[med-svn] [python-bx] 02/09: New upstream version 0.7.4
Steffen Möller
moeller at moszumanska.debian.org
Sat Jan 14 11:13:02 UTC 2017
This is an automated email from the git hooks/post-receive script.
moeller pushed a commit to branch master
in repository python-bx.
commit e7bcf977e01a9f320840f3a50a28e0c4e56d1d45
Author: Steffen Moeller <moeller at debian.org>
Date: Fri Jan 13 11:34:00 2017 +0100
New upstream version 0.7.4
---
.hgignore => .gitignore | 5 +-
.hg_archival.txt | 6 -
.hgtags | 1 -
.travis.yml | 25 +
README.md | 25 +
distribute_setup.py | 546 -
ez_setup.py | 391 +
lib/bx/bbi/bbi_file.c | 11136 ++++++++++-----------
lib/bx/bbi/bbi_file.pyx | 94 +-
lib/bx/bbi/bigbed_file.c | 7127 ++++++-------
lib/bx/bbi/bigbed_file.pyx | 44 +-
lib/bx/bbi/bigwig_file.c | 9666 +++++++++---------
lib/bx/bbi/bigwig_file.pyx | 60 +-
lib/bx/bbi/bigwig_tests.py | 8 +-
lib/bx/phylo/newick_tests.py | 7 +-
lib/bx/seqmapping_tests.py | 15 +-
script_tests/bnMapper_tests.py | 3 +-
script_tests/maf_extract_ranges_indexed_tests.py | 2 +-
script_tests/out_to_chain_tests.py | 3 +-
scripts/bnMapper.py | 2 +-
setup.cfg | 12 +-
setup.py | 80 +-
22 files changed, 13608 insertions(+), 15650 deletions(-)
diff --git a/.hgignore b/.gitignore
similarity index 89%
rename from .hgignore
rename to .gitignore
index b619417..f4b5694 100644
--- a/.hgignore
+++ b/.gitignore
@@ -1,5 +1,3 @@
-syntax: glob
-
# Build directory
build
@@ -21,3 +19,6 @@ bx_python.egg-info
# nose egg
nose*.egg
+
+# .eggs directory
+.eggs
diff --git a/.hg_archival.txt b/.hg_archival.txt
deleted file mode 100644
index b52ef42..0000000
--- a/.hg_archival.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-repo: 075807ec108016807156d50f8618799cb107c128
-node: da37e3aa45dc610ab4fc2f60949de90f93f84401
-branch: default
-latesttag: bnMapper freeze
-latesttagdistance: 9
-changessincelatesttag: 11
diff --git a/.hgtags b/.hgtags
deleted file mode 100644
index a02cc1b..0000000
--- a/.hgtags
+++ /dev/null
@@ -1 +0,0 @@
-83b6d153f88995ad6e223391281b4442e1f38f5a bnMapper freeze
diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..2664193
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,25 @@
+language: python
+sudo: false
+os:
+ - linux
+ ## - osx
+python:
+ - 2.7
+addons:
+ apt:
+ packages:
+ - liblzo2-dev
+before_install:
+ # Use miniconda for dependencies, pip is too slow -- https://gist.github.com/zonca/9958333
+ - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+ - chmod +x miniconda.sh
+ - ./miniconda.sh -b
+ - export PATH=/home/travis/miniconda2/bin:$PATH
+ - conda update --yes conda
+install:
+ - conda create --yes -n testenv python=$TRAVIS_PYTHON_VERSION Cython numpy nose
+ - source activate testenv
+ - python setup.py build_ext --inplace
+ - python setup.py install
+script:
+ - nosetests
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..86eee22
--- /dev/null
+++ b/README.md
@@ -0,0 +1,25 @@
+[](https://travis-ci.org/bxlab/bx-python)
+
+# bx-python
+
+The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are:
+
+ * Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats)
+ * Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optomized for use over network filesystems)
+ * Data structures for working with intervals on sequences
+ * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly
+ * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation
+
+## Installing
+
+The package can be installed with pip:
+
+```pip install bx-python```
+
+It is available in [bioconda](https://anaconda.org/bioconda/bx-python) (recommended):
+
+```conda install -c bioconda bx-python```
+
+Or can be built from a checkout of the repository:
+
+```python setup.py install```
diff --git a/distribute_setup.py b/distribute_setup.py
deleted file mode 100644
index a447f7e..0000000
--- a/distribute_setup.py
+++ /dev/null
@@ -1,546 +0,0 @@
-#!python
-"""Bootstrap distribute installation
-
-If you want to use setuptools in your package's setup.py, just include this
-file in the same directory with it, and add this to the top of your setup.py::
-
- from distribute_setup import use_setuptools
- use_setuptools()
-
-If you want to require a specific version of setuptools, set a download
-mirror, or use an alternate download directory, you can do so by supplying
-the appropriate options to ``use_setuptools()``.
-
-This file can also be run as a script to install or upgrade setuptools.
-"""
-import os
-import shutil
-import sys
-import time
-import fnmatch
-import tempfile
-import tarfile
-import optparse
-
-from distutils import log
-
-try:
- from site import USER_SITE
-except ImportError:
- USER_SITE = None
-
-try:
- import subprocess
-
- def _python_cmd(*args):
- args = (sys.executable,) + args
- return subprocess.call(args) == 0
-
-except ImportError:
- # will be used for python 2.3
- def _python_cmd(*args):
- args = (sys.executable,) + args
- # quoting arguments if windows
- if sys.platform == 'win32':
- def quote(arg):
- if ' ' in arg:
- return '"%s"' % arg
- return arg
- args = [quote(arg) for arg in args]
- return os.spawnl(os.P_WAIT, sys.executable, *args) == 0
-
-DEFAULT_VERSION = "0.6.35"
-DEFAULT_URL = "http://pypi.python.org/packages/source/d/distribute/"
-SETUPTOOLS_FAKED_VERSION = "0.6c11"
-
-SETUPTOOLS_PKG_INFO = """\
-Metadata-Version: 1.0
-Name: setuptools
-Version: %s
-Summary: xxxx
-Home-page: xxx
-Author: xxx
-Author-email: xxx
-License: xxx
-Description: xxx
-""" % SETUPTOOLS_FAKED_VERSION
-
-
-def _install(tarball, install_args=()):
- # extracting the tarball
- tmpdir = tempfile.mkdtemp()
- log.warn('Extracting in %s', tmpdir)
- old_wd = os.getcwd()
- try:
- os.chdir(tmpdir)
- tar = tarfile.open(tarball)
- _extractall(tar)
- tar.close()
-
- # going in the directory
- subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
- os.chdir(subdir)
- log.warn('Now working in %s', subdir)
-
- # installing
- log.warn('Installing Distribute')
- if not _python_cmd('setup.py', 'install', *install_args):
- log.warn('Something went wrong during the installation.')
- log.warn('See the error message above.')
- # exitcode will be 2
- return 2
- finally:
- os.chdir(old_wd)
- shutil.rmtree(tmpdir)
-
-
-def _build_egg(egg, tarball, to_dir):
- # extracting the tarball
- tmpdir = tempfile.mkdtemp()
- log.warn('Extracting in %s', tmpdir)
- old_wd = os.getcwd()
- try:
- os.chdir(tmpdir)
- tar = tarfile.open(tarball)
- _extractall(tar)
- tar.close()
-
- # going in the directory
- subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
- os.chdir(subdir)
- log.warn('Now working in %s', subdir)
-
- # building an egg
- log.warn('Building a Distribute egg in %s', to_dir)
- _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir)
-
- finally:
- os.chdir(old_wd)
- shutil.rmtree(tmpdir)
- # returning the result
- log.warn(egg)
- if not os.path.exists(egg):
- raise IOError('Could not build the egg.')
-
-
-def _do_download(version, download_base, to_dir, download_delay):
- egg = os.path.join(to_dir, 'distribute-%s-py%d.%d.egg'
- % (version, sys.version_info[0], sys.version_info[1]))
- if not os.path.exists(egg):
- tarball = download_setuptools(version, download_base,
- to_dir, download_delay)
- _build_egg(egg, tarball, to_dir)
- sys.path.insert(0, egg)
- import setuptools
- setuptools.bootstrap_install_from = egg
-
-
-def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
- to_dir=os.curdir, download_delay=15, no_fake=True):
- # making sure we use the absolute path
- to_dir = os.path.abspath(to_dir)
- was_imported = 'pkg_resources' in sys.modules or \
- 'setuptools' in sys.modules
- try:
- try:
- import pkg_resources
- if not hasattr(pkg_resources, '_distribute'):
- if not no_fake:
- _fake_setuptools()
- raise ImportError
- except ImportError:
- return _do_download(version, download_base, to_dir, download_delay)
- try:
- pkg_resources.require("distribute>=" + version)
- return
- except pkg_resources.VersionConflict:
- e = sys.exc_info()[1]
- if was_imported:
- sys.stderr.write(
- "The required version of distribute (>=%s) is not available,\n"
- "and can't be installed while this script is running. Please\n"
- "install a more recent version first, using\n"
- "'easy_install -U distribute'."
- "\n\n(Currently using %r)\n" % (version, e.args[0]))
- sys.exit(2)
- else:
- del pkg_resources, sys.modules['pkg_resources'] # reload ok
- return _do_download(version, download_base, to_dir,
- download_delay)
- except pkg_resources.DistributionNotFound:
- return _do_download(version, download_base, to_dir,
- download_delay)
- finally:
- if not no_fake:
- _create_fake_setuptools_pkg_info(to_dir)
-
-
-def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
- to_dir=os.curdir, delay=15):
- """Download distribute from a specified location and return its filename
-
- `version` should be a valid distribute version number that is available
- as an egg for download under the `download_base` URL (which should end
- with a '/'). `to_dir` is the directory where the egg will be downloaded.
- `delay` is the number of seconds to pause before an actual download
- attempt.
- """
- # making sure we use the absolute path
- to_dir = os.path.abspath(to_dir)
- try:
- from urllib.request import urlopen
- except ImportError:
- from urllib2 import urlopen
- tgz_name = "distribute-%s.tar.gz" % version
- url = download_base + tgz_name
- saveto = os.path.join(to_dir, tgz_name)
- src = dst = None
- if not os.path.exists(saveto): # Avoid repeated downloads
- try:
- log.warn("Downloading %s", url)
- src = urlopen(url)
- # Read/write all in one block, so we don't create a corrupt file
- # if the download is interrupted.
- data = src.read()
- dst = open(saveto, "wb")
- dst.write(data)
- finally:
- if src:
- src.close()
- if dst:
- dst.close()
- return os.path.realpath(saveto)
-
-
-def _no_sandbox(function):
- def __no_sandbox(*args, **kw):
- try:
- from setuptools.sandbox import DirectorySandbox
- if not hasattr(DirectorySandbox, '_old'):
- def violation(*args):
- pass
- DirectorySandbox._old = DirectorySandbox._violation
- DirectorySandbox._violation = violation
- patched = True
- else:
- patched = False
- except ImportError:
- patched = False
-
- try:
- return function(*args, **kw)
- finally:
- if patched:
- DirectorySandbox._violation = DirectorySandbox._old
- del DirectorySandbox._old
-
- return __no_sandbox
-
-
-def _patch_file(path, content):
- """Will backup the file then patch it"""
- f = open(path)
- existing_content = f.read()
- f.close()
- if existing_content == content:
- # already patched
- log.warn('Already patched.')
- return False
- log.warn('Patching...')
- _rename_path(path)
- f = open(path, 'w')
- try:
- f.write(content)
- finally:
- f.close()
- return True
-
-_patch_file = _no_sandbox(_patch_file)
-
-
-def _same_content(path, content):
- f = open(path)
- existing_content = f.read()
- f.close()
- return existing_content == content
-
-
-def _rename_path(path):
- new_name = path + '.OLD.%s' % time.time()
- log.warn('Renaming %s to %s', path, new_name)
- os.rename(path, new_name)
- return new_name
-
-
-def _remove_flat_installation(placeholder):
- if not os.path.isdir(placeholder):
- log.warn('Unkown installation at %s', placeholder)
- return False
- found = False
- for file in os.listdir(placeholder):
- if fnmatch.fnmatch(file, 'setuptools*.egg-info'):
- found = True
- break
- if not found:
- log.warn('Could not locate setuptools*.egg-info')
- return
-
- log.warn('Moving elements out of the way...')
- pkg_info = os.path.join(placeholder, file)
- if os.path.isdir(pkg_info):
- patched = _patch_egg_dir(pkg_info)
- else:
- patched = _patch_file(pkg_info, SETUPTOOLS_PKG_INFO)
-
- if not patched:
- log.warn('%s already patched.', pkg_info)
- return False
- # now let's move the files out of the way
- for element in ('setuptools', 'pkg_resources.py', 'site.py'):
- element = os.path.join(placeholder, element)
- if os.path.exists(element):
- _rename_path(element)
- else:
- log.warn('Could not find the %s element of the '
- 'Setuptools distribution', element)
- return True
-
-_remove_flat_installation = _no_sandbox(_remove_flat_installation)
-
-
-def _after_install(dist):
- log.warn('After install bootstrap.')
- placeholder = dist.get_command_obj('install').install_purelib
- _create_fake_setuptools_pkg_info(placeholder)
-
-
-def _create_fake_setuptools_pkg_info(placeholder):
- if not placeholder or not os.path.exists(placeholder):
- log.warn('Could not find the install location')
- return
- pyver = '%s.%s' % (sys.version_info[0], sys.version_info[1])
- setuptools_file = 'setuptools-%s-py%s.egg-info' % \
- (SETUPTOOLS_FAKED_VERSION, pyver)
- pkg_info = os.path.join(placeholder, setuptools_file)
- if os.path.exists(pkg_info):
- log.warn('%s already exists', pkg_info)
- return
-
- log.warn('Creating %s', pkg_info)
- try:
- f = open(pkg_info, 'w')
- except EnvironmentError:
- log.warn("Don't have permissions to write %s, skipping", pkg_info)
- return
- try:
- f.write(SETUPTOOLS_PKG_INFO)
- finally:
- f.close()
-
- pth_file = os.path.join(placeholder, 'setuptools.pth')
- log.warn('Creating %s', pth_file)
- f = open(pth_file, 'w')
- try:
- f.write(os.path.join(os.curdir, setuptools_file))
- finally:
- f.close()
-
-_create_fake_setuptools_pkg_info = _no_sandbox(
- _create_fake_setuptools_pkg_info
-)
-
-
-def _patch_egg_dir(path):
- # let's check if it's already patched
- pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO')
- if os.path.exists(pkg_info):
- if _same_content(pkg_info, SETUPTOOLS_PKG_INFO):
- log.warn('%s already patched.', pkg_info)
- return False
- _rename_path(path)
- os.mkdir(path)
- os.mkdir(os.path.join(path, 'EGG-INFO'))
- pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO')
- f = open(pkg_info, 'w')
- try:
- f.write(SETUPTOOLS_PKG_INFO)
- finally:
- f.close()
- return True
-
-_patch_egg_dir = _no_sandbox(_patch_egg_dir)
-
-
-def _before_install():
- log.warn('Before install bootstrap.')
