diff --git a/AUTHORS b/AUTHORS new file mode 100644 index 00000000..59988333 --- /dev/null +++ b/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. diff --git a/COPYING b/COPYING new file mode 100644 index 00000000..82fa2f4e --- /dev/null +++ b/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. \ No newline at end of file diff --git a/INSTALL b/INSTALL new file mode 100644 index 00000000..132e50c1 --- /dev/null +++ b/INSTALL @@ -0,0 +1,40 @@ +System Requirements +=================== + +SAMtools depends on the zlib library . 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 +, 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. diff --git a/KNOWN_BUGS b/KNOWN_BUGS new file mode 100644 index 00000000..e69de29b diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 00000000..cd0beee2 --- /dev/null +++ b/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 + diff --git a/doc/api.rst b/doc/api.rst index d80624f6..fada0d8f 100644 --- a/doc/api.rst +++ b/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 diff --git a/pysam/csamtools.pyx b/pysam/csamtools.pyx index 1ef39007..b469e784 100644 --- a/pysam/csamtools.pyx +++ b/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, diff --git a/setup.py b/setup.py index f9515d85..7a7ab7ea 100644 --- a/setup.py +++ b/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': "andreas.heger@gmail.com", - 'license': "GPL", + 'license': "MIT", 'platforms': "ALL", 'url': "http://code.google.com/p/pysam/", 'py_modules': [