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History of the file that is called apps/qctool.cpp at check-in e11ef8d5cb296342
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2025-03-01
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| 16:14 | Bingwa: work toward supporting multiple variants (i.e. hptest support) file: [a45aa551cb] check-in: [8bbdb57401] user: gav branch: gb:bingwa-multivariant, size: 118187 | |
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2024-08-14
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| 11:23 | Fix catch-by-value warning file: [89201ab28f] check-in: [cd581b3883] user: gav branch: master, size: 118179 | |
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2024-05-26
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| 21:28 | Import bingwa from seperate bingwa repository. file: [fb0e3eb272] check-in: [f81765423c] user: gav branch: master, size: 118172 | |
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2023-09-25
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| 16:08 | qctool: fix documentation to not say that -incl/excl-range take comma-separated lists of ranges file: [689a580449] check-in: [9e0e19be02] user: gav branch: master, size: 118200 | |
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2021-11-12
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| 22:31 | Revise package_revision_autogenerated.hpp build code, fix [0ca1159b29] file: [fb200d13d1] check-in: [1c3816a97f] user: gav branch: master, size: 118268 | |
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2021-07-31
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| 13:33 | qctool: add -sqlite-dont-link-variants and -sqlite-store-alt-identifiers. Don't store alt identifiers by default. Bump version to 2.2.0-rc3 file: [6493ccde45] check-in: [e666e186cc] user: gav branch: master, size: 118257 | |
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2021-05-16
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| 21:07 | qctool: add -sqlite-dont-link-variants; bump to 2.2.0-rc2 file: [b709460fa3] check-in: [f96603cda3] user: gav branch: master, size: 118065 | |
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2021-04-04
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| 21:49 | Merged from v2.0.8. Bump to v2.2.0-rc1 file: [5a341adec7] check-in: [45978a8ebc] user: gav branch: master, size: 117669 | |
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2020-06-30
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| 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 file: [d395577eaf] check-in: [69ce5b9cd4] user: gav branch: b952a6be-fix, size: 116263 | |
| 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. file: [c09af1070f] check-in: [500cd8c3bd] user: gav branch: b952a6be-fix, size: 115946 | |
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2020-04-13
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| 20:27 | Finish work on compilation with new waf version file: [a2f2f45191] check-in: [406a471f34] user: gav branch: master, size: 115007 | |
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2019-10-03
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| 13:19 | Update to output program version in output files. file: [5813fe35b9] check-in: [233cdcdf03] user: gavin.band@well.ox.ac.uk branch: master, size: 115085 | |
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2019-08-27
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| 08:05 | qctool: pull -incl-samples changes from beta branch file: [758081216b] check-in: [02165adf99] user: gavin.band@well.ox.ac.uk branch: master, size: 115073 | |
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2019-08-22
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| 08:53 | qctool: header include simplification file: [90fdf08b88] check-in: [d2e07d63f4] user: gavin.band@well.ox.ac.uk branch: master, size: 115055 | |
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2019-05-29
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| 21:19 | Pull qctool change from master branch file: [a0266bb6da] check-in: [c159f99246] user: gavin.band@well.ox.ac.uk branch: origin/beta, size: 115840 | |
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2019-01-22
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| 21:07 | multifinemap: implement -incl-range[s\ and -excl-range[s] file: [6fa261b42e] check-in: [e8ebd4e124] user: gavin.band@well.ox.ac.uk branch: master, size: 115227 | |
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2019-01-16
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| 15:06 | Fix anonymous sample IDs, allowing tests to pass again. Also fix docs for -infer-ploidy-from-sex file: [709c74a5ce] check-in: [097e63e723] user: gavin.band@well.ox.ac.uk branch: master, size: 115288 | |
| 13:57 | Remove db/ in favour of genfile/db/ file: [2191c63f7e] check-in: [81ec55fbb8] user: gavin.band@well.ox.ac.uk branch: master, size: 117298 | |
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2018-08-04
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| 13:35 | qctool: bugfix -incl-ranges and -excl-ranges argument processing file: [40fd7b6c27] check-in: [964614d1bb] user: gavin.band@well.ox.ac.uk branch: master, size: 117254 | |
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2018-08-02
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| 19:35 | qctool: implement -[in|ex]cl-ranges, which loads from a file. Support -ofiletype list file: [5dee130129] check-in: [db7751eea1] user: gavin.band@well.ox.ac.uk branch: master, size: 117176 | |
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2018-07-19
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| 08:54 | Merged from beta branch file: [bc419989cd] check-in: [2c71cd2d9f] user: gavin.band@well.ox.ac.uk branch: master, size: 115734 | |
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2018-05-03
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| 21:25 | qctool: fix use of CountingCohortIndividualSource file: [c9ea825145] check-in: [b90831c0a7] user: gavin.band@well.ox.ac.uk branch: master, size: 115752 | |
| 16:39 | qctool: implement rename file: [3122e47385] check-in: [7ecaffe917] user: gavin.band@well.ox.ac.uk branch: master, size: 115844 | |
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2018-03-26
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| 11:28 | qctool: error message fix file: [2aaccb500f] check-in: [037627a0b6] user: gavin.band@well.ox.ac.uk branch: origin/beta, size: 115822 | |
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2018-03-20
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| 16:16 | Remove cruft code, add sync_with_stdio(false) file: [a8a95b723c] check-in: [da8c21158c] user: gavin.band@well.ox.ac.uk branch: master, size: 115840 | |
| 15:46 | Merged changes from beta branch file: [9155523f2f] check-in: [f56170c361] user: gavin.band@well.ox.ac.uk branch: master, size: 116046 | |
| 15:09 | qctool: fix crashing bug on mismatching number of samples file: [6880d80160] check-in: [fa1ea28ea6] user: gavin.band@well.ox.ac.uk branch: master, size: 115938 | |
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2018-02-27
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| 09:02 | qctool: use std::sync_with_stdio(false) file: [77a34556f2] check-in: [afa7c9d384] user: gavin.band@well.ox.ac.uk branch: master, size: 116059 | |
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2018-02-05
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| 14:13 | Changes to make streaming of vcf input possible file: [3bc3cf2669] check-in: [75ea7a893c] user: gavin.band@well.ox.ac.uk branch: master, size: 115951 | |
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2018-01-25
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| 14:45 | qctool: implement -bgen-permitted-input-rounding-error file: [d4cdc0d6ce] check-in: [e34102699b] user: gavin.band@well.ox.ac.uk branch: master, size: 115373 | |
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2018-01-16
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| 11:50 | qctool: rename -threshhold -threshold file: [b433b5250b] check-in: [b3ac69a352] user: gavin.band@well.ox.ac.uk branch: master, size: 114640 | |
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2018-01-08
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| 09:47 | Remove -flat-file and -flat-table options, which are unused file: [2e06142612] check-in: [a3e88b54da] user: gavin.band@well.ox.ac.uk branch: master, size: 114645 | |
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2017-12-19
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| 14:21 | qctool: fix bug in -merge-in. Bump to -rc7 file: [29d68083f1] check-in: [f300bdfd01] user: gavin.band@well.ox.ac.uk branch: master, size: 115226 | |
| 14:09 | qctool: factor out open_snp_data_sources() to be reuseable, use it in -compute-ld-with file: [349b2bb154] check-in: [676e06a041] user: gavin.band@well.ox.ac.uk branch: master, size: 115050 | |
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2017-10-26
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| 10:12 | genfile: Implement PloidyConvertingSNPDataSource, qctool -infer-ploidy-from file: [683e799b59] check-in: [56a7df90c2] user: gavin.band@well.ox.ac.uk branch: master, size: 109768 | |
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2017-10-06
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| 14:15 | Add -help documentation for -reorder file: [a6f29a30ef] check-in: [3143636330] user: gavin.band@well.ox.ac.uk branch: master, size: 108044 | |
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2017-09-27
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| 22:30 | PCAComputer: send output to -osample not -PCs. file: [9618ee7668] check-in: [9571708915] user: gavin.band@well.ox.ac.uk branch: master, size: 107708 | |
| 12:56 | qctool: rename -snp-match-fields -> -compare-variants-by, -excl-snps-matching -> -excl-variants-matching, as per udpated docs file: [394bdc4868] check-in: [6e71af08ab] user: gavin.band@well.ox.ac.uk branch: master, size: 107546 | |
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2017-09-18
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| 15:31 | qctool.cpp: update doc for -analysis-name file: [a963307520] check-in: [5894930afd] user: gavin.band@well.ox.ac.uk branch: master, size: 107841 | |
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2017-08-31
