v1.26.0 - subtract ➖

New Features

• seqfu subtract — new command to output sequences from that are absent from . Matching can be done by sequence name (default) or by sequence content
  (--by-seq / MD5 hash). Options include --strip-comment, --strip-pair (ignore /1//2 suffixes), and --relaxed (don't error when contains names absent from ).

Improvements

• seqfu stats — JSON output now emits proper numeric types for all numeric fields (previously all fields were quoted strings).
• seqfu stats — --sort-by is now validated early with a descriptive error on unknown keys; sort logic refactored to a clean enum-based comparator.
• seqfu stats — %GC no longer produces NaN/Inf in MultiQC reports when --gc is not explicitly requested; GC is silently computed whenever a MultiQC report is requested.
• fu-primers — major refactor of reverse-complement primer matching; switched internal threading from threadpool to malebolgia; improved test coverage.

⚠️ Bug Fixes

• seqfu tab — fixed wrong sequence being printed in paired-end mode (src/fastx_tabulate.nim) (fixes #31 thanks to @wiedenhoeft)
• seqfu metadata — --force-csv flag was not being honoured; now correctly switches output to CSV format.

v1.25.1

• Fix bioconda build -lphreads

v1.25.0 - 📈 Stats

Improvements

• Multithreading counts and other improvements
  • Experimental table view in counts
• Multithreading stats and other improvements
  • multithreading support via --threads INT; multiple files are now processed in parallel when threads > 1 and stdin is not involved.
  • stats now outputs a JSON with integer/float values (before it was strings only)

v1.23.0 - Convert to FASTA 🔀

• add seqfu tofasta that extracts sequences from GenBank, EMBL, GFF, etc (port of any2fasta)

v1.22.3 — 😸 cat fix

• seqfu cat --anvio fixed: it was requiring explicit --report to work

v1.22.2 — 📐L50 stats

• Add support for L50,75,90 statistics in seqfu stats using --index
  • ⚠️ this is experimental, the flag can change and the final output too

SeqFu 1.22.0 - 🌊 EBAME9

• Moved tests and code to fully support Nim 2.0
• SeqFu cat bug fix on prefixes, and addess --anvio shortcut to replicate anvi-script-reformat-fasta (for pipelines preparing data for Anvi'o
• SeqFu metadata now offers nf-core/rnaseq, nf-core/ampliseq and bactopia filesheets (experimental)
• SeqFu derep, improved docs
• Various fixes and documentation updates

Thanks to dialvarezs for Ignore incompatible-pointer-types error and to martin-g for improving Makefile and actions.

--

What's Changed

• compile by @microbiomes in #22
• Make use of makes implicit variables by @martin-g in #23
• Ignore incompatible-pointer-types error by @dialvarezs in #25

New Contributors

• @microbiomes made their first contribution in #22
• @martin-g made their first contribution in #23
• @dialvarezs made their first contribution in #25

SeqFu v1.20.3

• Bugfix interleave/deinterleave #21

SeqFu v1.20.2 - 🇬🇲 Fajara

• Migrating to Nim 2.0

SeqFu v1.20.1 - 🇬🇲 Gambia

• Bugfix in seqfu metadata when producing a Manifest file for single end #18
• Added --translate to fu-orf