.gitignore

+PyVCF.egg-info
+build
+dist
+*.pyc
+docs/_build
+.ropeproject
+1kg.prof
+.noseids
+.tox
+.DS_Store
+vcf/cparse.c
+vcf/cparse.so
+.coverage

.travis.yml

+# Validate this file using http://lint.travis-ci.org/
+language: python
+sudo: false
+cache:
+  directories:
+    - $HOME/.cache/pip
+python:
+  - "2.7"
+  - "3.4"
+  - "3.5"
+  - "3.6"
+  - "nightly"
+  - "pypy"
+  - "pypy3"
+install:
+  - if [[ "$TRAVIS_PYTHON_VERSION" =~ ^pypy ]]; then pip install -r requirements/pypy-requirements.txt; else pip install -r requirements/common-requirements.txt; fi
+  - python setup.py install
+script: python setup.py test

LICENSE

+Copyright (c) 2011-2012, Population Genetics Technologies Ltd, All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.  
+
+2. Redistributions in binary form must reproduce the above copyright notice, this
+list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.  
+
+3. Neither the name of the Population Genetics Technologies Ltd nor the names of
+its contributors may be used to endorse or promote products derived from this
+software without specific prior written permission.  
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+Copyright (c) 2011 John Dougherty
+
+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.

PKG-INFO

-Metadata-Version: 1.1
-Name: PyVCF
-Version: 0.6.8
-Summary: Variant Call Format (VCF) parser for Python
-Home-page: https://github.com/jamescasbon/PyVCF
-Author: James Casbon and @jdoughertyii
-Author-email: casbon@gmail.com
-License: UNKNOWN
-Description: UNKNOWN
-Keywords: bioinformatics
-Platform: UNKNOWN
-Classifier: Development Status :: 4 - Beta
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Cython
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 2
-Classifier: Programming Language :: Python :: 2.6
-Classifier: Programming Language :: Python :: 2.7
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.2
-Classifier: Programming Language :: Python :: 3.3
-Classifier: Programming Language :: Python :: 3.4
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics

debian/changelog

+python-pyvcf (0.6.8+git20170215.476169c-1) UNRELEASED; urgency=medium
+
+  * d/watch: use git mode
+  * drop unneeded get-orig-source target
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.5
+  * Testsuite: autopkgtest-pkg-python
+  * Lintian override for Suggests which is correct
+
+ -- Andreas Tille <tille@debian.org>  Wed, 18 Jul 2018 10:55:07 +0200
+
 python-pyvcf (0.6.8-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-10
+11

debian/control

@@ -2,8 +2,9 @@ Source: python-pyvcf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille@debian.org>
 Section: python
+Testsuite: autopkgtest-pkg-python
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                dh-python,
                cython,
                python-dev,
@@ -11,9 +12,9 @@ Build-Depends: debhelper (>= 10),
                cython3,
                python3-all-dev,
                python3-setuptools
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-pyvcf.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/python-pyvcf.git
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/python-pyvcf
+Vcs-Git: https://salsa.debian.org/med-team/python-pyvcf.git
 Homepage: https://pypi.python.org/pypi/PyVCF
 
 Package: python-pyvcf

debian/get-orig-source

-#!/bin/sh
-# Test-Data needs to be fetched separately from Git
-
-set -e
-
-PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-
-if ! echo $@ | grep -q upstream-version ; then
-    VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
-    uscan --verbose --force-download
-else
-    VERSION=`echo $@ | sed 's?^.*--upstream-version \([0-9.]\+\).*?\1?'`
-    if echo "$VERSION" | grep -q "upstream-version" ; then
-	echo "Unable to parse version number"
-        exit
-    fi
-fi
-
-TARDIR="$PKG"-"$VERSION"
-cd ..
-mkdir -p tarballs
-cd tarballs
-
-tar xaf ../PyVCF-${VERSION}.tar.gz
-mv PyVCF-${VERSION} ${TARDIR}
-find . -name "*.egg-info" -type d | xargs rm -rf
-git clone https://github.com/jamescasbon/PyVCF.git
-rsync -a --exclude '*.py' PyVCF/vcf/test ${TARDIR}/vcf
-
-GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX --exclude-vcs -caf "$PKG"_"$VERSION".orig.tar.xz ${TARDIR}
-rm -rf ${TARDIR} PyVCF

debian/lintian-overrides

+# The example package works for both Python versions
+python-pyvcf-examples: python-package-depends-on-package-from-other-python-variant Suggests: python3-pyvcf
+

