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Rc vs 1365 hatcher testing parquet#8845

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RoriCremer wants to merge 42 commits intoah_var_storebroadinstitute/gatk:ah_var_storefrom rc-vs-1365-hatcher_testing_parquetbroadinstitute/gatk:rc-vs-1365-hatcher_testing_parquetCopy head branch name to clipboard

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Commits

Commits on Oct 11, 2023

• Funcotator Update for Datasource Release V1.8 (#8512)

  jamesemery

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  d40a485

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• Fixed Funcotator VCF output renderer to correctly preserve B37 contig names on output for B37 aligned files (#8539)

  jamesemery

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  423d106

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Commits on Nov 3, 2023

• Fix for events not in minimal representation (#8567)

  meganshand

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  2900e01

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Commits on Nov 13, 2023

• Ultima.flow annotations.fix (#8442)

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  dror27

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  683eaa8

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• Removes unnecessary and buggy validation check (#8580)

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  ilyasoifer

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  e6e4dea

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Commits on Nov 14, 2023

• Update our HTSJDK dependency to 4.0.2 (#8584)

  droazen

  authored
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Commits on Nov 15, 2023

• Update picard to 3.1.1 (#8585)

  lbergelson

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Commits on Nov 26, 2023

• Add option to AnalyzeSaturationMutagenesis to keep disjoint mates (#8557)

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  odcambc

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Commits on Nov 28, 2023

• New/Updated Flow Based Read tools (#8579)

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  dror27

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Commits on Dec 6, 2023

• GroundTruthScorer doc update (#8597)

  dror27

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  e37b344

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Commits on Dec 8, 2023

• Add a native GATK implementation for 2bit references, and remove the dependency on the ADAM library (#8606)

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  droazen

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  bf24519

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• Update dependencies to address security vulnerabilities, and add a security scanner to build.gradle (#8607)

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  droazen

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Commits on Dec 9, 2023

• Update http-nio and wire its new settings (#8611)

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  lbergelson

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  3b8b5bf

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• PrintFileDiagnostics for cram, crai and bai. (#8577)

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  cmnbroad

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• Allow GenomicsDBImport to connect to az:// files without interference (#8438)

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  3 peopleauthored
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Commits on Dec 11, 2023

• Disable line-by-line codecov comments (#8613)

  droazen

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• Support for custom ploidy regions in HaplotypeCaller (#8609)

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  3 peopleauthored
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Commits on Dec 12, 2023

• Update the GATK base image to a newer LTS ubuntu release (#8610)

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  droazen

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Commits on Dec 13, 2023

• build_docker_remote: add ability to specify the RELEASE arg to the cloud-based docker build, and add a release script (#8247)

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  droazen

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  75f5104

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• Update to htsjdk 4.1.0 (#8620)

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  lbergelson

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  23c8071

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• Fix the Spark version in the GATK jar manifest, and used the right constant in build.gradle (#8625)

  droazen

  authored
  70ee553

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• Update http-nio to 1.1.0 which implements Path.resolve() methods (#8626)

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  lbergelson

  authored
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Commits on Dec 14, 2023

• Fix GT header in PostprocessGermlineCNVCalls's --output-genotyped-intervals output (#8621)

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  jmarshall

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  fd873e9

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• Output the new image name at the end of a successful cloud docker build (#8627)

  droazen

  authored
  39cfbba

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• Reduce SVConcordance memory footprint (#8623)

  mwalker174

  authored
  b68fadc

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Commits on Jan 23, 2024

• Rewrite complex SV functional annotation in SVAnnotate (#8516)

  epiercehoffman

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Commits on Jan 26, 2024

• Improvements to Mutect2's Permutect training data mode (#8663)

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  davidbenjamin

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  2d50cf8

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Commits on Jan 30, 2024

• normal artifact lod is now defined without the extra minus sign (#8668)

  davidbenjamin

  authored
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Commits on Feb 7, 2024

• Parameterize the logging frequency for ProgressLogger in GatherVcfsCloud. (#8662)

  gbggrant

  authored
  bbc028b

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Commits on Feb 15, 2024

• Handle CTX_INV subtype in SVAnnotate (#8693)

  epiercehoffman

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Commits on Mar 5, 2024

• manually merging build.gradle

  koncheto-broad

  committed
  e8f71e4

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• updating from master

  koncheto-broad

  committed
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• updating from master

  koncheto-broad

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• Updating org.apache.commons package change to get the branch building

  koncheto-broad

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Commits on Mar 12, 2024

• Messy, but functionally converting a local gvcf to a parquet file output

  koncheto-broad

  committed
  4501d90

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• Cleaning it up a tad

  koncheto-broad

  committed
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Commits on Mar 19, 2024

• non-compatible tweaks to ingestion to write our parquet files

  koncheto-broad

  committed
  dc68776

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Commits on Mar 20, 2024

• small update

  koncheto-broad

  committed
  bd9b766

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• finally getting the parquet copying part sorted out

  koncheto-broad

  committed
  b1b7577

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• suffering a file name clash and overriding the same file. Changing to make file names unique

  koncheto-broad

  committed
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• suffering a file name clash and overriding the same file. Changing to make file names unique

  koncheto-broad

  committed
  7a9d105

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Commits on Jun 26, 2024

• add reference and header parquet writers

  RoriCremer

  committed
  e852dcf

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