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| 10:51 | Merged file: [3afb378c23] check-in: [3cc783f153] user: gavin.band@well.ox.ac.uk branch: master, size: 107909 | |
| 10:41 | compilation fixes. Move config.hpp to single file in config/ dir. Fix some compiler warnings. file: [4cfba7a8fd] check-in: [5611f8881d] user: gavin.band@well.ox.ac.uk branch: master, size: 107779 | |
| 08:51 | Remove MGL and BZIP2 from wscript. Remove ClusterPlotter file: [b63f2bb9ee] check-in: [adebe5faf1] user: gavin.band@well.ox.ac.uk branch: master, size: 107772 | |
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2017-07-27
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| 12:45 | qctool: update revision / version display as per bgenix. Bump to v2.0-rc5 file: [5dc541746d] check-in: [f9be11b2d9] user: gavin.band@well.ox.ac.uk branch: master, size: 108236 | |
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2017-07-14
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| 13:37 | Fix bug with wrong file being loadd by -incl-snpids. file: [0a3e513bb1] check-in: [51b9879050] user: gavin.band@well.ox.ac.uk branch: master, size: 108106 | |
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2017-07-12
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| 22:32 | qctool: uniformify filename parsing. file: [52d9797d41] check-in: [c81b319b48] user: gavin.band@well.ox.ac.uk branch: master, size: 108106 | |
| 09:37 | qctool: further tweaks to -help output file: [0e98fc05b2] check-in: [a8adc60e5d] user: gavin.band@well.ox.ac.uk branch: master, size: 108092 | |
| 09:32 | Fix documentation for -strand file: [8e89e0d86f] check-in: [8b2d705d97] user: gavin.band@well.ox.ac.uk branch: master, size: 108035 | |
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2017-07-11
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| 23:09 | Merged: respect -snp-match-fields in -map-id-data; additional checks on sample counts file: [7aa0e4bedb] check-in: [7f817c53bd] user: gavin.band@well.ox.ac.uk branch: master, size: 107895 | |
| 22:32 | qctool: make chromosome_hint be missing chromosome if filename match is empty file: [5f90d06255] check-in: [4beeec0710] user: gavin.band@well.ox.ac.uk branch: master, size: 107735 | |
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2017-04-20
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| 11:10 | Make -map-id-data respect -snp-match-fields file: [69948f3fd0] check-in: [12c1fd4ef7] user: gavin.band@well.ox.ac.uk branch: master, size: 107912 | |
| 10:27 | qctool: allow up to a thousand instances of -g file: [098cb68961] check-in: [88929657ee] user: gavin.band@well.ox.ac.uk branch: master, size: 107754 | |
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2017-02-21
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| 10:11 | qctool.cpp: remove commented out typedef file: [f8e835dbfb] check-in: [d2ba48be85] user: gavin.band@well.ox.ac.uk branch: master, size: 107752 | |
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2016-11-30
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| 22:22 | Remove unneeded reset_to_start() calls. file: [099d5a8f80] check-in: [d3c9f865d0] user: gavin.band@well.ox.ac.uk branch: master, size: 107884 | |
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2016-11-01
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| 14:17 | qctool: speed up testing of samples with filter for large samples file: [a490a8a034] check-in: [93178318e3] user: gavin.band@well.ox.ac.uk branch: master, size: 107913 | |
| 13:04 | qctool.cpp: work around bind to push_back file: [c8b869eca5] check-in: [1d3127e102] user: gavin.band@well.ox.ac.uk branch: master, size: 107885 | |
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2016-10-16
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| 13:38 | qctool: added -bgen-compression option. Support zstandard as compression option file: [71066eb1ef] check-in: [1b1594aa3e] user: gavin.band@well.ox.ac.uk branch: master, size: 107808 | |
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2016-08-23
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| 16:44 | qctool.cpp: Allow -incl/-excl-range to have multiple arguemnts, not comma-separated file: [1c684b3939] check-in: [ff24ed598c] user: gavin.band@well.ox.ac.uk branch: master, size: 107401 | |
| 14:18 | qctool: use predefined boost::format object for slight speedup when processing samples file: [0a237b177a] check-in: [320b767773] user: gavin.band@well.ox.ac.uk branch: master, size: 107533 | |
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2016-08-18
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| 23:01 | qctool: allow -incl-snps-matching and -excl-snps-matching to take multipe arguments. file: [3adaf301c8] check-in: [ca38da1c4b] user: gavin.band@well.ox.ac.uk branch: master, size: 107520 | |
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2016-08-01
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| 21:35 | qctool: remove unwanted options file: [fecaa79c99] check-in: [7002f7cd77] user: gavin.band@well.ox.ac.uk branch: master, size: 107692 | |
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2016-05-14
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| 09:15 | Removed unwanted old code file: [0446f19a55] check-in: [dc878e6763] user: gavin.band@well.ox.ac.uk branch: master, size: 109103 | |
| 08:58 | Removed more unneeded cruft file: [0445316f1e] check-in: [d26b4f4a1b] user: gavin.band@well.ox.ac.uk branch: master, size: 109498 | |
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2016-05-10
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| 22:37 | Merged file: [9b65464a42] check-in: [2581c41802] user: gavin.band@well.ox.ac.uk branch: master, size: 109754 | |
| 22:31 | qctool: make wildcard get non-sex chromosomes only. file: [630d91ec9e] check-in: [626284efde] user: gavin.band@well.ox.ac.uk branch: master, size: 109168 | |
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2016-05-09
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| 13:33 | qctool: indentation fix file: [f069317a6f] check-in: [279ab192f8] user: gavin.band@well.ox.ac.uk branch: master, size: 109746 | |
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2016-04-30
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| 08:52 | qctool: add -precision argument for gen file output. Create random file test for BGEN file: [25c4c89c41] check-in: [7d0524a1c4] user: gavin.band@well.ox.ac.uk branch: master, size: 109762 | |
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2016-04-23
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| 08:54 | qctool: make hom the default haploid coding. Move -sample-data after merge-in file: [16b0813ae1] check-in: [eb5bbb301a] user: gavin.band@well.ox.ac.uk branch: master, size: 109191 | |
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2016-02-01
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| 21:45 | Merged multiple_alleles branches file: [37ed44217d] check-in: [f6c882caf4] user: gavin.band@well.ox.ac.uk branch: origin/multiple_alleles, size: 109160 | |
| 21:42 | qctool: implement -spec file: [7f2506f49a] check-in: [cbc310a75d] user: gavin.band@well.ox.ac.uk branch: origin/multiple_alleles, size: 109159 | |
| 10:05 | Merge from default branch file: [ac0dfeb597] check-in: [d2b80e8f59] user: gavin.band@well.ox.ac.uk branch: origin/multiple_alleles, size: 109121 | |
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2016-01-23
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| 00:13 | qctool: fix intensity field mapping file: [5f22c6a88a] check-in: [3b80ac3033] user: gavin.band@well.ox.ac.uk branch: master, size: 108826 | |
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2016-01-01
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| 03:03 | Update to use VariantIdentifyingData (which supports multiple alleles). Update gen-grep to potentially output more than one allele. Make compilation successful again. file: [9f7a16982e] check-in: [56134be00a] user: gavin.band@well.ox.ac.uk branch: origin/multiple_alleles, size: 109120 | |
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2015-10-27
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| 09:08 | qctool: workaround missing line count in strand files file: [659657421f] check-in: [fc6ed8a833] user: gavin.band@well.ox.ac.uk branch: master, size: 108825 | |
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2015-09-02
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| 10:01 | qctool -reorder: support -reorder <file> where file contains list of ordered samples file: [61e31f4cd3] check-in: [0ceb822fa3] user: gavin.band@well.ox.ac.uk branch: master, size: 108790 | |
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2015-08-12
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| 16:13 | Implement -filetype long file: [8914ea388c] check-in: [c5d14e7da4] user: gavin.band@well.ox.ac.uk branch: master, size: 107184 | |
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2015-08-03
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| 09:06 | statfile: make number_of_rows() return an optional. Make StatSources implement operator bool(), which is greedy (i.e. reflects 'are there any more rows of data'?) file: [f4720fe35d] check-in: [8f833252fb] user: gavin.band@well.ox.ac.uk branch: master, size: 106759 | |
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2015-05-02
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| 22:33 | Merged file: [80a851f61c] check-in: [4f5b4c7c6c] user: gavin.band@well.ox.ac.uk branch: master, size: 106550 | |
| 22:07 | qctool: load_snp_dictionary(): tolerate repeated SNPs if they have the same data. file: [b3045e75ee] check-in: [675f3a3e74] user: gavin.band@well.ox.ac.uk branch: master, size: 106312 | |
| 21:58 | -bgen-suppress-sample-identifier-block => -bgen-omit-sample-identifier-block file: [1c17e624b3] check-in: [a00bcb4dfc] user: gavin.band@well.ox.ac.uk branch: master, size: 106000 | |
| 21:54 | qctool: bgen: write sample identifier block by default if -s is given. Add -bgen-suppress-sample-identifer-block to change this behaviour file: [056d71eabf] check-in: [472432bbfe] user: gavin.band@well.ox.ac.uk branch: master, size: 106008 | |
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2015-05-01
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| 08:42 | ClusterFitComputation: turn off debug statuements file: [d3e13ab353] check-in: [2f88f56a2f] user: gavin.band@well.ox.ac.uk branch: master, size: 105762 | |