debian/rules

@@ -27,6 +27,3 @@ override_dh_install:
 	    mv $${py} $(helperdir)/bin/`basename $${py} .py` ; \
 	done
 	rm -rf debian/python-$(PYBUILD_NAME)/usr/bin
-
-get-orig-source:
-	. debian/get-orig-source

debian/watch

-# Test-Data needs to be fetched separately from Git so wee need to call get-orig-source
 version=4
-http://pypi.debian.net/PyVCF/PyVCF-(.+)\.(?:tar(?:\.gz|\.bz2)?|tgz) \
-  debian debian/get-orig-source
+
+opts="mode=git,pretty=0.6.8+git%cd.%h" \
+    https://github.com/jamescasbon/PyVCF.git HEAD

docs/API.rst

+API
+===
+
+vcf.Reader
+----------
+
+.. autoclass:: vcf.Reader
+   :members:
+
+vcf.Writer
+----------
+
+.. autoclass:: vcf.Writer
+   :members:
+
+vcf.model._Record
+-----------------
+
+.. autoclass:: vcf.model._Record
+   :members:
+
+vcf.model._Call
+---------------
+
+.. autoclass:: vcf.model._Call
+   :members:
+
+vcf.model._AltRecord
+--------------------
+
+.. autoclass:: vcf.model._AltRecord
+   :members:
+
+vcf.model._Substitution
+-----------------------
+
+.. autoclass:: vcf.model._Substitution
+   :members:
+
+vcf.model._SV
+-------------
+
+.. autoclass:: vcf.model._SV
+   :members:
+
+vcf.model._SingleBreakend
+-------------------------
+
+.. autoclass:: vcf.model._SingleBreakend
+   :members:
+
+vcf.model._Breakend
+-------------------
+
+.. autoclass:: vcf.parser._Breakend
+   :members:

