Captus v1.5.1

• Setting --tolerance to -1 in captus align disables the removal of divergent sequences when using the informed paralog filter.
• VSEARCH is now limited by --threads in captusd.
• Captus version and Command correctly printed to the HTML reports of captusd.

Captus v1.5.0

• New options for captusd_cluster: --align_method to select MAFFT's algorithm and --align_max_copies to avoid aligning clusters with an excessive number of potential copies.
• Fixed a bug in captus extract caused when no BLAT hits pass the filters.

Captus v1.4.9

• ClipKIT now preserves reading frame when trimming NT format (=CDS)
• Fixed bug in captusd cluster

Captus v1.4.8

• Fixed a bug in TAPER caused by lower case sequences. Now all sequences are capitalized before being processed with TAPER.

Captus v1.4.7

• Fix for Salmon command, now allows single-contig assemblies

Captus v1.4.6

• Fixed an integer division bug in the extract step, potentially affecting extractions from full-chromosome quality assemblies.

Captus v1.4.5

• Smarter parallelization for the extract step, the size of the assemblies are taken into account to reserve RAM for BLAT and divide CPUs accordingly.

Captus v1.4.4

• Fixed bugs causing inconsistent TAPER correction (TAPER's code was translated by AI from Julia into Python and two off-by-one errors were introduced, I guess AI won't replace us for now).

Captus v1.4.2

New in extract: parameter --paralog_tolerance now accepts decimal values

Captus v1.4.1

• Maximum overlap between loci increased from 1% to 5% in HIT_MAX_PCT_OVERLAP in settings.py
• new_targets_from_alignments works with alignments not made in Captus (though the directory structure must match the Captus alignments directory)
• Bug fix for a math error caused by a target locus is not found in the data