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2015-04-27
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| 19:50 | qctool: rename -adjust-id-data -> -map-id-data file: [92285b2cb3] check-in: [543333cead] user: gavin.band@well.ox.ac.uk branch: master, size: 105727 | |
| 19:22 | qctool: rename -adjust-id-data to -update-id-data file: [e74fc8c327] check-in: [2b0e476910] user: gavin.band@well.ox.ac.uk branch: master, size: 105736 | |
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2015-04-23
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| 16:54 | qctool: replace -translate-snp-positions with -adjust-id-data. file: [76ac43f5ab] check-in: [43e3a1b24c] user: gavin.band@well.ox.ac.uk branch: master, size: 105736 | |
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2015-04-17
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| 23:31 | qctool: add -cluster-fit which now works and estimates normal or t-distribution clusters. file: [958674a319] check-in: [ba5cee02cd] user: gavin.band@well.ox.ac.uk branch: master, size: 105718 | |
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2015-04-15
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| 15:33 | qctool: -reorder randomly: get a random seed from /dev/urandom. file: [e7093f0987] check-in: [a62cc648af] user: gavin.band@well.ox.ac.uk branch: master, size: 105966 | |
| 10:41 | qctool: implement -reorder randomly and -reorder backwards file: [cefccdba2b] check-in: [62fd8fe433] user: gavin.band@well.ox.ac.uk branch: master, size: 105638 | |
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2015-04-08
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| 12:12 | qctool: remove -ip and -op file: [039ccb59be] check-in: [c9f08ba372] user: gavin.band@well.ox.ac.uk branch: master, size: 103283 | |
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2015-03-12
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| 16:49 | Fix -compare-to. Fix DosageFileSNPDataSource.cpp to report sample size where it should. file: [c7a30d0ecb] check-in: [760e5e2b29] user: gavin.band@well.ox.ac.uk branch: master, size: 105207 | |
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2015-03-08
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| 00:02 | Port genfile and statfile from dev branch, rev 14e7950ed137 file: [a586597f72] check-in: [11abe24082] user: gavin.band@well.ox.ac.uk branch: origin/qctool-1.5, size: 91605 | |
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2015-03-06
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| 22:38 | qctool: omit sex chromosomes from wildcard file: [0a9bc6bb84] check-in: [99965bd71d] user: gavin.band@well.ox.ac.uk branch: origin/qctool-1.5, size: 93051 | |
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2015-02-27
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| 23:40 | Fix bug in SampleFilteringSNPDataSource that prevented correct sampel counts. file: [6346b462fa] check-in: [9ae68ed4fd] user: gavin.band@well.ox.ac.uk branch: master, size: 104722 | |
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2015-01-23
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| 23:29 | qctool: add a -bgen-bits option. genfile: fix input of bgen v1.0 alleles. file: [9a0af72982] check-in: [edacf54865] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 104683 | |
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2014-12-17
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| 09:51 | qctool: rig up pass-through of VCF metadata to output file. file: [acae7cf8b4] check-in: [7b07db498c] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 104462 | |
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2014-12-15
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| 12:38 | qctool: check for '-osnp' before using it. file: [a81cf1bb6d] check-in: [570a8d16f3] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 104421 | |
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2014-10-28
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| 20:55 | qctool: whitespace change file: [88bda6c74d] check-in: [fc4fffeb97] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 104534 | |
| 08:19 | qctool: make sure and finalise storage. VCFFormatSNPDataSource: support files with no samples. file: [75d6667096] check-in: [d31152416b] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 104535 | |
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2014-10-27
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| 16:59 | Fix qctool.cpp for typo file: [67aaf18277] check-in: [d122738b7f] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 104456 | |
| 16:14 | merged file: [c9b33f69cd] check-in: [76daedd4f1] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 104468 | |
| 16:14 | qctool: respect -snp-match-fields when writing to -osnp database file: [15ba67cb6f] check-in: [4a2258ddaa] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 104352 | |
| 16:11 | qctool: fixes to handline of -flip-to-match-allele and sqlite format oututs. file: [509dc19b57] check-in: [d6993fa2bc] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 104410 | |
| 12:50 | qctool: implement -flip-to-match-allele file: [252bb6bed8] check-in: [54b84d9fec] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 104297 | |
| 10:53 | qctool: implement -vcf-output-fields option file: [152939281e] check-in: [189d45967f] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 102553 | |
| 08:32 | qctool: some work towards combined strand alignment and allele flipping. file: [b676dc6b4b] check-in: [2c6e49c583] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 101907 | |
|
2014-10-23
| ||
| 13:30 | qctool: add a -permissive argument to be permissive about vcf errors. file: [81f173191d] check-in: [cc7a8b038d] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 101256 | |
|
2014-10-15
| ||
| 16:02 | qctool: add a -no-clobber option file: [d407227208] check-in: [5b025f9be3] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 100871 | |
|
2014-09-04
| ||
| 16:06 | SNPOutputComponent: make SQLiteGenotypesSNPDataSink and SQLiteHaplotypesSNPDataSink output all the sample data in the same way. file: [e870a3944f] check-in: [e7e353e3c8] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 99708 | |
| 13:38 | qctool: output with 6dps of precision, not 15. Throw an error if an unrecognised filetype is supplied. Finisht he progress bar before printing totals. file: [bffaa0bacd] check-in: [c99976aad3] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 99576 | |
|
2014-09-02
| ||
| 22:51 | qctool: work towards new way of specifying output: -osnp and -osample. file: [19c8d0cff3] check-in: [2120e4bccb] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 99543 | |
| 20:47 | More compliation warning fixes. file: [f657fe9970] check-in: [0c8aa6f4eb] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 96796 | |
|
2014-08-27
| ||
| 13:03 | qctool: update code slightly. Implement -include-sex-chromosome which makes qctool output autosomal-like stats for the sex chromosomes. file: [7f131446e2] check-in: [be425bf1b9] user: gavin.band@well.ox.ac.uk branch: origin/qctool-1.5, size: 93490 | |
|
2014-08-19
| ||
| 13:42 | SQLiteGenotypesSNPDataSink: output all columns of the sample file to the output. file: [d8599acd7d] check-in: [7eedd2c94a] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 97066 | |
| 11:42 | qctool: make DBOutputter respect -snp-match-fields for -ofiletype sqlite_genotypes. Remove SQLiteIntensitiesSNPDataSink.hpp file: [214c14ccb5] check-in: [c820c6c2cd] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 97047 | |
|
2014-08-18
| ||
| 15:47 | apps/qctool.cpp: Fix field mapping file: [dc803af764] check-in: [dbbef64348] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 97438 | |
| 15:18 | Make each source support :genotypes: and possibly :intensities: fields. file: [d50f57573c] check-in: [e9dcaa44fc] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 97169 | |
| 14:14 | SQLiteGenotypesSNPDataSink: output GP/XY by default. file: [01776879a5] check-in: [278e96baf6] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 97635 | |
|
2014-08-12
| ||
| 13:45 | qctool.cpp: remove unused variable file: [08fb8cf816] check-in: [172d1a0b5e] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 97017 | |
|
2014-08-08
| ||
| 22:54 | Work on -merge-in. Make it respect assume-chromosome and -metadata. file: [987c0c3177] check-in: [c609c39c6a] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 97068 | |
| 07:47 | genfile: Name fields as GT or GP in input files. file: [9820b4fb4f] check-in: [fef4097992] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 96636 | |
|
2014-05-01
| ||
| 16:17 | qcdb: work on database structure. Split analyses into Analysis table. Replace analysis description with -analysis-chunk. Put chromosome/position in flat results tables. file: [fc8f45f342] check-in: [0b7c7e59a7] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 96634 | |
|
2014-04-24
| ||
| 16:31 | Add a risk score computation. Update SampleSummaryComponent to output a flat table. file: [fc721abf95] check-in: [f09af816f7] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 96679 | |
|
2014-03-11
| ||
| 12:53 | Update hapdb Haplotype data storage to use 255 not 254 to denote nonexistent haplotypes, this makes downstream code simpler. file: [a4ae7db381] check-in: [6165660615] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 96541 | |
|
2014-03-10
| ||
| 15:54 | qctool: set genotype source expected ploidy from sex information in sample file. file: [50703b74f6] check-in: [86c0c9dae9] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 96551 | |
|
2014-03-08
| ||
| 21:11 | Make qctool compile (on Mac OS X) using integrated copy of boost. Fixes based on compilation warnings. file: [dfa42bae70] check-in: [b008a8733a] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 96314 | |
|
2014-01-27
| ||
| 16:04 | Fix sample mapping for LD computation file: [cc535f75f4] check-in: [0e41471770] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 96341 | |
| 15:53 | qctool: make -compute-ld-with match samples like -merge-in file: [a30b07400c] check-in: [6efccdd934] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 96384 | |
|
2014-01-24
| ||
| 15:05 | Move merge-in work after samples have been loaded. file: [13e76fe06c] check-in: [79eb59e24a] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 95259 | |
