-in: 1cf8e08d68 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 14:01 | Closing nolock branch which has been merged Leaf check-in: c146119c99 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:57 | Merged from default branch check-in: 7617fce049 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:46 | Merge nolock branch changes into default branch check-in: 4e2e9c03b8 user: gavin.band@well.ox.ac.uk tags: trunk, master | |
| 13:35 | bgenix -vcf: refactor 8-bit code slightly check-in: 429fc1bbfd user: gavin.band@well.ox.ac.uk tags: trunk, origin/fixvcf | |
| 13:23 | bgenix -vcf: use std::ostringstream, not boost::format, to format probabilities, avoiding truncation of trailing zeros check-in: 6724062f68 user: gavin.band@well.ox.ac.uk tags: trunk, origin/fixvcf | |
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2018-03-27
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| 20:33 | Merged from master branch check-in: e031c6cf63 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 20:32 | Added changes for sqlite3 nolock check-in: e77c04e157 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2018-03-23
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| 15:11 | Merge from default branch check-in: 6513879ff7 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:11 | bgenix: use fixed-point formatting in vcf lookup table output check-in: 124f3297e5 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:10 | bgen::View: call anonymous samples (anonymous_sample_n) check-in: 3c9922d6a8 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:16 | bitbucket-pipelines.yml: use waf not waf-1.8.13 check-in: c48923cf17 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:16 | bitbucket-pipelines.yml: use waf not waf-1.8.13 check-in: a378c2afb0 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:52 | wscript: fix waf release stub for non-osx platforms check-in: 1f932081bc user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:49 | Merge from default branch. Bump version to v1.1.1 check-in: 27e74dc8e2 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:47 | rbgen: doc update check-in: df5ecfa093 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:14 | README.md: use waf not waf-1.8.13 check-in: 63c1dd62b8 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:13 | tests.txt: add trailing newline check-in: 7e3af21d2e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:04 | rbgen: remove need for C++11 in Makevars check-in: 2e41929fee user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:03 | boost: implement patch from boost TRAC ticket #10125, re: thread/pthread/once.hpp variadic template error check-in: d7e6c9f583 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:51 | IndexQuery.hpp: include \<ctime\>. rbgen: don't compile sqlite3 shell check-in: 90263172c5 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:40 | rbgen: improve man page check-in: b9e8104e7e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:33 | wscript: build_rbgen tweaks, don't put platform name in rbgen package tarball name check-in: fa0ca2757d user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:30 | wscript: Use False not FALSE check-in: b1f5e53467 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:28 | added genfile/wscript check-in: 44c01bb1fc user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:26 | rbgen: add man page, update build to use waf build_rbgen instead of being built in build dir check-in: d6ef8fc9a2 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:15 | waf: update do recent waf, call it just waf check-in: 2d85682d8e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:46 | appcontext: remove reliance on boost iostreams check-in: 91073aee35 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2018-03-22
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| 13:37 | Merged from master branch check-in: 07e802f9d7 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:36 | bgenix: more dps in fast vcf output check-in: 069414ebc9 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2018-03-14
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| 10:54 | wscript: bump version to 1.2-dev check-in: afc98e0bf8 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:48 | bgenix -vcf: add a progress meter check-in: 74d50eaa1d user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:45 | bgenix: lookup table implementation of -vcf check-in: 7ae899262b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:44 | bitbucket-pipelines.yml: changes from master check-in: 90bbe9223b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:44 | bgen.hpp: convenience overload of v12::parse_probability_data taking GenotypeDataBlock as parameter check-in: 21c73d7021 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2018-03-06
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| 14:42 | Merge README.md changes from default branch check-in: 91d11f0592 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:41 | README.md edited online with Bitbucket check-in: 0fc493489f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:37 | Merged two master branches check-in: bb4b7ca41b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:36 | Merged pipeline changes from default check-in: 4a27a075ab user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:26 | bitbucket-pipelines.yml: use correct waf version check-in: dacea57b11 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:24 | Merge pipelines changes from master check-in: f8d118f2c4 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:21 | Fixes to bitbucket-pipelines.yml check-in: 3c0275fd96 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:20 | README.md edited online with Bitbucket check-in: 806509f2e0 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:18 | Merged, this actually turns on bitbucket pipelines check-in: efe6ba7d3f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:17 | Initial Bitbucket Pipelines configuration check-in: cfb8758ce1 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:16 | Remove unwanted comments from bitbucket-pipelines.yml check-in: 3e6809ce73 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:15 | Added bitbucket-pipelines.yml check-in: 7063da6410 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:13 | Added test/wscript check-in: 5dd03986a2 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:13 | Added robot test framework-based testing stub, and bitbucket pipelines check-in: 52278eeec3 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2018-03-05
