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CHANGELOG.md

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Changelog

0.8.6

  • Update dependencies
  • Include update from atglib to fix bug in GTF parsing of gene records

0.8.4.

  • Unpin serde, the issue from 0.8.3 has been fixed
  • Update other dependencies, fix security issue in dependencies

0.8.3.

0.8.0

  • Add QC-filter option
  • Add option to specify custom genetic codes
  • Allow using S3 objects for Fasta reference files (using S3Reader)
  • Switch to ATGLib 0.2.0
  • Switch to clap v4 and use Derive

0.7.0

  • Switch to ATGlib 0.1.4
  • Add spliceai ouput format

0.6.0

  • Switch to ATGlib 0.1.3
    • ncExons in feature-sequence for non-coding transcripts
    • Add QC module

0.5.1

  • Uncouple the lib from the CLI, make an extra atglib crate
  • Fix exon sorting to take the transcirpt orientation into account

0.5

  • Add exon numbers in GTF output
  • Refactor GTF parsing to improve performance
  • Add GenePredExt Reader and Writer
  • Add GenePred Writer
  • Remove chr prefixing during parsing of chromosomes/contigs
  • Improve docs
  • Add more integration tests

0.4

  • Support writing Fasta files
  • Support sequence output per feature
  • Improved error handling

0.3

  • Support writing bed files
  • Update CICD and proper release guidelines

0.2

  • Improve performance and memory usage
  • Remove unused GTF attributes fields
  • Improve logging

0.1

  • Inital release