Code

Read from vcz#1

Code

Merged

Will-Tyler merged 28 commits intomainsgkit-dev/SAIGE-VCZ:mainfrom read-from-vczsgkit-dev/SAIGE-VCZ:read-from-vczCopy head branch name to clipboardOct 1, 2024

Commits

Commits on Sep 9, 2024

• Create genotype_100markers.vcz

  Will-Tyler

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  5c30bbd

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• Add vczFile option to step2 script

  Will-Tyler

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• Add vczFile to SPAGMMATtest

  Will-Tyler

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• Add vczFile parameter to setGenoInput and checkGenoInput

  Will-Tyler

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Commits on Sep 10, 2024

• Invert if-statement

  Will-Tyler

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  b6e91b5

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• Add VCZ case to SAIGE.Marker

  Will-Tyler

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• Add C++ code skeleton

  Will-Tyler

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Commits on Sep 12, 2024

• Setup tensorstore

  Will-Tyler

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Commits on Sep 14, 2024

• TensorStore working!

  Will-Tyler

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Commits on Sep 17, 2024

• Improve Makevars

  Will-Tyler

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Commits on Sep 18, 2024

• Add VCZ method implementations

  Will-Tyler

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• Use pimpl idiom to hide tensorstore

  Will-Tyler

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• Add debug flags in Makevars

  Will-Tyler

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  de35a62

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• Update r-base version

  Will-Tyler

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• Load utils library (helps debugging)

  Will-Tyler

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Commits on Sep 19, 2024

• Make build an order-only prereq

  Will-Tyler

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• Disable optimization in cmake

  Will-Tyler

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Commits on Sep 20, 2024

• Remove cmake verbose

  Will-Tyler

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• Code is reading with TS and terminating successfully

  Will-Tyler

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Commits on Sep 24, 2024

• Output with VCZ is similar to output with VCF

  Will-Tyler

  committed
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• Add ChunkCacher class

  Will-Tyler

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• Rechunk example VCZ file

  Will-Tyler

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• Implement chunk caching

  Will-Tyler

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• Update genotype_100markers.vcz

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  e5ac26f

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• Change build mode to release

  Will-Tyler

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Commits on Sep 27, 2024

• Improve CMakeLists.txt

  Will-Tyler

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Commits on Sep 28, 2024

• Make VCZ faster with pointer arithmetic

  Will-Tyler

  committed
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Commits on Sep 30, 2024

• Tidy up VCZ.cpp

  Will-Tyler

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  498f5c1

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