Rnachipintegrator

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* Fix the broken ``--promoter_region`` option which was being
ignored.

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* ``--compact`` now only changes the output format from "multi-line"
(i.e. one hit pair per line) to "single-line" (i.e. all hits on
the same line). The same fields are reported in both modes.
* The explanatory text for the dist_closest field has been updated
to make it clearer what this means.

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* Executable now installs as ``RnaChipIntegrator`` (i.e. no ``.py``
extension)
* Specify feature type (e.g. ``gene``, ``transcript`` etc) to be used
in output using ``--feature`` option.
* New ``direction`` field in output indicates whether hits are
up- or downstream from reference.
* Specify arbitrary columns from input peaks file using new
``--peak_cols`` options to set chromosome, start and end.
* ``--pad`` option is automatically implied by the ``--compact``
option (i.e. single line output is always padded).

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* Complete reimplementation of RnaChipIntegrator to unify internal
algorithms, simplify usage and substantially update the
documentation.
* No distinction is now made between 'summits' and 'peaks'; the
same algorithm is applied in each case.
* The program always finds the nearest features to each peak, and
vice versa. The same distance cutoff and maximum number of hits
are applied to both and can be specified using the ``--cutoff``
and ``--number`` options.
* By default nearest distances between peaks and features are
calculated from the TSS of the feature to whichever of the peak
edges are closer; alternatively distances can be calculated
between the nearest pair of peak/feature edges by specifying the
``--edge=both`` option.
* Any differential expression flags in the input features file
are ignored unless the ``--only-DE`` option is specified, in which
case only the differentially expressed features are considered
in the analyses.
* By default each peak/feature pair is reported on a separate
line; the ``--compact`` option reports all nearest features/peaks
on a single line of output.
* Excel output is only produced if the ``--xls`` option is specified;
summary output is only produced if ``--summary`` is specified.
* The ``rearrange_columns.py`` utility has been dropped.

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* Use ``/usr/bin/env`` rather than ``/bin/env`` to invoke Python
interpreter in RnaChipIntegrator.py (was broken for e.g. Ubuntu
linux).

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* Update ``--pad`` output so that requested number of lines appears
for peaks even when there are no hits, and "empty" lines contain
the chromosome, start and end positions for the peak in question.

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