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| 17:04 | merge from default branch check-in: 37642835c6 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 17:03 | merge doc changes check-in: b166d18d04 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:48 | Merged from default branch check-in: 46f35d03a3 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:47 | Move example/compute_dosages.cpp -> example/compute_expected_dosage.cpp check-in: 1c6f47bc09 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:14 | Merged check-in: 19d91c1d6d user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:32 | Merged changes from rescomp check-in: f8fc792d68 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:27 | rbgen: compilation fixes check-in: 216e440e78 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:26 | example/compute_dosages.cpp: compute expected dosage only check-in: a588c2fb78 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:16 | Merged from default branch check-in: 7032354d18 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:13 | Added doc symlink: index.html check-in: 711bfd5bb9 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:24 | doc: move bgen_format.html to bgen_format_v1.3.html, and make a soft link to it check-in: fec4246319 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:22 | doc: update reference to uk biobank data check-in: c3cac568d4 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:20 | Doc: update list of supporting tools check-in: 1b9574ae34 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:20 | Added tool images check-in: 2f2be772ba user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:45 | bgen::View: remove need for boost::lexical_cast, use sstream instead check-in: 186e4ff86c user: gavin.band@well.ox.ac.uk tags: trunk | |
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2018-02-06
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| 16:14 | rbgen: put back -std=c++11, since this appears to be required for some compiler / library versions check-in: 86f0d6fc03 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:55 | rbgen: fix use of std::map, turn of -std=c++11. check-in: 3f40c82305 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:48 | rbgen: use std::map, not unordered_map, to avoid C++11 requirement check-in: ca8623994f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:24 | rbgen: bgen.load(): support rsids argument and fix samples argument check-in: fbc56379fb user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:41 | bgen.hpp: sync with qctool revision 9a701ba5ed9d: improve output on failing prob limit test check-in: 6ea022f44a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:40 | bgenix: be more sensible about behaviour when there's an existing .tmp file check-in: 6ccbfa524f user: gavin.band@well.ox.ac.uk tags: trunk | |
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2018-01-31
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| 22:23 | bgen.hpp: fixes from rescomp check-in: 005a656470 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:19 | bgen.hpp: remove unwanted SampleStatus:: check-in: 62efe07ed1 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:15 | bgenix: add sync_with_stdio(false), set default compression level for v11 files to 9 check-in: b67d20665b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:13 | compute_dosages.cpp: call sync_with_stdio(false) check-in: b189ccbd1f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:11 | Fix some names and comments in compute_dosages.cpp check-in: 1bb6df99bc user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:10 | Added example program: compute_dosages.cpp check-in: aff165a320 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:43 | ProbSetCheck: require values >= 0.0 check-in: bfee56c868 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2018-01-30
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| 15:40 | bgen: clamp remainder values to 0 to avoid small -ve values. check-in: 568e278e64 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:56 | genfile::bgen::View: make get_sample_ids() a const method check-in: 5b042d7878 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:56 | bgen.hpp: further optimise data parsing for non-multiple of 8 sizes check-in: ce1f0deb43 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:55 | rbgen: added sample subset method check-in: e064189fc7 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2018-01-29
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| 14:23 | bgen.hpp: remove unwanted #if check-in: 383fd56e17 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:30 | bgen.hpp: remove unused variables check-in: 221a14f9b1 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:29 | bgen::v12: implement optimised parse implementation for all-diploid case, and for common bit sizes check-in: e31bdac839 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2018-01-25
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| 14:44 | bgen: allow configurable input error in GenotypeDataBlockWriter check-in: c7dd09b57a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:20 | bgen::v12: Further work on bounds checking, allow epsilon in addition to specified rounding error, check per-probabilty and per sum. check-in: 64fbff3410 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:08 | bgen: implement 'completely missing' samples as in qctool revision 51b1a9bae043. bgen::v12: update probability bounds check to insist values are within specific maximum error bound check-in: 389eeebcf1 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:36 | Pull bgen parsing optimisation from qctool revision 51b1a9bae043 check-in: c7b187cf8e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:15 | bgenix: pull -vcf fixes from master branch check-in: d08ddc8867 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:13 | Merged from master branch check-in: c255e55686 user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
| 10:13 | Bump to v1.0.2. bgenix: fix vcf output for metadata and unneeded additional tab characters. check-in: 8a5f1f2468 user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
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2018-01-12
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| 11:26 | count_alleles.cpp: comment fix check-in: f583f93c2a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:25 | bgen::v12: make inner loop functions inline for performance. Handle case of writing a 'completely missing' sample as if 0 ploid and missing. check-in: 08771f05b0 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2018-01-08
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| 13:27 | Fix build to exclude boost/iostreams/bzip2 which we do not link. Test plain R by default check-in: 1a408e7107 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:17 | Fix db/wscript trailing line check-in: 6ea5e4f31d user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:10 | Merged from default branch Leaf check-in: 235c860cc3 user: gavin.band@well.ox.ac.uk tags: trunk, origin/query_experiment | |
| 13:06 | Closed. check-in: 168025337a user: gavin.band@well.ox.ac.uk tags: trunk, origin/query_experiment | |
| 13:05 | IndexQuery: add comments to methods to clarify that list provided must be unique check-in: fe3a9e741e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:05 | Fix build to copy .cpp and .c files into rbgen directory for compilation during R CMD INSTALL check-in: 184fea42ae user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-09-05
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| 21:42 | Pull bgenix -vcf rsid fix from master. Update to use faster floor() check-in: 53faa821b8 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2017-07-27
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| 10:56 | Merged from release branch check-in: e0ea109e36 user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
| 10:43 | bgenix -vcf: correctly output ID field. Bump to v1.0.1 check-in: 0372e99b23 user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
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2017-07-13