- _fake_setuptools()
-
-
-def _under_prefix(location):
- if 'install' not in sys.argv:
- return True
- args = sys.argv[sys.argv.index('install') + 1:]
- for index, arg in enumerate(args):
- for option in ('--root', '--prefix'):
- if arg.startswith('%s=' % option):
- top_dir = arg.split('root=')[-1]
- return location.startswith(top_dir)
- elif arg == option:
- if len(args) > index:
- top_dir = args[index + 1]
- return location.startswith(top_dir)
- if arg == '--user' and USER_SITE is not None:
- return location.startswith(USER_SITE)
- return True
-
-
-def _fake_setuptools():
- log.warn('Scanning installed packages')
- try:
- import pkg_resources
- except ImportError:
- # we're cool
- log.warn('Setuptools or Distribute does not seem to be installed.')
- return
- ws = pkg_resources.working_set
- try:
- setuptools_dist = ws.find(
- pkg_resources.Requirement.parse('setuptools', replacement=False)
- )
- except TypeError:
- # old distribute API
- setuptools_dist = ws.find(
- pkg_resources.Requirement.parse('setuptools')
- )
-
- if setuptools_dist is None:
- log.warn('No setuptools distribution found')
- return
- # detecting if it was already faked
- setuptools_location = setuptools_dist.location
- log.warn('Setuptools installation detected at %s', setuptools_location)
-
- # if --root or --preix was provided, and if
- # setuptools is not located in them, we don't patch it
- if not _under_prefix(setuptools_location):
- log.warn('Not patching, --root or --prefix is installing Distribute'
- ' in another location')
- return
-
- # let's see if its an egg
- if not setuptools_location.endswith('.egg'):
- log.warn('Non-egg installation')
- res = _remove_flat_installation(setuptools_location)
- if not res:
- return
- else:
- log.warn('Egg installation')
- pkg_info = os.path.join(setuptools_location, 'EGG-INFO', 'PKG-INFO')
- if (os.path.exists(pkg_info) and
- _same_content(pkg_info, SETUPTOOLS_PKG_INFO)):
- log.warn('Already patched.')
- return
- log.warn('Patching...')
- # let's create a fake egg replacing setuptools one
- res = _patch_egg_dir(setuptools_location)
- if not res:
- return
- log.warn('Patching complete.')
- _relaunch()
-
-
-def _relaunch():
- log.warn('Relaunching...')
- # we have to relaunch the process
- # pip marker to avoid a relaunch bug
- _cmd1 = ['-c', 'install', '--single-version-externally-managed']
- _cmd2 = ['-c', 'install', '--record']
- if sys.argv[:3] == _cmd1 or sys.argv[:3] == _cmd2:
- sys.argv[0] = 'setup.py'
- args = [sys.executable] + sys.argv
- sys.exit(subprocess.call(args))
-
-
-def _extractall(self, path=".", members=None):
- """Extract all members from the archive to the current working
- directory and set owner, modification time and permissions on
- directories afterwards. `path' specifies a different directory
- to extract to. `members' is optional and must be a subset of the
- list returned by getmembers().
- """
- import copy
- import operator
- from tarfile import ExtractError
- directories = []
-
- if members is None:
- members = self
-
- for tarinfo in members:
- if tarinfo.isdir():
- # Extract directories with a safe mode.
- directories.append(tarinfo)
- tarinfo = copy.copy(tarinfo)
- tarinfo.mode = 448 # decimal for oct 0700
- self.extract(tarinfo, path)
-
- # Reverse sort directories.
- if sys.version_info < (2, 4):
- def sorter(dir1, dir2):
- return cmp(dir1.name, dir2.name)
- directories.sort(sorter)
- directories.reverse()
- else:
- directories.sort(key=operator.attrgetter('name'), reverse=True)
-
- # Set correct owner, mtime and filemode on directories.
- for tarinfo in directories:
- dirpath = os.path.join(path, tarinfo.name)
- try:
- self.chown(tarinfo, dirpath)
- self.utime(tarinfo, dirpath)
- self.chmod(tarinfo, dirpath)
- except ExtractError:
- e = sys.exc_info()[1]
- if self.errorlevel > 1:
- raise
- else:
- self._dbg(1, "tarfile: %s" % e)
-
-
-def _build_install_args(options):
- """
- Build the arguments to 'python setup.py install' on the distribute package
- """
- install_args = []
- if options.user_install:
- if sys.version_info < (2, 6):
- log.warn("--user requires Python 2.6 or later")
- raise SystemExit(1)
- install_args.append('--user')
- return install_args
-
-def _parse_args():
- """
- Parse the command line for options
- """
- parser = optparse.OptionParser()
- parser.add_option(
- '--user', dest='user_install', action='store_true', default=False,
- help='install in user site package (requires Python 2.6 or later)')
- parser.add_option(
- '--download-base', dest='download_base', metavar="URL",
- default=DEFAULT_URL,
- help='alternative URL from where to download the distribute package')
- options, args = parser.parse_args()
- # positional arguments are ignored
- return options
-
-def main(version=DEFAULT_VERSION):
- """Install or upgrade setuptools and EasyInstall"""
- options = _parse_args()
- tarball = download_setuptools(download_base=options.download_base)
- return _install(tarball, _build_install_args(options))
-
-if __name__ == '__main__':
- sys.exit(main())
diff --git a/ez_setup.py b/ez_setup.py
new file mode 100644
index 0000000..3762bd8
--- /dev/null
+++ b/ez_setup.py
@@ -0,0 +1,391 @@
+#!/usr/bin/env python
+
+"""
+Setuptools bootstrapping installer.
+
+Run this script to install or upgrade setuptools.
+"""
+
+import os
+import shutil
+import sys
+import tempfile
+import zipfile
+import optparse
+import subprocess
+import platform
+import textwrap
+import contextlib
+import warnings
+
+from distutils import log
+
+try:
+ from urllib.request import urlopen
+except ImportError:
+ from urllib2 import urlopen
+
+try:
+ from site import USER_SITE
+except ImportError:
+ USER_SITE = None
+
+DEFAULT_VERSION = "18.0.1"
+DEFAULT_URL = "https://pypi.python.org/packages/source/s/setuptools/"
+DEFAULT_SAVE_DIR = os.curdir
+
+
+def _python_cmd(*args):
+ """
+ Execute a command.
+
+ Return True if the command succeeded.
+ """
+ args = (sys.executable,) + args
+ return subprocess.call(args) == 0
+
+
+def _install(archive_filename, install_args=()):
+ """Install Setuptools."""
+ with archive_context(archive_filename):
+ # installing
+ log.warn('Installing Setuptools')
+ if not _python_cmd('setup.py', 'install', *install_args):
+ log.warn('Something went wrong during the installation.')
+ log.warn('See the error message above.')
+ # exitcode will be 2
+ return 2
+
+
+def _build_egg(egg, archive_filename, to_dir):
+ """Build Setuptools egg."""
+ with archive_context(archive_filename):
+ # building an egg
+ log.warn('Building a Setuptools egg in %s', to_dir)
+ _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir)
+ # returning the result
+ log.warn(egg)
+ if not os.path.exists(egg):
+ raise IOError('Could not build the egg.')
+
+
+class ContextualZipFile(zipfile.ZipFile):
+
+ """Supplement ZipFile class to support context manager for Python 2.6."""
+
+ def __enter__(self):
+ return self
+
+ def __exit__(self, type, value, traceback):
+ self.close()
+
+ def __new__(cls, *args, **kwargs):
+ """Construct a ZipFile or ContextualZipFile as appropriate."""
+ if hasattr(zipfile.ZipFile, '__exit__'):
+ return zipfile.ZipFile(*args, **kwargs)
+ return super(ContextualZipFile, cls).__new__(cls)
+
+
+ at contextlib.contextmanager
+def archive_context(filename):
+ """
+ Unzip filename to a temporary directory, set to the cwd.
+
+ The unzipped target is cleaned up after.
+ """
+ tmpdir = tempfile.mkdtemp()
+ log.warn('Extracting in %s', tmpdir)
+ old_wd = os.getcwd()
+ try:
+ os.chdir(tmpdir)
+ with ContextualZipFile(filename) as archive:
+ archive.extractall()
+
+ # going in the directory
+ subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
+ os.chdir(subdir)
+ log.warn('Now working in %s', subdir)
+ yield
+
+ finally:
+ os.chdir(old_wd)
+ shutil.rmtree(tmpdir)
+
+
+def _do_download(version, download_base, to_dir, download_delay):
+ """Download Setuptools."""
+ egg = os.path.join(to_dir, 'setuptools-%s-py%d.%d.egg'
+ % (version, sys.version_info[0], sys.version_info[1]))
+ if not os.path.exists(egg):
+ archive = download_setuptools(version, download_base,
+ to_dir, download_delay)
+ _build_egg(egg, archive, to_dir)
+ sys.path.insert(0, egg)
+
+ # Remove previously-imported pkg_resources if present (see
+ # https://bitbucket.org/pypa/setuptools/pull-request/7/ for details).
+ if 'pkg_resources' in sys.modules:
+ del sys.modules['pkg_resources']
+
+ import setuptools
+ setuptools.bootstrap_install_from = egg
+
+
+def use_setuptools(
+ version=DEFAULT_VERSION, download_base=DEFAULT_URL,
+ to_dir=DEFAULT_SAVE_DIR, download_delay=15):
+ """
+ Ensure that a setuptools version is installed.
+
+ Return None. Raise SystemExit if the requested version
+ or later cannot be installed.
+ """
+ to_dir = os.path.abspath(to_dir)
+
+ # prior to importing, capture the module state for
+ # representative modules.
+ rep_modules = 'pkg_resources', 'setuptools'
+ imported = set(sys.modules).intersection(rep_modules)
+
+ try:
+ import pkg_resources
+ pkg_resources.require("setuptools>=" + version)
+ # a suitable version is already installed
+ return
+ except ImportError:
+ # pkg_resources not available; setuptools is not installed; download
+ pass
+ except pkg_resources.DistributionNotFound:
+ # no version of setuptools was found; allow download
+ pass
+ except pkg_resources.VersionConflict as VC_err:
+ if imported:
+ _conflict_bail(VC_err, version)
+
+ # otherwise, unload pkg_resources to allow the downloaded version to
+ # take precedence.
+ del pkg_resources
+ _unload_pkg_resources()
+
+ return _do_download(version, download_base, to_dir, download_delay)
+
+
+def _conflict_bail(VC_err, version):
+ """
+ Setuptools was imported prior to invocation, so it is
+ unsafe to unload it. Bail out.
+ """
+ conflict_tmpl = textwrap.dedent("""
+ The required version of setuptools (>={version}) is not available,
+ and can't be installed while this script is running. Please
+ install a more recent version first, using
+ 'easy_install -U setuptools'.
+
+ (Currently using {VC_err.args[0]!r})
+ """)
+ msg = conflict_tmpl.format(**locals())
+ sys.stderr.write(msg)
+ sys.exit(2)
+
+
+def _unload_pkg_resources():
+ del_modules = [
+ name for name in sys.modules
+ if name.startswith('pkg_resources')
+ ]
+ for mod_name in del_modules:
+ del sys.modules[mod_name]
+
+
+def _clean_check(cmd, target):
+ """
+ Run the command to download target.
+
+ If the command fails, clean up before re-raising the error.
+ """
+ try:
+ subprocess.check_call(cmd)
+ except subprocess.CalledProcessError:
+ if os.access(target, os.F_OK):
+ os.unlink(target)
+ raise
+
+
+def download_file_powershell(url, target):
+ """
+ Download the file at url to target using Powershell.
+
+ Powershell will validate trust.
+ Raise an exception if the command cannot complete.
+ """
+ target = os.path.abspath(target)
+ ps_cmd = (
+ "[System.Net.WebRequest]::DefaultWebProxy.Credentials = "
+ "[System.Net.CredentialCache]::DefaultCredentials; "
+ "(new-object System.Net.WebClient).DownloadFile(%(url)r, %(target)r)"
+ % vars()
+ )
+ cmd = [
+ 'powershell',
+ '-Command',
+ ps_cmd,
+ ]
+ _clean_check(cmd, target)
+
+
+def has_powershell():
+ """Determine if Powershell is available."""
+ if platform.system() != 'Windows':
+ return False
+ cmd = ['powershell', '-Command', 'echo test']
+ with open(os.path.devnull, 'wb') as devnull:
+ try:
+ subprocess.check_call(cmd, stdout=devnull, stderr=devnull)
+ except Exception:
+ return False
+ return True
+download_file_powershell.viable = has_powershell
+
+
+def download_file_curl(url, target):
+ cmd = ['curl', url, '--silent', '--output', target]
+ _clean_check(cmd, target)
+
+
+def has_curl():
+ cmd = ['curl', '--version']
+ with open(os.path.devnull, 'wb') as devnull:
+ try:
+ subprocess.check_call(cmd, stdout=devnull, stderr=devnull)
+ except Exception:
+ return False
+ return True
+download_file_curl.viable = has_curl
+
+
+def download_file_wget(url, target):
+ cmd = ['wget', url, '--quiet', '--output-document', target]
+ _clean_check(cmd, target)
+
+
+def has_wget():
+ cmd = ['wget', '--version']
+ with open(os.path.devnull, 'wb') as devnull:
+ try:
+ subprocess.check_call(cmd, stdout=devnull, stderr=devnull)
+ except Exception:
+ return False
+ return True
+download_file_wget.viable = has_wget
+
+
+def download_file_insecure(url, target):
+ """Use Python to download the file, without connection authentication."""
+ src = urlopen(url)
+ try:
+ # Read all the data in one block.
+ data = src.read()
+ finally:
+ src.close()
+
+ # Write all the data in one block to avoid creating a partial file.
+ with open(target, "wb") as dst:
+ dst.write(data)
+download_file_insecure.viable = lambda: True
+
+
+def get_best_downloader():
+ downloaders = (
+ download_file_powershell,
+ download_file_curl,
+ download_file_wget,
+ download_file_insecure,
+ )
+ viable_downloaders = (dl for dl in downloaders if dl.viable())
+ return next(viable_downloaders, None)
+
+
+def download_setuptools(
+ version=DEFAULT_VERSION, download_base=DEFAULT_URL,
+ to_dir=DEFAULT_SAVE_DIR, delay=15,
+ downloader_factory=get_best_downloader):
+ """
+ Download setuptools from a specified location and return its filename.
+
+ `version` should be a valid setuptools version number that is available
+ as an sdist for download under the `download_base` URL (which should end
+ with a '/'). `to_dir` is the directory where the egg will be downloaded.
