LSUx 0.99.8

Fix a bug in find_amplicon() when marking the primer locations.

LSUx 0.99.7

Added tests for most functionality.
Reimplemented truncate_alignment() using narrow() method for Stockholm alignments from inferrnal 0.99.8. It now handles interleaved Stockholm files.
Added find_amplicon() to locate and mark or extract the region defined by a primer pair. Also exported are helper functions find_primer() and gap_fill().

LSUx 0.99.6

When input sequences to lsux() are unnamed, use index (as character) for seq_id field in output. Previously, the result would be missing seq_id in this case.
Fix some issues in coercion between sequence types (migrated from tzara).
Don't return 0-length (or shorter) regions in lsux.
Add functions to truncate Stockholm alignments and repair secondary structure annotations.
Add option "quiet" to lsux() to suppress cmsearch output.
Multiple values can be passed to mxsize and cpu arguments of lsux(). In this case, on failure of cmalign, it will be restarted with the second, third, etc. values.

LSUx 0.99.5

Support fastq files in lsux.

LSUx 0.99.4

Handle queries where no sequences have a 5.8S match (by returning a 0-row result).
Pass mxsize argument to cmalign.

LSUx 0.99.3

lsux now protects the names of input sequences, which can sometimes be mangled by Infernal if they contain nonstandard characters.
lsux supports inputs as FASTA filenames, named character vectors, and objects of types DNAStringSet, RNAStringSet, ShortRead, and ShortReadQ.

LSUx 0.99.2

Breaking change: Change return value of lsux from wide to long, to match merge_5_8S and rITSx, as well as the inputs for tzara.

LSUx 0.99.1

Added a NEWS.md file to track changes to the package.
Added support for ShortRead objects as input.
Change from "seq" and "seq_name" to "seq_id" in position tables, to match rITSx and tzara.