diff --git a/README.rst b/README.rst index 4e5efa3..f2d7a74 100644 --- a/README.rst +++ b/README.rst @@ -304,97 +304,11 @@ A lower-level Faidx class is also available: - Start and end coordinates are 1-based. -Changes +Changelog ------- -*New in version 0.3.4*: -- `--delimiter` option for cli script and `split_char` argument for `Fasta` and `Faidx` - -*New in version 0.3.3*: - -- `--split-files` option writes each returned sequence to an individual file. Names are generated based on the sequence name and region coordinates. -- `--stats` option prints the name and sequence length for each entry, suitable for use as a UCSC-style [chrom.sizes](http://genome.ucsc.edu/goldenpath/help/hg19.chrom.sizes) file. -- Sequence `longname` attribute allows access to "chr:start-end (complement)" formatted names - - -*New in version 0.3.2*: - -- Fasta `__getitem__` no longer initializes new FastaRecord classes -- Faidx `read_ahead` attribute implementaion avoids unnecessary disk hits (`#34 `_) - -*New in version 0.3.1*: - -- Fasta can now accept an integer index in addition to string keys. - -*New in version 0.3.0*: - -- FastaRecord now works as a line-based iterator (`#30 `_) -- Added MutableFastaRecord class that allows same-length in-place replacement for FASTA (`#29 `_) - -*New in version 0.2.9*: - -- Added read-ahead buffer for fast sequential sequence access (`#26 `_) -- Fixed a condition where `as_raw` parameter was not respected (`#27 `_) - -*New in version 0.2.8*: - -- Small internal refactoring - -*New in version 0.2.7*: - -- Faidx and Fasta `strict_bounds` bounds checking logic is more correct -- Fasta `default-seq` parameter now works -- CLI script `faidx` now takes a BED file for fetching regions from a fasta - -*New in version 0.2.6*: - -- Faidx no longer has `raw_index` attribute or `rebuild_index` method (reduce memory footprint) -- Faidx index memory usage decreased by 31-40% -- .fai creation is streaming, performance increase for very large indices -- Possible speed regression when performing many small queries using `Fasta` class - -*New in version 0.2.5*: - -- Fasta and Faidx can take `default-seq` in addition to `as_raw`, `key_function`, - and `strict_bounds` parameters. -- Fixed issue `#20 `_ -- Faidx has attribute `raw_index` which is a list representing the fai file. -- Faidx has `rebuild_index` and `write_fai` functions for building and writing - `raw_index` to file. -- Extra test cases, and test cases against Biopython SeqIO - -*New in version 0.2.4*: - -- Faidx index order is stable and non-random - -*New in version 0.2.3*: - -- Fixed a bug affecting Python 2.6 - -*New in version 0.2.2*: - -- `Fasta` can receive the `strict_bounds` argument - -*New in version 0.2.1*: - -- `FastaRecord` str attribute returns a string -- `Fasta` is now an iterator - -*New in version 0.2.0*: - -- `as_raw` keyword arg for `Faidx` and `Fasta` allows a simple string return type -- `__str__` method for `FastaRecord` returns entire contig sequence - -*New in version 0.1.9*: - -- line wrapping of ``faidx`` is set based on the wrapping of the indexed - fasta file -- added ``--reverse`` and ``--complement`` arguments to ``faidx`` - -*New in version 0.1.8*: - -- ``key_function`` keyword argument to ``Fasta`` allows lookup based on function - output +Please see the `releases `_ for a +comprehensive list of version changes. Acknowledgements ---------------- diff --git a/pyfaidx/__init__.py b/pyfaidx/__init__.py index 6c8bb6e..8302884 100644 --- a/pyfaidx/__init__.py +++ b/pyfaidx/__init__.py @@ -20,7 +20,7 @@ dna_bases = re.compile(r'([ACTGNactgnYRWSKMDVHBXyrwskmdvhbx]+)') -__version__ = '0.3.4' +__version__ = '0.3.5' class FastaIndexingError(Exception):