+ `delay` is the number of seconds to pause before an actual download
+ attempt.
+
+ ``downloader_factory`` should be a function taking no arguments and
+ returning a function for downloading a URL to a target.
+ """
+ # making sure we use the absolute path
+ to_dir = os.path.abspath(to_dir)
+ zip_name = "setuptools-%s.zip" % version
+ url = download_base + zip_name
+ saveto = os.path.join(to_dir, zip_name)
+ if not os.path.exists(saveto): # Avoid repeated downloads
+ log.warn("Downloading %s", url)
+ downloader = downloader_factory()
+ downloader(url, saveto)
+ return os.path.realpath(saveto)
+
+
+def _build_install_args(options):
+ """
+ Build the arguments to 'python setup.py install' on the setuptools package.
+
+ Returns list of command line arguments.
+ """
+ return ['--user'] if options.user_install else []
+
+
+def _parse_args():
+ """Parse the command line for options."""
+ parser = optparse.OptionParser()
+ parser.add_option(
+ '--user', dest='user_install', action='store_true', default=False,
+ help='install in user site package (requires Python 2.6 or later)')
+ parser.add_option(
+ '--download-base', dest='download_base', metavar="URL",
+ default=DEFAULT_URL,
+ help='alternative URL from where to download the setuptools package')
+ parser.add_option(
+ '--insecure', dest='downloader_factory', action='store_const',
+ const=lambda: download_file_insecure, default=get_best_downloader,
+ help='Use internal, non-validating downloader'
+ )
+ parser.add_option(
+ '--version', help="Specify which version to download",
+ default=DEFAULT_VERSION,
+ )
+ parser.add_option(
+ '--to-dir',
+ help="Directory to save (and re-use) package",
+ default=DEFAULT_SAVE_DIR,
+ )
+ options, args = parser.parse_args()
+ # positional arguments are ignored
+ return options
+
+
+def _download_args(options):
+ """Return args for download_setuptools function from cmdline args."""
+ return dict(
+ version=options.version,
+ download_base=options.download_base,
+ downloader_factory=options.downloader_factory,
+ to_dir=options.to_dir,
+ )
+
+
+def main():
+ """Install or upgrade setuptools and EasyInstall."""
+ options = _parse_args()
+ archive = download_setuptools(**_download_args(options))
+ return _install(archive, _build_install_args(options))
+
+if __name__ == '__main__':
+ sys.exit(main())
diff --git a/lib/bx/bbi/bbi_file.c b/lib/bx/bbi/bbi_file.c
index 7fefe6a..fe3f17b 100644
--- a/lib/bx/bbi/bbi_file.c
+++ b/lib/bx/bbi/bbi_file.c
@@ -1,26 +1,13 @@
-/* Generated by Cython 0.22 */
+/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
#define PY_SSIZE_T_CLEAN
-#ifndef CYTHON_USE_PYLONG_INTERNALS
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#else
-#include "pyconfig.h"
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 1
-#else
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#endif
-#endif
-#endif
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000)
- #error Cython requires Python 2.6+ or Python 3.2+.
+#elif PY_VERSION_HEX < 0x02040000
+ #error Cython requires Python 2.4+.
#else
-#define CYTHON_ABI "0_22"
-#include <stddef.h>
+#include <stddef.h> /* For offsetof */
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
@@ -54,29 +41,80 @@
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
-#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag)
-#define Py_OptimizeFlag 0
+#if PY_VERSION_HEX < 0x02050000
+ typedef int Py_ssize_t;
+ #define PY_SSIZE_T_MAX INT_MAX
+ #define PY_SSIZE_T_MIN INT_MIN
+ #define PY_FORMAT_SIZE_T ""
+ #define CYTHON_FORMAT_SSIZE_T ""
+ #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
+ #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
+ #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
+ (PyErr_Format(PyExc_TypeError, \
+ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
+ (PyObject*)0))
+ #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
+ !PyComplex_Check(o))
+ #define PyIndex_Check __Pyx_PyIndex_Check
+ #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
+ #define __PYX_BUILD_PY_SSIZE_T "i"
+#else
+ #define __PYX_BUILD_PY_SSIZE_T "n"
+ #define CYTHON_FORMAT_SSIZE_T "z"
+ #define __Pyx_PyIndex_Check PyIndex_Check
+#endif
+#if PY_VERSION_HEX < 0x02060000
+ #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
+ #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
+ #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
+ #define PyVarObject_HEAD_INIT(type, size) \
+ PyObject_HEAD_INIT(type) size,
+ #define PyType_Modified(t)
+ typedef struct {
+ void *buf;
+ PyObject *obj;
+ Py_ssize_t len;
+ Py_ssize_t itemsize;
+ int readonly;
+ int ndim;
+ char *format;
+ Py_ssize_t *shape;
+ Py_ssize_t *strides;
+ Py_ssize_t *suboffsets;
+ void *internal;
+ } Py_buffer;
+ #define PyBUF_SIMPLE 0
+ #define PyBUF_WRITABLE 0x0001
+ #define PyBUF_FORMAT 0x0004
+ #define PyBUF_ND 0x0008
+ #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
+ #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
+ #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
+ #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
+ #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
+ #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
+ #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
+ typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
+ typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
-#define __PYX_BUILD_PY_SSIZE_T "n"
-#define CYTHON_FORMAT_SSIZE_T "z"
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
- #define __Pyx_DefaultClassType PyClass_Type
+ PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
- #define __Pyx_DefaultClassType PyType_Type
+#endif
+#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
+ #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
- #define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE)
- #define Py_TPFLAGS_HAVE_FINALIZE 0
+#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
+ #define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
#define CYTHON_PEP393_ENABLED 1
@@ -84,34 +122,13 @@
0 : _PyUnicode_Ready((PyObject *)(op)))
#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u)
- #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
#define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
#else
#define CYTHON_PEP393_ENABLED 0
#define __Pyx_PyUnicode_READY(op) (0)
#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE))
- #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
- #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if CYTHON_COMPILING_IN_PYPY
- #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b)
- #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b)
- #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s)
-#else
- #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b)
- #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \
- PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
- #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s)
-#endif
-#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
-#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b)
-#else
- #define __Pyx_PyString_Format(a, b) PyString_Format(a, b)
+ #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#endif
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
@@ -120,12 +137,27 @@
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
- #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
-#else
- #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj))
- #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
+#if PY_VERSION_HEX < 0x02060000
+ #define PyBytesObject PyStringObject
+ #define PyBytes_Type PyString_Type
+ #define PyBytes_Check PyString_Check
+ #define PyBytes_CheckExact PyString_CheckExact
+ #define PyBytes_FromString PyString_FromString
+ #define PyBytes_FromStringAndSize PyString_FromStringAndSize
+ #define PyBytes_FromFormat PyString_FromFormat
+ #define PyBytes_DecodeEscape PyString_DecodeEscape
+ #define PyBytes_AsString PyString_AsString
+ #define PyBytes_AsStringAndSize PyString_AsStringAndSize
+ #define PyBytes_Size PyString_Size
+ #define PyBytes_AS_STRING PyString_AS_STRING
+ #define PyBytes_GET_SIZE PyString_GET_SIZE
+ #define PyBytes_Repr PyString_Repr
+ #define PyBytes_Concat PyString_Concat
+ #define PyBytes_ConcatAndDel PyString_ConcatAndDel
+#endif
+#if PY_VERSION_HEX < 0x02060000
+ #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
+ #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#endif
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
@@ -146,17 +178,11 @@
#define PyInt_AsSsize_t PyLong_AsSsize_t
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
- #define PyNumber_Int PyNumber_Long
#endif
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
-#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY
- #ifndef PyUnicode_InternFromString
- #define PyUnicode_InternFromString(s) PyUnicode_FromString(s)
- #endif
-#endif
-#if PY_VERSION_HEX < 0x030200A4
+#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
#define __Pyx_PyInt_AsHash_t PyInt_AsLong
@@ -164,61 +190,42 @@
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
+#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
+ #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
+ #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
#else
- #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
-#endif
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
- #elif defined(_MSC_VER)
- #define CYTHON_INLINE __inline
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
+ #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
+ #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
-#ifndef CYTHON_RESTRICT
- #if defined(__GNUC__)
- #define CYTHON_RESTRICT __restrict__
- #elif defined(_MSC_VER) && _MSC_VER >= 1400
- #define CYTHON_RESTRICT __restrict
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_RESTRICT restrict
- #else
- #define CYTHON_RESTRICT
- #endif
+#if PY_MAJOR_VERSION >= 3
+ #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
-#ifdef NAN
-#define __PYX_NAN() ((float) NAN)
+#if PY_VERSION_HEX < 0x02050000
+ #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
+ #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
+ #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
#else
-static CYTHON_INLINE float __PYX_NAN() {
- /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
- a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
- a quiet NaN. */
- float value;
- memset(&value, 0xFF, sizeof(value));
- return value;
-}
+ #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
+ #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
+ #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
-#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None)
-#ifdef __cplusplus
-template<typename T>
-void __Pyx_call_destructor(T* x) {
- x->~T();
-}
-template<typename T>
-class __Pyx_FakeReference {
- public:
- __Pyx_FakeReference() : ptr(NULL) { }
- __Pyx_FakeReference(T& ref) : ptr(&ref) { }
- T *operator->() { return ptr; }
- operator T&() { return *ptr; }
- private:
- T *ptr;
-};
+#if PY_VERSION_HEX < 0x02050000
+ #define __Pyx_NAMESTR(n) ((char *)(n))
+ #define __Pyx_DOCSTR(n) ((char *)(n))
+#else
+ #define __Pyx_NAMESTR(n) (n)
+ #define __Pyx_DOCSTR(n) (n)
#endif
@@ -258,6 +265,17 @@ class __Pyx_FakeReference {
#define CYTHON_WITHOUT_ASSERTIONS
#endif
+#ifndef CYTHON_INLINE
+ #if defined(__GNUC__)
+ #define CYTHON_INLINE __inline__
+ #elif defined(_MSC_VER)
+ #define CYTHON_INLINE __inline
+ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define CYTHON_INLINE inline
+ #else
+ #define CYTHON_INLINE
+ #endif
+#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
@@ -271,157 +289,40 @@ class __Pyx_FakeReference {
# define CYTHON_UNUSED
# endif
#endif
-typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
- const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
-
-#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
-#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
-#define __PYX_DEFAULT_STRING_ENCODING ""
-#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
-#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \
- (sizeof(type) < sizeof(Py_ssize_t)) || \
- (sizeof(type) > sizeof(Py_ssize_t) && \
- likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX) && \
- (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \
- v == (type)PY_SSIZE_T_MIN))) || \
- (sizeof(type) == sizeof(Py_ssize_t) && \
- (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX))) )
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
-#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
-#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
-#define __Pyx_PyBytes_FromString PyBytes_FromString
-#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#else
- #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
-#endif
-#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s)
-#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s)
-#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s)
-#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s)
-#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
-#if PY_MAJOR_VERSION < 3
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
-{
- const Py_UNICODE *u_end = u;
- while (*u_end++) ;
- return (size_t)(u_end - u - 1);
-}
-#else
-#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
-#endif
-#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
-#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
-#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
+typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
+
+#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
+#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
+static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
#else
#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
-static int __Pyx_sys_getdefaultencoding_not_ascii;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys;
- PyObject* default_encoding = NULL;
- PyObject* ascii_chars_u = NULL;
- PyObject* ascii_chars_b = NULL;
- const char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (!sys) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
- Py_DECREF(sys);
- if (!default_encoding) goto bad;
- default_encoding_c = PyBytes_AsString(default_encoding);
- if (!default_encoding_c) goto bad;
- if (strcmp(default_encoding_c, "ascii") == 0) {
- __Pyx_sys_getdefaultencoding_not_ascii = 0;
- } else {
- char ascii_chars[128];
- int c;
- for (c = 0; c < 128; c++) {
- ascii_chars[c] = c;
- }
- __Pyx_sys_getdefaultencoding_not_ascii = 1;
- ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
- if (!ascii_chars_u) goto bad;
- ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
- if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
- PyErr_Format(
- PyExc_ValueError,
- "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
- default_encoding_c);
- goto bad;
- }
- Py_DECREF(ascii_chars_u);
- Py_DECREF(ascii_chars_b);
- }
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return -1;
-}
-#endif
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
-#else
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
-static char* __PYX_DEFAULT_STRING_ENCODING;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys;
- PyObject* default_encoding = NULL;
- char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (!sys) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- Py_DECREF(sys);
- if (!default_encoding) goto bad;
- default_encoding_c = PyBytes_AsString(default_encoding);
- if (!default_encoding_c) goto bad;
- __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
- if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
- strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(default_encoding);
- return -1;
-}
-#endif
-#endif
-/* Test for GCC > 2.95 */
-#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))
- #define likely(x) __builtin_expect(!!(x), 1)
- #define unlikely(x) __builtin_expect(!!(x), 0)
-#else /* !__GNUC__ or GCC < 2.95 */
+#ifdef __GNUC__
+ /* Test for GCC > 2.95 */
+ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
+ #define likely(x) __builtin_expect(!!(x), 1)
+ #define unlikely(x) __builtin_expect(!!(x), 0)
+ #else /* __GNUC__ > 2 ... */
+ #define likely(x) (x)
+ #define unlikely(x) (x)
+ #endif /* __GNUC__ > 2 ... */
+#else /* __GNUC__ */
#define likely(x) (x)
#define unlikely(x) (x)
#endif /* __GNUC__ */
-
+
static PyObject *__pyx_m;
-static PyObject *__pyx_d;
static PyObject *__pyx_b;
static PyObject *__pyx_empty_tuple;
static PyObject *__pyx_empty_bytes;
@@ -453,23 +354,23 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
- "bx/bbi/bbi_file.pyx",
- "bx/bbi/bbi_file.pxd",
- "__init__.pxd",
- "bx/bbi/bpt_file.pxd",
- "bx/bbi/cirtree_file.pxd",
+ "bbi_file.pyx",
+ "bbi_file.pxd",
+ "numpy.pxd",
+ "bpt_file.pxd",
+ "cirtree_file.pxd",
"type.pxd",
};
#define IS_UNSIGNED(type) (((type) -1) > 0)
struct __Pyx_StructField_;
#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0)
typedef struct {
- const char* name;
+ const char* name; /* for error messages only */
struct __Pyx_StructField_* fields;
- size_t size;
- size_t arraysize[8];
+ size_t size; /* sizeof(type) */
+ size_t arraysize[8]; /* length of array in each dimension */
int ndim;
- char typegroup;
+ char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject, c_H_ar */
char is_unsigned;
int flags;
} __Pyx_TypeInfo;
@@ -582,7 +483,7 @@ typedef int __pyx_t_2bx_3bbi_5types_signed32;
*/
typedef int __pyx_t_2bx_3bbi_5types_boolean;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":726
+/* "numpy.pxd":723
* # in Cython to enable them only on the right systems.
