fixed distribution

AUTHORS

@@ -0,0 +1,23 @@
+Andreas Heger, Martin Goodson, Tildon Grant Belgard, Leo Goodstadt
+all contributed to the code for pysam. Gerton Lunter advised.
+
+The sources in the directory samtools are from the samtools project:
+http://samtools.sourceforge.net/. All of these are available under the
+MIT licence. The attributions for this code are as follows:
+
+Heng Li from the Sanger Institute wrote most of the initial source codes
+of SAMtools and various converters.
+
+Bob Handsaker from the Broad Institute is a major contributor to the
+SAM/BAM specification. He designed and implemented the BGZF format, the
+underlying indexable compression format for the BAM format. BGZF does
+not support arithmetic between file offsets.
+
+Jue Ruan for the Beijing Genome Institute designed and implemented the
+RAZF format, an alternative indexable compression format. RAZF supports
+arithmetic between file offsets, at the cost of increased index file
+size and the full compatibility with gzip. RAZF is optional and only
+used in `faidx' for indexing RAZF compressed fasta files.
+
+Colin Hercus updated novo2sam.pl to support gapped alignment by
+novoalign.

COPYING

@@ -0,0 +1,21 @@
+The MIT License
+
+Copyright (c) 2008-2009 Genome Research Ltd.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

INSTALL

@@ -0,0 +1,40 @@
+System Requirements
+===================
+
+SAMtools depends on the zlib library <http://www.zlib.net>. The latest
+version 1.2.3 is preferred and with the latest version you can compile
+razip and use it to compress a FASTA file. SAMtools' faidx is able to
+index a razip-compressed FASTA file to save diskspace. Older zlib also
+works with SAMtools, but razip cannot be compiled.
+
+The text-based viewer (tview) requires the GNU ncurses library
+<http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and
+most of the modern Linux/Unix distributions. If you do not have this
+library installed, you can still compile the rest of SAMtools by
+manually modifying one line in Makefile.
+
+Pysam requires pyrex (0.9.8 or greater) and python (2.6 or greater).
+It has not been tested on many other platforms.
+
+Compilation
+===========
+
+Unpack the distribution and enter the pysam directory. Type 
+
+python setup.py build
+
+to compile.
+
+Installation
+============
+
+Type 
+
+   python setup.py install
+
+to install it within the site-packages directory of your python
+distribution. Type
+
+   python setup.py install --help 
+
+for more options.

MANIFEST.in

@@ -0,0 +1,14 @@
+#
+# Use .add_data_files and .add_data_dir methods in a appropriate
+# setup.py files to include non-python files such as documentation,
+# data, etc files to distribution. Avoid using MANIFEST.in for that.
+#
+include MANIFEST.in
+include COPYING
+include INSTALL
+include KNOWN_BUGS
+include THANKS
+include pysam/csamtools.pxd
+include pysam/pysam_util.h
+include samtools/*.h
+

doc/api.rst

@@ -24,8 +24,6 @@ To give::
     EAS51_64:3:190:727:308	0	102	<<<<<<<<<<<<<<<<<<<<<<<<<<<::<<<844	99	GGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGG	99	18	1
     ...
 
-
-
 You can also write to a :class:`~pysam.Samfile`::
 
    import pysam

pysam/csamtools.pyx

@@ -293,7 +293,7 @@ cdef class Samfile:
         return self.samfile.header.target_name[tid]
 
     def getNumReferences( self ):
-        """return the number of :ref:`reference` sequences."""
+        """return the number of :term:`reference` sequences."""
         return self.samfile.header.n_targets
 
     def _parseRegion( self, reference = None, start = None, end = None, 

setup.py

@@ -32,7 +32,6 @@
 from distutils.core import setup, Extension
 from Pyrex.Distutils import build_ext
 
-
 name = "pysam"
 version = "0.1"
 
@@ -49,10 +48,9 @@
 Topic :: Scientific/Engineering :: Bioinformatics
 """
 
-
 pysam = Extension(
     "pysam/csamtools",                   # name of extension
-    [ "pysam/csamtools.pyx",]  +\
+    [ "pysam/csamtools.pyx" ]  +\
        [ "pysam/%s" % x for x in (
              "pysam_util.c", )] +\
        glob.glob( os.path.join( "samtools", "*.c" ) ),
@@ -69,7 +67,7 @@
     'long_description': __doc__,
     'author': "Andreas Heger",
     'author_email': "[email protected]",
-    'license': "GPL",
+    'license': "MIT",
     'platforms': "ALL",
     'url': "http://code.google.com/p/pysam/",
     'py_modules': [