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50 check-ins related to "master" plus check-in "2015-02-10 16:16:25" occurring around 2015-02-10 16:16:25.
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2015-03-03
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| 12:08 | RelatednessComponent: write sample files in csv format etc. if requested. Write full sample files when doing projections. Get projection names right. check-in: 0aa6da8de5 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 11:57 | RelatednessComputer::PCAProjector: use a shared, not unique ptr, to avoid a dangling reference check-in: ed7fe831e8 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 11:56 | RelatednessComponent: get the maf filter right in PCAProjector check-in: 8fc9104ac8 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 11:55 | RelatednessComponent: just use sample id_1, not both sample ids check-in: b49dc67ee2 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 11:55 | bingwa: only output max bf and max posterior if one exists check-in: 5b6b9a12a5 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 11:54 | genfile::DosageFileSNPDataSource: accomodate comment lines at top of file check-in: 8d6450a894 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 11:31 | bgen: fix bug in bgen format reading by putting total payload size before uncompressed size. This breaks the new bgen format. check-in: 940fcd2cff user: gavin.band@well.ox.ac.uk tags: master, trunk | |
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2015-03-02
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| 22:17 | qctool: make projection onto loadings work out. check-in: b30daceeeb user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 21:51 | qctool: allow -PCAs and -UDUT with -kinship. check-in: c4aa72cd8d user: gavin.band@well.ox.ac.uk tags: master, trunk | |
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2015-02-27
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| 23:40 | Fix bug in SampleFilteringSNPDataSource that prevented correct sampel counts. check-in: 9ae68ed4fd user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 16:46 | open.hapdb.R: open in read-only mode check-in: e84882bfa8 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
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2015-02-24
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| 14:58 | Merged check-in: fd4c17e496 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 14:43 | bingwa: allow -simple-prior models to have names. check-in: 24adf588e8 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 13:38 | DosageFileSNPDataSource.cpp: fix metadata check-in: 59fc67cd1c user: gavin.band@well.ox.ac.uk tags: master, trunk | |
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2015-02-23
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| 22:41 | BasicBGenFileSNPDataSink: add some comments check-in: a30e7ca9e0 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 22:40 | Merged check-in: 17a1d48cbd user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 22:38 | DosageFileSNPDataSource: fix this up for order type. check-in: cef5b885e8 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 22:38 | bingwa: use ApproximateBayesianMetaAnalysis again check-in: 891ac6ccd8 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 22:01 | genfile::bgen: fix sample identifier block. check-in: 91982bb263 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 14:34 | genfile::BGenFileSNPDataSink: do write the sample information block. check-in: 5c9c483575 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 14:33 | Remove dead code in RelatednessComponent check-in: adf33610b6 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 13:14 | ModifiedNewtonRaphson.hpp: update code comments check-in: 97b474b161 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
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2015-02-18
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| 13:40 | BGenFileSNPDataSink: attempt to write the correct offset. check-in: 264f3a5c7c user: gavin.band@well.ox.ac.uk tags: master, trunk | |
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2015-02-11
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| 00:21 | RiskScoreComputation: allow extra columns after effect size ones. check-in: 58692c7da3 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
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2015-02-10
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| 16:16 | KinshipCoefficientComputer: turn on output again. check-in: 167be3afd0 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 10:14 | inthinnerator: don't write log file by default check-in: 42e58fae18 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
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2015-02-08
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| 23:12 | Work to test integration::ModifiedCholesky check-in: 097f029953 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 23:12 | bingwa: name frequentist columns FixedEffectMetaAnalysis again. check-in: 21052c7119 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 23:11 | statfile::DelimitedStatSink: put quotes around strings containing the delimiter check-in: f9b81fa796 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
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2015-02-03
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| 23:22 | KinshipCoefficientComputer: Added a comment about multi-lookup tables check-in: 1cc7853ca7 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 22:50 | KinshipCoefficientComputer: Fix initialisation of lookup tables check-in: 14242958f6 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 22:24 | qctool: -kinship:use four lookup tables, not one check-in: da249f8ab0 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 21:17 | KinshipCoefficientComputer: print computation properties. check-in: 37440c22a2 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 21:09 | Make -kinship use new fast computation by default. check-in: e6296e95a1 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 17:36 | KinshipCoefficientComputer.cpp: add get_matrix_lower_diagonal_strip_tiling which tiles by sample. check-in: 0d59c5f1a6 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 17:36 | CallReader.hpp: add Types.hpp it depends on check-in: 4d9241c888 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 16:38 | KinshipCoefficientComputer: make sure and pass parameters by reference in bind() check-in: 05b0ad5b95 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 15:25 | qctool: implement -fast-kinship, which is faster than -kinship and uses a lookup table. check-in: 016281d91e user: gavin.band@well.ox.ac.uk tags: master, trunk | |
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2015-01-31
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| 10:44 | KinshipCoefficientComputer: slight refactor check-in: f1f0e47732 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 10:43 | HaplotypeFrequencyComponent: remove unwanted get. check-in: b830462a30 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
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2015-01-29
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| 21:54 | genfile:: gen format, speed up reading by sharing buffer. check-in: d5fcc970fb user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 21:03 | BGenFileSNPDataSource.cpp: get metadata right. check-in: 14677a9fba user: gavin.band@well.ox.ac.uk tags: master, trunk | |
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2015-01-28
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| 21:18 | genfile::bgen: fix bug where EOF is not correctly recognised check-in: 14873335e2 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 15:56 | Fix bug in genfile::vcf::CallReader::set_order_type() check-in: 233cd82ec7 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 15:30 | Fix VCF output format. Fix metadata when threshholding genotype calls check-in: ded538b5d1 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 14:46 | genfile::OffsetFlippedAlleleSetter: intercept set_number_of_samples appropriately check-in: 323bccfab9 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 14:45 | Make Gen file source get Type right in metadata. check-in: 54327e7de9 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 12:01 | statfile::SNPDataSourceAdapter: make suer and support inthinnerator output files with alternate_ids in check-in: 68180de9ed user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 11:45 | statfile_utils.cpp: only peek at file if it actually is possible. check-in: d91572b1e2 user: gavin.band@well.ox.ac.uk tags: master, trunk | |
| 11:45 | ImputeHaplotypesSNPDataSource.cpp: get metadata right check-in: d94c403a53 user: gavin.band@well.ox.ac.uk tags: master, trunk | |