*
* ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
@@ -591,7 +492,7 @@ typedef int __pyx_t_2bx_3bbi_5types_boolean;
*/
typedef npy_int8 __pyx_t_5numpy_int8_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":727
+/* "numpy.pxd":724
*
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
@@ -600,7 +501,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t;
*/
typedef npy_int16 __pyx_t_5numpy_int16_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":728
+/* "numpy.pxd":725
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
@@ -609,7 +510,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t;
*/
typedef npy_int32 __pyx_t_5numpy_int32_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":729
+/* "numpy.pxd":726
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
@@ -618,7 +519,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t;
*/
typedef npy_int64 __pyx_t_5numpy_int64_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":733
+/* "numpy.pxd":730
* #ctypedef npy_int128 int128_t
*
* ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
@@ -627,7 +528,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t;
*/
typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":734
+/* "numpy.pxd":731
*
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
@@ -636,7 +537,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t;
*/
typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":735
+/* "numpy.pxd":732
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
@@ -645,7 +546,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t;
*/
typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":736
+/* "numpy.pxd":733
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
@@ -654,7 +555,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t;
*/
typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":740
+/* "numpy.pxd":737
* #ctypedef npy_uint128 uint128_t
*
* ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
@@ -663,7 +564,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t;
*/
typedef npy_float32 __pyx_t_5numpy_float32_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":741
+/* "numpy.pxd":738
*
* ctypedef npy_float32 float32_t
* ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
@@ -672,7 +573,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t;
*/
typedef npy_float64 __pyx_t_5numpy_float64_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":750
+/* "numpy.pxd":747
* # The int types are mapped a bit surprising --
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t # <<<<<<<<<<<<<<
@@ -681,7 +582,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t;
*/
typedef npy_long __pyx_t_5numpy_int_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":751
+/* "numpy.pxd":748
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
@@ -690,7 +591,7 @@ typedef npy_long __pyx_t_5numpy_int_t;
*/
typedef npy_longlong __pyx_t_5numpy_long_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":752
+/* "numpy.pxd":749
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
@@ -699,7 +600,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t;
*/
typedef npy_longlong __pyx_t_5numpy_longlong_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":754
+/* "numpy.pxd":751
* ctypedef npy_longlong longlong_t
*
* ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
@@ -708,7 +609,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t;
*/
typedef npy_ulong __pyx_t_5numpy_uint_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":755
+/* "numpy.pxd":752
*
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
@@ -717,7 +618,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":756
+/* "numpy.pxd":753
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
@@ -726,7 +627,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":758
+/* "numpy.pxd":755
* ctypedef npy_ulonglong ulonglong_t
*
* ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
@@ -735,7 +636,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
*/
typedef npy_intp __pyx_t_5numpy_intp_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":759
+/* "numpy.pxd":756
*
* ctypedef npy_intp intp_t
* ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
@@ -744,7 +645,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t;
*/
typedef npy_uintp __pyx_t_5numpy_uintp_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":761
+/* "numpy.pxd":758
* ctypedef npy_uintp uintp_t
*
* ctypedef npy_double float_t # <<<<<<<<<<<<<<
@@ -753,7 +654,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t;
*/
typedef npy_double __pyx_t_5numpy_float_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":762
+/* "numpy.pxd":759
*
* ctypedef npy_double float_t
* ctypedef npy_double double_t # <<<<<<<<<<<<<<
@@ -762,7 +663,7 @@ typedef npy_double __pyx_t_5numpy_float_t;
*/
typedef npy_double __pyx_t_5numpy_double_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":763
+/* "numpy.pxd":760
* ctypedef npy_double float_t
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
@@ -792,15 +693,15 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
/*--- Type declarations ---*/
-struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile;
-struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile;
struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock;
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData;
struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler;
-struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile;
+struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile;
+struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData;
struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel;
+struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile;
+struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":765
+/* "numpy.pxd":762
* ctypedef npy_longdouble longdouble_t
*
* ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
@@ -809,7 +710,7 @@ struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel;
*/
typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":766
+/* "numpy.pxd":763
*
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
@@ -818,7 +719,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
*/
typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":767
+/* "numpy.pxd":764
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
@@ -827,7 +728,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
*/
typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":769
+/* "numpy.pxd":766
* ctypedef npy_clongdouble clongdouble_t
*
* ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
@@ -836,7 +737,7 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
*/
typedef npy_cdouble __pyx_t_5numpy_complex_t;
-/* "bx/bbi/bbi_file.pyx":45
+/* "bx/bbi/bbi_file.pyx":43
* cdef inline int imin(int a, int b): return a if a <= b else b
*
* cdef enum summary_type: # <<<<<<<<<<<<<<
@@ -851,23 +752,36 @@ enum __pyx_t_2bx_3bbi_8bbi_file_summary_type {
__pyx_e_2bx_3bbi_8bbi_file_summary_type_sd = 4
};
-/* "bpt_file.pxd":5
- * from types cimport *
+/* "bx/bbi/bbi_file.pxd":8
+ * cimport numpy
*
- * cdef class BPTFile: # <<<<<<<<<<<<<<
+ * cdef class SummaryBlock: # <<<<<<<<<<<<<<
* """
- * On disk B+ tree compatible with Jim Kent's bPlusTree.c
+ * A block of summary data from disk
*/
-struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile {
+struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock {
PyObject_HEAD
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- __pyx_t_2bx_3bbi_5types_bits32 block_size;
- __pyx_t_2bx_3bbi_5types_bits32 key_size;
- __pyx_t_2bx_3bbi_5types_bits32 value_size;
- __pyx_t_2bx_3bbi_5types_bits64 item_count;
- __pyx_t_2bx_3bbi_5types_bits64 root_offset;
+ __pyx_t_2bx_3bbi_5types_bits32 chrom_id;
+ __pyx_t_2bx_3bbi_5types_bits32 start;
+ __pyx_t_2bx_3bbi_5types_bits32 end;
+ __pyx_t_2bx_3bbi_5types_bits32 valid_count;
+ double min_val;
+ double max_val;
+ double sum_data;
+ double sum_squares;
+};
+
+
+/* "bx/bbi/bbi_file.pxd":39
+ * cdef class BBIFile
+ *
+ * cdef class BlockHandler: # <<<<<<<<<<<<<<
+ * """
+ * Callback for `BBIFile.visit_blocks_in_region`
+ */
+struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtab;
};
@@ -895,26 +809,6 @@ struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile {
};
-/* "bx/bbi/bbi_file.pxd":8
- * cimport numpy
- *
- * cdef class SummaryBlock: # <<<<<<<<<<<<<<
- * """
- * A block of summary data from disk
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock {
- PyObject_HEAD
- __pyx_t_2bx_3bbi_5types_bits32 chrom_id;
- __pyx_t_2bx_3bbi_5types_bits32 start;
- __pyx_t_2bx_3bbi_5types_bits32 end;
- __pyx_t_2bx_3bbi_5types_bits32 valid_count;
- double min_val;
- double max_val;
- double sum_data;
- double sum_squares;
-};
-
-
/* "bx/bbi/bbi_file.pxd":21
* cdef public double sum_squares
*
@@ -936,16 +830,22 @@ struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData {
};
-/* "bx/bbi/bbi_file.pxd":39
- * cdef class BBIFile
+/* "bx/bbi/bbi_file.pyx":279
+ * return closest_level
*
- * cdef class BlockHandler: # <<<<<<<<<<<<<<
- * """
- * Callback for `BBIFile.visit_blocks_in_region`
+ * cdef class ZoomLevel: # <<<<<<<<<<<<<<
+ * cdef BBIFile bbi_file
+ * cdef public bits32 reduction_level
*/
-struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler {
+struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel {
PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtab;
+ struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_vtab;
+ struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *bbi_file;
+ __pyx_t_2bx_3bbi_5types_bits32 reduction_level;
+ __pyx_t_2bx_3bbi_5types_bits32 reserved;
+ __pyx_t_2bx_3bbi_5types_bits64 data_offset;
+ __pyx_t_2bx_3bbi_5types_bits64 index_offset;
+ int item_count;
};
@@ -978,41 +878,28 @@ struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile {
};
-/* "bx/bbi/bbi_file.pyx":281
- * return closest_level
+/* "bpt_file.pxd":5
+ * from types cimport *
*
- * cdef class ZoomLevel: # <<<<<<<<<<<<<<
- * cdef BBIFile bbi_file
- * cdef public bits32 reduction_level
+ * cdef class BPTFile: # <<<<<<<<<<<<<<
+ * """
+ * On disk B+ tree compatible with Jim Kent's bPlusTree.c
*/
-struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel {
+struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile {
PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_vtab;
- struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *bbi_file;
- __pyx_t_2bx_3bbi_5types_bits32 reduction_level;
- __pyx_t_2bx_3bbi_5types_bits32 reserved;
- __pyx_t_2bx_3bbi_5types_bits64 data_offset;
- __pyx_t_2bx_3bbi_5types_bits64 index_offset;
- int item_count;
+ PyObject *file;
+ PyObject *reader;
+ __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
+ __pyx_t_2bx_3bbi_5types_bits32 block_size;
+ __pyx_t_2bx_3bbi_5types_bits32 key_size;
+ __pyx_t_2bx_3bbi_5types_bits32 value_size;
+ __pyx_t_2bx_3bbi_5types_bits64 item_count;
+ __pyx_t_2bx_3bbi_5types_bits64 root_offset;
};
-/* "bx/bbi/bbi_file.pyx":58
- * pass
- *
- * cdef class SummarizedData: # <<<<<<<<<<<<<<
- * """
- * The result of using SummaryBlocks read from the file to produce a
- */
-
-struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData {
- PyObject *(*accumulate_interval_value)(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float);
-};
-static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtabptr_2bx_3bbi_8bbi_file_SummarizedData;
-
-
-/* "bx/bbi/bbi_file.pyx":112
+/* "bx/bbi/bbi_file.pyx":110
* pass
*
* cdef class BBIFile: # <<<<<<<<<<<<<<
@@ -1032,7 +919,7 @@ struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile {
static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile *__pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile;
-/* "bx/bbi/bbi_file.pyx":105
+/* "bx/bbi/bbi_file.pyx":103
* min_val[j] = val
*
* cdef class BlockHandler: # <<<<<<<<<<<<<<
@@ -1046,7 +933,21 @@ struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler {
static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtabptr_2bx_3bbi_8bbi_file_BlockHandler;
-/* "bx/bbi/bbi_file.pyx":281
+/* "bx/bbi/bbi_file.pyx":56
+ * pass
+ *
+ * cdef class SummarizedData: # <<<<<<<<<<<<<<
+ * """
+ * The result of using SummaryBlocks read from the file to produce a
+ */
+
+struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData {
+ PyObject *(*accumulate_interval_value)(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float);
+};
+static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtabptr_2bx_3bbi_8bbi_file_SummarizedData;
+
+
+/* "bx/bbi/bbi_file.pyx":279
* return closest_level
*
* cdef class ZoomLevel: # <<<<<<<<<<<<<<
@@ -1059,8 +960,6 @@ struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_ZoomLevel {
PyObject *(*_summarize)(struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int);
};
static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_vtabptr_2bx_3bbi_8bbi_file_ZoomLevel;
-
-/* --- Runtime support code (head) --- */
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
@@ -1074,7 +973,7 @@ static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_vtabptr_2bx_3
void (*FinishContext)(void**);
} __Pyx_RefNannyAPIStruct;
static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
- static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname);
+ static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); /*proto*/
#define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
#ifdef WITH_THREAD
#define __Pyx_RefNannySetupContext(name, acquire_gil) \
@@ -1111,193 +1010,151 @@ static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_vtabptr_2bx_3
#define __Pyx_XDECREF(r) Py_XDECREF(r)
#define __Pyx_XGOTREF(r)
#define __Pyx_XGIVEREF(r)
-#endif
-#define __Pyx_XDECREF_SET(r, v) do { \
- PyObject *tmp = (PyObject *) r; \
- r = v; __Pyx_XDECREF(tmp); \
- } while (0)
-#define __Pyx_DECREF_SET(r, v) do { \
- PyObject *tmp = (PyObject *) r; \
- r = v; __Pyx_DECREF(tmp); \
- } while (0)
+#endif /* CYTHON_REFNANNY */
#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
- PyTypeObject* tp = Py_TYPE(obj);
- if (likely(tp->tp_getattro))
- return tp->tp_getattro(obj, attr_name);
-#if PY_MAJOR_VERSION < 3
- if (likely(tp->tp_getattr))
- return tp->tp_getattr(obj, PyString_AS_STRING(attr_name));
-#endif
- return PyObject_GetAttr(obj, attr_name);
-}
-#else
-#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
-#endif
-
-static PyObject *__Pyx_GetBuiltinName(PyObject *name);
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
- Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found);
+ Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
-static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);
+static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
- const char* function_name);
-
-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name);
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
-#else
-#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
-#endif
+ const char* function_name); /*proto*/
-static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type);
+static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj,
__Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack);
static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info);
-#ifndef __PYX_FORCE_INIT_THREADS
- #define __PYX_FORCE_INIT_THREADS 0
-#endif
-
-static void __Pyx_RaiseBufferIndexError(int axis);
+static void __Pyx_RaiseBufferIndexError(int axis); /*proto*/
#define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0)
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb);
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb);
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
-#endif
-
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
-#else
-#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL)
-#endif
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
- PyListObject* L = (PyListObject*) list;
- Py_ssize_t len = Py_SIZE(list);
- if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) {
- Py_INCREF(x);
- PyList_SET_ITEM(list, len, x);
- Py_SIZE(list) = len+1;
- return 0;
+static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
+ if (likely(PyList_CheckExact(L))) {
+ if (unlikely(PyList_Append(L, x) < 0)) return NULL;
+ Py_INCREF(Py_None);
+ return Py_None; /* this is just to have an accurate signature */
+ } else {
+ PyObject *r, *m;
+ m = __Pyx_GetAttrString(L, "append");
+ if (!m) return NULL;
+ r = PyObject_CallFunctionObjArgs(m, x, NULL);
+ Py_DECREF(m);
+ return r;
}
- return PyList_Append(list, x);
}
-#else
-#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
-#endif
-
-static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg);
-
-static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x);
