Code

feat: adding the annotaTR tool#226

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gymreklab merged 80 commits intomastergymrek-lab/TRTools:masterfrom annotaTRgymrek-lab/TRTools:annotaTRCopy head branch name to clipboardAug 23, 2024

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Commits

Commits on Aug 7, 2024

• adding initial annotatr tool

  

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• adding dosage fields to vcf output

  

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• draft dosage functions

  

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Commits on Aug 8, 2024

• add multiple outputs and add dslen to pvar

  

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• initial version of beagle annotation

  

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• add pgenlib as dependency, remove tensorqtl output for now

  

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Commits on Aug 9, 2024

• adding tests for dosages in tr harmonizer

  

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• drafting annotatr readme

  

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• updating annotatr docs

  

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• updating annotatr docs

  

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• adding first test of beagle type dosages

  

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Commits on Aug 10, 2024

• adding tests for beagle dosages

  

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• adding first annotatr tests

  

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• update cyvcf2 version to have num_records

  

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Commits on Aug 11, 2024

• adding outtype tests

  

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• added unit tests for annotaTR

  

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• annotatr fail if no operation

  

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• remove unnecessary vcfwriter function

  

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• adding documentation to annotatr functions

  

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• updating annotaTR readme

  

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• adding notes to callers documentation

  

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Commits on Aug 12, 2024

• updating pgenlib dependency version

  

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• update pgenlib version in dev-env

  

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• making annotatr test file smaller

  

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• further reducing file sizes

  

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• update pgenlib version in dev-env

  

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• updating cyvcf2 version

  

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• adding back modified large associatr files

  

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• adding missing docs file for annotatr

  

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• only count dup locus if both ref and alt the same

  

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• fix docs typos

  

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• more docs typo fixes

  

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• change how we access AP1

  

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Commits on Aug 13, 2024

• updating how AP1 and AP2 format fields accessed

  

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• updating how format is accessed in tests

  

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• updated missing docs file

  

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Commits on Aug 14, 2024

• adding more options for matching refpanel

  

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• typo in match option

  

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• don't load samples in ref panel

  

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• better warning for invalid pgen output

  

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• updating annotatr docs

  

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• add message about loading ref panel

  

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• adding debug option

  

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• updating how we trim alleles

  

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• don't sort alt alleles when getting locuskey

  

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• updating how we get variant ct for refpanel

  

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• updating variant count message

  

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• Merge branch 'master' into annotaTR

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• bug in psam output

  

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• Merge branch 'annotaTR' of https://github.com/gymrek-lab/TRTools into annotaTR

  

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Commits on Aug 15, 2024

• typo on readme - annotatr link pointed to prancstr

  

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• minor change to annotatr readme

  

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Commits on Aug 22, 2024

• Apply suggestions from code review

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• Apply suggestions from code review

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• Update doc/CALLERS.rst

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• Update doc/CALLERS.rst

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• Update doc/CALLERS.rst

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• Update trtools/utils/tests/test_trharmonizer.py

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• Update trtools/utils/tests/test_trharmonizer.py

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• Update pyproject.toml

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• adding poetry.lock file suggested from code review

  

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• make it clear annotatr requires bgzipped and indexed vcf

  

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• add test for beagle input but no refpanel specified

  

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• add type suggestion to GetDosages function

  

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• Update test/cmdline_tests.sh

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• input set for sample order rather than list

  

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• Merge branch 'annotaTR' of https://github.com/gymrek-lab/TRTools into annotaTR

  

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Commits on Aug 23, 2024

• remove numpy typing suggestion

  

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• added check to dosages for case of no samples to return None

  

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• expose pgen batch size

  

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• typos in batch size argparse

  

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• clean up checking input vcftype

  

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• update to checking vcftype

  

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• restore old beagle test files

  

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• minor changes to make pvars valid vcfs

  

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• add test for vcfs not zipped or indexed

  

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• adding file tests for annotatr

  

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• updated CEU subset unzip/index files to have variants

  

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• making unzipped example smaller

  

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• Update trtools/utils/tr_harmonizer.py

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