v0.24.4

--info

• Fix typo with indropsv3

ref

• If any input (FASTA or GTF) files are provided as gzip files, they are uncompressed to the temporary directory, instead of being streamed directly. This is because ref relies on being able to access arbitrary locations of the files quickly. Working with decompressed files results in a considerable speedup.

count

• For --lamanno: spliced and unspliced busfiles no longer contain the .s suffix. This was done to make the output consistent with the normal (non--lamanno) command
• Implemented --filter with --lamanno
• Support for single nuclei RNA-seq with --nuclei. The only difference between --nuclei and --lamanno is how the spliced and unspliced matrices are combined. Specifically, --nuclei sums the matrices. Using --nuclei with neither --loom nor --h5ad results in behavior identical with --lamanno.