=============
2011-04-21
- refactoring of GenomicArray class:
- field ``step_vectors`` replaced with ``chrom_vector``. These now contain
dicts of dicts of ``ChromVector`` objects rather than ``StepVector`` ones.
- ``chrom_vectors`` is now always a dict of dict, even for unstranded GenomicArrays
to make it easier to loop over them. (The inner dict has either keys ``"+"``
and ``"-"``, or just one key, ``"."``.)
- The new ``ChromVector`` class wraps the actual vector and supports three different
storage modes: ``step``, ``ndarray`` and ``memmap``, the latter two being numpy
arrays, without and with memory mapping.
- The ``GenomicArray`` constructor now take two new arguments, one for the storage
class, one for the memmap directory (if needed).
- The ``add_value`` methods had been replaced with an ``__iadd__`` method, to
enable the ``+=`` semantics.
- Similarily, ``+=`` for ``GenomicArrayOfSets`` adds an element to the sets.
- Instead of ``get_steps``, now use ``steps``.
- new parser class ``VCF_Reader`` and record class ``VariantCall``
- new parser class ``BAM_Reader``, to add BAM support (including indexed random access)
(requires PySam to be installed)
- new documentation page :ref:`tss`
- ``Fasta_Reader`` now allows indexed access to Fasta files (requires Pysam to be
installed)
- peek function removed
Patch Versions:
- v0.5.0p1 (2011-04-22):
- build was incomplete; fixed
- v0.5.0p2 (2011-04-22):
- build was still faulty; new try
- v0.5.0p3 (2011-04-26)
- fixed regression bug in htseq-count