Skip to content

Latest commit

 

History

History
99 lines (85 loc) · 3.9 KB

CHANGELOG.md

File metadata and controls

99 lines (85 loc) · 3.9 KB
Raw

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.

[v0.3.16] - 2024-09-04

Added

  • Read mean Qscore and alignment flag added to stats_from_bam output.
  • Add option to filter_bam to keep unmapped reads that pass (non-alignment) filters.
  • Enable multithreaded bam file reading and writing in filter_bam.

Changed

  • Pin numpy<2.0.

[v0.3.15] - 2023-12-18

Added

  • mini_align can take a bam as input and optionally retain all or subset of bam tags.

Changed

  • Drop porechop dependency from pypi package due to blocking package uploads. Add warning to the user if porechop is called by mini_assemble but does not exist.

[v0.3.14] - 2023-10-25

Changed

  • subsample_bam and coverage_from_bam now have unified read filtering options and logic.

Added

  • filter_bam to filter a bam with the same logic used in subsample_bam.

Fixed

  • subsample_bam was previously subsampling proportionally before filtering resulting in lower than expected depth.

[v0.3.13] - 2023-06-23

Changed

  • subsample_bam: --force_low_coverage saves contigs with coverage below the target
  • subsample_bam: --force_non_primary saves multimapping for the subsampled reads
  • coverage_from_bam: --primary_only considers only primary reads when computing the depth
  • bedtools: upgraded to v2.31
  • porechop: switched to using Artic version

Added

  • Option -C for mini_align to copy fastx comments into bam tags

Fixed

  • Minor compatibility fixes to support pandas>=2.0

[v0.3.12] - 2023-02-09

Changed

  • subsample_bam: --quality filtering now uses mean error probability, not mean of quality scores as previously.
  • subsample_bam: enable filtering for proportional subsampling.

[v0.3.11] - 2022-11-16

Fixed

  • Fix crashes in subsample_bam with alignment filtering and common_errors_from_bam
  • assess_assembly -H uses correct output directory.
  • Handling of comments in bed files.

Changed

  • Added Q(sub) to summary output.
  • Ported bed file handling from intervaltrees to ncls, speeding up assessment and multithreading efficiency.

Added

[v0.3.10] - 2022-02-22

Fixed

  • stats_from_bam: handle cigar strings using = and X instead of M.

Changed

  • Include mapping quality in stats_from_bam output.

Added

  • Handling of LRA bams in which NM tag is number of matches rather than edit distance.
  • Added an option (-y) to assess_assembly and mini_align to include supplementary alignments.
  • Added an option (-d) to mini_align and assess_assembly to select minimap2 alignment preset.
  • Added accumulation of errors over a number of chunks (-a option in summary_from_stats and assess_assembly) to get better stats.
  • Use -L option for minimap2.
  • Updated versions of minimap2, samtools, bcftools, bedtools, seqkit in Makefile to the most recent ones.

[v0.3.9] - 2021-08-18

Fixed

  • Reduced memory consumption of catalogue_errors.
  • fast_convert qa now properly outputs a fasta file
  • Fixed long_fastx --others option
  • Fixed split_fastx fastq output

Added

  • assess_homopolymers can use multiple threads

[v0.3.8] - 2021-06-22

Changed

  • Install paftools.js from minimap2 and k8

[v0.3.7] - 2021-05-10

Changed

  • Speed improvements to several benchmarking and analysis scripts

Fixed

  • Quoted all variables in mini_align to handle spaces in inputs.

[v0.3.6] - 2020-02-17

Changed

  • stats_from_bam no longer throws exception when no alignments have been proceseed.

Added

  • coverage_from_bam now has a --one_file option to better specify the output in the common usage.

[v0.3.5] - 2020-02-01

Removed

  • Python 3.5 support

Added

  • Python >3.6 support