Kindel - 1.2.1

• Fixes crash for certain BAMs, reported by @sivico26 (https://github.com/bede/kindel/issues/25)

Scientific Software - Peer-reviewed - Python
Published by bede 6 months ago

Kindel - 1.2.0

• Fixes crashes with certain BAMs (#23 )
• Fixes coordinate system used in kindel plot. Coordinates now match alignment viewers and Samtools depth.
• Improved tests
• Updated usage notebook
• Minimum Python version is now 3.9 (was 3.8)

Scientific Software - Peer-reviewed - Python
Published by bede about 1 year ago

Kindel - 1.1.0

• Restores, tests kindel weights and kindel features subcommands
• Fully removes kindel variants subcommand
• Adds clip start and clip end frequencies to kindel weights

Scientific Software - Peer-reviewed - Python
Published by bede about 1 year ago

Kindel - 1.0.0

Main improvements - Significantly improved consensus calling accuracy around small deletions - Significantly improved consensus calling accuracy around large clip-dominant deletions in --realign mode for some alignments - Fixed issue with difflib.SequenceMatcher where identifying overlaps in clip-dominant regions could fail unexpectedly - Fixes related TypeError with --realign enabled (reported by @sivico26) - Faster installation and consensus generation

Other changes - Added support for Python versions up to 3.13, offering significant performance improvements - Minimum Python version increased from 3.6 to 3.8 - Replaced Biopython with dnaio for sequence IO - Testing improvements: - Expected consensus sequences now are validated by the test suite, guarding against regressions - Added clip-dominant test case helpfully shared by @sivico26 (#23) - Test suite now runs in CI with both newest and oldest supported Python versions - Moved to pyproject.toml with Flit build backend - Added Ruff pre-commit

Breaking changes - Removed: - kindel variants - Plotting functions other than kindel plot-clips (renamed in this release to kindel plot)

Please open an issue if this release causes problems or breaks your workflow.

Scientific Software - Peer-reviewed - Python
Published by bede about 1 year ago

Kindel - 0.4.4

• Python 3.8
• min_depth defaults to 1 in both CLI and Python API (CLI default was 2)
• Removes <unknown description> from generated fasta headers

Scientific Software - Peer-reviewed - Python
Published by bede over 5 years ago

Kindel - 0.4.3

• Fixes crash for reference sequences <100bp
• Counts SAM 1.4 CIGAR X records
• Changes to stdout report format

Scientific Software - Peer-reviewed - Python
Published by bede over 5 years ago

Kindel - 0.4.2

• Works with Minimap2 BAMs
• Tested against bacterial alignment (performance is poor; be warned)

Scientific Software - Peer-reviewed - Python
Published by bede over 6 years ago

Kindel - 0.4.1

Fixes SAM parsing regression in 0.4.0 (thanks to @mdshw5)

Scientific Software - Peer-reviewed - Python
Published by bede over 6 years ago

Kindel - 0.4.0

• Support for BAMs with more than one reference chromosome
  • Generates a consensus sequence for each reference contig with one or more primary alignments

Scientific Software - Peer-reviewed - Python
Published by bede over 6 years ago

Kindel - 0.3.0

• Basic documentation and JOSS paper
• Tidies up tabular output of weights()

Scientific Software - Peer-reviewed - Python
Published by bede over 8 years ago

Kindel - 0.2.0

• Refactored handling of consensus inference at clip-dominant regions
• Basic tests and CI

Scientific Software - Peer-reviewed - Python
Published by bede over 8 years ago

Kindel - 0.1.4

Reconciles substitutions and CIGAR specified indels

Scientific Software - Peer-reviewed - Python
Published by bede over 9 years ago