docs/FILTERS.rst

+Filtering VCF files
+===================
+
+The filter script: vcf_filter.py
+--------------------------------
+
+Filtering a VCF file based on some properties of interest is a common enough 
+operation that PyVCF offers an extensible script.  ``vcf_filter.py`` does 
+the work of reading input, updating the metadata and filtering the records.
+
+
+Existing Filters
+----------------
+
+.. autoclass:: vcf.filters.SiteQuality
+
+.. autoclass:: vcf.filters.VariantGenotypeQuality
+
+.. autoclass:: vcf.filters.ErrorBiasFilter
+
+.. autoclass:: vcf.filters.DepthPerSample
+
+.. autoclass:: vcf.filters.AvgDepthPerSample
+
+.. autoclass:: vcf.filters.SnpOnly
+
+
+
+
+Adding a filter
+---------------
+
+You can reuse this work by providing a filter class, rather than writing your own filter.
+For example, lets say I want to filter each site based on the quality of the site.
+I can create a class like this::
+   
+    import vcf.filters
+    class SiteQuality(vcf.filters.Base):
+        'Filter sites by quality'
+
+        name = 'sq'
+
+        @classmethod
+        def customize_parser(self, parser):
+            parser.add_argument('--site-quality', type=int, default=30,
+                    help='Filter sites below this quality')
+
+        def __init__(self, args):
+            self.threshold = args.site_quality
+
+        def __call__(self, record):
+            if record.QUAL < self.threshold:
+                return record.QUAL
+
+
+This class subclasses ``vcf.filters.Base`` which provides the interface for VCF filters.
+The docstring  and ``name`` are metadata about the parser.  The docstring provides
+the help for the script, and the first line is included in the FILTER metadata when 
+applied to a file.
+
+The ``customize_parser`` method allows you to add arguments to the script.
+We use the ``__init__`` method to grab the argument of interest from the parser.
+Finally, the ``__call__`` method processes each record and returns a value if the 
+filter failed.  The base class uses the ``name`` and ``threshold`` to create
+the filter ID in the VCF file.
+
+To make vcf_filter.py aware of the filter, you can either use the local script option
+or declare an entry point.  To use a local script, simply call vcf_filter::
+
+    $ vcf_filter.py --local-script my_filters.py ...
+
+To use an entry point, you need to declare a ``vcf.filters`` entry point in your ``setup``::
+
+    setup(
+        ...
+        entry_points = {
+            'vcf.filters': [
+                'site_quality = module.path:SiteQuality',
+            ]
+        }
+    )
+
+Either way, when you call vcf_filter.py, you should see your filter in the list of available filters::
+
+    usage: vcf_filter.py [-h] [--no-short-circuit] [--no-filtered] 
+                  [--output OUTPUT] [--local-script LOCAL_SCRIPT]
+                  input filter [filter_args] [filter [filter_args]] ...
+                
+
+    Filter a VCF file
+
+    positional arguments:
+      input                 File to process (use - for STDIN) (default: None)
+
+    optional arguments:
+      -h, --help            Show this help message and exit. (default: False)
+      --no-short-circuit    Do not stop filter processing on a site if any filter
+                            is triggered (default: False)
+      --output OUTPUT       Filename to output [STDOUT] (default: <open file
+                            '<stdout>', mode 'w' at 0x1002841e0>)
