seqfu - v1.22.3 — 😸 cat fix

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

- Nim
Published by telatin over 1 year ago

seqfu - v1.22.2 — 📐L50 stats

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

- Nim
Published by telatin over 1 year ago

seqfu - 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 https://github.com/telatin/seqfu2/pull/22
• Make use of makes implicit variables by @martin-g in https://github.com/telatin/seqfu2/pull/23
• Ignore incompatible-pointer-types error by @dialvarezs in https://github.com/telatin/seqfu2/pull/25

New Contributors

• @microbiomes made their first contribution in https://github.com/telatin/seqfu2/pull/22
• @martin-g made their first contribution in https://github.com/telatin/seqfu2/pull/23
• @dialvarezs made their first contribution in https://github.com/telatin/seqfu2/pull/25

- Nim
Published by telatin over 1 year ago

seqfu - SeqFu v1.20.3

• Bugfix interleave/deinterleave #21

- Nim
Published by telatin over 2 years ago

seqfu - SeqFu v1.20.2 - 🇬🇲 Fajara

• Migrating to Nim 2.0

- Nim
Published by telatin over 2 years ago

seqfu - SeqFu v1.20.1 - 🇬🇲 Gambia

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

- Nim
Published by telatin over 2 years ago

seqfu - SeqFu v1.20.0 — Align faster ⇉

• Added genetic code 15 to fu-orf
• Rewrote Smith-Waterman code in nim without external libraries, with a 2X speed bump

- Nim
Published by telatin almost 3 years ago

seqfu - v.1.18.0 — ✂️shred more

• Added paired end support for fu-shred
• Added --noheader in seqfu stats
• Minor fixes

- Nim
Published by telatin almost 3 years ago

seqfu - v1.17.1 – detabulate bug fix 🐛

• Fixed bug on seqfu tabulate when detabulating FASTQ files

- Nim
Published by telatin over 3 years ago

seqfu - v1.17.0 – 🧵 no threads

- Nim
Published by telatin over 3 years ago

seqfu - SeqFu 1.16.0 — 🖍 crayon

• Update color schemes for fu-msa, added aminoacid
• Bugfix in seqfu check to ensure matching of the correct files when using --dir
• Bugfix in seqfu bases to ensure --abs and --basename are honored
• Update unit tests
• Code refactoring on several tools

- Nim
Published by telatin over 3 years ago

seqfu - SeqFu 1.15.3 – 🫧 Bath Hackathon edition

Experimental seqfu bases

- Nim
Published by telatin over 3 years ago

seqfu - SeqFu 1.15.0 — 🕵️‍♂️ Sherlock edition

• New SeqFu check program to validate the integrity of FASTQ datasets
• Bug fix in seqfu qual that was printing debug information in non-debug runs

- Nim
Published by telatin over 3 years ago

seqfu - SeqFu v1.14.0 — 🥒 slicing edition

• First release officially shipping fu-split
  • fu-split now can use a different SeqFu than specified in path, setting $SEQFU_BIN or --bin option
  • fu-split version check fixed
• SeqFu grep will die if fed with non existing files (to ensure no wrong parameters were passed)
• SeqFu grep will match oligos case insensitive by default
• Addedd invert match -v to seqfu grep
• Improved fu-tabcheck, notably added --inspect option to print columns info
• :warning: Bugfix in seqfu tab: was not working with FASTA files
• SeqFu head and SeqFu tail migrated to readfq library

- Nim
Published by telatin almost 4 years ago

seqfu - SeqFu v1.13.2

• added --print-last option to seqfu cat and seqfu heda
• updated fu-split, with support for paired end reads, improved performance thanks to --print-last, new tests

- Nim
Published by telatin almost 4 years ago

seqfu - SeqFu v1.13.1

• added fu-split (experimental)

- Nim
Published by telatin almost 4 years ago

seqfu - SeqFu v1.13.0 — 💎🐈‍⬛ rich cat edition

• seqfu cat now can skip a set of initial sequences (--skip-first INT) or start from a specific sequence (--jump-to AFTERTHIS)
• Minor updates in the test suite, github actions (including rich_codex) and documentation updates

