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TRGTdb#6

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ACEnglish wants to merge 102 commits intoPacificBiosciences:mainPacificBiosciences/trgt:mainfrom ACEnglish:mainCopy head branch name to clipboard

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Commits on Feb 3, 2023

• Starting wrapping

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• create command works

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• dna_decode compliment

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Commits on Feb 4, 2023

• code clean

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• logging

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• testing file formats

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• moving to parquet focus

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Commits on Feb 5, 2023

• progress

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Commits on Feb 8, 2023

• append prototype

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• initital test and clean

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• beginning refactor

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• working on structure

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• Merge branch 'feature/simplecreate' into develop

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Commits on Feb 9, 2023

• Allele change. Multi-sample

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• code clean

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• fixing sample name fetching

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• fix samp

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• turn off encoding

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• new query

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• setting dtypes and turning on encoding

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• in-code doc

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• Merge branch 'release/tdb_v0.1'

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Commits on Feb 10, 2023

• turning off sequence dtype

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• fixing monref query

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• beginning direct write to parquet.

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• pylint 10/10

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• playing with uint8 array

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• fixing develop

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• starting gtmerge query

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• Merge branch 'main' into develop

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• metadata query

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• consolidate bug fix

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• bug fixes and huge simplification

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• Sort gtmerge output

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• Merge branch 'release/tdb_v0.2'

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• Recovering sample_consolidator change and encoding

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• Merge branch 'release/tdb_v0.3'

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Commits on Feb 11, 2023

• query has output destination/type parameters

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• Using pyarrow

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• Merge branch 'release/tdb_v0.4'

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• speeding tdb reading

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• working with latest trgt vcfs

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• load filtering and programmatic queries

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• tutorial, importing queries, load_tdb fix

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• Merge branch 'develop'

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• Update tdb_tutorial.md

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• Update tdb_tutorial.md

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• Update tdb_tutorial.md

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Commits on Feb 12, 2023

• Update tdb_tutorial.md

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• Update tdb_tutorial.md

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• Update tdb_tutorial.md

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• Update tdb_tutorial.md

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• Update tdb_tutorial.md

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• query gtmerge bug

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Commits on Feb 13, 2023

• minor code clean

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• Merge branch 'develop'

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Commits on Feb 15, 2023

• updating requirements

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• Merge branch 'develop'

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Commits on Mar 18, 2023

• ac bugfix

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• Merge branch 'PacificBiosciences:main' into main

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Commits on Mar 29, 2023

• Adding AM to Sample

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• Merge branch 'main' of https://github.com/ACEnglish/trgt

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• correcting type casting

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• new methyl query

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• improving allele queries

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• expanding methyl query

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Commits on Mar 30, 2023

• variant_length query

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Commits on Mar 31, 2023

• cleaning log lines

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• create from tdb fix

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Commits on Apr 1, 2023

• searching for the bug

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• removing encoding allele_sequence

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Commits on Apr 2, 2023

• Update dbutils.py

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Commits on Apr 10, 2023

• Faster/fulller allele_cnts

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• optional index writing

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Commits on Apr 12, 2023

• Adding notebook, fixing methyl

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Commits on Apr 13, 2023

• Merge branch 'PacificBiosciences:main' into main

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• intermediate jaccard push

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• Merge branch 'main' of https://github.com/ACEnglish/trgt

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• Fixed comp

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• code cleaning and locus_ji query

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• removing jaccard debug and adding parameters

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• update gitignore

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• jaccard clean, add polymorphism score queries

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• adding by-seq AF filtering to polymorphism scores

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• Working on tutorials and queries

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Commits on Apr 14, 2023

• allele summary tutorial cleaning

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Commits on Apr 15, 2023

• Finishing allele summary tutorial

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Commits on Apr 16, 2023

• faster monref query

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Commits on Apr 24, 2023

• Adding new tutorial

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Commits on Apr 27, 2023

• updating CpG notebook

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Commits on Apr 28, 2023

• small changes

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Commits on May 5, 2023

• adding deid

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• optional sample shuffle in deid

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Commits on Jul 6, 2023

• Adding proband-only example notebook

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• removing unused imports

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• adding a summary plot

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Commits on Jul 7, 2023

• Setting AM to float

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• Updating LongExpansions

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• LongExpansions clean

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Commits on Jul 9, 2023

• AM float fix

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Commits on Oct 20, 2023

• fail on redundant samples during create

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• Merge branch 'main' of https://github.com/ACEnglish/trgt

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