sam2lca v1.1.4

Changelog

• bugfix: 53fc0aa allows user provided taxonomy dump files

sam2lca v1.1.3

Fixes a minor bug when sam2lca crashes if at given identity the LCA algorithm doesn't assign any reads to taxids #13
Thanks @alexhbnr for the fix !

sam2lca v1.1.2

Performance improvement when writing bam split by TAXID

sam2lca v1.1.1

Patch release for 1.1.0: Fix the index of bam alignment sam2lca output files when split by rank

sam2lca v1.1.0

• Added the option to split bam ouput file by TAXID at specified rank

sam2lca v1.0.0

sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files

Version 1.0.0-beta

Changelog

Added

• Added sam2lca tutorial
• Add Custom acc2tax with json
• Total number of reads is computed early on to provide progress bar
• unit and integration testing with PyTest
• Total Descendant read counts for each taxon
• GTDB taxonomy and acc2tax added
• 18s acc2tax added
• XN and XR flag in bam output for, respectively, Taxon name and rank
• Add edit distance threshold filtering
• JOSS article

Changed

• Code refactoring for speedup, making use of multithreading on shared dictionaries
• Improve logging and replace prints statements with logging.info
• ete3 has been replaced by taxopy
• Unclassified TAXID is now 12908 by default
• RocksDB params changed
• TAXID of LCA is only attributed to alignment segments passing threshold
• Identity threshold is now a range selection in CLI.

Dependencies

• ete3 removed
• ordered-set removed
• pytest-console-scripts 1.3.1
• scipy
• Jinja2 pinned version ot 3.1 (see RTD issue )

sam2lca v0.3.3

Changelog

What's Changed

• Subset list to references with aligned reads to improve speed by @alexhbnr in #3
• Identify unique combinations of taxids before running NCBI topology by @alexhbnr in #4
• The TAXID as computed by the LCA is optionally written as XT tag for each read in the alignment file.

New Contributors

• @alexhbnr made their first contribution in #3

Full Changelog: 0.3.1...0.3.3

sam2lca 0.3.1 - beta version

Changelog

• Add check for ultraconserved regions

sam2lca 0.3 - beta version

Added subcommand to download/update acc2tax and taxonomy database