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE int __Pyx_IterFinish(void);
+static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected);
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
static CYTHON_INLINE long __Pyx_div_long(long, long); /* proto */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause);
-
-#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \
- (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \
- __Pyx_GetItemInt_Generic(o, to_py_func(i))))
-#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
- (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck);
-#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
- (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck);
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck);
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) {
- PyListObject* L = (PyListObject*) list;
- Py_ssize_t len = Py_SIZE(list);
- if (likely(L->allocated > len)) {
- Py_INCREF(x);
- PyList_SET_ITEM(list, len, x);
- Py_SIZE(list) = len+1;
- return 0;
- }
- return PyList_Append(list, x);
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
+ PyObject *r;
+ if (!j) return NULL;
+ r = PyObject_GetItem(o, j);
+ Py_DECREF(j);
+ return r;
}
+#define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_List_Fast(o, i) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
#else
-#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x)
+ return PySequence_GetItem(o, i);
#endif
-
-#if PY_MAJOR_VERSION >= 3
-static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
- PyObject *value;
- value = PyDict_GetItemWithError(d, key);
- if (unlikely(!value)) {
- if (!PyErr_Occurred()) {
- PyObject* args = PyTuple_Pack(1, key);
- if (likely(args))
- PyErr_SetObject(PyExc_KeyError, args);
- Py_XDECREF(args);
- }
- return NULL;
+}
+#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_Tuple_Fast(o, i) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
- Py_INCREF(value);
- return value;
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
+#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_Fast(o, i) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (PyList_CheckExact(o)) {
+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ }
+ else if (PyTuple_CheckExact(o)) {
+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ } else { /* inlined PySequence_GetItem() */
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return NULL;
+ i += l;
+ }
+ return m->sq_item(o, i);
+ }
+ }
#else
- #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
+ if (PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
+ }
#endif
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+}
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable);
-
-static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name);
-
-typedef struct {
- int code_line;
- PyCodeObject* code_object;
-} __Pyx_CodeObjectCacheEntry;
-struct __Pyx_CodeObjectCache {
- int count;
- int max_count;
- __Pyx_CodeObjectCacheEntry* entries;
-};
-static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
-static PyCodeObject *__pyx_find_code_object(int code_line);
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
+static void __Pyx_RaiseBufferFallbackError(void); /*proto*/
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename);
+static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/
typedef struct {
Py_ssize_t shape, strides, suboffsets;
@@ -1324,23 +1181,7 @@ typedef struct {
static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0};
static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1};
-static CYTHON_INLINE unsigned int __Pyx_PyInt_As_unsigned_int(PyObject *);
-
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_int(unsigned int value);
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_As_unsigned_short(PyObject *);
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_As_unsigned_PY_LONG_LONG(PyObject *);
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_PY_LONG_LONG(unsigned PY_LONG_LONG value);
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_short(unsigned short value);
+static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name);
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
@@ -1354,7 +1195,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_short(unsigned short va
#define __Pyx_CREAL(z) ((z).real)
#define __Pyx_CIMAG(z) ((z).imag)
#endif
-#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX
+#if defined(_WIN32) && defined(__cplusplus) && CYTHON_CCOMPLEX
#define __Pyx_SET_CREAL(z,x) ((z).real(x))
#define __Pyx_SET_CIMAG(z,y) ((z).imag(y))
#else
@@ -1440,10 +1281,42 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
#endif
#endif
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
+static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
+
+static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
+
+static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *);
+
+static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *);
+
+static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *);
+
+static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *);
+
+static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *);
+
+static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *);
+
+static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *);
+
+static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *);
+
+static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *);
+
+static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *);
+
+static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *);
+
+static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *);
+
+static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);
+
+static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
static int __Pyx_check_binary_version(void);
+static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
+
#if !defined(__Pyx_PyIdentifier_FromString)
#if PY_MAJOR_VERSION < 3
#define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
@@ -1452,23 +1325,29 @@ static int __Pyx_check_binary_version(void);
#endif
#endif
-static PyObject *__Pyx_ImportModule(const char *name);
+static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+
+typedef struct {
+ int code_line;
+ PyCodeObject* code_object;
+} __Pyx_CodeObjectCacheEntry;
+struct __Pyx_CodeObjectCache {
+ int count;
+ int max_count;
+ __Pyx_CodeObjectCacheEntry* entries;
+};
+static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
+static PyCodeObject *__pyx_find_code_object(int code_line);
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict);
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename); /*proto*/
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t);
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval_value(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_s, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_e, float __pyx_v_val); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_8bbi_file_12BlockHandler_handle_block(CYTHON_UNUSED struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_block_data, CYTHON_UNUSED struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_bbi_file); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_8bbi_file_7BBIFile_visit_blocks_in_region(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_chrom_id, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler *__pyx_v_handler); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_8bbi_file_7BBIFile_summarize(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, char *__pyx_v_chrom, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_v_summary_size, int __pyx_skip_dispatch); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_8bbi_file_7BBIFile_summarize_from_full(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, char *__pyx_v_chrom, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_v_summary_size, int __pyx_skip_dispatch); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_8bbi_file_7BBIFile_query(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, char *__pyx_v_chrom, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_v_summary_size, int __pyx_skip_dispatch); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_8bbi_file_7BBIFile__get_chrom_id_and_size(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, char *__pyx_v_chrom); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_8bbi_file_7BBIFile__summarize_from_full(CYTHON_UNUSED struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, CYTHON_UNUSED __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_chrom_id, CYTHON_UNUSED __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, CYTHON_UNUSED __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, CYTHON_UNUSED int __pyx_v_summary_size); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_8bbi_file_7BBIFile__best_zoom_level(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, int __pyx_v_desired_reduction); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_8bbi_file_9ZoomLevel__get_summary_slice(CYTHON_UNUSED struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_base_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_base_end, PyObject *__pyx_v_summaries); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_8bbi_file_9ZoomLevel__summarize(CYTHON_UNUSED struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_v_self, CYTHON_UNUSED __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_chrom_id, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_v_summary_size); /* proto*/
/* Module declarations from 'bx.bbi.types' */
@@ -1527,7 +1406,6 @@ int __pyx_module_is_main_bx__bbi__bbi_file = 0;
/* Implementation of 'bx.bbi.bbi_file' */
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_range;
-static PyObject *__pyx_builtin_zip;
static PyObject *__pyx_builtin_RuntimeError;
static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_8chrom_id___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self); /* proto */
static int __pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_8chrom_id_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
@@ -1590,183 +1468,171 @@ static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel_12index_offset___get__(s
static int __pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel_12index_offset_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
-static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_SummaryBlock(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_SummarizedData(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_BBIFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_BlockHandler(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_ZoomLevel(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static char __pyx_k_B[] = "B";
-static char __pyx_k_H[] = "H";
-static char __pyx_k_I[] = "I";
-static char __pyx_k_L[] = "L";
-static char __pyx_k_O[] = "O";
-static char __pyx_k_Q[] = "Q";
-static char __pyx_k_b[] = "b";
-static char __pyx_k_d[] = "d";
-static char __pyx_k_f[] = "f";
-static char __pyx_k_g[] = "g";
-static char __pyx_k_h[] = "h";
-static char __pyx_k_i[] = "i";
-static char __pyx_k_l[] = "l";
-static char __pyx_k_q[] = "q";
-static char __pyx_k_II[] = "II";
-static char __pyx_k_Zd[] = "Zd";
-static char __pyx_k_Zf[] = "Zf";
-static char __pyx_k_Zg[] = "Zg";
-static char __pyx_k_np[] = "np";
-static char __pyx_k_end[] = "end";
-static char __pyx_k_max[] = "max";
-static char __pyx_k_min[] = "min";
-static char __pyx_k_nan[] = "nan";
-static char __pyx_k_zip[] = "zip";
-static char __pyx_k_file[] = "file";
-static char __pyx_k_find[] = "find";
-static char __pyx_k_main[] = "__main__";
-static char __pyx_k_math[] = "math";
-static char __pyx_k_mean[] = "mean";
-static char __pyx_k_open[] = "open";
-static char __pyx_k_read[] = "read";
-static char __pyx_k_seek[] = "seek";
-static char __pyx_k_size[] = "size";
-static char __pyx_k_sqrt[] = "sqrt";
-static char __pyx_k_test[] = "__test__";
-static char __pyx_k_zlib[] = "zlib";
-static char __pyx_k_chrom[] = "chrom";
-static char __pyx_k_deque[] = "deque";
-static char __pyx_k_dtype[] = "dtype";
-static char __pyx_k_names[] = "names";
-static char __pyx_k_numpy[] = "numpy";
-static char __pyx_k_query[] = "query";
-static char __pyx_k_range[] = "range";
-static char __pyx_k_start[] = "start";
-static char __pyx_k_zeros[] = "zeros";
-static char __pyx_k_append[] = "append";
-static char __pyx_k_extend[] = "extend";
-static char __pyx_k_import[] = "__import__";
-static char __pyx_k_uint32[] = "uint32";
-static char __pyx_k_unpack[] = "unpack";
-static char __pyx_k_float32[] = "float32";
-static char __pyx_k_float64[] = "float64";
-static char __pyx_k_max_val[] = "max_val";
-static char __pyx_k_min_val[] = "min_val";
-static char __pyx_k_std_dev[] = "std_dev";
-static char __pyx_k_StringIO[] = "StringIO";
-static char __pyx_k_chrom_id[] = "chrom_id";
-static char __pyx_k_coverage[] = "coverage";
-static char __pyx_k_sum_data[] = "sum_data";
-static char __pyx_k_cStringIO[] = "cStringIO";
-static char __pyx_k_summarize[] = "summarize";
-static char __pyx_k_type_name[] = "type_name";
-static char __pyx_k_ValueError[] = "ValueError";
-static char __pyx_k_decompress[] = "decompress";
-static char __pyx_k_fromstring[] = "fromstring";
-static char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
-static char __pyx_k_collections[] = "collections";
-static char __pyx_k_read_uint16[] = "read_uint16";
-static char __pyx_k_read_uint32[] = "read_uint32";
-static char __pyx_k_read_uint64[] = "read_uint64";
-static char __pyx_k_sum_squares[] = "sum_squares";
-static char __pyx_k_valid_count[] = "valid_count";
-static char __pyx_k_RuntimeError[] = "RuntimeError";
-static char __pyx_k_expected_sig[] = "expected_sig";
-static char __pyx_k_summary_size[] = "summary_size";
-static char __pyx_k_byteswap_needed[] = "byteswap_needed";
-static char __pyx_k_BinaryFileReader[] = "BinaryFileReader";
-static char __pyx_k_bx_misc_binary_file[] = "bx.misc.binary_file";
-static char __pyx_k_summarize_from_full[] = "summarize_from_full";
-static char __pyx_k_find_overlapping_blocks[] = "find_overlapping_blocks";
-static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous";
-static char __pyx_k_Core_implementation_for_reading[] = "\nCore implementation for reading UCSC \"big binary indexed\" files.\n\nThere isn't really any specification for the format beyond the code, so this\nmirrors Jim Kent's 'bbiRead.c' mostly. \n";
-static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
-static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd";
-static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported";
-static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous";
-static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short.";
-static PyObject *__pyx_n_s_BinaryFileReader;
-static PyObject *__pyx_kp_u_Format_string_allocated_too_shor;
-static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2;
-static PyObject *__pyx_n_s_II;
-static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor;
-static PyObject *__pyx_n_s_RuntimeError;
-static PyObject *__pyx_n_s_StringIO;
-static PyObject *__pyx_n_s_ValueError;
-static PyObject *__pyx_n_s_append;
-static PyObject *__pyx_n_s_bx_misc_binary_file;
-static PyObject *__pyx_n_s_byteswap_needed;
-static PyObject *__pyx_n_s_cStringIO;
-static PyObject *__pyx_n_s_chrom;
-static PyObject *__pyx_n_s_chrom_id;
-static PyObject *__pyx_n_s_collections;
-static PyObject *__pyx_n_s_coverage;
-static PyObject *__pyx_n_s_decompress;
-static PyObject *__pyx_n_s_deque;
-static PyObject *__pyx_n_s_dtype;
-static PyObject *__pyx_n_s_end;
-static PyObject *__pyx_n_s_expected_sig;
-static PyObject *__pyx_n_s_extend;
-static PyObject *__pyx_n_s_file;
-static PyObject *__pyx_n_s_find;
-static PyObject *__pyx_n_s_find_overlapping_blocks;
-static PyObject *__pyx_n_s_float32;
-static PyObject *__pyx_n_s_float64;
-static PyObject *__pyx_n_s_fromstring;
-static PyObject *__pyx_n_s_import;
-static PyObject *__pyx_n_s_main;
-static PyObject *__pyx_n_s_math;
-static PyObject *__pyx_n_s_max;
-static PyObject *__pyx_n_s_max_val;
-static PyObject *__pyx_n_s_mean;
-static PyObject *__pyx_n_s_min;
-static PyObject *__pyx_n_s_min_val;
-static PyObject *__pyx_n_s_names;
-static PyObject *__pyx_n_s_nan;
-static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous;
-static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou;
-static PyObject *__pyx_n_s_np;
-static PyObject *__pyx_n_s_numpy;
-static PyObject *__pyx_n_s_open;
-static PyObject *__pyx_n_s_pyx_vtable;
-static PyObject *__pyx_n_s_query;
-static PyObject *__pyx_n_s_range;
-static PyObject *__pyx_n_s_read;
-static PyObject *__pyx_n_s_read_uint16;
