v0.4.0-beta.3 (2025-01-05)

Release Notes

Besides dependency updates, the release includes:

• The ability to append records to the output file(s) instead of overwriting
  (--append) (7fe1893). This is especially useful for the split command.
• A new --counts option in the split command, which returns the record counts
  for each file (565b42c). This saves an extra st count command.
• Added some error messages to prevent panics (d91b1fc, 8156c45)

Install seqtool 0.4.0-beta.3

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/markschl/seqtool/releases/download/v0.4.0-beta.3/seqtool-installer.sh | sh

Install prebuilt binaries via powershell script

powershell -ExecutionPolicy ByPass -c "irm https://github.com/markschl/seqtool/releases/download/v0.4.0-beta.3/seqtool-installer.ps1 | iex"

Install prebuilt binaries via Homebrew

brew install seqtool

Download seqtool 0.4.0-beta.3

File	Platform	Checksum
seqtool-aarch64-apple-darwin.tar.xz	Apple Silicon macOS	checksum
seqtool-x86_64-apple-darwin.tar.xz	Intel macOS	checksum
seqtool-x86_64-pc-windows-msvc.zip	x64 Windows	checksum
seqtool-x86_64-pc-windows-msvc.msi	x64 Windows	checksum
seqtool-aarch64-unknown-linux-gnu.tar.xz	ARM64 Linux	checksum
seqtool-x86_64-unknown-linux-gnu.tar.xz	x64 Linux	checksum
seqtool-x86_64-unknown-linux-musl.tar.xz	x64 MUSL Linux	checksum

v0.4.0-beta.2 (pre-release)

Release Notes

This release comes with substantial improvements and lots of internal code improvements
and also some notable bugfixes.
See CHANGELOG for all details.

Download seqtool 0.4.0-beta.2

File	Platform	Checksum
seqtool-aarch64-apple-darwin.tar.xz	Apple Silicon macOS	checksum
seqtool-x86_64-apple-darwin.tar.xz	Intel macOS	checksum
seqtool-x86_64-pc-windows-msvc.zip	x64 Windows	checksum
seqtool-x86_64-pc-windows-msvc.msi	x64 Windows	checksum
seqtool-x86_64-unknown-linux-gnu.tar.xz	x64 Linux	checksum

v0.3.0

Binary renamed: The binary was renamed from seqtool to st, because
typing the rather long name repeatedly can be tiring (-: The documentation
was updated accordingly

New commands:

• view command for viewing sequences in terminal with colored background

Changes / additions:

• Seqtool now handles quality scores associated with sequences. This includes:

  • Support for converting between FASTQ format variants
  • The exp_err statistics variable, which represents the total number of expected
    errors in a sequence, according to the quality scores. This allows filtering
    by sequence quality as done by fastq_filter from USEARCH and VSEARCH
  • 454-style QUAL files can be read an written

• --format renamed to --fmt, and --outformat renamed to --to

• The former txt format is now tsv (including the option --to-tsv).

Bug fixes:

• seq_io was updated, containing two small bug fixes. Both bugs were very
  unlikely to be hit and of low severity

v0.2.3

New commands:

• concat command
• interleave command

Changes / additions:

• The find command is now much faster for approximate searching.
  The starting position (f:start variable) can be different in some
  cases where several alignments with the same distance and end position are
  possible.
  Note: Pattern length for approximate searching is now limited to 64.

• Added a shortcut -T for --read-thread. Adding this option
  (and eventually --write-thread) can speed up many commands.
  Since there are no comprehensive benchmarks, the default
  is to read/write in the main thread.

• New dirname variable

Bug fixes:

• Compressed files produced by the split command were still truncated
  in some cases (related to bug fixed in v0.2.2). This is fixed now.
• Pattern type recognition in find command was not always correct

v0.2.2

Important bugfixes:

• Writing compressed files was partly broken (truncated files) and was fixed
  now, along with many unit tests
• With --fields/--txt/--csv, column indices are now correctly interpreted
  as 1-based, not 0-based
• Fixed handling of NaN values in 'count' command
• tail returned one sequence too much.

Changes to behaviour:

• -n option removed from slice command, use a range (..n) instead.

New features:

• Added ZSTD (de-)compression which is almost as fast as LZ4, but has a better
  compression ratio
• Now allows for changing the compression level (--compr-level)
• Writing attributes to sequences removed by filtering (--dropped option of
  find and filter) is now possible.
• Other small improvements and better testing, almost all options have tests now.

v0.2.1

• recognize '.tsv' and uppercase extensions
• report names of missing files
• small performance improvements

v0.2.0

• added more advanced math expressions (ExprTk library)
• filter command
• renamed 'properties' to 'attributes'
• bug fixes, cleanups and more tests

v0.1.1

v0.1.1 release