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| 21:27 | README.md edited online with Bitbucket check-in: dea59ce70a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:27 | README.md edited online with Bitbucket check-in: 6662ade010 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:26 | README.md edited online with Bitbucket check-in: b1cbcffaae user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:12 | README.md edited online with Bitbucket check-in: 0dc98a2d49 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 20:59 | README.md edited online with Bitbucket check-in: 9713d7f21f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 20:58 | README.md edited online with Bitbucket check-in: 09244899a9 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 20:30 | README.md edited online with Bitbucket check-in: 3f87c1be94 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 20:28 | README.md edited online with Bitbucket check-in: 0e30c4dd70 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:54 | README.md edited online with Bitbucket check-in: 028646b170 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:53 | README.md edited online with Bitbucket check-in: 9de7cfa7a4 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:53 | README.md edited online with Bitbucket check-in: cd48a7fd7c user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:51 | README.md edited online with Bitbucket check-in: e8f29fefb0 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:50 | README.md edited online with Bitbucket check-in: 967d1dc3d7 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:49 | README.md edited online with Bitbucket check-in: fd12135a9a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:30 | Merged from release brnach check-in: 2b72290b29 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:03 | Merged from release branch check-in: 81d4aa2889 user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
| 13:45 | rbgen: be better about C++ exceptions. Allow specifying index file. Allow specifying R version in test script check-in: 62ab7167e9 user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
| 13:44 | bgenix: add -i option to allow specifiying index. check-in: ab2c782140 user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
| 13:08 | README.md edited online with Bitbucket check-in: 0c853a1519 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:07 | README.md edited online with Bitbucket check-in: bb97d34644 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:06 | README.md edited online with Bitbucket check-in: b45a7bb2af user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:06 | README.md edited online with Bitbucket check-in: 77862230a4 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:05 | README.md edited online with Bitbucket check-in: 5e3404e23f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:55 | README.md edited online with Bitbucket check-in: d58a6180d3 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:38 | README.md edited online with Bitbucket check-in: 42a9a9598c user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:38 | README.md edited online with Bitbucket check-in: e58ece4c07 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:36 | README.md edited online with Bitbucket check-in: cfff5bfb12 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:29 | README.md edited online with Bitbucket check-in: 067cc73913 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:53 | Get wscript fixes from master branch check-in: eb6a6cd7de user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
| 10:51 | wscript: name release tarball for linux distro used check-in: bc846c9923 user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
| 10:29 | Merged release branch changes check-in: 2a4f8b5c62 user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
| 10:28 | Add a 'release' method to build script check-in: a47fe1438a user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
| 09:59 | Merge edits for v1.0 release from release/master branch check-in: 2f45e4835e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:57 | Merge edits from master that should have been made here. check-in: 140f94e89a user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
| 09:55 | Tag this as version 1.0 check-in: afa2948151 user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
| 09:54 | Added tag v1.0 for changeset ec2434a33522 check-in: 21ff086ac4 user: gavin.band@well.ox.ac.uk tags: origin/nolock, trunk | |
| 09:53 | Added tag 1.0 for changeset ec4a336f2a30 check-in: f036fa67f0 user: gavin.band@well.ox.ac.uk tags: trunk, v1.0 | |
| 09:53 | Added tag 1.0-rc1 for changeset c208cac2e16b check-in: cf01ceab10 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:52 | bgenix: hotfixes: better report version in output check-in: d87c46000b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:37 | Merged into master from release branch check-in: 5baeae292b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:11 | Started experiment with rejigged Query object check-in: a961170912 user: gavin.band@well.ox.ac.uk tags: trunk, origin/query_experiment | |
|
2017-06-22
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| 09:51 | Merged changes from release branch check-in: a270a441ed user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-06-20
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| 14:25 | View.cpp: resize, not reserve space in m_postheader_data, fix broken index generation. check-in: 9c1cdfb6ad user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:38 | Started release branch in preparation for 1.0 release check-in: 3a871e3d2e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:48 | Merged from default branch Leaf check-in: 4eaf7aed8b user: gavin.band@well.ox.ac.uk tags: trunk, 1.0-rc1 | |
| 08:56 | Do not install example programs or tests check-in: c9db87cabc user: gavin.band@well.ox.ac.uk tags: trunk | |
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2017-06-16
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| 09:43 | README.md edited online with Bitbucket check-in: 412ed18719 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:42 | README.md edited online with Bitbucket check-in: 45272662d7 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:30 | README.md edited online with Bitbucket check-in: ecc08c5e2b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:29 | README.md edited online with Bitbucket check-in: 283ffa2632 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:47 | README.md edited online with Bitbucket check-in: 1aec43556a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:47 | README.md edited online with Bitbucket check-in: 6633650591 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:46 | README.md edited online with Bitbucket check-in: b5969ab427 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:45 | README.md edited online with Bitbucket check-in: 54f25634f0 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:42 | README.md edited online with Bitbucket check-in: fdb13fda8f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:40 | README.md edited online with Bitbucket check-in: 57d53c0fdd user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:39 | README.md edited online with Bitbucket check-in: a1e7dd20bf user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-06-11
