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Commits on Mar 26, 2018

• qctool: error message fix

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• HaplotypeFrequencyComponent: avoid short-cutting when computing stratified ld metrics

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Commits on Mar 20, 2018

• tests.txt: update to -rc9

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• Remove cruft code, add sync_with_stdio(false)

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• doc: update info on ld prior

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• wscript: bump to -rc9

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• HaplotypeFrequencyComponent: use a dirichlet(.25, .25, .25, .25) prior by default. Add -prior-ld-weight to allow setting prior weights

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• qctool: fix crashing bug on mismatching number of samples

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Commits on Mar 14, 2018

• bgen.hpp: fix clamping of 1 - sum to 0

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Commits on Feb 6, 2018

• options: update to include new bgen allowed precision option

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Commits on Feb 5, 2018

• Doc update for vcf streaming

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• Bump version to -rc8

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• Pull SNPDataSource.cpp from default branch, implement input from stdin for vcf

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• qctool -read-test: take more performant implementation from default branch

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• qctool: merge from default branch: implement -bgen-permitted-input-rounding-error, allow for streaming input of VCF, more performant bgen read implementation

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Commits on Jan 23, 2018

• Merged

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• VCFFormatSNPDataSource: work around gcc 5 C++ ABI exception bug

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Commits on Jan 22, 2018

• doc update for -threshold

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• Update tests for -threshhold -> -threshold change

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• -threshhold -> -threshold in option names

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Commits on Jan 12, 2018

• genfile::ToGP: output better debug

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• bgen: sync with bgen repo revision 706cfdb3eaaf

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Commits on Jan 8, 2018

• Remove -flat-file and -flat-table options, which are unused

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Commits on Dec 21, 2017

• Remove redundant SNPSummaryComponent code determing sample sex; now use -infer-ploidy-from instead

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• wscript: configure: look for blas, cblas, openblas libraries

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• GenFileSNPDataSink.cpp: fix message in a thrown error

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Commits on Dec 20, 2017

• pipeline: fix pybot invocation

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• pipeline: add an xUnit test report output

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Commits on Dec 19, 2017

• qctool: fix bug in -merge-in. Bump to -rc7

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• wscript: bump to rc7

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• qctool: factor out open_snp_data_sources() to be reuseable, use it in -compute-ld-with

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• SNPDataSourceChain: remove set_expected_ploidy()

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• ReorderingSNPDataSource: update to store data then output, fulfilling contract that it sends sample data in the original order, making it useable with all clients. Also, allow arbitrary sample mapp…

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• VCFFormatSNPDataSink: update to handle 'completely missing' samples

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• KinshipCoefficientComputer: use posterior estimate of frequency for sd

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