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CHANGELOG.md

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Changelog

All notable changes to the PipeVal tool.

The format is based on Keep a Changelog.

This project adheres to Semantic Versioning.

[Unreleased]

Changed

  • Update pysam version to 0.22.1

[5.1.0] - 2024-07-08

Added

  • Add validation flowchart
  • Add support for unmapped BAM
  • Add additional MIME type for GZIP compressed files
  • Add support for checksum files formatted with any whitespace separator

[5.0.0] - 2024-02-16

Added

  • Validation skip functionality for checksums

[5.0.0-rc.3] - 2023-12-07

Added

  • Integrity test for compressed files

[5.0.0-rc.2] - 2023-12-06

Added

  • FASTQ validator

[5.0.0-rc.1] - 2023-11-22

Changed

  • Restructured CLI to have common main command pipeval

[4.0.0] - 2023-11-22

Added

  • Parallelize validation

[4.0.0-rc.2] - 2023-04-24

Changed

  • Resolve potential symlinks before validation

[4.0.0-rc.1] - 2023-04-11

Added

  • Add check for empty BAM files (valid header but no reads).
  • Add auto-build workflow to push image to uclahs-cds registry
  • Add repo source label to Dockerfile
  • Add check for existence of index file
  • Add references for VCFtools and Pysam in README
  • Unit tests for existing functions
  • Unit tests for main runner functions
  • Add separate checks for SAM and CRAM files
  • Compression validation and detection through python-magic

Changed

  • Make -t optional, default to file-input
  • Explicitly set Python version to 3.10
  • Split validation and checksum generation into different CLI commands
  • Re-organize functions
  • Change builder image to mambaforge in Dockerfile
  • Update README input tables and command examples
  • Re-structure README with details of current tool

Fixed

Removed

  • Remove deprecated parameter options from README
  • Remove inaccessible design doc link from README
  • Remove directory checking
  • Remove user-specified file type option

[3.0.0] - 2022-08-03

Updated

  • Updated bl-base to 1.1.0
  • Installed tools using mamba

Added

  • Add bldocker user and group to Dockerfile
  • Add support for mutliple input files

Changed

  • Convert module to Python CLI package; now runs directly from commandline with validate.
  • Single source package version from __init__.py
  • Use pysam instead of samtools in bam file validation.

Fixed

  • Add handling for valid file types whose validation is not yet implemented.

[2.1.6] - 2021-10-18

Changed

  • File type detection update to properly detect file type when filename contains multiple .

Fixed

  • Fixed bug with detecting fasta files