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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, and this project adheres to Semantic Versioning.

[v2.1.5]

Fixed

  • Capitalised modified base tags additionally removed from monomers if no modified bases for a monomer.

[v2.1.4]

Fixed

  • MN tag is now amended when monomer records are created.

Added

  • All potential minimap2 SAM tags are removed from input records before processing.

[v2.1.3]

Fixed

  • Output ML tag is now correctly a byte array tag.

[v2.1.2]

Added

  • Full example to README.

Changed

  • The command-line option --stdout now behaves as a more traditional boolean option.

Fixed

  • A regression whereby mv tag in BAM was not being dropped.

[v2.1.1]

Changed

  • Updated requirements of conda package.

[v2.1.0]

Added

  • Option max_monomers to digest command to remove reads containing more than max monomers. Excluded reads can be output to second BAM file and/or a text file of read names.

Removed

  • --max_reads argument from digest command, as it was non-functional.

[v2.0.6]

Fixed

  • Chromunity parquet file output contains columns required for use with Chromunity.

[v2.0.5]

Changed

  • Updated LICENSE to Oxford Nanopore Technologies PLC. Public License Version 1.0.

[v2.0.4]

Fixed

  • Chromunity writer group colinear output error.
  • Modified bases digest step and associated tests.

[v2.0.3]

Added

  • Digest sub command will accept stdin input.

[v2.0.2]

Added

  • Threads parameter to chunk_bam sub command.

[v2.0.1]

Fixed

  • Annotate sub command check of existing files.

[v2.0.0]

Added

  • Stdout options for annotate and digest sub commands.

Changed

  • Simplified logging for easier parsing.
  • Rewrote CLI, removing utils and keeping only those programs which are used.
  • Parse bam subcommand renamed annotate.

Removed

  • A lot of code and dependencies.

[v1.0.0]

Changed

  • Tidy up for release as a conda package in the EPI2MELabs channel

[v0.7.2]

Fixed

  • digest: don't strip mod base tags by default

[v0.7.1]

Added

  • create-chunked-ubam: break an unaligned bam into chunks

[v0.7.0]

Added

  • bam: add PG tag to bam files produced
  • export: add separate export subcommand
  • paired-end-export: enable filtering paired end read export to cis only and distance bounds
  • chromunity: add option to merge fragments colinear in the read and genome into a single 'monomer'
  • cli.py: add option to remove SAM tags from input, rename and move subcommands
  • digest: move digest to top-level command, add option to remove sam tags from output
  • aligns.py: add functions to group alignments colinear in the genome

Fixed

  • model.py: fix mixed up sam tags

Changed

  • remove kw_only from dataclass (requires python 3.10 or higher)
  • overlaps.py: remove fragment overlap code
  • dataclasses: replace attrs uses with dataclasses
  • mappy: remove genome index and mappy uses

[v0.6.0]

Added

  • io.py: write basic summary stats in json format
  • io.py: write a chromunity-compatible parquet file

Fixed

  • model.py: use read start,end coords as monomer id
  • Snakefile: fix integration tests

[v0.5.1]

Fixed

  • aligns.py: fix bug caused by change in lru_cache signature

Changed

  • sam_tags.py: rename to sam_utils to reflect broader functoin
  • utils.py: remove utils.py put functionaliy into io and sam_tags
  • sam_tags.py: move sam tag processing to separate module
  • model.py: make pore-s-specific tags into global settings

[v0.5.0]

Fixed

  • variants.py: remove partial phasing code
  • testing.py: fix phased vcf generation

[v0.4.0]

Changed

  • model.py: set paired end fields and add walk metadata
  • model.py: downgrade mm tags to work with pysam, ease roundtrip of tag data
  • cli.py: analyse the first n reads

Fixed

  • hatch.toml: fix type

[0.3.0]

Fixed

  • model.py: handle case where read is 1-base long and has '*' as quak

Changed

  • refactor model.py

[0.2.0]

Added

  • aligns.py: Further annotation of alignments
  • aligns.py: extract pairwise alignments
  • aligns.py: sort alignments by concatemer_index
  • cli.py: add cli tool to generate test data
  • align.py: group algnments by concatemer id
  • porec: refactor to use generators to avoid memory issues
  • utils.py: code to handle sam flags
  • io.py: write aligments to sorted bam
  • log.py: remove loguru dependency add remora-inspired logging setup
  • map.py: find fragment overlaps for alignments
  • map.py: add data structure to hold alignments for a concatemer
  • index.py: move indexing code to separate file
  • test_digest: initial implementation of virtual digest
  • Initial-commit: iniital commit

Fixed

  • monomers.py: fix edge case for empty cuts
  • pyproject.toml: fix broken toml

Changed

  • pyproject.toml: remove testw command, can't get it to work
  • model.py: move some method logic to functions
  • map.py: add multithreaded alignment
  • cli.py: update mapping cli
  • map.py: move test code into place
  • digest.py: use filecollection to manage multiple output
  • digest.py: refactor to support mapping
  • digest.py: dataclass and pandera schema for digest
  • digest.py: move functions out of test code
  • pyscaffold: remove old pyscaffold files