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Commits on Dec 19, 2017

• ReorderingCohortIndividualSource: UPdate comment

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• genfile:SNPDataSource classes: remove set_expected_ploidy()

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• SNPDataSource: remove set_expected_ploidy()

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• BGenFileSNPDataSink.cpp: remove cruft

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• metro: add an improved comment

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• release: add test data for -compute-ld-with

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• -compute-ld-with: update to handle phased, unphased, and haploid genotypes.

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Commits on Dec 18, 2017

• bgen: update to handle completely missing samples

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• VariableInSetSampleFilter: update implementation to use a std::map, as it was sloooow

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Commits on Dec 15, 2017

• ToGP.hpp: fix debug statement

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Commits on Nov 9, 2017

• Doc update: fix menu header on two pages, fix computing_pcs page

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Commits on Nov 3, 2017

• SNPSummaryComponent: update for -infer-ploidy-from: get ploidy directly from genotype source, not from sample sex

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• tests.txt: add test for -merge-in targetting bgen

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• Added merge1_merged_merge2 for bgen merge test

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• genfile::SampleMappingSNPDataSource: correctly call finalise(), resolving issues with bgen and -merge-in

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• Minor doc updates

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Commits on Nov 1, 2017

• test updates: test bed annotation

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• Doc updates

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• Doc updates

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• doc updates

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• README.md: add acknowledgements

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• Disable avx and sse2 again

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Commits on Oct 31, 2017

• Doc updates

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Commits on Oct 26, 2017

• Make ploidy inference test work again, revert change to test.gen that breaks bgen test

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• Merge build / test changes from default

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• merged

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• SNPSummaryComponent: fix option description for -snp-stats

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• wscript: bump to 2.0-rc6

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• qcdb::DBOutputter: revert change that matches NULL chromosomes in Vairant table, as this is a performance regression.

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• genfile: Implement PloidyConvertingSNPDataSource, qctool -infer-ploidy-from

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Commits on Oct 6, 2017

• Merged from beta branch

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• Merged

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• Implement -reorder for all output types. Test for it.

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• MergingSNPDataSource.cpp: remove unwanted print

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• Add -help documentation for -reorder

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