v1.2.0

Highlights from previous stable release

• Locus-level TE quantification. Use -l or --locus to enable it. This will add a tilde followed by a number to TE feature name (e.g. L1PA7~123).
• Support for UMI-less libraries (e.g. smart-seq). Use with --no-umi.
• Dramatically improved memory usage efficiency and run time.
• A copy of the TE annotation generated on the fly with the -g <genome_assembly> flag will be saved in the output directory.
• Support for strand-specific count, for stranded libraries and in case knowing the orientation of transcribed TEs is relevant. Use --strandedness forward or --strandedness reverse to activate it.
• Support Python versions from 3.10 to 3.14 (NB: installation time on Python 3.14 is a few minutes longer, until Pysam's wheels update).

What's Changed

• Fix invalid escape sequence warning message by @bepoli in #19
• Set multiple verbosity level by @bepoli in #21
• Implement EM convergence with tolerance threshold of log-likelihood change by @bepoli in #20
• Add Python 3.13 test by @bepoli in #22
• SMART-seq support by @marco-cominelli01 in #27
• drop python 3.8 support by @bepoli in #28
• add test for --no-umi mode by @bepoli in #29
• Update error message for unsorted BAM in map.py by @marco-cominelli01 in #31
• Update get_ranges in misc.py by @marco-cominelli01 in #32
• Use sparse matrices in EM by @marco-cominelli01 in #35
• dependencies update by @bepoli in #36
• Support library strandedness by @bepoli in #38
• Add locus-level quantification option by @bepoli in #39
• Fix string formatting in bam file testing message by @marco-cominelli01 in #40

New Contributors

• @marco-cominelli01 made their first contribution in #27

Full Changelog: v1.1.2...v1.2.0