|
2013-12-13
| ||
| 13:56 | qctool: Add a sqlite_intensities output format file: [40112f823b] check-in: [5014ba442a] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 95250 | |
| 13:19 | qctool: Added support for sqlite_genotypes output filetype. file: [10cccd93b6] check-in: [3f5ec88a9c] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 94791 | |
|
2013-12-12
| ||
| 23:23 | Add some more text for description of -strand file: [27724f2fee] check-in: [0a2b511e95] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 94283 | |
|
2013-10-22
| ||
| 09:35 | Add a sqlite_haplotypes output method using UBJSON or BITPACK to encode the data. file: [d077bc858c] check-in: [e5fb472d61] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 94128 | |
|
2013-10-07
| ||
| 13:39 | qctool: report the SQL when there's a DB error. file: [b19657c9db] check-in: [362b58652c] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 93627 | |
|
2013-09-30
| ||
| 13:48 | Update to use merged genfile lib file: [85ae801827] check-in: [8f88a5bbce] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 93372 | |
|
2013-09-28
| ||
| 21:59 | qctool: use -snp-missing-call-rate not -missing-call-rate file: [fe2486f8ca] check-in: [9a1bf3a95d] user: gavin.band@well.ox.ac.uk branch: origin/qctool-release, size: 92987 | |
|
2013-08-19
| ||
| 15:35 | Pull implementation of fix_sex_chromosome_genotypes from snptest. file: [4a0841b534] check-in: [6f0e0788f6] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 93353 | |
| 15:04 | Added a -sex_column option. file: [186468c26e] check-in: [8e5643b287] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 93088 | |
|
2013-07-02
| ||
| 09:59 | FromFileCohortIndividualSource: index the sample id field for efficient lookup. file: [733eb060cd] check-in: [7aab188547] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 92926 | |
| 09:58 | Remove lots of crap that we don't use any more. file: [44c78b80a4] check-in: [d7e4a66438] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 92876 | |
| 09:03 | qctool: don't insist on having ID_1 and missing columns in sample file. file: [fd3309446f] check-in: [747b226bfc] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 93845 | |
|
2013-06-26
| ||
| 14:21 | qctool: implement -sample-data file: [e3d681651d] check-in: [de49a5817a] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 92458 | |
| 10:12 | Don't do SNP output when only -os is specified. file: [7881f14037] check-in: [e7f5cb7951] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 90886 | |
|
2013-06-23
| ||
| 21:46 | qctool: implement -threshhold file: [dc51e3b35f] check-in: [8ecb4e1f22] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 90914 | |
|
2013-06-20
| ||
| 14:59 | Fixes to improve the SNP progress counter and speed up relatedness computation. file: [7401ea18e0] check-in: [849f99f363] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 89583 | |
| 14:40 | Fix to avoid long setup cost in progress timer. file: [3f06970ee9] check-in: [b51ec955a3] user: gavin.band@well.ox.ac.uk branch: origin/dev, size: 89469 | |
|
2013-06-14
| ||
| 16:01 | qctool: fix the sample filter. file: [ff84263781] check-in: [df22415dab] user: gavin.band@well.ox.ac.uk branch: origin/sample.filter, size: 88661 | |
|
2013-05-30
| ||
| 10:05 | qctool: add -table-name option. Make -annotate- options not be stratified by -stratify. file: [0870fc33f9] check-in: [ca3a15d92b] user: gavin.band@well.ox.ac.uk branch: origin/sample.filter, size: 88526 | |
| 09:07 | qctool: don't keep reloading the SNP filter: reuse it. file: [ae815138a7] check-in: [dba5ae44cd] user: gavin.band@well.ox.ac.uk branch: origin/sample.filter, size: 88400 | |
|
2013-05-29
| ||
| 11:08 | Fix sample filter failure count. file: [12bab1439d] check-in: [90f784542e] user: gavin.band@well.ox.ac.uk branch: origin/sample.filter, size: 88349 | |
| 09:55 | Support haplotypic output in ShapeIT format using -ofiletype option. file: [eb7a5384e2] check-in: [d8e6eab42e] user: gavin.band@well.ox.ac.uk branch: origin/sample.filter, size: 88302 | |
|
2013-05-28
| ||
| 08:06 | Work towards sample filter spec parsing. file: [1d06f47e64] check-in: [bd51248557] user: gavin.band@well.ox.ac.uk branch: origin/sample.filter, size: 87800 | |
|
2013-05-24
| ||
| 20:26 | Work towards new sample filtering. file: [84bf26cc58] check-in: [08e21cfa3a] user: gavin.band@well.ox.ac.uk branch: master, size: 90813 | |
|
2013-05-01
| ||
| 15:14 | qctool: be permissive about duplicate lines in strand file, as long as they agree on the strand. file: [fc3d376e36] check-in: [12c092bdbc] user: gavin.band@well.ox.ac.uk branch: master, size: 88676 | |
|
2013-04-09
| ||
| 11:27 | Don't allow writing to the same analysis. file: [c365120d2e] check-in: [48a73c004e] user: gavin.band@well.ox.ac.uk branch: master, size: 88624 | |
|
2013-04-03
| ||
| 14:08 | -[in|ex]cl-snps: don't try to read input in GEN format, as this gets it wrong. file: [67702e9750] check-in: [8de5b2d727] user: gavin.band@well.ox.ac.uk branch: master, size: 88380 | |
|
2013-03-26
| ||
| 12:53 | qctool: Be nicer about error message when the wrong number of strand files are supplied. Make -strand respect -snp-match-fields file: [3039395ae0] check-in: [56bc5d4623] user: gavin.band@well.ox.ac.uk branch: master, size: 88829 | |
| 10:34 | qctool: make -quantile-normalise respect exclusions, i.e. only use those samples not excluded. file: [94057912d3] check-in: [d91752cbf2] user: gavin.band@well.ox.ac.uk branch: master, size: 88366 | |
| 10:32 | qctool: re-implement -os file: [e71036e7ef] check-in: [f0288a0d27] user: gavin.band@well.ox.ac.uk branch: master, size: 88349 | |
|
2013-03-25
| ||
| 14:33 | qctool: really don't list SNPs when using -match-alleles-to-cohort1 file: [b4f4f2e72e] check-in: [1de2533bf9] user: gavin.band@well.ox.ac.uk branch: master, size: 89152 | |
| 14:31 | qctool: do not pre-scan data for joining multiple cohorts. Make -strand possible strand alignments for alleles. file: [add5ada4b7] check-in: [e01586c724] user: gavin.band@well.ox.ac.uk branch: master, size: 89384 | |
|
2013-03-22
| ||
| 22:45 | qctool: Make -strand respect -snp-match-fields. file: [67b23164cf] check-in: [ce1dfb5641] user: gavin.band@well.ox.ac.uk branch: master, size: 89712 | |
|
2013-03-21
| ||
| 11:43 | -merge-in: support -match-sample-ids, allowing merged-in source to differ in number of samples. file: [2a12da6325] check-in: [e67012d584] user: gavin.band@well.ox.ac.uk branch: master, size: 89668 | |
|
2013-03-20
| ||
| 17:24 | Added SampleMappingSNPDataSource. file: [2f7be3df67] check-in: [63dec1e8bb] user: gavin.band@well.ox.ac.uk branch: master, size: 88810 | |
|
2013-02-26
| ||
| 14:40 | qctool: implement -write-index file: [f1536bfda8] check-in: [24ed71d1e0] user: gavin.band@well.ox.ac.uk branch: master, size: 88730 | |
|
2013-02-25
| ||
| 11:44 | qctool.cpp: remove some unused code. file: [6617854ef5] check-in: [08452fb5e5] user: gavin.band@well.ox.ac.uk branch: master, size: 88358 | |
|
2012-12-11
| ||
| 12:15 | qctool: implement -haplotypic which currently affects -compare-to. file: [c9cf8b97ad] check-in: [855dc521d4] user: gavin.band@well.ox.ac.uk branch: master, size: 88590 | |
|
2012-11-05
| ||
| 16:56 | qctool: move CallComparerComponent to run from SNPSummaryComponent. file: [7d87646204] check-in: [df4fefddc7] user: gavin.band@well.ox.ac.uk branch: master, size: 88557 | |
| 11:49 | qctool: add a -flat-table output format. file: [2da5d534c9] check-in: [666bd120bc] user: gavin.band@well.ox.ac.uk branch: master, size: 88976 | |
|
2012-10-31
| ||
| 11:36 | qctool: make -[in|ex]cl-snps respect -snp-match-fields. file: [eb732dc5c8] check-in: [ea8aa8938a] user: gavin.band@well.ox.ac.uk branch: master, size: 88682 | |
| 11:05 | qctool: pull -[in|ex]cl-snps options and associated functionality from qctool-release. Update to read from GEN style files too. file: [073f070eb4] check-in: [01cd612d1b] user: gavin.band@well.ox.ac.uk branch: master, size: 88438 | |
|
2012-10-30
| ||
| 17:09 | qctool: Make -ip and -op work again. file: [ce0e74bf24] check-in: [2098cd90d8] user: gavin.band@well.ox.ac.uk branch: master, size: 86171 | |
|
2012-10-26
| ||
| 21:39 | CallComparerComponent: add glue to use SNPSummaryComponent outputters. file: [59ecb68d2f] check-in: [ed509e4fcb] user: gavin.band@well.ox.ac.uk branch: master, size: 86166 | |
|
2012-10-18
| ||
| 21:22 | qctool: rename -odb to -o, and remove cruft. file: [b7a1b9dbc2] check-in: [0ad1c0a8eb] user: gavin.band@well.ox.ac.uk branch: master, size: 86165 | |
|
2012-10-17
| ||
| 13:59 | KinshipCoefficientComputer2: fix bug overwriting data of running tasks. qctool: add a -buffer-snps option. file: [04bc4c177a] check-in: [81f8e108e3] user: gavin.band@well.ox.ac.uk branch: master, size: 94512 | |
| 13:21 | genfile:: implement AsynchronousSNPDataSource which loads SNPs in the background. qctool: Use the AsynchronousSNPDataSource if -threads is specified. file: [15d8896b3f] check-in: [47b0cd07e8] user: gavin.band@well.ox.ac.uk branch: master, size: 94302 | |
|
2012-10-11
| ||
| 08:51 | rename -nodb -> -flat-file file: [b3542358c3] check-in: [fff3bb1c5b] user: gavin.band@well.ox.ac.uk branch: master, size: 94108 | |
| 08:42 | qctool: fix SNP data source opening before sample files. file: [a08d9de7f2] check-in: [c9608d9649] user: gavin.band@well.ox.ac.uk branch: master, size: 94103 | |
|
2012-10-10
| ||
| 21:01 | qctool: Fix usage with no sample file. Fix bug inferring chromosome for ShapeIT haplotypes. file: [fa8524cf05] check-in: [8fd63ad66f] user: gavin.band@well.ox.ac.uk branch: master, size: 95069 | |
|
2012-08-29
| ||
| 11:17 | Changed branch to qctool-release file: [93faacb96f] check-in: [7d9e0d9880] user: gavin.band@well.ox.ac.uk branch: origin/qctool-release, size: 92983 | |
|
2012-08-28
| ||
| 20:47 | Full implementation and fixes for -[in|ex]-cl-snps file: [e490dbea71] check-in: [4f27771b10] user: gavin.band@well.ox.ac.uk branch: origin/qctool-1.1, size: 92984 | |
| 19:49 | qctool: Add a -[in|ex]-cl-snps option which reads them in the format output by -write-snp-excl-list. Not fully working yet. file: [428901adbb] check-in: [16fba5251b] user: gavin.band@well.ox.ac.uk branch: origin/qctool-1.1, size: 92769 | |
|
2012-08-08
| ||
| 11:01 | Merged changes from qctool-1.2 branch. file: [030794869f] check-in: [da1894139e] user: gavin.band@well.ox.ac.uk branch: master, size: 94842 | |
