Skip to content

Releases: yhoogstrate/fastafs

v1.10.0

22 Jan 14:53
654ea09
Compare
Choose a tag to compare

2023-01-22

  • v.10.0
  • Better ninja/meson support
  • Code clean-ups
  • Restructured the chunked_reader class and subclasses according to
    the desgin patterns philisopy

v1.9.0

12 Feb 16:12
a86e1a1
Compare
Choose a tag to compare

v1.9.0:

  • Bugfix thanks to @Y4NG333 [out of bound checking fastafs version] #63

v1.8.1

25 Jan 08:28
c955a71
Compare
Choose a tag to compare

v1.8.1

  • More structured way of building using cmake and libfastafs.
  • Improved building using meson / ninja

v1.8.0

28 Dec 13:16
d29011f
Compare
Choose a tag to compare
  • v1.8.0
  • Support for zstd-seekable
  • Support for protein sequences using 8-to-5 byte compression
  • Object type for chunked/buffered file reading
  • Requires libzstd (1.4.5 and above) as dependency
  • Awesome and complex per-system-id & per-git-revision Python benchmark system 😎 which exports stats into the git tree

v1.7.5

03 Mar 15:01
Compare
Choose a tag to compare

v1.7.5:

  • Added argument check -5/--md5sum to do file verification using md5sums as well
  • Fixed error code returned after fastafs check --help

v1.7.4:

  • Added argument cache --2bit to force 2bit compression when this gives suboptimal compression ratio's (needed for statistical analysis)

v1.7.3

26 Feb 15:35
Compare
Choose a tag to compare
2020-20-26  Youri Hoogstrate

   * v1.7.3
   * Small decoy function added for basic snakemake compatiblity

2020-02-04  Youri Hoogstrate

   * v1.7.2
   * Reduce file read syscalls and gain performance
   * Functional testing in python, for both view to stdout as mounting
   * Added templating for cleaner code
   * Auto conversion to fourbit if that is more efficient compression

v1.7.1

01 Feb 17:50
87dc480
Compare
Choose a tag to compare

2020-02-01 Youri Hoogstrate

  • v1.7.1
  • Fixed an errornous syscall (when ls -l requests a certain xattr)
  • Set chmods to 0555 to 0444

v1.7.0

29 Jan 20:51
c52232b
Compare
Choose a tag to compare
  • fastafs cache -o for custom output files and bypassing the config
  • Random access subsequence retrieval diretly via filesystem: <mount>/seq/chr1:100-200
  • Implements CRC32 checksums for whole-file integritity
  • Converting to meson because of insane build times using cmake+make and re-building files that have not changed
  • fastafs view|mount -m/--no-masking virtualises fasta files without masking (uppercase)
  • Minor support for building with meson and ninja
  • cmake template allows building for guix (+guix file provided)
  • Changed requirement from c++17 on c++14 to avoid large compatibility issues
  • Implements bitflags with corresponding class
  • Implements fourbit (and automatically switches over if non ACTGUN chars are found
  • Implements functions is_fasta_file, and is_ucsc2bit_file using file MAGIC
  • Creates by FASTAFS files that are first flagged as incomplete, that are unflagged after conversion has completed
  • MD5sums working for fourbit compressed sequences
  • Implements fastafs cache -o to export to desired output fastafs file
  • Adds compression type to fastafs list output
  • More and improved testing, including file integrity detection

v1.6.2

06 Sep 07:31
04eaa80
Compare
Choose a tag to compare
  • Rewritten argument parsing of fuse/mounting
  • Added binary mount.fastafs only for mounting, without the toolkit, to use in /etc/fstab
  • fastafs --version will now also output whether the binary was compiled as debug or release.

v1.6.1

21 Aug 15:08
e80c1df
Compare
Choose a tag to compare
  • Adds process' pid to fastafs ps