-static PyObject *__pyx_n_s_read_uint32;
-static PyObject *__pyx_n_s_read_uint64;
-static PyObject *__pyx_n_s_seek;
-static PyObject *__pyx_n_s_size;
-static PyObject *__pyx_n_s_sqrt;
-static PyObject *__pyx_n_s_start;
-static PyObject *__pyx_n_s_std_dev;
-static PyObject *__pyx_n_s_sum_data;
-static PyObject *__pyx_n_s_sum_squares;
-static PyObject *__pyx_n_s_summarize;
-static PyObject *__pyx_n_s_summarize_from_full;
-static PyObject *__pyx_n_s_summary_size;
-static PyObject *__pyx_n_s_test;
-static PyObject *__pyx_n_s_type_name;
-static PyObject *__pyx_n_s_uint32;
-static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd;
-static PyObject *__pyx_n_s_unpack;
-static PyObject *__pyx_n_s_valid_count;
-static PyObject *__pyx_n_s_zeros;
-static PyObject *__pyx_n_s_zip;
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int big_bed_sig;
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__Pyx_RefNannySetupContext("range_intersection", 0);
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__pyx_t_1 = __pyx_v_start2;
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__pyx_t_4 = __pyx_t_1;
} else {
__pyx_t_4 = __pyx_t_2;
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goto __pyx_L0;
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-
- /* function exit code */
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__pyx_L0:;
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} else {
__pyx_t_1 = __pyx_v_b;
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goto __pyx_L0;
- /* function exit code */
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__Pyx_RefNannyFinishContext();
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int __pyx_t_1;
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} else {
__pyx_t_1 = __pyx_v_b;
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__Pyx_RefNannyFinishContext();
return __pyx_r;
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static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_8chrom_id___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self) {
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static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_5start___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self) {
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* self.sum_data = numpy.zeros( self.size, dtype=numpy.float64 )
* self.sum_squares = numpy.zeros( self.size, dtype=numpy.float64 )
* cdef accumulate_interval_value( self, bits32 s, bits32 e, float val ): # <<<<<<<<<<<<<<
@@ -2944,7 +2756,7 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
__pyx_pybuffernd_sum_squares.data = NULL;
__pyx_pybuffernd_sum_squares.rcbuffer = &__pyx_pybuffer_sum_squares;
- /* "bx/bbi/bbi_file.pyx":76
+ /* "bx/bbi/bbi_file.pyx":74
* cdef double overlap_factor, interval_weight
* # We locally cdef the arrays so all indexing will be at C speeds
* cdef numpy.ndarray[numpy.float64_t, ndim=1] valid_count = self.valid_count # <<<<<<<<<<<<<<
@@ -2957,14 +2769,14 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
__Pyx_BufFmt_StackElem __pyx_stack[1];
if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_valid_count.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {
__pyx_v_valid_count = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_valid_count.rcbuffer->pybuffer.buf = NULL;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
} else {__pyx_pybuffernd_valid_count.diminfo[0].strides = __pyx_pybuffernd_valid_count.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_valid_count.diminfo[0].shape = __pyx_pybuffernd_valid_count.rcbuffer->pybuffer.shape[0];
}
}
__pyx_v_valid_count = ((PyArrayObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "bx/bbi/bbi_file.pyx":77
+ /* "bx/bbi/bbi_file.pyx":75
* # We locally cdef the arrays so all indexing will be at C speeds
* cdef numpy.ndarray[numpy.float64_t, ndim=1] valid_count = self.valid_count
* cdef numpy.ndarray[numpy.float64_t, ndim=1] min_val = self.min_val # <<<<<<<<<<<<<<
@@ -2977,14 +2789,14 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
__Pyx_BufFmt_StackElem __pyx_stack[1];
if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_min_val.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {
__pyx_v_min_val = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_min_val.rcbuffer->pybuffer.buf = NULL;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
} else {__pyx_pybuffernd_min_val.diminfo[0].strides = __pyx_pybuffernd_min_val.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_min_val.diminfo[0].shape = __pyx_pybuffernd_min_val.rcbuffer->pybuffer.shape[0];
}
}
__pyx_v_min_val = ((PyArrayObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "bx/bbi/bbi_file.pyx":78
+ /* "bx/bbi/bbi_file.pyx":76
* cdef numpy.ndarray[numpy.float64_t, ndim=1] valid_count = self.valid_count
* cdef numpy.ndarray[numpy.float64_t, ndim=1] min_val = self.min_val
* cdef numpy.ndarray[numpy.float64_t, ndim=1] max_val = self.max_val # <<<<<<<<<<<<<<
@@ -2997,14 +2809,14 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
__Pyx_BufFmt_StackElem __pyx_stack[1];
if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_max_val.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {
__pyx_v_max_val = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_max_val.rcbuffer->pybuffer.buf = NULL;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
} else {__pyx_pybuffernd_max_val.diminfo[0].strides = __pyx_pybuffernd_max_val.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_max_val.diminfo[0].shape = __pyx_pybuffernd_max_val.rcbuffer->pybuffer.shape[0];
}
}
__pyx_v_max_val = ((PyArrayObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "bx/bbi/bbi_file.pyx":79
+ /* "bx/bbi/bbi_file.pyx":77
* cdef numpy.ndarray[numpy.float64_t, ndim=1] min_val = self.min_val
* cdef numpy.ndarray[numpy.float64_t, ndim=1] max_val = self.max_val
* cdef numpy.ndarray[numpy.float64_t, ndim=1] sum_data = self.sum_data # <<<<<<<<<<<<<<
@@ -3017,14 +2829,14 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
__Pyx_BufFmt_StackElem __pyx_stack[1];
if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_sum_data.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {
__pyx_v_sum_data = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_sum_data.rcbuffer->pybuffer.buf = NULL;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
} else {__pyx_pybuffernd_sum_data.diminfo[0].strides = __pyx_pybuffernd_sum_data.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_sum_data.diminfo[0].shape = __pyx_pybuffernd_sum_data.rcbuffer->pybuffer.shape[0];
}
}
__pyx_v_sum_data = ((PyArrayObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "bx/bbi/bbi_file.pyx":80
+ /* "bx/bbi/bbi_file.pyx":78
* cdef numpy.ndarray[numpy.float64_t, ndim=1] max_val = self.max_val
* cdef numpy.ndarray[numpy.float64_t, ndim=1] sum_data = self.sum_data
* cdef numpy.ndarray[numpy.float64_t, ndim=1] sum_squares = self.sum_squares # <<<<<<<<<<<<<<
@@ -3037,24 +2849,24 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
__Pyx_BufFmt_StackElem __pyx_stack[1];
if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_sum_squares.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {
__pyx_v_sum_squares = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_sum_squares.rcbuffer->pybuffer.buf = NULL;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
} else {__pyx_pybuffernd_sum_squares.diminfo[0].strides = __pyx_pybuffernd_sum_squares.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_sum_squares.diminfo[0].shape = __pyx_pybuffernd_sum_squares.rcbuffer->pybuffer.shape[0];
}
}
__pyx_v_sum_squares = ((PyArrayObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "bx/bbi/bbi_file.pyx":82
+ /* "bx/bbi/bbi_file.pyx":80
* cdef numpy.ndarray[numpy.float64_t, ndim=1] sum_squares = self.sum_squares
* # Trim interval down to region of interest
* if s < self.start: # <<<<<<<<<<<<<<
* s = self.start
* if e > self.end:
*/
- __pyx_t_2 = ((__pyx_v_s < __pyx_v_self->start) != 0);
+ __pyx_t_2 = (__pyx_v_s < __pyx_v_self->start);
if (__pyx_t_2) {
- /* "bx/bbi/bbi_file.pyx":83
+ /* "bx/bbi/bbi_file.pyx":81
* # Trim interval down to region of interest
* if s < self.start:
* s = self.start # <<<<<<<<<<<<<<
@@ -3067,17 +2879,17 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
}
__pyx_L3:;
- /* "bx/bbi/bbi_file.pyx":84
+ /* "bx/bbi/bbi_file.pyx":82
* if s < self.start:
* s = self.start
* if e > self.end: # <<<<<<<<<<<<<<
* e = self.end
* if s >= e:
*/
- __pyx_t_2 = ((__pyx_v_e > __pyx_v_self->end) != 0);
+ __pyx_t_2 = (__pyx_v_e > __pyx_v_self->end);
if (__pyx_t_2) {
- /* "bx/bbi/bbi_file.pyx":85
+ /* "bx/bbi/bbi_file.pyx":83
* s = self.start
* if e > self.end:
* e = self.end # <<<<<<<<<<<<<<
@@ -3090,17 +2902,17 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
}
__pyx_L4:;
- /* "bx/bbi/bbi_file.pyx":86
+ /* "bx/bbi/bbi_file.pyx":84
* if e > self.end:
* e = self.end
* if s >= e: # <<<<<<<<<<<<<<
* return
* base_step = ( self.end - self.start ) / self.size
*/
- __pyx_t_2 = ((__pyx_v_s >= __pyx_v_e) != 0);
+ __pyx_t_2 = (__pyx_v_s >= __pyx_v_e);
if (__pyx_t_2) {
- /* "bx/bbi/bbi_file.pyx":87
+ /* "bx/bbi/bbi_file.pyx":85
* e = self.end
* if s >= e:
* return # <<<<<<<<<<<<<<
@@ -3110,9 +2922,11 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
__Pyx_XDECREF(__pyx_r);
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
+ goto __pyx_L5;
}
+ __pyx_L5:;
- /* "bx/bbi/bbi_file.pyx":88
+ /* "bx/bbi/bbi_file.pyx":86
* if s >= e:
* return
* base_step = ( self.end - self.start ) / self.size # <<<<<<<<<<<<<<
@@ -3121,18 +2935,12 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
*/
__pyx_t_3 = (__pyx_v_self->end - __pyx_v_self->start);
if (unlikely(__pyx_v_self->size == 0)) {
- #ifdef WITH_THREAD
- PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();
- #endif
- PyErr_SetString(PyExc_ZeroDivisionError, "integer division or modulo by zero");
- #ifdef WITH_THREAD
- PyGILState_Release(__pyx_gilstate_save);
- #endif
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyErr_Format(PyExc_ZeroDivisionError, "integer division or modulo by zero");
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_v_base_step = (__pyx_t_3 / __pyx_v_self->size);
- /* "bx/bbi/bbi_file.pyx":89
+ /* "bx/bbi/bbi_file.pyx":87
* return
* base_step = ( self.end - self.start ) / self.size
* for j from 0 <= j < self.size: # <<<<<<<<<<<<<<
@@ -3142,7 +2950,7 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
__pyx_t_4 = __pyx_v_self->size;
for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_4; __pyx_v_j++) {
- /* "bx/bbi/bbi_file.pyx":90
+ /* "bx/bbi/bbi_file.pyx":88
* base_step = ( self.end - self.start ) / self.size
* for j from 0 <= j < self.size:
* base_start = self.start + ( base_step * j ) # <<<<<<<<<<<<<<
@@ -3151,7 +2959,7 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
*/
__pyx_v_base_start = (__pyx_v_self->start + (__pyx_v_base_step * __pyx_v_j));
- /* "bx/bbi/bbi_file.pyx":91
+ /* "bx/bbi/bbi_file.pyx":89
* for j from 0 <= j < self.size:
* base_start = self.start + ( base_step * j )
* base_end = base_start + base_step # <<<<<<<<<<<<<<
@@ -3160,7 +2968,7 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
*/
__pyx_v_base_end = (__pyx_v_base_start + __pyx_v_base_step);
- /* "bx/bbi/bbi_file.pyx":92
+ /* "bx/bbi/bbi_file.pyx":90
* base_start = self.start + ( base_step * j )
* base_end = base_start + base_step
* overlap = range_intersection( base_start, base_end, s, e ) # <<<<<<<<<<<<<<
@@ -3169,17 +2977,17 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
*/
__pyx_v_overlap = __pyx_f_2bx_3bbi_8bbi_file_range_intersection(__pyx_v_base_start, __pyx_v_base_end, __pyx_v_s, __pyx_v_e);
- /* "bx/bbi/bbi_file.pyx":93
+ /* "bx/bbi/bbi_file.pyx":91
* base_end = base_start + base_step
* overlap = range_intersection( base_start, base_end, s, e )
* if overlap > 0: # <<<<<<<<<<<<<<
* interval_size = e - s
* overlap_factor = <double> overlap / interval_size
*/
- __pyx_t_2 = ((__pyx_v_overlap > 0) != 0);
+ __pyx_t_2 = (__pyx_v_overlap > 0);
if (__pyx_t_2) {
- /* "bx/bbi/bbi_file.pyx":94
+ /* "bx/bbi/bbi_file.pyx":92
* overlap = range_intersection( base_start, base_end, s, e )
* if overlap > 0:
* interval_size = e - s # <<<<<<<<<<<<<<
@@ -3188,7 +2996,7 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
*/
__pyx_v_interval_size = (__pyx_v_e - __pyx_v_s);
- /* "bx/bbi/bbi_file.pyx":95
+ /* "bx/bbi/bbi_file.pyx":93
* if overlap > 0:
* interval_size = e - s
* overlap_factor = <double> overlap / interval_size # <<<<<<<<<<<<<<
@@ -3196,18 +3004,12 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
* valid_count[j] += interval_weight
*/
if (unlikely(__pyx_v_interval_size == 0)) {
- #ifdef WITH_THREAD
- PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();
- #endif
- PyErr_SetString(PyExc_ZeroDivisionError, "float division");
- #ifdef WITH_THREAD
- PyGILState_Release(__pyx_gilstate_save);
- #endif
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyErr_Format(PyExc_ZeroDivisionError, "float division");
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_v_overlap_factor = (((double)__pyx_v_overlap) / __pyx_v_interval_size);
- /* "bx/bbi/bbi_file.pyx":96
+ /* "bx/bbi/bbi_file.pyx":94
* interval_size = e - s
* overlap_factor = <double> overlap / interval_size
* interval_weight = interval_size * overlap_factor # <<<<<<<<<<<<<<
@@ -3216,7 +3018,7 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
*/
__pyx_v_interval_weight = (__pyx_v_interval_size * __pyx_v_overlap_factor);
- /* "bx/bbi/bbi_file.pyx":97
+ /* "bx/bbi/bbi_file.pyx":95
* overlap_factor = <double> overlap / interval_size
* interval_weight = interval_size * overlap_factor
* valid_count[j] += interval_weight # <<<<<<<<<<<<<<
@@ -3231,11 +3033,11 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
} else if (unlikely(__pyx_t_5 >= __pyx_pybuffernd_valid_count.diminfo[0].shape)) __pyx_t_6 = 0;
if (unlikely(__pyx_t_6 != -1)) {
__Pyx_RaiseBufferIndexError(__pyx_t_6);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 97; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_valid_count.rcbuffer->pybuffer.buf, __pyx_t_5, __pyx_pybuffernd_valid_count.diminfo[0].strides) += __pyx_v_interval_weight;
- /* "bx/bbi/bbi_file.pyx":98
+ /* "bx/bbi/bbi_file.pyx":96
* interval_weight = interval_size * overlap_factor
* valid_count[j] += interval_weight
* sum_data[j] += val * interval_weight # <<<<<<<<<<<<<<
@@ -3250,11 +3052,11 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
} else if (unlikely(__pyx_t_6 >= __pyx_pybuffernd_sum_data.diminfo[0].shape)) __pyx_t_7 = 0;
if (unlikely(__pyx_t_7 != -1)) {
__Pyx_RaiseBufferIndexError(__pyx_t_7);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 96; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_sum_data.rcbuffer->pybuffer.buf, __pyx_t_6, __pyx_pybuffernd_sum_data.diminfo[0].strides) += (__pyx_v_val * __pyx_v_interval_weight);
- /* "bx/bbi/bbi_file.pyx":99
+ /* "bx/bbi/bbi_file.pyx":97
* valid_count[j] += interval_weight
* sum_data[j] += val * interval_weight
* sum_squares[j] += val * val * interval_weight # <<<<<<<<<<<<<<
@@ -3269,11 +3071,11 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
} else if (unlikely(__pyx_t_7 >= __pyx_pybuffernd_sum_squares.diminfo[0].shape)) __pyx_t_8 = 0;
if (unlikely(__pyx_t_8 != -1)) {
__Pyx_RaiseBufferIndexError(__pyx_t_8);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 97; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_sum_squares.rcbuffer->pybuffer.buf, __pyx_t_7, __pyx_pybuffernd_sum_squares.diminfo[0].strides) += ((__pyx_v_val * __pyx_v_val) * __pyx_v_interval_weight);
- /* "bx/bbi/bbi_file.pyx":100
+ /* "bx/bbi/bbi_file.pyx":98
* sum_data[j] += val * interval_weight
* sum_squares[j] += val * val * interval_weight
* if max_val[j] < val: # <<<<<<<<<<<<<<
@@ -3288,12 +3090,12 @@ static PyObject *__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval
} else if (unlikely(__pyx_t_8 >= __pyx_pybuffernd_max_val.diminfo[0].shape)) __pyx_t_9 = 0;
if (unlikely(__pyx_t_9 != -1)) {
__Pyx_RaiseBufferIndexError(__pyx_t_9);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_2 = (((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_max_val.rcbuffer->pybuffer.buf, __pyx_t_8, __pyx_pybuffernd_max_val.diminfo[0].strides)) < __pyx_v_val) != 0);
+ __pyx_t_2 = ((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_max_val.rcbuffer->pybuffer.buf, __pyx_t_8, __pyx_pybuffernd_max_val.diminfo[0].strides)) < __pyx_v_val);
if (__pyx_t_2) {
- /* "bx/bbi/bbi_file.pyx":101
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__pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2)));
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":230
+ /* "numpy.pxd":227
* # This is allocated as one block, strides first.