| 09:12 | qctool: Added -[in|ex]cl-positions and a test case. file: [554e6a9f5d] check-in: [ce74adf091] user: gavin.band@well.ox.ac.uk branch: origin/qctool-1.1, size: 91288 | |
|
2012-08-07
| ||
| 15:45 | qctool: update for sorting of vcf files. Add tests for this. Run functional test when waf test is run. Update changelog appropriately file: [54b3e89c32] check-in: [32bc6201cd] user: gavin.band@well.ox.ac.uk branch: origin/qctool-1.1, size: 90021 | |
|
2012-07-24
| ||
| 15:26 | Add SNPSummaryComponent if -annotate-[ancestral|reference] options are used. file: [ce68d889de] check-in: [99d1244b02] user: gavin.band@well.ox.ac.uk branch: master, size: 94744 | |
| 11:02 | Tweaks to SequenceAnnotation. file: [c2610f15c2] check-in: [e0af0870dc] user: gavin.band@well.ox.ac.uk branch: master, size: 94690 | |
|
2012-07-13
| ||
| 13:51 | qctool: implement -[in|ex]cl-positions. file: [d1d99f540e] check-in: [80c4639b5e] user: gavin.band@well.ox.ac.uk branch: master, size: 94688 | |
|
2012-07-03
| ||
| 15:51 | genfile::SNPDataSink: make a set_sample_names method that must be called before SNPs are output. file: [a3d98806b3] check-in: [d0f777f769] user: gavin.band@well.ox.ac.uk branch: master, size: 93329 | |
|
2012-06-27
| ||
| 10:08 | Make -snp-stats and -sample-stats and -compute-ld-with output data into argument given by -odb. file: [4c5273b15c] check-in: [29b48e86e6] user: gavin.band@well.ox.ac.uk branch: master, size: 93192 | |
| 09:59 | qctool: bug fix relating to last change. Remove default value for -compute-ld-file. file: [5675be31c7] check-in: [2811ff233f] user: gavin.band@well.ox.ac.uk branch: master, size: 93015 | |
| 09:45 | Add a -max-ld-distance argument to only compute LD within a specified distance. Also, open LD file in the same way as other files (with the same filtering, etc.) file: [5952b1c28c] check-in: [4680d12c07] user: gavin.band@well.ox.ac.uk branch: master, size: 93468 | |
|
2012-06-20
| ||
| 12:50 | qctool: use -sample-stats not -sample-stats-old file: [8bd0aa6281] check-in: [9669ad5d76] user: gavin.band@well.ox.ac.uk branch: master, size: 92589 | |
| 12:43 | qctool: unhide options again file: [31fbf8dd8b] check-in: [f03939e99b] user: gavin.band@well.ox.ac.uk branch: master, size: 92593 | |
|
2012-04-20
| ||
| 09:39 | qctool.cpp: include the right components file: [606412b432] check-in: [aa4f4f973b] user: gavin.band@well.ox.ac.uk branch: master, size: 92746 | |
|
2012-04-19
| ||
| 09:17 | Fix -snp-stats and -sample-stats options again. file: [075327117b] check-in: [b2dd580f3d] user: gavin.band@well.ox.ac.uk branch: master, size: 93031 | |
|
2012-04-18
| ||
| 16:15 | Merge changes from qctool v1.1 file: [1a0006deba] check-in: [6d63528ea2] user: gavin.band@well.ox.ac.uk branch: master, size: 93011 | |
|
2012-04-17
| ||
| 12:47 | Fixes to SNP visitation - don't visit them unless we need to. file: [61668451eb] check-in: [42225947b7] user: gavin.band@well.ox.ac.uk branch: origin/qctool-1.1, size: 89923 | |
| 11:58 | Docs: add link to GTOOL to the overview page. Fixes and links to help file. qctool: more tweaks to options. file: [d94a169cce] check-in: [9e64ee646d] user: gavin.band@well.ox.ac.uk branch: origin/qctool-1.1, size: 91560 | |
|
2012-04-15
| ||
| 20:36 | Fix compilation by removing unwanted files. file: [1843e0fc40] check-in: [6e5f3f4c0f] user: gavin.band@well.ox.ac.uk branch: origin/qctool-1.1, size: 92450 | |
|
2012-04-13
| ||
| 21:35 | In -sample-stats, make output column names ID_1 and ID_2 (not ID1 and ID2) file: [de01ad33f1] check-in: [2ed3ba6aa0] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 92440 | |
| 21:31 | Bug fixes to -snp-stats output columns. Add A_allele and B_allele columns. file: [630b06aca2] check-in: [10290dd3b6] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 92518 | |
|
2012-04-12
| ||
| 23:13 | Cosmetic tweaks file: [234aa71bd5] check-in: [1d93241cae] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 92498 | |
| 23:04 | Tweaks and fixes for the tutorial page. file: [5f29708c60] check-in: [33c3e0297f] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 92499 | |
| 22:19 | qctool: 1: ensure only filtered-in SNPs are used in sample stats computation. 2: make -sample-stats imply -os. Doc fixes. file: [41aa23a275] check-in: [6dc038c3de] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 92371 | |
| 21:51 | Always provide a cohort individual source (a dummy one if -s is not given). Output all excluded SNPs if -write-snp-excl-list is given. file: [000eb28ec2] check-in: [e217c310fb] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 92311 | |
| 10:55 | Fix quantile normalisation to really put quantile-normalised columns in output. file: [efdb5eae18] check-in: [2a7f7037fb] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 91754 | |
| 10:42 | qctool: Use statfile in -write-sample-excl-list. Update quantile normalisation to add extra columns file: [493171d2d7] check-in: [89bad54cad] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 91628 | |
|
2012-04-11
| ||
| 21:05 | Added license to each cpp/hpp file. file: [b0e5bc51c9] check-in: [702d5dc76a] user: gavin.band@well.ox.ac.uk branch: master, size: 92097 | |
| 20:46 | Added license to all files. file: [5ae12c8d40] check-in: [64358eb9f2] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 91613 | |
|
2012-04-09
| ||
| 22:46 | Replace -vcf-field-map with -vcf-genotype-field. Further fixes for web page tutorial file: [afff662896] check-in: [36fda6f593] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 91397 | |
|
2012-04-08
| ||
| 23:27 | Updated documentation and according fixes to qctool file: [6d0ba7a87c] check-in: [3bbf6bad1e] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 91835 | |
|
2012-04-07
| ||
| 21:31 | Fix bug where SNP filter values are not output correctly, sometimes appearing as zero although non-zero. file: [36fae68fe6] check-in: [d0bd7f1659] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 91440 | |
| 20:34 | Added CHANGELOG. Work on sanitising options and other useability tweaks. file: [f9481159f4] check-in: [f17064bd85] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 91268 | |
|
2012-03-28
| ||
| 12:25 | Amet: first working version. file: [021803b6ae] check-in: [d73f243b1e] user: gavin.band@well.ox.ac.uk branch: master, size: 91881 | |
|
2012-03-22
| ||
| 23:07 | ConsensusCaller: slight refactor. file: [6ebef2656b] check-in: [b13dcdbe56] user: gavin.band@well.ox.ac.uk branch: master, size: 91845 | |
|
2012-03-17
| ||
| 00:26 | Work on SampleSummaryComponent. file: [131c6abaf9] check-in: [6bb95318d4] user: gavin.band@well.ox.ac.uk branch: master, size: 91702 | |
|
2012-03-13
| ||
| 17:01 | Really hide -translate-snp-position options. file: [5bff641098] check-in: [f3e0bcba89] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 92085 | |
| 17:01 | Hide -strand and -translate-snp-position options. file: [d35db54770] check-in: [2a8c7a761c] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 92079 | |
| 16:53 | Release 1.1 branch. Various changes. Re-instate original snp-stats and filtering code. file: [e8b3cc5ee5] check-in: [301f1bac05] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 92068 | |
| 14:41 | Port OptionProcessor from snptest/dev. file: [3d7043664f] check-in: [7923ce9620] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 91311 | |
|
2012-03-09
| ||
| 10:35 | Print a summary from the SNPSummaryComponent. file: [2a939c5692] check-in: [d44fefeaa4] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 91463 | |
|
2012-03-08
| ||
| 17:45 | tweak qctool for SNPSummaryCOmponent changes. file: [2f67eaffe1] check-in: [0e175e2114] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 91284 | |
|
2012-03-07
| ||
| 14:51 | Add a -filetype option to qctool; this overrides the auto-generated file type. file: [107cece83f] check-in: [2c0dc05ae0] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 91227 | |
| 13:11 | genfile: work towards reading of ShapeIT-phased haplotype files. file: [d70e0d627a] check-in: [e539c664cd] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90043 | |
|
2012-03-06
| ||
| 23:04 | Lots of work on PCA component, now renamed as RelatednessComponent. file: [f1466d3185] check-in: [e11ef8d5cb] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89821 | |
| 14:45 | Only visit SNPs if -loadings is specified when doing -PCAs. file: [dc5fa5386b] check-in: [de0ca6fe93] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89765 | |
|
2012-03-03
| ||
| 22:53 | qctool: make analysis name use qctool and datestamp by default. file: [1277897c72] check-in: [5fd89e51b8] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89625 | |
|
2012-03-02
| ||
| 22:55 | qctool: check again that number of samples match file: [8dde577b35] check-in: [42ad04ba5d] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89513 | |
| 16:59 | qctool: don't write a sample file unless told to. file: [016c9f2959] check-in: [0c3858b26d] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89226 | |
|
2012-02-28
| ||
| 15:00 | More OptionProcessor fixes. Put partial specialisation of get_value(s) back in. file: [77f60b201e] check-in: [f75a56683b] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90548 | |
|
2012-02-22
| ||
| 16:35 | Compilation tweaks to CallComparerComponent. file: [a618768c3e] check-in: [cb3e1c9bf9] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90521 | |
|
2012-02-21
| ||
| 23:02 | Work on ConsensusCaller. file: [b42396c79e] check-in: [f49bb85caf] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90697 | |
| 10:11 | Lots of work on removing need for number of SNPs / list of SNPs. file: [999a0156c1] check-in: [95e0b6c7e9] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90696 | |
|
2012-02-20
| ||
| 23:38 | qctool: work towards removing need for snp lists / number of snps. file: [b3e8c903f9] check-in: [8104fd7e7c] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90444 | |
| 22:13 | Work to make SNPDataSource::total_number_of_snps() return an optional value. file: [e7007f7630] check-in: [f732cb24c5] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90450 | |
| 12:49 | Fix some warnings/compilation errors. file: [01a55b1f67] check-in: [0e71811c73] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90408 | |
|
2012-02-09
| ||
| 15:44 | Merged file: [67b2de9488] check-in: [ebbf36ffd2] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90427 | |
| 15:43 | qctool: minor argument tweaks. Allow -excl-rsids or -excl-snpids more than once. file: [375f38d5c5] check-in: [43e6b2a34e] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90498 | |
