This is the changelog for FASTX::Reader. Version prior to v 0.1 are preliminary (alpha) release, not to be used in production.
Some APIs *can change* with the release of the first stable release (v 1.0).
Version 0.61 has been available via BioConda
1.12.0 2023-09-24
* 5.16 minimum Perl version required
* minor updates to POD, tests
1.11.0 2023-08-22
* added `translate()` method to FASTX::Seq
1.10.0 2023-01-13
* `new()` FASTX::Reader method now supports a named parameter instantiation, e.g. `FASTX::Reader->new(-file => 'file.fastq')`
* `new()` FASTX::Seq method now supports a named parameter instantiation, e.g. `FASTX::Seq->new(-seq => 'CACCA')`
* Added `copy()` method to FASTX::Seq
* Added quality methods to FASTX::Seq:
* `qualities()` to get an array of scores, `trim_until(int)` and `trim_after(int)`
* functions like `char2qual()` and `qual2char()` to convert between ASCII and integer scores
* `$record->offset(new)` to change offset (default is 33)
* Test updates, minor changes
1.9.0 2023-01-12
* Added `slice(from, len)` method to FASTX::Seq (works as substr)
* Added `string()` method to get the sequence as a string (FASTQ or FASTA according to the record), with `as_string()` as alias
* Added `is_fasta()` and `is_fastq()` methods to FASTX::Seq
* Added `as_fasta()` and `as_fastq()` aliases to FASTX::Seq (for syntax consistency)
1.8.1 2023-01-09
* Updated tests
* Update POD documentation
1.8.0 2023-01-08
* **CRITICAL BUG FIX ** in `next()` method used in while loops
1.7.0 2022-12-12
* FASTX::Seq has more stringent requirements, undef seq not allowed (but empty are fine)
1.6.1 2022-12-08
* POD fixes
1.6.0 2022-12-02
* FASTX::Reader now uses FASTX::Seq internally
* Experimental FASTX::PE renamed FASTX::ReaderPaired. Remains **experimental** and not for use in production.
1.5.1 2022-12-01
* Bug fixes, documentation and functionality update for `fqlen.pl`
* Minor changes
1.5.0 2022-06-24
* FASTX::Seq with undef name is now rendered as FASTA/Q with name "sequence"
1.4.1 2022-06-22
* Added PerlIO::encoding in prerequisites (in core since 5.8.0)
1.4.0 2022-06-19
* Updated documentation
* Added a len() method for FASTX::Seq
1.3.0 2021-11-04
* Standalone FASTX::Seq class
1.2.1 2021-11-01
* Fix changelog mismatching version
* Minor fix in test "nonillumina.t"
1.2.0 2021-11-01
* Introduction of "next()" method that returns a blessed object instead of a scalard, test n. 21
* Minor code improvements (perlcritic)
1.1.0 2021-08-04
* Support for Windows line endings (experimental)
1.0.5 2021-04-21
* Improved test suite
* Minor code cleanup
1.0.4 2021-04-19
* Documentation updates
1.0.2 2021-03-25
* Documentation updates
* Improved tests for PE reader
* ScriptHelper verbose() function now tolerant when passing multiple strings
1.0.1 2021-03-24
* Migration of Continuous Integration from TravisCI to GitHub actions
* META.yaml ships with the package (for GitHub Actions)
1.0.0 2021-03-20
* BUG FIX: Multiple instances of the same object were conflicting when mixing filetypes (tests 40_*)
* Semantic versioning
* Improved test suite
0.94 2020-06-01
* Accessory script updates
* Requirements: File::Fetch
0.93 2020-05-29
* Markdown updated
0.91 2020-05-06
* Updated ScriptHelper (new function download[url, destdir])
0.90 2020-05-03
* Updated dist.ini dependency
0.89 2020-05-02
* added run() function in ScriptHelper
* unit test for ScriptHelper
0.88 2020-04-13
* getFileFormat() also supports gzipped files
* FASTX::PE strips /1 /2 _1 _2 _R1 _R2 from interleaved read names
* Preliminary release of FASTX::ScriptHelper
* Bug fixes
0.87 2020-04-05
* POD fixes
* Minor updates
* Fixed bug in auto reverse file finding [FASTX::PE]
0.85 2020-04-05
* Alpha release of FASTX::PE, updated with improved tests and documentation
0.82 2020-04-03
* Alpha release of FASTX::PE
0.80 2020-03-31
* Added the `getIlluminaRead()` method that parses the read name to populate extra attributes.
0.70 2020-01-20
* Added attribute 'loadseqs' in method new(), will load all sequence in %{ $self-{seqs} }. Values can be 'name' or 'seq' (that is the key of the resulting hash)
0.61 2019-10-10
* When using 'which', standard error is redirected to /dev/null
0.60 2019-06-17
* FIXED: Comment retainment: comments were truncated
* File::Which only recommended (might be removed as requirement in the future)
0.50 2019-06-13
* Added a control in new() that will stop parsing the file if it's binary (and not .gz)
* Added a new control in getFastqRead() to report truncated FASTQ files
* 'fqc': file without reads will print n/a instead of 0
0.40 2019-06-13
* 'fqc': added '--verbose' feature, renamed tabular output switch to '-x/--screen' for consistency with Proch::N50
* 'fqc': improved handling of non existing files, improved documentation
0.32 2019-06-12
* Ships a script to count FASTA/FASTQ sequences called 'fqc' (see)
* Reader object new property 'compressed' (1 if reading .gz files, 0 otherwise)
* POD documentation Updated
0.31 2019-06-12
* POD documentation Updated
0.30 2019-06-11
* Improved getFastqRead() error handling
* Improved unit tests, in particular for getFastqRead() method
* Added 'bad.fastq': malformed FASTQ file
* Shipping FastqReader.pl demo script to see how getFastqRead() works
* NOTE: This release focuses on getFastqRead(FASTQ), that is 12% faster than the generic getRead(FASTX)
0.20 2019-06-10
* Added preliminary support to read .gz files
0.11 2019-06-03
* Cleanup via dist.ini
0.10 2019-06-03
* FIXED Comments parser was not working for FASTA files
* Added unit tests for comments
* Moved release tests to xt/release
* Added 'Counter.pl' sample script, counting sequences in FASTA/FASTQ files
0.09 2019-05-16
* Removed test/ directory
0.08 2019-05-16
* Dist::Zilla configuration updated
* Renamed experimental files
0.07 2019-05-15
* GitHub repository restructured to allow TravisCI tests
0.06 2019-05-15
* BUG FIX author test moved to xt
0.05 2019-05-09
* Improved test coverage
* BUG FIX on getFileFormat()
0.02 2019-05-07
* Reader parses STDIN
* Updated documentation
0.01 2019-05-05
* Initial release of a working parser