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| 23:00 | rbgen: allow specifying a maximum number of entries per sample, by default 3. Allow phased data. Remove restriction on number of alleles. check-in: ece41bd600 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:56 | Allow index files that don't have metadata again check-in: 0ef03a9523 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:23 | Merged check-in: c23c024693 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:21 | IndexQuery: revert to using in-query ranges. check-in: 65144e1823 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:19 | Add SQLITE_MAX_EXPR_DEPTH=10000 to sqlite build for greater number of includable variants check-in: 9d7e223b3f user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-05-19
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| 22:37 | load.cpp: usr genfile::bgen::uint32_t check-in: a8abce62ec user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:34 | add R/package/src/load.cpp, msitakenly missed out check-in: c65ddd1dd3 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:18 | Removed unwanted rbgen/ stuff, now in R/package check-in: 58c4e4168a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:18 | R/package: update to use bgen.load() not giveMeMyData() check-in: d9a7fe2ec4 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-05-16
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| 12:04 | fix R/package/test.sh to refer to existing indexed file check-in: af1894edac user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:02 | Add missing file R/package/src/Makevars check-in: 839ba068c6 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:01 | Add missing file R/wscript check-in: 59129a4df2 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:01 | rbgen: construct rbgen source package in build dir during waf build. COmpile with -fPIC to allow R shared object to work. check-in: 16988ef0e9 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:00 | example: regenerate index files using up-to-date bgenix check-in: 3e0f8370b9 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:47 | Added test.sh as simple test of rbgen package check-in: b78fc1bbd9 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:56 | added Makevars check-in: 3cfa6df503 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:35 | Compilation fixes, link to boost thread pthread once_atomic, not once.cpp check-in: e8dfa50261 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:34 | rbgen::giveMeMyData(): add samples and variant names to result data check-in: 4c3ec5d20f user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-05-15
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| 23:06 | IndexQuery: revert to using query for include_range check-in: b4874f0919 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:06 | View: implement missing method check-in: fc3914572d user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:06 | Added code in rbgen/ for bgen R package check-in: 0d0a2da1a9 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-05-11
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| 14:07 | Rejig to use IndexQuery::GenomicRange instead of boost::tuple check-in: 88988c19bf user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:06 | IndexQuery: rejig to use a GenomicRange struct instead of a boost::tuple check-in: 0ac4fcd718 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-04-18
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| 09:17 | Added index file for example/haplotypes.bgen check-in: 6aa76813c2 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:30 | Added example files containing haplotypes check-in: 2c6cf1ea3e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:30 | Fix View.cpp sample_ids issue check-in: 3dcc8e43e3 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-03-31
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| 22:32 | Fix build of count_alleles for dl rt pthread check-in: 8d1df58592 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:18 | count_alleles.cpp: Fix usage statement check-in: 5ca9369a21 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:16 | count_alleles.cpp: Move output code to separate function. Comment fixes. check-in: bcb47c33b1 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:04 | count_alleles: simplify getting ids check-in: 5ba2d13237 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:01 | IndexQuery: move query methods to base class check-in: b8a3c0524d user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:59 | count_alleles.cpp: use a using statement to simplify code check-in: 3b87d8674e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:57 | Added a new example program example/count_alleles.cpp, updated some methods to match check-in: 60780fe286 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2017-03-30
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| 12:08 | genfile::bgen::View: remove use of c++11 features, rely on boost instead check-in: d2ec6760b5 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:03 | Added genfile/include/genfile/bgen/View.hpp check-in: 7974e158e3 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:02 | Merged with tip check-in: c2d9293743 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:00 | bgenix: factor BgenParser into genfile::bgen::View check-in: 76d2655cb4 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:42 | Compilation fixes check-in: 28393b322a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:22 | Added convenience header db/sqlite3.hpp check-in: 3a68772d16 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:18 | bgenix: work on error messages check-in: b9012b6764 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:09 | Check metadata when not doing transcoding. check-in: 05aa36096f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:05 | Use -table option for index table. check-in: 887ac1c137 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:59 | bgenix: implement -compression-level for -v11 check-in: 4d8e90111b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:39 | bgenix: factor out index query to genfile/bgen/index_query.hpp check-in: ffc58f9b8e user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-03-29
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| 13:38 | bgenix: use 'bgenView' for the main processing object check-in: ded2e11136 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:44 | bgenix: refactor to use a BgenIndex base class, rename BgenProcessor -> BgenView and allow it to use the index check-in: e1b8ed6ae4 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-03-22
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| 10:24 | bgenix: comment code. check-in: 88c5d17184 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:09 | example/complex.bgen: rebuild index check-in: 614f6a063b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:08 | bgen.hpp: implement a method to unpack bgen v1.2 data without full parse check-in: 7270bd4b5d user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:08 | bgenix: fix bug with metadata for files < 1000 bytes in size. Implement -vcf and update docs for -vcf and -v11 check-in: 00d6162f88 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-03-03
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| 22:42 | Merged changes from default branch check-in: c64c4050e9 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-02-08