+      --no-filtered         Output only sites passing the filters (default: False)
+      --local-script LOCAL_SCRIPT
+                            Python file in current working directory with the
+                            filter classes (default: None)
+
+    sq:
+      Filter sites by quality
+
+      --site-quality SITE_QUALITY
+                            Filter sites below this quality (default: 30)
+
+The filter base class: vcf.filters.Base
+---------------------------------------
+
+.. autoclass:: vcf.filters.Base
+   :members:
+
+
+
+Utilities
+=========
+
+.. automodule:: vcf.utils
+
+Simultaneously iterate two or more files
+----------------------------------------
+
+.. autofunction:: vcf.utils.walk_together
+
+Trim common suffix
+--------------------
+.. autofunction:: vcf.utils.trim_common_suffix
+
+
+vcf_melt
+--------
+
+This script converts a VCF file from wide format (many calls per row) 
+to a long format (one call per row).  This is useful if you want to grep per sample
+or for really quick import into, say, a spreadsheet::
+
+    $ vcf_melt < vcf/test/gatk.vcf 
+    SAMPLE	AD	DP	GQ	GT	PL	FILTER	CHROM	POS	REF	ALT	ID	info.AC	info.AF	info.AN	info.BaseQRankSum	info.DB	info.DP	info.DS	info.Dels	info.FS	info.HRun	info.HaplotypeScore	info.InbreedingCoeff	info.MQ	info.MQ0	info.MQRankSum	info.QD	info.ReadPosRankSum
+    BLANK	6,0	6	18.04	0/0	0,18,211	.	chr22	42522392	G	[A]	rs28371738	2	0.143	14	0.375	True	1506	True	0.0	0.0	0	123.5516		253.92	0	0.685	5.9	0.59
+    NA12878	138,107	250	99.0	0/1	1961,0,3049	.	chr22	42522392	G	[A]	rs28371738	2	0.143	14	0.375	True	1506	True	0.0	0.0	0	123.5516		253.92	0	0.685	5.9	0.59
+    NA12891	169,77	250	99.0	0/1	1038,0,3533	.	chr22	42522392	G	[A]	rs28371738	2	0.143	14	0.375	True	1506	True	0.0	0.0	0	123.5516		253.92	0	0.685	5.9	0.59
+    NA12892	249,0	250	99.0	0/0	0,600,5732	.	chr22	42522392	G	[A]	rs28371738	2	0.143	14	0.375	True	1506	True	0.0	0.0	0	123.5516		253.92	0	0.685	5.9	0.59
+    NA19238	248,1	250	99.0	0/0	0,627,6191	.	chr22	42522392	G	[A]	rs28371738	2	0.143	14	0.375	True	1506	True	0.0	0.0	0	123.5516		253.92	0	0.685	5.9	0.59
+    NA19239	250,0	250	99.0	0/0	0,615,5899	.	chr22	42522392	G	[A]	rs28371738	2	0.143	14	0.375	True	1506	True	0.0	0.0	0	123.5516		253.92	0	0.685	5.9	0.59
+    NA19240	250,0	250	99.0	0/0	0,579,5674	.	chr22	42522392	G	[A]	rs28371738	2	0.143	14	0.375	True	1506	True	0.0	0.0	0	123.5516		253.92	0	0.685	5.9	0.59
+    BLANK	13,4	17	62.64	0/1	63,0,296	.	chr22	42522613	G	[C]	rs1135840	6	0.429	14	16.289	True	1518	True	0.03	0.0	0	142.5716		242.46	0	2.01	9.16	-1.731
+    NA12878	118,127	246	99.0	0/1	2396,0,1719	.	chr22	42522613	G	[C]	rs1135840	6	0.429	14	16.289	True	1518	True	0.03	0.0	0	142.5716		242.46	0	2.01	9.16	-1.731
+    NA12891	241,0	244	99.0	0/0	0,459,4476	.	chr22	42522613	G	[C]	rs1135840	6	0.429	14	16.289	True	1518	True	0.03	0.0	0	142.5716		242.46	0	2.01	9.16	-1.731
+    NA12892	161,85	246	99.0	0/1	1489,0,2353	.	chr22	42522613	G	[C]	rs1135840	6	0.429	14	16.289	True	1518	True	0.03	0.0	0	142.5716		242.46	0	2.01	9.16	-1.731
+    NA19238	110,132	242	99.0	0/1	2561,0,1488	.	chr22	42522613	G	[C]	rs1135840	6	0.429	14	16.289	True	1518	True	0.03	0.0	0	142.5716		242.46	0	2.01	9.16	-1.731
+    NA19239	106,135	242	99.0	0/1	2613,0,1389	.	chr22	42522613	G	[C]	rs1135840	6	0.429	14	16.289	True	1518	True	0.03	0.0	0	142.5716		242.46	0	2.01	9.16	-1.731
+    NA19240	116,126	243	99.0	0/1	2489,0,1537	.	chr22	42522613	G	[C]	rs1135840	6	0.429	14	16.289	True	1518	True	0.03	0.0	0	142.5716		242.46	0	2.01	9.16	-1.731
+