- Nim
Published by telatin almost 4 years ago

seqfu - SeqFu v1.12.0 – 🇨🇦 Canadian edition

• Expanded "fu-index": also reports run infos, not only indexes
• Minor bugfix

- Nim
Published by telatin almost 4 years ago

seqfu - SeqFu v1.11.0 – 👑 jubilee edition

• Improved seqfu stats: added sorting option and JSON output, added GC content, improved test suite.
• bugfix Seqfu tabulate -d (detabulate) was too stringent in requiring forward and reverse reads to have the same length :facepalm:

- Nim
Published by telatin almost 4 years ago

seqfu - SeqFu v1.10.0 – 🤍 Bianca edition

• Added support for MetaPhage to seqfu metadata
• Added --header to fu-tabcheck
• Minor fixes

- Nim
Published by telatin about 4 years ago

seqfu - SeqFu v1.9.3

• bugfix: seqfu cat controls the length of operations (truncate, trim)
• improved: seqfu cat improved renaming options (basename and strip-name will now add a progressive number automatically)

- Nim
Published by telatin about 4 years ago

seqfu - SeqFu v1.9.2

• Bugfix on Seqfu Detabulate

- Nim
Published by telatin about 4 years ago

seqfu - v1.9.1

• Fixes #8
• This is a re-release finally with all the necessary commits... What a mess :)

- Nim
Published by telatin over 4 years ago

seqfu - v1.9.0 – 🎅 Santa edition

• seqfu grep now has -w (word) and -f (full) match options. default behaviour unchanged.
• seqfu cat now has a filter for Ns (--max-ns INT)
• seqfu cat now has a filter for the total expected errors (--max-ee FLOAT), and can report --add-ee and --add-initial-ee
• Added header line in seqfu metadata when using "irida" formats

- Nim
Published by telatin over 4 years ago

seqfu - SeqFu v1.8.9

• Improved fu-msa

- Nim
Published by telatin over 4 years ago

seqfu - SeqFu v1.8.8

• Introduced the experimental multiple alignment viewer fu-msa

- Nim
Published by telatin over 4 years ago

seqfu - SeqFu v1.8.7

• Improved performance
• Added Makefile

- Nim
Published by telatin over 4 years ago

seqfu - SeqFu v1.8.6

• Added seqfu rotate

- Nim
Published by telatin over 4 years ago

seqfu - v1.8.5 fu-orf

Supporting NCBI Genetic Codes in fu-orf

- Nim
Published by telatin over 4 years ago

seqfu - SeqFu v1.8.4

• fu-orf
  • Fixed bug in fu-orf to allow for single sequences
  • Introduced -r, --scan-reverse to include reverse complement in the ORF finder
  • fu-orf also prints frame in the sequence comment
• Expanded test suite

- Nim
Published by telatin over 4 years ago

seqfu - SeqFu v1.8.3

• Markdown documentation improvements
• Splashscreen for fu-virfilter fixed
• Argument parser for fu-cov improved
• Now seqfu --version and seqfu version will print the version number and exit
• Added test for fu-cov
• Added citation in main command and repository

- Nim
Published by telatin over 4 years ago

seqfu - SeqFu v1.8.2

• Added fu-virfilter to filter VirFinder results
• Bugfix in seqfu cat --basename: the last update made it working only when prefix was also specified

- Nim
Published by telatin over 4 years ago

seqfu - SeqFu v1.8.1

• introduced fu-homocomp to compress homopolymers

- Nim
Published by telatin over 4 years ago

seqfu - SeqFu v1.8.0

• added seqfu list to extract sequences via a list

- Nim
Published by telatin over 4 years ago

seqfu - SeqFu v1.7.2

• seqfu grep supports for comments

- Nim
Published by telatin over 4 years ago

seqfu - SeqFu v1.7.1

• Bugfix release: seqfu cat with no parameters was stripping the reads name

- Nim
Published by telatin over 4 years ago

seqfu - v1.6.3

• In seqfu head you must use --quiet and the short version is no longer allowed.