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| 17:58 | Merged doc changes check-in: 25fc1c6bb7 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 17:57 | bgenix.cpp: better message when the file doesn't exist check-in: be9f5dbaca user: gavin.band@well.ox.ac.uk tags: trunk | |
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2017-02-04
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| 22:20 | Merged check-in: e59ddba5c8 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2017-01-26
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| 11:53 | Doc update for v1.2 UK Biobank banner check-in: b69afe7dbd user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:50 | bgenix: fix doc string for -index option, as in master branch check-in: 100fb7a968 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:49 | Merge doc changes check-in: c49afa3e79 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 11:49 | Update doc pages to add banner re: UK Biobank check-in: 9969b8a9fb user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-01-25
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| 16:39 | Merged with doc changes made online check-in: 41e0f1e69b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 16:38 | bgenix -v11: output progress and use lowest zlib compression. check-in: 74355812a2 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 16:37 | bgen.hpp: use highest zlib compression by default check-in: d8f9ee36a7 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 16:37 | zlib.hpp: zlib_compress(): pass on compression setting correctly check-in: f44572fa08 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:18 | Fix -v11 error message check-in: d7b5a383fc user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:08 | README.md edited online with Bitbucket check-in: 81e752298e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:07 | README.md edited online with Bitbucket check-in: de9549a417 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:36 | Merged check-in: 0f5f3cb2f6 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-01-24
| ||
| 10:16 | bgenix: make error message better on failed bgen read check-in: bf06dfaf6d user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:12 | bgenix.cpp: debug in case of bgen file error. check-in: 0d6d636b0f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:11 | bgen.hpp: add debug statements on failed read of v1.1 variant check-in: 7e63418030 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:48 | bgenix: implement -v11 flag which transcodes to BGEN v1.1. Remove sample identifiers from example BGEN v1.1 file. check-in: 149626d6da user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:30 | zlib.cpp: pull implementation including compressionLevel from qctool check-in: 10d3a17f05 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:29 | zlib.hpp: whitespace change check-in: 3360acdb20 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:29 | bgen.hpp: fix bug in v11 output for missing samples check-in: 715c4b09ac user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-01-18
| ||
| 12:25 | Removed bgen_format_v1.3.html as it is the same as bgen_format.html check-in: f8ca422927 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2017-01-17
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| 12:25 | edit-bgen: make -g required check-in: 19812913dd user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:16 | Fix link in v1.3 doc check-in: efd9a7759f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:15 | docs: links between versions included check-in: acc080f47d user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:13 | docs: links between versions included check-in: d77ad45d93 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:06 | Update code for to v1.3 spec nomenclature, Layout0, Layout1, Layout2 etc. check-in: 15d67c9d5d user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:05 | doc updates for v1.3 check-in: 024b71f740 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:07 | Update to README check-in: 5c826d4e2b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:00 | Added edit-bgen check-in: ad9e901696 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-12-15
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| 17:50 | Pull CHAR_BIT check from master check-in: f67c3a92cf user: gavin.band@well.ox.ac.uk tags: trunk | |
| 17:50 | Fix CHAR_BIT check check-in: c454aa7304 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 17:43 | Merged from default branch check-in: 20ebff1e9e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 17:42 | Remove dependence on CHAR_BIT. Verify it equals 8. check-in: 2abaf1d8e5 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 17:34 | Merge check-in: 8db91b9c17 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-12-07
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| 09:09 | Update doc to forbid zstandard compression in bgen v1.1 files check-in: 98697becb3 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-12-06
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| 14:57 | README.md edited online with Bitbucket check-in: ef33170849 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:57 | README.md edited online with Bitbucket check-in: 4a5249e134 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:34 | Fix help string for -index option check-in: b257368207 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-12-01
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| 23:05 | Pull doc changes from master check-in: 221de0b446 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:05 | Update doc pages check-in: 9d4dbeae7b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:59 | Merged from default branch check-in: add61c3857 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:54 | Update bgenix -help check-in: 274f1c5ca9 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:46 | doc updates check-in: c69af25520 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:46 | bgenix: implement -index. Implement a Metadata table that must be correct (if present) for bgenix to do its work. check-in: 7231ade40b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:46 | db: implement blob reading/writing. Fix opening in read-only mode. check-in: 4ecce90921 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-11-12
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| 21:57 | Doc updates for finalised spec check-in: b925ab4f64 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:26 | Add support for zstandard check-in: 37be7a56aa user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-07-07
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| 15:46 | README.md edited online with Bitbucket check-in: ad39b7fa0c user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:44 | README.md edited online with Bitbucket check-in: 83451dcdb6 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:33 | CHANGELOG.md edited online with Bitbucket check-in: 39641ccb3d user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:28 | README.md edited online with Bitbucket check-in: 9893677ccb user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:28 | README.md edited online with Bitbucket check-in: e964b35115 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:26 | README.md edited online with Bitbucket check-in: 8fc511b1d0 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:26 | README.md edited online with Bitbucket check-in: 572f25eff6 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:21 | README.md edited online with Bitbucket check-in: a996db62d7 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-07-06