docs/HISTORY.rst

+Development
+===========
+
+Please use the `PyVCF repository <https://github.com/jamescasbon/PyVCF/>`_.
+Pull requests gladly accepted.
+Issues should be reported at the github issue tracker.
+
+Running tests
+-------------
+
+Please check the tests by running them with::
+
+    python setup.py test
+
+New features should have test code sent with them.
+
+Changes
+=======
+
+0.6.7 Release
+-------------
+
+* Include missing .pyx files
+
+0.6.6 Release
+-------------
+
+* better walk together record ordering (Thanks @datagram, #141)
+
+0.6.5 Release
+-------------
+
+* Better contig handling (#115, #116, #119 thanks Martijn)
+* INFO lines with type character (#120, #121 thanks @AndrewUzilov, Martijn)
+* Single breakends fix (#126 thanks @pkrushe)
+* Speedup by losing ordering of INFO (#128 thanks Martijn)
+* HOMSEQ and other missing fields in INFO (#130 thanks Martijn)
+* Add aaf property, (thanks @mgymrek #131)
+* Custom equality for walk_together, thanks bow #132
+* Change default line encoding to '\n'
+* Improved __eq__ (#134, thanks bow)
+
+
+0.6.4 Release
+-------------
+
+* Handle INFO fields with multiple values, thanks
+* Support writing records without GT data #88, thanks @bow
+* Pickleable call data #112, thanks @superbobry
+* Write files without FORMAT #95 thanks Martijn
+* Strict whitespace mode, thanks Martijn, Lee Lichtenstein and Manawsi Gupta
+* Add support for contigs in header, thanks @gcnh and Martijn
+* Fix GATK header parsing, thanks @alimanfoo
+
+0.6.3 Release
+-------------
+
+* cython port of #79
+* correct writing of meta lines #84
+
+0.6.2 Release
+-------------
+
+* issues #78, #79 (thanks Sean, Brad)
+
+0.6.1 Release
+-------------
+
+* Add strict whitespace mode for well formed VCFs with spaces
+  in sample names (thanks Marco)
+* Ignore blank lines in files (thanks Martijn)
+* Tweaks for handling missing data (thanks Sean)
+* bcftools tests (thanks Martijn)
+* record.FILTER is always a list
+
+0.6.0 Release
+-------------
+
+* Backwards incompatible change: _Call.data is now a
+  namedtuple (previously it was a dict)
+* Optional cython version, much improved performance.
+* Improvements to writer (thanks @cmclean)
+* Improvements to inheritance of classes (thanks @lennax)
+
+
+0.5.0 Release
+-------------
+
+* VCF 4.1 support:
+  - support missing genotype #28 (thanks @martijnvermaat)
+  - parseALT for svs #42, #48 (thanks @dzerbino)
+* `trim_common_suffix` method #22 (thanks @martijnvermaat)
+* Multiple metadata with the same key is stored (#52)
+* Writer improvements:
+  - A/G in Number INFO fields #53 (thanks @lennax)
+  - Better output #55 (thanks @cmclean)
+* Allow malformed INFO fields #49 (thanks @ilyaminkin)
+* Added bayes factor error bias VCF filter
+* Added docs on vcf_melt
+* filters from @libor-m (SNP only, depth per sample, avg depth per sample)
+* change to the filter API, use docstring for filter description
+
+0.4.6 Release
+-------------
+
+* Performance improvements (#47)
+* Preserve order of INFO column (#46)
+
+0.4.5 Release
+-------------
+
+* Support exponent syntax qual values (#43, #44) (thanks @martijnvermaat)
+* Preserve order of header lines (#45)
+
+0.4.4 Release
+-------------
+
+* Support whitespace in sample names
+* SV work (thanks @arq5x)
+* Python 3 support via 2to3 (thanks @marcelm)
+* Improved filtering script, capable of importing local files
+
+0.4.3 Release
+-------------
+
+* Single floats in Reader._sample_parser not being converted to float #35
+* Handle String INFO values when Number=1 in header #34
+
+0.4.2 Release
+-------------
+
+* Installation problems
+
+0.4.1 Release
+-------------
+
+* Installation problems
+
+0.4.0 Release
+-------------
+
+* Package structure
+* add ``vcf.utils`` module with ``walk_together`` method
+* samtools tests
+* support Freebayes' non standard '.' for no call
+* fix vcf_melt
+* support monomorphic sites, add ``is_monomorphic`` method, handle null QUALs
+* filter support for files with monomorphic calls
+* Values declared as single are no-longer returned in lists
+* several performance improvements
+
+
+0.3.0 Release
+-------------
+
+* Fix setup.py for python < 2.7
+* Add ``__eq__`` to ``_Record`` and ``_Call``
+* Add ``is_het`` and ``is_variant`` to ``_Call``
+* Drop aggressive parse mode: we're always aggressive.
+* Add tabix fetch for single calls, fix one->zero based indexing
+* add prepend_chr mode for ``Reader`` to add `chr` to CHROM attributes
+
+0.2.2 Release
+-------------
+
+Documentation release
+
+0.2.1 Release
+-------------
+
+* Add shebang to vcf_filter.py
+
+0.2 Release
+-----------
+
+* Replace genotype dictionary with a ``Call`` object
+* Methods on ``Record`` and ``Call`` (thanks @arq5x)
+* Shortcut parse_sample when genotype is None
+
+0.1 Release
+-----------
+
+* Added test code
+* Added Writer class
+* Allow negative number in ``INFO`` and ``FORMAT`` fields (thanks @martijnvermaat)
+* Prefer ``vcf.Reader`` to ``vcf.VCFReader``
+* Support compressed files with guessing where filename is available on fsock
+* Allow opening by filename as well as filesocket
+* Support fetching rows for tabixed indexed files
+* Performance improvements (see ``test/prof.py``)
+* Added extensible filter script (see FILTERS.md), vcf_filter.py
+
+Contributions
+=============
+
+Project started by @jdoughertyii and taken over by @jamescasbon on 12th January 2011.
+Contributions from @arq5x, @brentp, @martijnvermaat, @ian1roberts, @marcelm.
+
+This project was supported by `Population Genetics <http://www.populationgenetics.com/>`_.

docs/INTRO.rst

+Introduction
+============
+
+.. include:: ../README.rst

docs/Makefile

+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/PyVCF.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/PyVCF.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/PyVCF"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/PyVCF"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	make -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."

docs/conf.py

+# -*- coding: utf-8 -*-
+#
+# PyVCF documentation build configuration file, created by
+# sphinx-quickstart on Wed Jan 25 12:29:23 2012.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+sys.path.insert(0, os.path.abspath('..'))
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.viewcode']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['.templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'PyVCF'
+copyright = u'2012, James Casbon, @jdoughertyii'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+import vcf
+version = vcf.VERSION
+# The full version, including alpha/beta/rc tags.
+release = vcf.VERSION
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['.build']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['.static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'PyVCFdoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'PyVCF.tex', u'PyVCF Documentation',
+   u'James Casbon, @jdoughertyii', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'pyvcf', u'PyVCF Documentation',
+     [u'James Casbon, @jdoughertyii'], 1)
+]

docs/index.rst

+
+PyVCF - A Variant Call Format Parser for Python 
+===============================================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   INTRO
+   API
+   FILTERS
+   HISTORY
+   
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

requirements/common-requirements.txt

+cython
+pysam!=0.8.0
+setuptools

requirements/pypy-requirements.txt

+setuptools