v0.3.4

Minor release

• upgrade to racon v1.4.13.
• --summary_only option to coverage_from_bam.
• stats_from_bam.py made faster.
• various changes to python package requirements.

v0.3.3

Minor release

• expose minimap2 alignment parameters in mini_align.
• stats_from_bam now works on unsorted bams.

v0.3.2

• Minor release with a couple of new command line utilities;
• tag_bam to add tags to a bam.
• reverse_bed to convert coordinates in a bed file to coordinates in the reverse sequence.
• install bgzip and tabix into the venv.

v0.3.0

• General tidy up.
• Removed several troublesome dependencies.
• Quite a few general tools added, see documentation.

v0.2.5

• Allow -T option with -b in assess_assembly #32
• Allow force creation of minimap index in mini_align nanoporetech/medaka#85

v0.2.4

Minor patch release

• Numerous minor tweaks

v0.2.2

CI/CD release

• Build and push python package to pypi

v0.2.1

• Adds --bed option to stats_from_sam for calculating statistics fore given regions.

v0.2.0

• New mini_assemble functionality:
  • option to correct specified depth of reads (not simply proportion of reads).
  • compress intermediates, and optionally delete.
• New options to subsample_from_bam:
  • simple proportional sampling.
  • quality, accuracy, and read coverage filters.
• mini_align filters to primary alignments by default.
• Remove many git submodules and simply use github release artifacts.
• Add a make target for building a conda environment.

v0.1.12

• Improvements and warnings in mini_assemble workflow
  • Skip some needless format conversions
  • Changes to read correction
• Changes to subsample_bam
  • Output a bam
  • change to faster sampling method