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Changelog
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Changelog
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2024-04-30
* v1.11.0
* Implements SHA1 and MD5 through OpenSSL's EVP interface as
old interface is deprecated as of OpenSSL 3.0
2023-01-22
* v1.10.0
* Better ninja/meson support
* Code clean-ups
* Restructured the chunked_reader class and subclasses according to
the desgin patterns philisopy
2020-04-29 Youri Hoogstrate
* v1.9.0
* Improved building
* Bugfix thanks to @Y4NG333 [out of bound checking fastafs version]
2020-04-29 Youri Hoogstrate
* 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
2020-03-03 Youri Hoogstrate
* v1.7.5
* Added argument `check -5/--md5sum` to do file verification using md5sums as well
* Fixed error code returned after `fastafs check --help`
2020-02-27 Youri Hoogstrate
* v1.7.4
* Added argument `cache --2bit` for statistical analysis
2020-02-26 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
2020-02-01 Youri Hoogstrate
* v1.7.1
* Fixed an errornous syscall (when `ls -l` requests a certain xattr
* Set chmods to 0555 and 0777
2020-01-27 Youri Hoogstrate
* v1.7.0
* `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
2019-09-06 Youri Hoogstrate
* v1.6.2
* Rewritten argument parsing of fuse/mounting
* Added binary `mount.fastafs` only for mounting, wihtout the toolkit
* `fastafs --version` will now also output whether the binary was compiled as debug or release.
2019-08-21 Youri Hoogstrate
* v1.6.1
* Adds process' pid to `fastafs ps`
2019-08-21 Youri Hoogstrate
* v1.6.0
* `fastafs list` now supports view running instances of the fastafs files
* function `lsfastafs()` allows finding all fuse mounted fastafs instances/mointpoints
by making use of the 'fastafs-file'-xattr (`getfattr -n fastafs-file /mnt/fastafs/test`)
* Adds `fastafs ps` listing all mounted fastafs instances and their corresponding
mountpoints (also that are not present in the 'database').
2019-08-02 Youri Hoogstrate
* v1.5.0
* Support mounting 2bit files (without FASTAFS file(s))
- Requires c++-17 for several std::filesystem calls
2019-06-05 Youri Hoogstrate
* Changed SHA1 to MD5 hashes for BAM compatibility
* Supports mounting `samtools dict` equivalent files
* Hotfix for more than 255 M-blocks
* Solves many warnings + various cleanups
* Fixed some memleaks
2019-05-21 Youri Hoogstrate
* Supports Masked regions (and conversion to/from UCSC TwoBit files)
2019-05-07 Youri Hoogstrate
* Full support for UCSC TwoBit files in `fastafs cache` (adding to db)
2019-04-30 Youri Hoogstrate
* Performance update.
2019-04-18 Youri Hoogstrate
* The forwards conversion (fasta to fastafs) code has been improved
and does not require to keep whole sequences in heap.
2019-04-11 Youri Hoogstrate
* The file format has been re-specified, backwards incompatible with
the test code. The fastafs to fasta projection has been enormously
improved and is way and way faster.
2018-10-26 Youri Hoogstrate
* fastafs_seq::sha1() is in concordance with CRAM standard; only
uppercase nucleotide chars are taken into consideration
2018-01-17 Youri Hoogstrate
* fastafs mount --padding 5 works
2018-01-10 Youri Hoogstrate
* fastafs mount provides appropriate file size
attributes resulting in correct files
2018-01-08 Youri Hoogstrate
* fastafs mount now also virtualizes faidx files
2017-12-27 Youri Hoogstrate
* Removal of some minor memory leaks
2017-12-22 Youri Hoogstrate
* First working prototype of `fastafs`
* fastafs cache
* fastafs list
* fastafs info
* fastafs view
* fastafs mount