- Nim
Published by telatin over 4 years ago

seqfu - SeqFu v1.6.0

• Improved STDIN messages, that can be disabled by $SEQFU_QUIET=1
• Added --format irida in seqfu metadata (for IRIDA uploader)
• Added --gc in seqfu qual: will print an additional column with the GC content
• Minor improvements on seqfu cat

- Nim
Published by telatin almost 5 years ago

seqfu - SeqFu v1.5.2

• seqfu cat has new options to manipulate the sequence name (like --append STRING) and to add comments (like --add-len, --add-gc)

- Nim
Published by telatin almost 5 years ago

seqfu - SeqFu v1.5.0

• seqfu count now multithreading and redesigned. The output format is identical but the order of the records is not protected (use seqfu count-legacy if needed)
• seqfu cat can print a list of sequences matching the criteria (--list)

- Nim
Published by telatin almost 5 years ago

seqfu - SeqFu v1.4.0

• Added fu-shred
• Added --reverse-read to fu-nanotags

- Nim
Published by telatin almost 5 years ago

seqfu - SeqFu v1.3.6

• Automatic release system
• Documentation updates
• Minor updates

- Nim
Published by telatin almost 5 years ago

seqfu -

- Nim
Published by telatin almost 5 years ago

seqfu - v1.3.2 - metadata for qiime2

seqfu metadata --format qiime2 now has its own implementation (the previous releases relied on the forward compatibility of mapping files)

- Nim
Published by telatin almost 5 years ago

seqfu - v1.2.3 - tabulate

• added seqfu tabulate

- Nim
Published by telatin almost 5 years ago

seqfu - v1.2.1 - nanotags

BUG FIX in seqfu rc: when a single sequence sequence was provided as argument, --only-rev was working at the opposite

New tool: fu-nanotags

- Nim
Published by telatin almost 5 years ago

seqfu - v1.2.0 - qualified regions

• Bug fix: SigPipe handling was not working since 1.0.0
• New: seqfu tabulate to generate metadata/mapping files from directories
• seqfu qual now automatically detects the qualified region of the reads using a sliding window.
• Minor improvements in documentation and implementation of seqfu head, seqfu cat

- Nim
Published by telatin almost 5 years ago

seqfu - v1.1.0

• Added tool to generate metadata (tabulate, now metadata from 1.2.+)
• seqfu rc can now --only-rev and has improved stdin handling
• Improved documentation
• Various Bugfixes, including derep #4;

- Nim
Published by telatin about 5 years ago

seqfu - v1.0.0 seqfu cat

• seqfu cat to print multiple files

- Nim
Published by telatin about 5 years ago

seqfu - v0.9.6 Windows release

• Refactored signal handling to support compilation from Windows
  • In this release we attach our compiled binaries that require a DLL library (zlib1.dll). We supply three versions and one should work when placed in the same directory as the other executables. We are not able to support Windows at the moment, but we found possible to compile and use SeqFu from Windows.
• Minor bugfix in fu-sw to handle missing files

- Nim
Published by telatin about 5 years ago

seqfu - v0.9.5 with core binaries

• Improved documentation thanks to reviewer's comments
• Improved seqfu view (support for ASCII encoding of quality scores)
• New tool fu-multirelabel
• Minor bug fixes

seqfu is the Linux binary, while seqfu_mac targets MacOS

- Nim
Published by telatin about 5 years ago

seqfu - v0.9.1 with binaries

• Improved seqfu view (collapsed visualization of multiple oligos per strand)
• Output of seqfu rc is a naked sequence when a single string is provided

- Nim
Published by telatin about 5 years ago

seqfu - v0.9.0

• seqfu qual function added

- Nim
Published by telatin about 5 years ago

seqfu - v0.8.13

• Update documentation
• Updated fu-sw for Smith Waterman alignments

- Nim
Published by telatin about 5 years ago

seqfu - v0.8.12

• Improved 'dadaist2-mergeseqs': mismatches allowed

- Nim
Published by telatin about 5 years ago

seqfu - v0.8.11 - with binaries

- Nim
Published by telatin over 5 years ago

seqfu - v0.8.10 - with binaries

• auxiliary tools transitioned argument parsing from argparse to docopt
• binaries released (Mac / Linux)

- Nim
Published by telatin over 5 years ago

seqfu - v0.8.8 fu-orf

- Nim
Published by telatin over 5 years ago

seqfu - Added "view" and "grep"

- Nim
Published by telatin over 5 years ago

seqfu - Added primer removal tool

- Nim
Published by telatin over 5 years ago

seqfu - Transition to nim

- Nim
Published by telatin over 5 years ago