* info.strides = <Py_ssize_t*>stdlib.malloc(sizeof(Py_ssize_t) * <size_t>ndim * 2)
* info.shape = info.strides + ndim # <<<<<<<<<<<<<<
@@ -9830,18 +9263,18 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim);
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":231
+ /* "numpy.pxd":228
* info.strides = <Py_ssize_t*>stdlib.malloc(sizeof(Py_ssize_t) * <size_t>ndim * 2)
* info.shape = info.strides + ndim
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* info.strides[i] = PyArray_STRIDES(self)[i]
* info.shape[i] = PyArray_DIMS(self)[i]
*/
- __pyx_t_4 = __pyx_v_ndim;
- for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
- __pyx_v_i = __pyx_t_5;
+ __pyx_t_5 = __pyx_v_ndim;
+ for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
+ __pyx_v_i = __pyx_t_6;
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":232
+ /* "numpy.pxd":229
* info.shape = info.strides + ndim
* for i in range(ndim):
* info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<<
@@ -9850,7 +9283,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
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- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":233
+ /* "numpy.pxd":230
* for i in range(ndim):
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* info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<<
@@ -9859,11 +9292,11 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
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}
- goto __pyx_L11;
+ goto __pyx_L7;
}
/*else*/ {
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":235
+ /* "numpy.pxd":232
* info.shape[i] = PyArray_DIMS(self)[i]
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* info.strides = <Py_ssize_t*>PyArray_STRIDES(self) # <<<<<<<<<<<<<<
@@ -9872,7 +9305,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self));
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":236
+ /* "numpy.pxd":233
* else:
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self)
* info.shape = <Py_ssize_t*>PyArray_DIMS(self) # <<<<<<<<<<<<<<
@@ -9881,9 +9314,9 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->shape = ((Py_ssize_t *)PyArray_DIMS(__pyx_v_self));
}
- __pyx_L11:;
+ __pyx_L7:;
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":237
+ /* "numpy.pxd":234
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self)
* info.shape = <Py_ssize_t*>PyArray_DIMS(self)
* info.suboffsets = NULL # <<<<<<<<<<<<<<
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*/
__pyx_v_info->suboffsets = NULL;
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":238
+ /* "numpy.pxd":235
* info.shape = <Py_ssize_t*>PyArray_DIMS(self)
* info.suboffsets = NULL
* info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<<
@@ -9901,16 +9334,16 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self);
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":239
+ /* "numpy.pxd":236
* info.suboffsets = NULL
* info.itemsize = PyArray_ITEMSIZE(self)
* info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<<
*
* cdef int t
*/
- __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0));
+ __pyx_v_info->readonly = (!PyArray_ISWRITEABLE(__pyx_v_self));
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":242
+ /* "numpy.pxd":239
*
* cdef int t
* cdef char* f = NULL # <<<<<<<<<<<<<<
@@ -9919,19 +9352,19 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_f = NULL;
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":243
+ /* "numpy.pxd":240
* cdef int t
* cdef char* f = NULL
* cdef dtype descr = self.descr # <<<<<<<<<<<<<<
* cdef list stack
* cdef int offset
*/
- __pyx_t_3 = ((PyObject *)__pyx_v_self->descr);
- __Pyx_INCREF(__pyx_t_3);
- __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_4 = ((PyObject *)__pyx_v_self->descr);
+ __Pyx_INCREF(__pyx_t_4);
+ __pyx_v_descr = ((PyArray_Descr *)__pyx_t_4);
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- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":247
+ /* "numpy.pxd":244
* cdef int offset
*
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@@ -9940,25 +9373,23 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr);
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":249
+ /* "numpy.pxd":246
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* # do not call releasebuffer
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*/
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+ __pyx_t_2 = (!__pyx_v_hasfields);
if (__pyx_t_2) {
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} else {
__pyx_t_1 = __pyx_t_2;
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}
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- __pyx_L15_bool_binop_done:;
if (__pyx_t_1) {
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":251
+ /* "numpy.pxd":248
* if not hasfields and not copy_shape:
* # do not call releasebuffer
* info.obj = None # <<<<<<<<<<<<<<
@@ -9970,11 +9401,11 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
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__Pyx_DECREF(__pyx_v_info->obj);
__pyx_v_info->obj = Py_None;
- goto __pyx_L14;
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/*else*/ {
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":254
+ /* "numpy.pxd":251
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@@ -9987,304 +9418,328 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__Pyx_DECREF(__pyx_v_info->obj);
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- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":256
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*
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* if ((descr.byteorder == c'>' and little_endian) or
*/
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if (__pyx_t_1) {
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":257
+ /* "numpy.pxd":254
*
* if not hasfields:
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*/
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- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":258
+ /* "numpy.pxd":255
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*/
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- __pyx_t_2 = (__pyx_v_little_endian != 0);
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- }
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- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":259
+ /* "numpy.pxd":256
* t = descr.type_num
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- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":260
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- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":261
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+ /* "numpy.pxd":968
* cdef PyObject* baseptr
* if base is None:
* baseptr = NULL # <<<<<<<<<<<<<<
@@ -11469,7 +10889,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
}
/*else*/ {
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":974
+ /* "numpy.pxd":970
* baseptr = NULL
* else:
* Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<<
@@ -11478,7 +10898,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
*/
Py_INCREF(__pyx_v_base);
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":975
+ /* "numpy.pxd":971
* else:
* Py_INCREF(base) # important to do this before decref below!
* baseptr = <PyObject*>base # <<<<<<<<<<<<<<
@@ -11489,7 +10909,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
}
__pyx_L3:;
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":976
+ /* "numpy.pxd":972
* Py_INCREF(base) # important to do this before decref below!
* baseptr = <PyObject*>base
* Py_XDECREF(arr.base) # <<<<<<<<<<<<<<
@@ -11498,7 +10918,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
*/
Py_XDECREF(__pyx_v_arr->base);
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":977
+ /* "numpy.pxd":973
* baseptr = <PyObject*>base
* Py_XDECREF(arr.base)
* arr.base = baseptr # <<<<<<<<<<<<<<
@@ -11507,19 +10927,10 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
*/
__pyx_v_arr->base = __pyx_v_baseptr;
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":969
- *
- *
- * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<<
- * cdef PyObject* baseptr
- * if base is None:
- */
-
- /* function exit code */
__Pyx_RefNannyFinishContext();
}
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":979
+/* "numpy.pxd":975
* arr.base = baseptr
*
* cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<<
@@ -11533,17 +10944,17 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
int __pyx_t_1;
__Pyx_RefNannySetupContext("get_array_base", 0);
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":980
+ /* "numpy.pxd":976
*
* cdef inline object get_array_base(ndarray arr):
* if arr.base is NULL: # <<<<<<<<<<<<<<
* return None
* else:
*/
- __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0);
+ __pyx_t_1 = (__pyx_v_arr->base == NULL);
if (__pyx_t_1) {
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":981
+ /* "numpy.pxd":977
* cdef inline object get_array_base(ndarray arr):
* if arr.base is NULL:
* return None # <<<<<<<<<<<<<<
@@ -11554,10 +10965,11 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
+ goto __pyx_L3;
}
/*else*/ {
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":983
+ /* "numpy.pxd":979
* return None
* else:
* return <object>arr.base # <<<<<<<<<<<<<<
@@ -11567,16 +10979,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
__pyx_r = ((PyObject *)__pyx_v_arr->base);
goto __pyx_L0;
}
+ __pyx_L3:;
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":979
- * arr.base = baseptr
- *
- * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<<
- * if arr.base is NULL:
- * return None
- */
-
- /* function exit code */
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
__Pyx_RefNannyFinishContext();
@@ -11584,22 +10989,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
}
static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_SummaryBlock(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- PyObject *o;
- if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
- o = (*t->tp_alloc)(t, 0);
- } else {
- o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
- }
- if (unlikely(!o)) return 0;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
return o;
}
static void __pyx_tp_dealloc_2bx_3bbi_8bbi_file_SummaryBlock(PyObject *o) {
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
(*Py_TYPE(o)->tp_free)(o);
}
@@ -11715,6 +11110,10 @@ static int __pyx_setprop_2bx_3bbi_8bbi_file_12SummaryBlock_sum_squares(PyObject
}
}
+static PyMethodDef __pyx_methods_2bx_3bbi_8bbi_file_SummaryBlock[] = {
+ {0, 0, 0, 0}
+};
+
static struct PyGetSetDef __pyx_getsets_2bx_3bbi_8bbi_file_SummaryBlock[] = {
{(char *)"chrom_id", __pyx_getprop_2bx_3bbi_8bbi_file_12SummaryBlock_chrom_id, __pyx_setprop_2bx_3bbi_8bbi_file_12SummaryBlock_chrom_id, 0, 0},
{(char *)"start", __pyx_getprop_2bx_3bbi_8bbi_file_12SummaryBlock_start, __pyx_setprop_2bx_3bbi_8bbi_file_12SummaryBlock_start, 0, 0},
@@ -11727,9 +11126,107 @@ static struct PyGetSetDef __pyx_getsets_2bx_3bbi_8bbi_file_SummaryBlock[] = {
{0, 0, 0, 0, 0}
};
+static PyNumberMethods __pyx_tp_as_number_SummaryBlock = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_SummaryBlock = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_SummaryBlock = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_SummaryBlock = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_SummaryBlock = {
PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bbi_file.SummaryBlock", /*tp_name*/
+ __Pyx_NAMESTR("bx.bbi.bbi_file.SummaryBlock"), /*tp_name*/
sizeof(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_2bx_3bbi_8bbi_file_SummaryBlock, /*tp_dealloc*/
@@ -11742,24 +11239,24 @@ static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_SummaryBlock = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ &__pyx_tp_as_number_SummaryBlock, /*tp_as_number*/
+ &__pyx_tp_as_sequence_SummaryBlock, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_SummaryBlock, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- "\n A block of summary data from disk\n ", /*tp_doc*/
+ &__pyx_tp_as_buffer_SummaryBlock, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("\n A block of summary data from disk\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- 0, /*tp_methods*/
+ __pyx_methods_2bx_3bbi_8bbi_file_SummaryBlock, /*tp_methods*/
0, /*tp_members*/
__pyx_getsets_2bx_3bbi_8bbi_file_SummaryBlock, /*tp_getset*/
0, /*tp_base*/
@@ -11778,22 +11275,16 @@ static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_SummaryBlock = {
0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
#endif
};
static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData __pyx_vtable_2bx_3bbi_8bbi_file_SummarizedData;
static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_SummarizedData(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *p;
- PyObject *o;
- if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
- o = (*t->tp_alloc)(t, 0);
- } else {
- o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
- }
- if (unlikely(!o)) return 0;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
p = ((struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *)o);
p->__pyx_vtab = __pyx_vtabptr_2bx_3bbi_8bbi_file_SummarizedData;
p->valid_count = ((PyArrayObject *)Py_None); Py_INCREF(Py_None);
@@ -11806,17 +11297,13 @@ static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_SummarizedData(PyTypeObject *t,
static void __pyx_tp_dealloc_2bx_3bbi_8bbi_file_SummarizedData(PyObject *o) {
struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *p = (struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *)o;
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
PyObject_GC_UnTrack(o);
Py_CLEAR(p->valid_count);
Py_CLEAR(p->min_val);
Py_CLEAR(p->max_val);
Py_CLEAR(p->sum_data);
Py_CLEAR(p->sum_squares);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -11842,8 +11329,8 @@ static int __pyx_tp_traverse_2bx_3bbi_8bbi_file_SummarizedData(PyObject *o, visi
}
static int __pyx_tp_clear_2bx_3bbi_8bbi_file_SummarizedData(PyObject *o) {
- PyObject* tmp;
struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *p = (struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *)o;
+ PyObject* tmp;
tmp = ((PyObject*)p->valid_count);
p->valid_count = ((PyArrayObject *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
@@ -11985,9 +11472,107 @@ static struct PyGetSetDef __pyx_getsets_2bx_3bbi_8bbi_file_SummarizedData[] = {
{0, 0, 0, 0, 0}
};
+static PyNumberMethods __pyx_tp_as_number_SummarizedData = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_SummarizedData = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_SummarizedData = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_SummarizedData = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_SummarizedData = {
PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bbi_file.SummarizedData", /*tp_name*/
+ __Pyx_NAMESTR("bx.bbi.bbi_file.SummarizedData"), /*tp_name*/
sizeof(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_2bx_3bbi_8bbi_file_SummarizedData, /*tp_dealloc*/
@@ -12000,17 +11585,17 @@ static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_SummarizedData = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ &__pyx_tp_as_number_SummarizedData, /*tp_as_number*/
+ &__pyx_tp_as_sequence_SummarizedData, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_SummarizedData, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- "\n The result of using SummaryBlocks read from the file to produce a \n aggregation over a particular range and resolution\n ", /*tp_doc*/
+ &__pyx_tp_as_buffer_SummarizedData, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("\n The result of using SummaryBlocks read from the file to produce a \n aggregation over a particular range and resolution\n "), /*tp_doc*/
__pyx_tp_traverse_2bx_3bbi_8bbi_file_SummarizedData, /*tp_traverse*/
__pyx_tp_clear_2bx_3bbi_8bbi_file_SummarizedData, /*tp_clear*/
0, /*tp_richcompare*/
@@ -12036,22 +11621,16 @@ static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_SummarizedData = {
0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
#endif
};
static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile __pyx_vtable_2bx_3bbi_8bbi_file_BBIFile;
static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_BBIFile(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *p;
- PyObject *o;
- if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
- o = (*t->tp_alloc)(t, 0);
- } else {
- o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
- }
- if (unlikely(!o)) return 0;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