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| 10:50 | README.md edited online with Bitbucket check-in: 8af0d50be1 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:49 | README.md edited online with Bitbucket check-in: 341bc1e8a8 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:48 | README.md edited online with Bitbucket check-in: a3557b305f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:48 | README.md edited online with Bitbucket check-in: 3b020ac7ee user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:47 | README.md edited online with Bitbucket check-in: effba325c4 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:46 | README.md edited online with Bitbucket check-in: f9ed97ab4f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:46 | README.md edited online with Bitbucket check-in: a1d05eb325 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:00 | bgenix: fix option help for -table option check-in: 543df57dcf user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:58 | Merged from default branch check-in: de1a8bdf65 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:24 | bgenix: fix -incl-rsids to be inclusive with -incl-range check-in: d9fced47b2 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 07:43 | bgenix: update to use temp tables for rsid queries. check-in: 19e239179f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 07:23 | Bgenix: update to use temp table for rsid restriction check-in: c2e57c3d4d user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-07-05
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| 22:38 | Discard old tweaks, use bgenix from b2c1c99e32ee check-in: 64af9260c4 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:37 | bgenix: work around int64_t issue in number of alleles check-in: 2591c139cd user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:34 | bgenix: get comment lines in -list output correct. check-in: 8d939198cd user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:29 | Merged check-in: c637667e8d user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:27 | bgenix: update, use int64_t for file positions (duh), get -incl-rsids working again check-in: e1715d6cac user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-07-01
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| 20:04 | bgenix: tweaks check-in: eb493ce771 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-06-18
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| 23:17 | bgenix: turn off debug again check-in: 1e42c6c624 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:15 | Merged check-in: fda6b07cc0 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:57 | bgenix.cpp: tweak index format for uk biobank files. check-in: 675ac25658 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-06-08
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| 10:56 | bgenix: update to make better use of indices when selecting check-in: 96d1ad951c user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-06-01
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| 12:03 | README.md edited online with Bitbucket check-in: d4347d3da5 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:22 | bgenix: include first allele in variant primary key. Update doc for -g check-in: 3ee374b971 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-05-26
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| 22:25 | Merge from default check-in: 1479c251b3 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:22 | Fix limit check in bgen.hpp check-in: 76737e03ab user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:14 | Merged single change applied to master. check-in: 1ee159b52b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:12 | bgen.hpp: add assert check for size of output check-in: e97b0f819f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:07 | Merge from default check-in: 2303dfc79c user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:07 | Turn off bgenix debug check-in: 69507a0327 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:01 | Merged from default branch check-in: dc946e7c97 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:45 | bgenix: Implement one-side ranges check-in: 45f8504a58 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 17:27 | bgenix: implement -index-table check-in: 38087074db user: gavin.band@well.ox.ac.uk tags: trunk | |
| 17:27 | Fix complex.bgen, complex.bgen.bgi to actually hold data check-in: 5682496d0a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 17:18 | bgenix: add -excl-rsids and -excl-range options check-in: 114435ddf0 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 16:57 | Merged from default branch check-in: 12071fc261 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-04-09
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| 22:48 | Added complex example files to example/ directory check-in: 14c40e31f3 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:43 | bgen.hpp: make sure buffer is big enough for multi-alleles / multiple ploidy check-in: 35c2380b3e user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-04-08
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| 08:17 | bgenix: implement -with-rowid check-in: af36965f03 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:09 | bgen.cpp: workaround bug in gcc std::istream::ignore() to allow indexing last SNP in file. check-in: eebc53dbf4 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-03-30
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| 22:08 | minor doc update check-in: 958de8f4bd user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:39 | bgenix.cpp: implement -list check-in: 96c47f39ee user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:14 | Doc update for v1.2 spec check-in: 410139e682 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:14 | cat-bgen: fix description of -set-free-data option - read from file not implemented check-in: 6dd8148531 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2016-03-21
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| 21:51 | docs: update order of probabilities check-in: 5f7084f32e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 16:49 | Run phased data SNP block output test. check-in: 52a47c4ca4 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 16:40 | implement output of multiple allele / multiple ploidy data. Update of tests to match check-in: 5870b61f70 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-12-14
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| 10:23 | Added a example/example.sample file, which lists sample IDs check-in: c42ceb972a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:41 | bgen::v12::ProbabilityDataWriter: enforce bound of [1.0/tolerance, tolerance] on total probability before rounding. Split tests and test for this. check-in: 79e3595408 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2015-12-08
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| 23:51 | round_probs_to_scaled_simplex() -> compute_approximate_probabilities(). Document this better. Throw error if probs don't sum near 1. check-in: 6b740eaec1 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:24 | Ensure probs are scaled to sum to one before rounding check-in: 73d37dfa5e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:53 | Fix warnings, thanks to Robert V. Baron check-in: b97e0bd19d user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-11-30
