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Changelog.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog,

[Unreleased]

  • Make genbank file with pfam annotation: desc field has format "tax:viral||anno:XXXX"
  • Check "suspicious" words in each contig: methyltransferase, epimerase, endonuclease
  • Mark short jobs as local_rules to optimaize for virsorter run --cluster mode
  • Add "all" in --include-groups
  • Change initial slide window to gene number based (4 genes) from bp size; apply the minimal prophage size at the end.

[2.2.4] - 2022-01-18

  • Fix issues with numpy v1.24 by limiting numpy version <1.24
  • Change "singularity" to "apptainer" in README
  • Add "PROVIRUS_MIN_HALLMARK_CNT" in template-config-original.yaml for tuning prophage search in provirus.py
  • Add new cols: "final_max_score_group" and "final_max_score" in final-viral-boundary.tsv to be consistent with "max_score_group" and "max_score" in final-viral-score.tsv
  • Remove records in final-viral-boundary.tsv but not in final-viral-score.tsv

[2.2.3] - 2021-04-20

  • Fix --seqname-suffix-off regex issues
  • Fix issues with pandas v1.3.0
  • Add email option (virsorter2 at gmail) for bug report

[2.2.2] - 2021-04-20

  • Fix bug with --seqname-suffix-off causing error with DRAMv

[2.2.1] - 2021-03-31

  • Fix minor bugs

[2.2] - 2021-03-30

  • Add --viral-gene-enrich-off option
  • Add --seqname-suffix-off option
  • Change default --include-groups from all groups to dsDNAphage and ssDNA
  • Add FAQ, viral identification SOP link in README

[2.1] - 2021-01-15

Added

  • Add --keep-original-seq option
  • Add --high-confidence-only option
  • Add --exclude-lt2gene option

Changed

  • Remove more itermediate files by default
  • Change HMMER3.3.1 to HMMER3.3; HMMER3.3.1 throws seg fault with low complexity sequences

[2.0] - 2020-12-01

Added

  • Add --viral-gene-required
  • Add --hallmark-required
  • Add --hallmark-required-on-short
  • Add --prep-for-dramv
  • Add --label in virsorter run to allow adding prefix to output files
  • Add shape to boundry file

Changed

  • Apply length prefilter to provirus.py; skip all seqs length < min(3000, MIN_GENOME_SIZE)
  • Limit max file splits to 1000

[2.0.beta] - 2020-06-19

Added

  • Make score table for trimmed viral seqs after provirus extraction
  • Add length to score table
  • Add subcommand virsorter train-feature and virsorter train-model for training customized classifiers of new viral groups, virsorter config for change configurations

[2.0.alpha] - 2020-06-07

Added

  • First release