v0.5.0

What's Changed

Core leviosam2 program updates

• Calculates the ref length of mate read using "MC:Z" when available by @milkschen in #67
• Corner case handling by @milkschen in #69
• Consistency check between chain target length and FAI file when indexing by @milkschen in #73
• Allow using multiple threads to (de)compress hts files by @milkschen in #74
• leviosam_utils refactor by @milkschen in #75
• Commit logic improvements by @milkschen in #76

Workflow updates

• CRAM support in the python workflow by @milkschen in #66
• Fix a typo in the Python workflow by @milkschen in #77
• use store_true for --use_preset by @milkschen in #79

Repo updates

• Use matrix in GitHub actions by @milkschen in #61
• Update README.md by @milkschen in #62
• Non-functional readability and testing improvements by @milkschen in #65
• Action update by @milkschen in #81
• Bump version to v0.5.0 by @milkschen in #80

Full Changelog: v0.4.2...v0.5.0

v0.4.2

Mostly python workflow bug fixes

What's Changed

• Minor changes: formatting and logging by @milkschen in #55
• Annotation workflow update by @milkschen in #56
• More consistent formatting by @milkschen in #57
• Workflow update by @milkschen in #58
• Version update (v0.4.2) by @milkschen in #59

Full Changelog: v0.4.1...v0.4.2

v0.4.1

This release includes no functional changes. It is intended for registering a DOI using Zenodo.

What's Changed

• Update README.md by @milkschen in #54

Full Changelog: v0.4.0...v0.4.1

v0.4.0

Highlights

• Arm64 support
• Ultima Genomics alignment tags
• Python-based workflow
• Erase source MAPQ information if a read is not liftable (new default value)

What's Changed

• Create integration-test.yml by @milkschen in #30
• Docker update by @milkschen in #31
• Reconcile random seed by @milkschen in #32
• Workflow improvement: support unaligned FASTQ inputs by @milkschen in #36
• Dark logo by @milkschen in #37
• Logi minor update by @milkschen in #38
• Integrate strobealign in the workflow by @milkschen in #39
• Add support for ARM architecture by @ch4rr0 in #43
• readme update by @milkschen in #44
• Add instruction to build leviosam2 with arm64 by @milkschen in #45
• Including htslib 1.17 in the tests by @milkschen in #46
• Workflow: adding strobealign by @milkschen in #48
• Use black for Python; python-based workflow (beta) by @milkschen in #42
• Prep for v0.4.0 by @milkschen in #49
• Erase MAPQ for alignments set to unmapped by @milkschen in #50
• Update cmake badge by @milkschen in #51
• Ultimate genomics BAM tags by @milkschen in #52
• Update Python-based workflow by @milkschen in #53

New Contributors

• @ch4rr0 made their first contribution in #43

Full Changelog: v0.3.0...v0.4.0

v0.3.0

Summary

• Improved long-read lift-over
• Now supports more flexible BED intersection logic -- adjusting -B <value> to decide the fraction/size of overlaps required for an read-interval intersection
• Workflow enhancements (using samtools merge)

What's Changed

• Fix for #18 by @jdidion in #19
• Fix typo for GitHub actions by @milkschen in #23
• Prep for the v0.3.0 release by @milkschen in #24
• Realign and CIGAR fixes for long reads by @milkschen in #22
• Formatting by @milkschen in #25
• Bed processing improvements by @milkschen in #26
• gitignore update by @milkschen in #27
• Fixes by @milkschen in #28
• Fix workflow by @milkschen in #29

New Contributors

• @jdidion made their first contribution in #19

Full Changelog: v0.2.2...v0.3.0

v0.2.2

Major changes

• [new feature] Support lifting over ONT alignments
• [new feature] Support input alignments using the extended cigar format (using X= instead of M). Output files still use regular CIGAR
• [bug fixed] Now correctly lifts alignments overlapping gaps in inverted chain regions

Minor changes

• [improvement] Error message improvement #14
• [improvement] CMakeLists improvement

New Contributors

• @sujunhao
• @maxrossi91
• @zhemingfan

Full Changelog: v0.2.1...v0.2.2

v0.2.1 release

• workflow update
• leviosam.cpp update: now skips re-alignment if -x is empty

v0.2.0 release

• Document updates
• LevioSAM2 pipeline updates

v0.1.0 release

Update README.md