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| 12:23 | test_bgen_snp_format.cpp: split out v10 and v11 tests, these updates were also applied to default branch. check-in: 0623cdeacf user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:04 | test_bgen_snp_format.cpp: split out v10 and v11 tests. check-in: 2874ea289e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:30 | wscript: build example utils again check-in: 9bca607f66 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:30 | wscript: build example utils again check-in: d06db60aad user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-11-24
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| 23:28 | Update bgen v11 to use ProbabilityDataWriter object. check-in: 8b44e070ad user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-11-17
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| 15:20 | Merged hotfix changes from master check-in: 592f09f4be user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:48 | Hotfix: included needed std headers in test code check-in: a018ac666c user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-11-16
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| 14:33 | bgen.hpp: remove unused variable 'm_phased'. check-in: ddb23f4423 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:14 | bgenix: guard against -ve size_in_bytes caused by final SNP in file check-in: b05df5a529 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:47 | Added missing std headers. check-in: d3692b8f65 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:41 | bgen_format_v1.2-beta1.html: typo fix check-in: 10643b69ab user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:38 | bgenix: create index on rsid. check-in: d533e943b1 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:34 | Test single-sample phased output as well as unphased output. Test ploidy==0 cases. check-in: 2294c08566 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:34 | bgen: remove unwanted print statement. check-in: b0a51c9101 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-11-13
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| 23:19 | Add test for phased data output (single sample). This currently fails. check-in: a9e13e36a2 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:21 | Make tests pass again by defining bgen writing behaviour in case of 0 samples. check-in: 4352266793 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-11-12
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| 23:42 | bgen: update v12::write_uncompressed_snp_probability_data to use ProbabilityDataWriter. Test this. check-in: 3b027c1dcc user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:06 | Merged changes from default branch check-in: c4c32ec083 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 13:04 | wscript: compile tests again. test_bgen_snp_format.cpp: remove unwanted print check-in: 976b82ec1a user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-11-11
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| 23:11 | README.md edited online with Bitbucket check-in: faf2a85c43 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:11 | README.md edited online with Bitbucket check-in: c856d5b8a1 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:09 | README.md edited online with Bitbucket check-in: b7fa880c15 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:08 | README.md edited online with Bitbucket check-in: afc0650fb1 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:08 | README.md edited online with Bitbucket check-in: 3267648cd5 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:45 | bgen.hpp: make this compile under C++03 again. check-in: b56a52b6f5 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:45 | appcontext: replace auto_ptr with unique_ptr to avoid deprecation warnings check-in: ff5de8b6c6 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-11-09
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| 13:12 | bgenix: write output message correctly check-in: 06d344843e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:41 | boost: use c++11 check-in: dd6f83e63a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:40 | appcontext: rely on c++11 check-in: 12e9c2ba65 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:40 | Make release default. Use c++11 not c++0x check-in: 87eeb11bc7 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 12:19 | no-unused-local-typedef -> no-unused-local-typedefs check-in: a28b85a162 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:03 | Use c++11 in db/wscript check-in: 871ad0aef1 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:53 | Merged check-in: dc88197078 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:52 | Update wscripts for linux build check-in: 31daccdbc0 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:52 | bgen.hpp: comment change check-in: 3ca07296b3 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:52 | genfile/types.hpp: include missing header check-in: ace69f380c user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:51 | bgenix.cpp: remove unused variable warning check-in: fb7f439b98 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:04 | README.md edited online with Bitbucket check-in: 07208f2db5 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:03 | README.md edited online with Bitbucket check-in: de10c6da6b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:02 | README.md edited online with Bitbucket check-in: 0c698dc383 user: gavin.band@well.ox.ac.uk tags: trunk | |
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| 08:57 | README.md edited online with Bitbucket check-in: f45f23f648 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:56 | README.md edited online with Bitbucket check-in: d0d3bff318 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:56 | README.md edited online with Bitbucket check-in: 1d96a5c4cd user: gavin.band@well.ox.ac.uk tags: trunk | |
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| 08:52 | README.md edited online with Bitbucket check-in: 9e83b552a3 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:52 | README.md edited online with Bitbucket check-in: 3dfb528388 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:48 | README.md edited online with Bitbucket check-in: 951fa8bb14 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:44 | README.md edited online with Bitbucket check-in: 35dc6ec2d3 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:39 | Pull CHANGELOG change from master check-in: 2e9a979a62 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:38 | CHANGELOG: add revision check-in: 3ccb375b04 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:36 | Fix CHANGELOG revision check-in: 272ad9f6ed user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:17 | Merged doc changes from master check-in: 4931a29b16 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:16 | Merge doc changes from default check-in: 8948aa5464 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 08:13 | CHANGELOG: added information about cat-bgen and bgenix check-in: 305b34a8f7 user: gavin.band@well.ox.ac.uk tags: trunk | |
|
2015-11-08