|
2012-02-08
| ||
| 21:12 | Merged. file: [db27664ec2] check-in: [21d11da18f] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90139 | |
| 21:12 | Add a get_spec() function to SNPDataSink. file: [771e1ae622] check-in: [a0ada37e93] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89237 | |
| 12:04 | qctool: make the drop strategy drop-duplicates as I think this is more descriptive. file: [0b723a738f] check-in: [3304f3ef10] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90210 | |
| 11:56 | qctool: make the sources loaded by -merge-in respect the snp filter. file: [1dc3154910] check-in: [fb66aafa69] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90199 | |
| 11:45 | qctool: add a -merge-strategy option to allow dropping duplicates in a merge. file: [0308e26636] check-in: [aa8fb0095e] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89608 | |
|
2012-02-01
| ||
| 11:22 | Added tests and fixes for snptest::case_control::LogLikelihood. NB we take more iterations than SNPTEST, usually, because our stopping condition is different. file: [28f55005a5] check-in: [fe903e4aa2] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89308 | |
|
2012-01-29
| ||
| 22:49 | Move SNPSummaryComponent into directory under components/ file: [d783e63685] check-in: [f81b163a38] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89306 | |
| 22:41 | Begun further rationalisation of associaton test code. LogLikelihood handles all of the exclusions now. file: [a0c520d889] check-in: [f528c7a915] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89275 | |
|
2012-01-27
| ||
| 20:11 | Move HaplotypeFrequencyComponent into components/ file: [220ec6a4dc] check-in: [b589b64a39] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89593 | |
|
2012-01-26
| ||
| 16:52 | Move CallComparerComponent into subdir of components/ file: [4d209c611c] check-in: [e6e17e58b3] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89554 | |
|
2012-01-25
| ||
| 10:23 | qctool: add a -merge-prefix option to add a prefix to the SNPID of merged-in SNPs. file: [492e231410] check-in: [75b4846179] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89521 | |
|
2012-01-12
| ||
| 12:28 | Do not output a log file by default. file: [bd72c251cd] check-in: [bd5ae9fc27] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89082 | |
|
2012-01-11
| ||
| 13:59 | Added sqlite3/extension-functions.c file: [bb2da9cb60] check-in: [2e9c8e3d02] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89160 | |
|
2012-01-10
| ||
| 16:57 | qctool: implement -merge-in file: [6283a2cebb] check-in: [e5b5912d23] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89165 | |
|
2012-01-09
| ||
| 17:03 | 1. merge 2. genfile: add SortingBGenFileSNPDataSink which sorts plain GEN and BGEN files. 3. SNPSummaryComponent: allow parallelism. Add analysis_id into SUmmaryData table and link to -cohort-name Entity with data specifying -g filename and sample nclusion/exclusion spec. file: [682332bed6] check-in: [59c931b826] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 88720 | |
|
2012-01-07
| ||
| 00:15 | qctool: implement -sort which will currently sort bgen and unzipped gen files. file: [4e47ce5e1b] check-in: [5b8a29525f] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 88009 | |
|
2012-01-06
| ||
| 21:17 | qctool: add -omit-chromosome. Add useful view to SNPSummaryComponent output. Allow unrecognised alleles in strand alignment. file: [4c9cc6fd6e] check-in: [8cb4a868b5] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 88347 | |
|
2012-01-04
| ||
| 15:15 | Replace genfile::FileNotOpenedError with genfile::ResourceNotOpenedError, and catch it in qctool. file: [11c7a5b9dc] check-in: [c91b833994] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 54128 | |
|
2011-12-20
| ||
| 20:50 | Make SNPSummaryComponent::DBOutputter the default output method. Also implement -nodb. file: [76e704bf4f] check-in: [ca60694067] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 87585 | |
| 14:29 | MakeSNPSummaryComponent write to a db by default. Remove -write-[snp|sample]-excl-list-file. file: [60f7d0b3c1] check-in: [bf339dca70] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 87303 | |
|
2011-12-19
| ||
| 13:59 | Minor tweaks. file: [0cb73cff1c] check-in: [e5b3a538e6] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89080 | |
|
2011-12-13
| ||
| 14:09 | Tweaks. Add version number to output. file: [6c6ab730fd] check-in: [223341f20f] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 53928 | |
| 14:05 | Hide some options. Implement threshholding. file: [9e4f73661e] check-in: [cfe237ede7] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 53850 | |
|
2011-12-07
| ||
| 21:51 | HaplotypeFrequencyComponent: write to sqlite database. Filter out filtered out samples. file: [d2a2bc84bc] check-in: [471a344152] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89080 | |
| 11:05 | HaplotypeFrequencyComponent: estimate frequency by EM algorithm. Write output to DB. file: [707e2b96da] check-in: [a85a1f178c] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 90145 | |
|
2011-12-06
| ||
| 17:35 | HaplotypeFrequencyComponent: implement likelihood, (which doesn't work). file: [bc3a2bce9f] check-in: [a67c215936] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89934 | |
|
2011-11-25
| ||
| 15:46 | qctool: fix problem where chromosome hint is not understood. file: [2a6e711f13] check-in: [3e97b9af88] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 53685 | |
| 14:48 | qctool: calculate SNP summary statistics using SNPSummaryComponent, not QCTool (which will be phased out.) file: [a2d2a24ee4] check-in: [003dc6227b] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89518 | |
|
2011-11-10
| ||
| 11:38 | qctool: Add -condition_on option, similar to SNPTEST file: [073424fdaf] check-in: [62c8004fba] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 89337 | |
|
2011-10-20
| ||
| 22:27 | qctool: make -incl-samples use union of all supplied files. file: [6510874324] check-in: [e8bf550836] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86951 | |
| 21:52 | Allow non-matching sample files. file: [599bd0e2e3] check-in: [67d575e5bd] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86761 | |
|
2011-10-18
| ||
| 08:29 | qctool: update description of -translate-snp-positions options file: [bb17a7e3f5] check-in: [6296702539] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86773 | |
|
2011-10-17
| ||
| 08:34 | qctool: work on cluster fitting and calling using IntensityModel file: [10c8903c6a] check-in: [0f59cf43b9] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86677 | |
|
2011-10-13
| ||
| 14:15 | qctool: add -plot-clusters option. file: [5b5be1d56d] check-in: [1874ce257a] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86558 | |
|
2011-10-12
| ||
| 16:01 | qctool: initial implementation of genotype call comparer using -compare-calls option. file: [20d38c428c] check-in: [67052ededa] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86206 | |
|
2011-10-04
| ||
| 15:27 | Make sure and add main QCTool processor if SNP filtering is done. file: [a1dd8a62fe] check-in: [5bdfba2ee2] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 85838 | |
| 13:35 | genfile::GenFileSNPDataSource: support metadata (number-of-variants) file: [3ab01dccf3] check-in: [ca05291e23] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 85757 | |
|
2011-09-15
| ||
| 10:53 | qctool: VCDB writer: tweaks. file: [03b8e6f14c] check-in: [d0d691094a] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 85515 | |
| 09:55 | VCDBDataStore / VCDBWriter, small refactor file: [929e2171f2] check-in: [dd0dc59305] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 85704 | |
|
2011-09-14
| ||
| 15:52 | qctool: use VCDBWriter not IntensityWriter. file: [ef5ca15f61] check-in: [3fdf796e6c] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 85963 | |
|
2011-09-06
| ||
| 15:17 | merged. file: [ae45ef39d7] check-in: [19cfec0e1f] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86001 | |
| 15:16 | Add a -load-kinship option to which -PCA is now linked. file: [2e7c571d14] check-in: [e82e43a73e] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86117 | |
| 11:02 | qctool: allow -snp-stats and -og at the same time. file: [bf91fbf537] check-in: [57955b6b48] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86024 | |
|
2011-09-05
| ||
| 21:52 | Give -PCA an option value, the file to save to. file: [1a21c8f3a1] check-in: [bc22123c77] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86140 | |
| 09:02 | KinshipCoefficientComputer: add a method to compute PCA (=eigenvalue decomposition of kinship matrix.) file: [b10242d2be] check-in: [4a57470ddb] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86124 | |
|
2011-09-02
| ||
| 12:44 | Slight refactor of KinshipCoefficientComputer, add an output callback. file: [144c7a3d4d] check-in: [4c0e415913] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86622 | |
|
2011-08-22
| ||
| 15:54 | qctool: add Chromosome to snp-stats output. file: [8e2f2e8b5c] check-in: [ab492f60fb] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86567 | |
|
2011-08-07
| ||
| 22:36 | worker: small fix file: [99e6b86e9f] check-in: [437b8cd248] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86555 | |
|
2011-08-04
| ||
| 16:34 | KinshipCoefficientComputer: another attempt at multi-thread. but I think the thread pool needs work. file: [ea6b726ec6] check-in: [171d113c12] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86577 | |
| 14:07 | qctool: add a ClusterFitter module. SingleSNPGenotypeProbabilities: be more tolerant about sum of probabilities. file: [c7838cfb3d] check-in: [2a6c0f7b92] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86879 | |
|
2011-08-03
| ||
| 16:27 | qctool: -kinship2 -> -kinship, which is renamed to -kinship-old. Add CallCountStatistic. file: [47fb316bb1] check-in: [60f2caf12d] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 87178 | |
|
2011-07-27
| ||
| 15:58 | qctool: add a -kinship2 option which does kinship a different way. file: [21e7df2694] check-in: [c90be26366] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 87151 | |
| 11:15 | qctool: fix bug in -read-test file: [6436c01c8c] check-in: [0a5a33b235] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86530 | |
