v5.2.1 release

Fix an issue for conda

v5.2 release (version naming system updated)

What's Changed

• Bed and vcf by @milkschen in #18
• Update genomic annotations by @milkschen in #19
• Integrate more genomic annotations by @milkschen in #20
• Dev by @milkschen in #22
• Ksw by @milkschen in #24

Full Changelog: v0.5.1...v5.2

v0.5.1 release

What's Changed

LevioSAM-asm

• Supported filtering using BED intervals
• Used dest FAI file as the header (for both ChainMap and VcfMap)
• Fixed bugs for reads overlapping multiple chain intervals
• Improved code readability and testability

Selective liftover

• Added leviosam collate to handle singletons
• Provided selective liftover pipelines (bash)

Full Changelog: v0.5.0...v0.5.1

v0.5.0 release

Support using a chain file as a lift-over map. See the wiki page for usage.

What's Changed

• instructions with pre-built indexes by @milkschen in #11
• Alpha version with chain support by @milkschen in #13
• added missing #include by @AndreaGuarracino in #14

New Contributors

• @AndreaGuarracino made their first contribution in #14

Full Changelog: v0.4.0...v0.5.0

v0.4.0 release

• logic for overlapping variants now follows that of bcftools consensus v1.11
• support for adding MD:z and NM:i tags to lifted alignments (-m option)
• fixed CMake compilation bugs
• added Dockerfile
• updated README.md
• added INSTALL.md to provide user with additional installation options
• added googletests
• additional bug fixes

v0.3.0 release

• Use htslib data structures for I/O
• Support read/write BAM format

v0.2.0 release

Changes in this release:

• Rename the software as levioSAM.
• Support multiple threads (with -t).
• Handle paired-end information as well (PNEXT and TLEN fields).
• Support local alignment.
• Support more CIGAR operators such as "S", "H" and "P".
• The orders of input SAM and output SAM headers are now the same.
• Minor bug fixes and refactorization.
• Better tests.

v0.1.0 release (refflow_preprint)

Update README.md