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| 22:58 | Re-rename bgen-cat as cat-bgen and bgen-index as bgenix. Make bgenix behave like tabix (in some usages). Fix appcontext::Timer to work in seconds. check-in: 36ae1d58d2 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 00:23 | Create a working implementation of bgen-index.cpp check-in: 9b14f8a17a user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-11-07
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| 00:02 | Update copyright notice to 2015 check-in: ef3b6a7482 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-11-06
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| 23:47 | Doc update check-in: 72ada911cd user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:42 | Add bgen-cat. Split wscript into subdirs. Move bgen_to_vcf to example/ subdir check-in: b23dd2841b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:41 | Added appcontext and db libs, taken from qctool check-in: cbe4ae855c user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:41 | Added sqlite3 v3.9.2 to the repo check-in: 48def9495e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:40 | Added boost libraries check-in: 0d03567e6a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:51 | Rename example files to remove leading zeroes from bits check-in: 43dde3ce45 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:40 | README.md edited online with Bitbucket check-in: a4d6d1b49f user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:39 | README.md edited online with Bitbucket check-in: 8f8487d9af user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:33 | README.md edited online with Bitbucket check-in: 325044ce5e user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:33 | Merged in default (pull request #1) check-in: 32ef0bc331 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:30 | Merged with online doc changes check-in: 40b39a0c15 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:30 | README.md edited online with Bitbucket check-in: 6980e366cb user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:30 | Added CHANGELOG check-in: 3e3b6486d3 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:29 | README.md edited online with Bitbucket check-in: 548d21398b user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:27 | Merged changes from default branch check-in: 3ab07eb442 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:26 | Merged with online doc change check-in: d99a0aea9c user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:26 | Fix warnings about unused/uninitialised variables check-in: 25b34ed194 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:26 | wscript: turn on -pedantic -Wall. check-in: 3d5a1ca344 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:12 | README.md edited online with Bitbucket check-in: 95a7039c07 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:09 | README.md edited online with Bitbucket check-in: 0406b0fae2 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 17:44 | Pull doc changes from default branch check-in: f1d4f1d7ed user: gavin.band@well.ox.ac.uk tags: trunk | |
| 17:43 | added beta-1 version of the spec. check-in: 69eac16e45 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 17:22 | Added bgen documentation check-in: 3f60de346a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 17:19 | Merged from default check-in: 7fd999e1f3 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:42 | bgen_to_vcf: report whether samples are named or not. check-in: f6377a6820 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 15:17 | Add example files with every possible number of bits. check-in: 58362e2942 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 14:05 | Rename operator() as set_value(). Include entry index in set_value(). check-in: 2834af1a8c user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:42 | README.md edited online with Bitbucket check-in: a68d2ea7e5 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:42 | README.md edited online with Bitbucket check-in: 3ee2bb6349 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:36 | Merged from dev (default) branch check-in: 8fda7137d7 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:35 | Merged check-in: 2613b06a8a user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:35 | test_bgen_snp_format.cpp: make every 13th sample have missing data and test for that. check-in: d8d77d07d0 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:34 | bgen.hpp: add ProbabilityDataWriter check-in: cc285264ae user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:33 | ProbSetCheck: allow for missing data check-in: 2f279c4f85 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 10:33 | example.gen: add some missing data. Generate bgen files at different bit sizes. check-in: c5a72b9a29 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:01 | README.md edited online with Bitbucket check-in: 9671b563a8 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 09:01 | README.md edited online with Bitbucket check-in: b6dcc87d00 user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-11-05
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| 21:28 | test: use genfile::byte_t instead of char. Add test for graceful failure on truncation and for two-sample datasets. check-in: 749d31aea3 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:27 | wscript: use CXXFLAGS not CFLAGS check-in: 8e0990e0d5 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:27 | ProbSetCheck: add expect_fail() method to allow testing of graceful failure situations. check-in: 036542f041 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:26 | genfile: add a byte_t typedef (which is uint8_t and use it for buffers in bgen check-in: 61d785fd07 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:26 | genfile: add a byte_t typedef (which is uint8_t and use it for buffers in bgen check-in: 87003aecec user: gavin.band@well.ox.ac.uk tags: trunk | |
| 21:25 | bgen_to_vcf.cpp: print alleles correctly. Use genfile::byte_t instead of char buffers check-in: fedc53f58b user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-11-04
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| 23:19 | ProbSetCheck: add set_min_max_ploidy() and finalise() methods. Make to_hex take an iterator range. check-in: 38f85e4459 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:18 | bgen: add support for optional set_min_max_ploidy() and finalise() methods of setter objects check-in: 34366f4d1c user: gavin.band@well.ox.ac.uk tags: trunk | |
| 23:18 | test_little_endian.cpp: fix min/max values check-in: 867e21fe7c user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-10-28
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| 23:59 | bgen.cpp: bgen v1.2 SPEC CHANGE: probabilities for missing samples are now stored as zeroes, not omitted. check-in: ace49dcc3f user: gavin.band@well.ox.ac.uk tags: trunk | |
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2015-10-27
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| 23:07 | test reformat check-in: b8aa1e0066 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:59 | test_little_endian: slight code move check-in: bdb9e38f88 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:58 | test_little_endian: test top and bottom bytes check-in: cb48f14dd6 user: gavin.band@well.ox.ac.uk tags: trunk | |
| 22:49 | Add test/ dir with tests driven by Catch check-in: 068cd1da35 user: gavin.band@well.ox.ac.uk tags: trunk | |