| 11:08 | qctool: add a -read-test option which just reads the data. file: [7d78f04d65] check-in: [01bd250cda] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86510 | |
|
2011-07-20
| ||
| 15:05 | qctool: fix single vcf file optimisation. Turn it off if we actually need the list of SNPs. QCTool.cpp: slight reworking. file: [5b20b42a14] check-in: [af9ad85e88] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 86241 | |
| 12:34 | qctool: add hack to open vcf files quickly. However, no filtering etc. can then be performed. file: [149296475e] check-in: [bd854fb695] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 85875 | |
|
2011-07-19
| ||
| 16:27 | genfile::VCFFormatSNPDataSource: if metadata is supplied to constructor, ignore the file metadata instead of parsing it. file: [2cc245711c] check-in: [e6fb423f78] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 85483 | |
|
2011-07-17
| ||
| 20:04 | merged. file: [174374dcc2] check-in: [ab5ac18db8] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 84945 | |
|
2011-07-15
| ||
| 16:03 | Updates for better serialization. file: [8e98c57a1f] check-in: [5714be6132] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 84918 | |
|
2011-07-11
| ||
| 08:19 | qctool: make sure -op works again. file: [986cda1c34] check-in: [a003796608] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 84891 | |
|
2011-07-08
| ||
| 15:37 | qctool: only do qctool_basic if needed. genfile::zlib.hpp: write length of data before data. file: [39870435e1] check-in: [c84e8330ae] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 84864 | |
| 13:28 | qctool: catch the DuplicateKeyError from last change and print out msg. file: [5bf55aa02a] check-in: [47fd90d035] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 84662 | |
| 10:53 | qctool: change -vcf-genotype-field and -vcf-intensity-field to -vcf-field-map. Make IntensityWriter output all fields \(float only\) available. file: [d66745beed] check-in: [be2829dbeb] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 84395 | |
|
2011-07-07
| ||
| 15:54 | qctool: add a method to write intensities to an sqlite3 database. This entails improvements to genfile::VariantDataReader and its implementations. file: [811ca97d2a] check-in: [a532bf539c] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 84292 | |
|
2011-07-05
| ||
| 22:31 | genfile/qctool: Added BedFileSNPDataSink, which writes plink binary-format files. Also work on making Ped files PLINK-compatible. file: [3ac94bda51] check-in: [99dd13d434] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 82854 | |
|
2011-07-01
| ||
| 10:01 | qctool: fix -write-snp-excl-list to not take value. file: [89d39d1471] check-in: [70107a6a6a] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 82396 | |
|
2011-06-28
| ||
| 12:48 | qctool: yet another case of catching a file-not-found and printing the msg. file: [0a82139ec3] check-in: [f1b3172f20] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 82423 | |
| 12:39 | qctool: Allow NA as well as ? in strand file file: [71cea1e6a9] check-in: [5f91a0d1b4] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 82190 | |
|
2011-06-27
| ||
| 22:28 | qctool: add -exclude-range option too. file: [aaf0086c18] check-in: [44b482523a] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 82172 | |
| 14:31 | qctool: add a -range option a la snptest. file: [94ef1f3183] check-in: [cb24f73924] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 81182 | |
|
2011-06-26
| ||
| 21:19 | qctool: minor cosmetic change. file: [e6f909a1aa] check-in: [a59aab2784] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 80511 | |
|
2011-06-24
| ||
| 08:42 | Catch FileNotFound error again and print message. file: [71d8cb2fd3] check-in: [4738c6a9e1] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 80378 | |
|
2011-06-14
| ||
| 13:34 | qctool: hook up kinship properyl. file: [b8598e5adf] check-in: [9effc24d0a] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 80163 | |
|
2011-06-10
| ||
| 11:21 | qctool: vcf format: work on allowing the use of an index file, or the number-of-variants=N key in the header info. file: [f2054c0000] check-in: [0c024f555d] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 80207 | |
|
2011-06-09
| ||
| 10:00 | Fix genfile::vcf::MetadataParser to allow taking an external file directly. file: [ea2dab1db8] check-in: [98c32e4bc2] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 80550 | |
| 08:28 | qctool: allow adding metdata from external file to VCF file. file: [d989919d02] check-in: [157588c3b7] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 80549 | |
| 08:10 | More refactorisation of association test. Mimic SNPTEST more closely. file: [b6c17e7933] check-in: [327ce6076b] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 80031 | |
|
2011-06-02
| ||
| 11:08 | genfile: support for gzipped VCF files. Update to use boost unit test, one test per subproject. file: [1377ddaf53] check-in: [23947b5a6e] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 79978 | |
|
2011-05-26
| ||
| 12:53 | Whoops: qctool: allow -excl/-incl-samples to be used no times again. file: [68b9209b4f] check-in: [60c80c7be3] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 80002 | |
| 12:50 | qctool: support multiple uses of -excl-samples or -incl-samples file: [c953c7f4e0] check-in: [cd7d26b5d6] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 80002 | |
|
2011-05-25
| ||
| 15:01 | qctool: relatotron: fix multithreading bug when waiting for tasks to complete file: [b97899461c] check-in: [29e7c6758b] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 79656 | |
| 14:35 | qctool: minor argument and file name changes file: [c7ec138ba6] check-in: [dfa3d1956e] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 79443 | |
|
2011-05-24
| ||
| 14:15 | qctool: add a -concordance option which produces concordnace.txt and pairwise_non_missing_count.txt file: [5f5405d3bb] check-in: [b4ef3491c0] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 79431 | |
|
2011-04-15
| ||
| 12:59 | qctool: dont write a sample file either if only doing snp stats. file: [0d500d2d22] check-in: [4d3e24f74a] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 53641 | |
| 10:39 | qctool: dont produce an output GEN file, by default, if -snp-stats is given. (Use -og to override.) file: [fcd8fe74b2] check-in: [10b44377cd] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 53554 | |
|
2011-03-21
| ||
| 12:39 | qctool: Operate on all chromosomes, even sex chromosomes, but ignore sex chromosomes for summary statistic calculation. file: [154e2bdb29] check-in: [e000329aa8] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 79371 | |
|
2011-03-18
| ||
| 15:52 | qctool: ignore sex chromosomes for snp and sample stats. (Do not filter them out based on stats either). file: [83d9582994] check-in: [0b65246d04] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 79405 | |
|
2011-03-16
| ||
| 21:31 | qctool: add -quantile-normalise and -missing-code options file: [9c245cc6ab] check-in: [48ddc1d5b7] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 79409 | |
|
2011-03-14
| ||
| 15:30 | qctool: More work on VCF support. Files must have a GT field now. file: [44e3ca2749] check-in: [a95662f685] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 76587 | |
|
2011-03-10
| ||
| 13:32 | qctool: First working VCF file support. file: [4712e6cce8] check-in: [3c8aa058aa] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 75749 | |
|
2011-03-09
| ||
| 13:23 | qctool: fix SNP dictionary loading problem file: [1fc84f86b3] check-in: [a0fd42a6ea] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 75542 | |
| 13:10 | qctool: implement -assume-chromosome option file: [f12d12f8ae] check-in: [37c61e209c] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 75455 | |
|
2011-03-01
| ||
| 15:48 | qctool: implement -test option which performs a frequentist case-control test on the given phenotype or phenotypes. file: [7f01ae0a62] check-in: [cf66603682] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 75072 | |
| 09:41 | qctool: Add hooks for association test. Output all phenotypes in PED file, dont make user specify. file: [3f2c986d9e] check-in: [b71fc11d87] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 75073 | |
|
2011-02-28
| ||
| 10:01 | fix small bug in qctool optoins file: [d9d583ab29] check-in: [eb631fe4fc] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 74904 | |
| 09:59 | Allow PED file to handle several phenotypes. file: [9a4a6dc1b9] check-in: [835f2ba71a] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 74903 | |
|
2011-02-24
| ||
| 16:37 | qctool: read pedigrees and write ped files using -ip/-op/-phenotype. file: [856462a493] check-in: [ec8389ddd7] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 75472 | |
|
2011-02-22
| ||
| 22:08 | qctool: rename some options. file: [04ebc2b8eb] check-in: [d02ddf7305] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 73339 | |
| 21:41 | qctool: always write a sample file if -os is given. file: [1de04a6f64] check-in: [58fe8aa982] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 73217 | |
|
2011-02-21
| ||
| 17:25 | Fix bugs in Affy strand file reading and SNP comparison file: [3629d914fe] check-in: [f6bf80a0c2] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 73217 | |
| 14:59 | qctool: fix bug in strand file loading. file: [23e8908ada] check-in: [3ca4ac692c] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 73064 | |
| 13:50 | gen-grep: make -help work. qctool: fix -excl-snps-matching and implement -snp-match-fields file: [5a2c87bf5a] check-in: [ab7a039664] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 73044 | |
|
2011-02-20
| ||
| 22:56 | qctool: fixes to strand file loading. Ignore lines that qctool cant understand. file: [b242da86ed] check-in: [c3790b8a8a] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 71777 | |
|
2011-02-18
| ||
| 15:28 | qctool: support strand alignment and matching alleles to the first cohort. file: [417645bd8a] check-in: [9efd1c486a] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 70824 | |
| 12:02 | qctool: be cleverer about detecting strand file columns. file: [15649c0185] check-in: [7ce27e9de8] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 69995 | |
| 11:26 | qctool: support -strand option. Load strand files and flip alleles where specified. file: [273bdd34f8] check-in: [788381db8e] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 70018 | |
|
2011-02-16
| ||
| 12:53 | Update to show hg revision at top of qctool output. file: [934675d815] check-in: [d5b16b0e07] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 65196 | |
| 10:13 | qctool: minor changes file: [5ab5bb5019] check-in: [0e8d5e48f4] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 65071 | |
|
2011-01-18
| ||
| 13:27 | qctool: option rationalisation. Apply exclusion lists in setup phase, not during processing. file: [01aaa1ea1c] check-in: [f556469289] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 65133 | |
|
2010-11-30
| ||
| 23:08 | qctool: load multiple sample files along with gen files. file: [f8a9c53d75] check-in: [d937c4f4fe] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 64153 | |
| 14:50 | qctool: minor bug fixes. file: [911af10937] check-in: [c72ab0c809] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 63263 | |
| 14:20 | Create rack implementation. Operate on several cohorts in parallel. (Or rather all together at once). file: [f05ace3035] check-in: [5d06b59934] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 63630 | |
| 10:45 | InputToOutputFilenameMapper: use genfile::wildcard. Slight rationalisation. I am getting rid of this anyway. file: [fbb4899a71] check-in: [c4f13a4815] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 63081 | |
|
2010-11-29
| ||
| 22:38 | qctool: get order of arguments right in load_snp_dictionary file: [cc2451678b] check-in: [ffda22a42b] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 61578 | |
| 17:25 | qctool: also support -incl-snps-matching file: [c3047e7f6f] check-in: [3ffb44464a] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 61578 | |
| 15:33 | qctool: replace -snpid-filter with -excl-snp-matches file: [df1c79f4e3] check-in: [5e03eebcdd] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 61025 | |
| 13:49 | qctool: initial implementation of -translate-snps option file: [5adcf9ea99] check-in: [6718a41b5b] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 61175 | |
|
2010-11-26
| ||
| 17:05 | qctool: filter SNPs before putting files in chain. file: [d290495328] check-in: [6cd3139033] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 58712 | |
| 09:48 | OptionProcessor: make sure empty argument list really is empty file: [87cdbdbfc3] check-in: [5b5700c5ff] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 58186 | |
| 09:31 | qctool: let relatotron do its work in multiple threads with -T option. file: [cc40684621] check-in: [1c9b83ad69] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 58183 | |
|
2010-11-25
| ||
| 14:41 | qctool: replace -snp-excl-list, -snp-incl-list with -excl-snpids -excl-rsids -incl-snpids -incl-rsids. Effect this filter first, in the context, not in the main qctool filtering section. file: [c9d9e84f07] check-in: [e2881e8739] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 57679 | |
| 13:07 | Relatotron: use -relatedness-sample-rows and -relatedness-sample-columns. Output only selected rows and columns. file: [d4dd4c9382] check-in: [3a33375c7a] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 56826 | |
| 12:46 | qctool: minor tweaks file: [ebfd793db2] check-in: [5942eb6bca] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 56514 | |
|
2010-11-24
| ||
| 23:35 | qctool: support rudimentary -relatedness-samples option file: [004c9016b7] check-in: [04f265f1df] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 56252 | |
|
2010-11-23
| ||
| 13:37 | Initial implementation of relatotron in qctool. file: [af21c56025] check-in: [cf6e80ad05] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 56266 | |
|
2010-11-22
| ||
| 13:38 | qctool: whoops, fix non-compiling bug from recent change. file: [99c630e42e] check-in: [ba694f9b43] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 56263 | |
| 12:34 | 1. qctool: make output snp exclusion lists have snpid, rsid, chromosome, position columns. 2. qctool: fix unwanted error check when using sample exclusion lists and outputting snp exclusion list. file: [431d9f4a25] check-in: [4c68670d7f] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 56273 | |
|
2010-11-19
| ||
| 23:30 | qctool: reworking to use appcontext/. Fix ensuing crashing bugs. file: [cb1a54be97] check-in: [10bfbc72f1] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 56172 | |
| 17:52 | qctool and others: update to use appcontext/. Compiles but probably does not run. file: [f8511c062e] check-in: [15fb654ac9] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 56314 | |
|
2010-11-18
| ||
| 17:09 | qctool: slight rename of vriables file: [932c668ccd] check-in: [127e1dbb89] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 53675 | |
| 14:39 | qctool: move QCToolProcessor->QCTool. Rework by making QCTool a client of a genfile::SNPDataSourceProcessor. file: [5d0072e52e] check-in: [01015b5c55] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 53639 | |
|
2010-11-17
| ||
| 17:33 | qctool et al: upgrade to most recent version of genfile library. file: [952e8a1418] check-in: [9eeeec04e2] user: gavin.band@well.ox.ac.uk branch: origin/release-1.1, size: 53483 | |
|
2010-11-01
| ||
| 22:33 | Add -missing-call-rate filter for missing_calls file: [9b91699103] check-in: [7f42a8c23e] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 53486 | |
| 21:44 | qctool: add missing_calls statistic. file: [5ddcad228f] check-in: [d68139af5f] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 53082 | |
|
2010-10-26
| ||
| 15:09 | Added entropy and hw_entropy statistics. Fix to mach_r2 statistics. file: [f74991b525] check-in: [5ec89a6d9f] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 53067 | |
| 13:37 | qctool: Add mach_r2 and filled_ and scaled_ variants file: [739828165a] check-in: [156507c0c8] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 53016 | |
| 11:06 | qctool: whoops, fix snp-stats-columns default value. file: [103fe7aa23] check-in: [ce73110ec8] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 52974 | |
| 10:58 | qctool: add filled_information and rescaled_information statistics, to work around problem with information and missing data. file: [c0c0c02860] check-in: [9aa56de0fe] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 53009 | |
|
2010-07-30
| ||
| 09:50 | qctool: make default output sample file <name>.qctool.sample as in WT course file: [49c86e1eba] check-in: [ab0bf9e440] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 52808 | |
| 08:47 | qctool: when no sample file is supplied, fix bug where output sample / sample-stats files begin with period. file: [183f252ec5] check-in: [cf3400d67f] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 52814 | |
| 08:36 | qctool: set up logging to screen even before options are processed. file: [df194a3625] check-in: [10c4b6aada] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 52613 | |
|
2010-07-26
| ||
| 15:16 | qctool: Allow file format conversion with -g -og -force file: [cb6448f931] check-in: [37457de104] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 52612 | |
|
2010-07-23
| ||
| 21:17 | qctool: Make default output sample file <file>.sample-stats.sample when using -sample-stats file: [02280bd0ab] check-in: [5459659d04] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 52251 | |
| 21:08 | qctool: minor tweak to sample output filename production code file: [ba6aa42b8e] check-in: [51791a7dd8] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 52182 | |
| 20:56 | qctool: get rid of -apply-excl-lists. Use common sense instead to know when to write output gen/sample files file: [2c61049f8d] check-in: [2918b4b6e9] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 52166 | |
|
2010-06-07
| ||
| 14:27 | qctool: fix line / column number in sample file error messages file: [98370e1c76] check-in: [07d93ee89c] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 52995 | |
| 13:40 | RFormatStatSink: add space before each comment line. qctool: Don't output comment line in stats file, as they might break existing pipelines. file: [3eb2522d91] check-in: [91665e0ec6] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 52987 | |
| 13:23 | qctool: write some descriptive text at top of stats files. file: [c56f9aa56c] check-in: [45a7a68e46] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 53193 | |
| 11:05 | qctool: catch genfile errors on sample reading. Fix default arguments in string_utils file: [bf7c9a4290] check-in: [7a114f4b7d] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 52857 | |
| 10:36 | qctool, SampleRow: use genfile::CohortIndividualSource to read sample files file: [0ad9166e2c] check-in: [fe45b1aef9] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 52554 | |
|
2010-05-20
| ||
| 22:29 | qctool: change qc-tool to qctool wherever it occured file: [beb374c0f0] check-in: [9d68a41269] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 53035 | |
|
2010-03-29
| ||
| 13:02 | genfile: Ported newer version from association-tools-dev file: [389d824e9b] check-in: [0560462274] user: gavin.band@well.ox.ac.uk branch: origin/release, size: 53040 | |
|
2009-10-01
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| 20:46 | Fix string_utils.cpp: to_upper(), to_lower(), which had the wrong adjustment applied! file: [5c9741a2cc] check-in: [c439c0f2d0] user: gav@gavin-bands-macbook-pro.local branch: origin/release, size: 53050 | |
| 20:26 | -sample-stats should not exclude -os file: [364bc64eb4] check-in: [c508cf50ad] user: gav@gavin-bands-macbook-pro.local branch: origin/release, size: 53015 | |
| 15:13 | qctool: Move exception handling into constructor to catch option processing exceptions. file: [4dd9fc1544] check-in: [d4ffc306af] user: gav@dhcp151.well.ox.ac.uk branch: origin/release, size: 53076 | |
| 09:58 | qctool: Clean up exclusion list handling. Make seperate option group for exclusion lists. file: [90b3777291] check-in: [25a16ea34a] user: gav@dhcp151.well.ox.ac.uk branch: origin/release, size: 53055 | |
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2009-09-30
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| 22:17 | qc-tool -> qctool. Implement a -write-sample-excl-list option and adjust option processing to allow its use. This resolves issue #1. file: [a879c34c62] check-in: [3644f7c76e] user: gav@gavin-bands-macbook-pro.local branch: origin/release, size: 51096 | |
| 13:09 | Added: Clean-up. Rename qc-tool to qctool. file: [ddc9ef23cb] check-in: [00307ab340] user: gav@dhcp151.well.ox.ac.uk branch: origin/release, size: 48341 | |