p = ((struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *)o);
p->__pyx_vtab = __pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile;
p->file = Py_None; Py_INCREF(Py_None);
@@ -12063,16 +11642,12 @@ static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_BBIFile(PyTypeObject *t, CYTHON
static void __pyx_tp_dealloc_2bx_3bbi_8bbi_file_BBIFile(PyObject *o) {
struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *p = (struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *)o;
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
PyObject_GC_UnTrack(o);
Py_CLEAR(p->file);
Py_CLEAR(p->reader);
Py_CLEAR(p->chrom_bpt);
Py_CLEAR(p->level_list);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -12095,8 +11670,8 @@ static int __pyx_tp_traverse_2bx_3bbi_8bbi_file_BBIFile(PyObject *o, visitproc v
}
static int __pyx_tp_clear_2bx_3bbi_8bbi_file_BBIFile(PyObject *o) {
- PyObject* tmp;
struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *p = (struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *)o;
+ PyObject* tmp;
tmp = ((PyObject*)p->file);
p->file = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
@@ -12168,10 +11743,10 @@ static int __pyx_setprop_2bx_3bbi_8bbi_file_7BBIFile_level_list(PyObject *o, PyO
}
static PyMethodDef __pyx_methods_2bx_3bbi_8bbi_file_BBIFile[] = {
- {"open", (PyCFunction)__pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_3open, METH_VARARGS|METH_KEYWORDS, __pyx_doc_2bx_3bbi_8bbi_file_7BBIFile_2open},
- {"summarize", (PyCFunction)__pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_5summarize, METH_VARARGS|METH_KEYWORDS, __pyx_doc_2bx_3bbi_8bbi_file_7BBIFile_4summarize},
- {"summarize_from_full", (PyCFunction)__pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_7summarize_from_full, METH_VARARGS|METH_KEYWORDS, __pyx_doc_2bx_3bbi_8bbi_file_7BBIFile_6summarize_from_full},
- {"query", (PyCFunction)__pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_9query, METH_VARARGS|METH_KEYWORDS, __pyx_doc_2bx_3bbi_8bbi_file_7BBIFile_8query},
+ {__Pyx_NAMESTR("open"), (PyCFunction)__pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_3open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_3bbi_8bbi_file_7BBIFile_2open)},
+ {__Pyx_NAMESTR("summarize"), (PyCFunction)__pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_5summarize, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_3bbi_8bbi_file_7BBIFile_4summarize)},
+ {__Pyx_NAMESTR("summarize_from_full"), (PyCFunction)__pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_7summarize_from_full, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_3bbi_8bbi_file_7BBIFile_6summarize_from_full)},
+ {__Pyx_NAMESTR("query"), (PyCFunction)__pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_9query, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_3bbi_8bbi_file_7BBIFile_8query)},
{0, 0, 0, 0}
};
@@ -12183,11 +11758,109 @@ static struct PyGetSetDef __pyx_getsets_2bx_3bbi_8bbi_file_BBIFile[] = {
{0, 0, 0, 0, 0}
};
-static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_BBIFile = {
- PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bbi_file.BBIFile", /*tp_name*/
- sizeof(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile), /*tp_basicsize*/
- 0, /*tp_itemsize*/
+static PyNumberMethods __pyx_tp_as_number_BBIFile = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_BBIFile = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_BBIFile = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_BBIFile = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_BBIFile = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("bx.bbi.bbi_file.BBIFile"), /*tp_name*/
+ sizeof(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
__pyx_tp_dealloc_2bx_3bbi_8bbi_file_BBIFile, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
@@ -12198,17 +11871,17 @@ static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_BBIFile = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ &__pyx_tp_as_number_BBIFile, /*tp_as_number*/
+ &__pyx_tp_as_sequence_BBIFile, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_BBIFile, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- "\n A \"big binary indexed\" file. Stores blocks of raw data and numeric \n summaries of that data at different levels of aggregation (\"zoom levels\").\n Generic enough to accommodate both wiggle and bed data. \n ", /*tp_doc*/
+ &__pyx_tp_as_buffer_BBIFile, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("\n A \"big binary indexed\" file. Stores blocks of raw data and numeric \n summaries of that data at different levels of aggregation (\"zoom levels\").\n Generic enough to accommodate both wiggle and bed data. \n "), /*tp_doc*/
__pyx_tp_traverse_2bx_3bbi_8bbi_file_BBIFile, /*tp_traverse*/
__pyx_tp_clear_2bx_3bbi_8bbi_file_BBIFile, /*tp_clear*/
0, /*tp_richcompare*/
@@ -12234,39 +11907,130 @@ static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_BBIFile = {
0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
#endif
};
static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler __pyx_vtable_2bx_3bbi_8bbi_file_BlockHandler;
static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_BlockHandler(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler *p;
- PyObject *o;
- if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
- o = (*t->tp_alloc)(t, 0);
- } else {
- o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
- }
- if (unlikely(!o)) return 0;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
p = ((struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler *)o);
p->__pyx_vtab = __pyx_vtabptr_2bx_3bbi_8bbi_file_BlockHandler;
return o;
}
static void __pyx_tp_dealloc_2bx_3bbi_8bbi_file_BlockHandler(PyObject *o) {
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
(*Py_TYPE(o)->tp_free)(o);
}
+static PyMethodDef __pyx_methods_2bx_3bbi_8bbi_file_BlockHandler[] = {
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_BlockHandler = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_BlockHandler = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_BlockHandler = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_BlockHandler = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_BlockHandler = {
PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bbi_file.BlockHandler", /*tp_name*/
+ __Pyx_NAMESTR("bx.bbi.bbi_file.BlockHandler"), /*tp_name*/
sizeof(struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_2bx_3bbi_8bbi_file_BlockHandler, /*tp_dealloc*/
@@ -12279,24 +12043,24 @@ static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_BlockHandler = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ &__pyx_tp_as_number_BlockHandler, /*tp_as_number*/
+ &__pyx_tp_as_sequence_BlockHandler, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_BlockHandler, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- "\n Callback for `BBIFile.visit_blocks_in_region`\n ", /*tp_doc*/
+ &__pyx_tp_as_buffer_BlockHandler, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("\n Callback for `BBIFile.visit_blocks_in_region`\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- 0, /*tp_methods*/
+ __pyx_methods_2bx_3bbi_8bbi_file_BlockHandler, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -12315,22 +12079,16 @@ static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_BlockHandler = {
0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
#endif
};
static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_ZoomLevel __pyx_vtable_2bx_3bbi_8bbi_file_ZoomLevel;
static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_ZoomLevel(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *p;
- PyObject *o;
- if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
- o = (*t->tp_alloc)(t, 0);
- } else {
- o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
- }
- if (unlikely(!o)) return 0;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
p = ((struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *)o);
p->__pyx_vtab = __pyx_vtabptr_2bx_3bbi_8bbi_file_ZoomLevel;
p->bbi_file = ((struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *)Py_None); Py_INCREF(Py_None);
@@ -12339,13 +12097,9 @@ static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_ZoomLevel(PyTypeObject *t, CYTH
static void __pyx_tp_dealloc_2bx_3bbi_8bbi_file_ZoomLevel(PyObject *o) {
struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *p = (struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *)o;
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
PyObject_GC_UnTrack(o);
Py_CLEAR(p->bbi_file);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -12359,8 +12113,8 @@ static int __pyx_tp_traverse_2bx_3bbi_8bbi_file_ZoomLevel(PyObject *o, visitproc
}
static int __pyx_tp_clear_2bx_3bbi_8bbi_file_ZoomLevel(PyObject *o) {
- PyObject* tmp;
struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *p = (struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *)o;
+ PyObject* tmp;
tmp = ((PyObject*)p->bbi_file);
p->bbi_file = ((struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
@@ -12410,7 +12164,7 @@ static int __pyx_setprop_2bx_3bbi_8bbi_file_9ZoomLevel_index_offset(PyObject *o,
}
static PyMethodDef __pyx_methods_2bx_3bbi_8bbi_file_ZoomLevel[] = {
- {"_summary_blocks_in_region", (PyCFunction)__pyx_pw_2bx_3bbi_8bbi_file_9ZoomLevel_1_summary_blocks_in_region, METH_VARARGS|METH_KEYWORDS, __pyx_doc_2bx_3bbi_8bbi_file_9ZoomLevel__summary_blocks_in_region},
+ {__Pyx_NAMESTR("_summary_blocks_in_region"), (PyCFunction)__pyx_pw_2bx_3bbi_8bbi_file_9ZoomLevel_1_summary_blocks_in_region, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_3bbi_8bbi_file_9ZoomLevel__summary_blocks_in_region)},
{0, 0, 0, 0}
};
@@ -12421,9 +12175,107 @@ static struct PyGetSetDef __pyx_getsets_2bx_3bbi_8bbi_file_ZoomLevel[] = {
{0, 0, 0, 0, 0}
};
+static PyNumberMethods __pyx_tp_as_number_ZoomLevel = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_ZoomLevel = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_ZoomLevel = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_ZoomLevel = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_ZoomLevel = {
PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bbi_file.ZoomLevel", /*tp_name*/
+ __Pyx_NAMESTR("bx.bbi.bbi_file.ZoomLevel"), /*tp_name*/
sizeof(struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_2bx_3bbi_8bbi_file_ZoomLevel, /*tp_dealloc*/
@@ -12436,16 +12288,16 @@ static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_ZoomLevel = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ &__pyx_tp_as_number_ZoomLevel, /*tp_as_number*/
+ &__pyx_tp_as_sequence_ZoomLevel, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_ZoomLevel, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ &__pyx_tp_as_buffer_ZoomLevel, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
__pyx_tp_traverse_2bx_3bbi_8bbi_file_ZoomLevel, /*tp_traverse*/
__pyx_tp_clear_2bx_3bbi_8bbi_file_ZoomLevel, /*tp_clear*/
@@ -12472,9 +12324,8 @@ static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_ZoomLevel = {
0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
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#else
PyModuleDef_HEAD_INIT,
#endif
- "bbi_file",
- __pyx_k_Core_implementation_for_reading, /* m_doc */
+ __Pyx_NAMESTR("bbi_file"),
+ __Pyx_DOCSTR(__pyx_k_18), /* m_doc */
-1, /* m_size */
__pyx_methods /* m_methods */,
NULL, /* m_reload */
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- {&__pyx_n_s_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 0, 1, 1},
- {&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1},
- {&__pyx_n_s_open, __pyx_k_open, sizeof(__pyx_k_open), 0, 0, 1, 1},
- {&__pyx_n_s_pyx_vtable, __pyx_k_pyx_vtable, sizeof(__pyx_k_pyx_vtable), 0, 0, 1, 1},
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- {&__pyx_n_s_read_uint16, __pyx_k_read_uint16, sizeof(__pyx_k_read_uint16), 0, 0, 1, 1},
- {&__pyx_n_s_read_uint32, __pyx_k_read_uint32, sizeof(__pyx_k_read_uint32), 0, 0, 1, 1},
- {&__pyx_n_s_read_uint64, __pyx_k_read_uint64, sizeof(__pyx_k_read_uint64), 0, 0, 1, 1},
- {&__pyx_n_s_seek, __pyx_k_seek, sizeof(__pyx_k_seek), 0, 0, 1, 1},
- {&__pyx_n_s_size, __pyx_k_size, sizeof(__pyx_k_size), 0, 0, 1, 1},
- {&__pyx_n_s_sqrt, __pyx_k_sqrt, sizeof(__pyx_k_sqrt), 0, 0, 1, 1},
- {&__pyx_n_s_start, __pyx_k_start, sizeof(__pyx_k_start), 0, 0, 1, 1},
- {&__pyx_n_s_std_dev, __pyx_k_std_dev, sizeof(__pyx_k_std_dev), 0, 0, 1, 1},
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- {&__pyx_n_s_uint32, __pyx_k_uint32, sizeof(__pyx_k_uint32), 0, 0, 1, 1},
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- {&__pyx_n_s_valid_count, __pyx_k_valid_count, sizeof(__pyx_k_valid_count), 0, 0, 1, 1},
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- {&__pyx_n_s_zlib, __pyx_k_zlib, sizeof(__pyx_k_zlib), 0, 0, 1, 1},
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@@ -12586,93 +12431,104 @@ static int __Pyx_InitCachedConstants(void) {
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+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_4));
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- __Pyx_GIVEREF(__pyx_tuple__3);
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+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_7));
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- __Pyx_GIVEREF(__pyx_tuple__4);
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- __Pyx_GOTREF(__pyx_tuple__6);
- __Pyx_GIVEREF(__pyx_tuple__6);
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+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_14));
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":806
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- __Pyx_GIVEREF(__pyx_tuple__7);
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+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_15));
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":826
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- __Pyx_GOTREF(__pyx_tuple__8);
- __Pyx_GIVEREF(__pyx_tuple__8);
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+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_17));
__Pyx_RefNannyFinishContext();
return 0;
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- __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+ __pyx_int_32 = PyInt_FromLong(32); if (unlikely(!__pyx_int_32)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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return 0;
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return -1;
@@ -12701,9 +12559,6 @@ PyMODINIT_FUNC PyInit_bbi_file(void)
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PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
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#if CYTHON_REFNANNY
__Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
@@ -12736,26 +12591,11 @@ PyMODINIT_FUNC PyInit_bbi_file(void)
#endif
/*--- Module creation code ---*/
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4("bbi_file", __pyx_methods, __pyx_k_Core_implementation_for_reading, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("bbi_file"), __pyx_methods, __Pyx_DOCSTR(__pyx_k_18), 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- Py_INCREF(__pyx_d);
- __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_PYPY
- Py_INCREF(__pyx_b);
- #endif
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- /*--- Initialize various global constants etc. ---*/
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- #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
- if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- if (__pyx_module_is_main_bx__bbi__bbi_file) {
- if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- }
#if PY_MAJOR_VERSION >= 3
{
PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -12764,6 +12604,16 @@ PyMODINIT_FUNC PyInit_bbi_file(void)
}
}
#endif
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_PYPY
+ Py_INCREF(__pyx_b);
+ #endif
+ if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ /*--- Initialize various global constants etc. ---*/
+ if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_module_is_main_bx__bbi__bbi_file) {
+ if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ }
/*--- Builtin init code ---*/
if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Constants init code ---*/
@@ -12772,16 +12622,14 @@ PyMODINIT_FUNC PyInit_bbi_file(void)
/*--- Variable export code ---*/
/*--- Function export code ---*/
/*--- Type init code ---*/
- if (PyType_Ready(&__pyx_type_2bx_3bbi_8bbi_file_SummaryBlock) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_type_2bx_3bbi_8bbi_file_SummaryBlock.tp_print = 0;
- if (PyObject_SetAttrString(__pyx_m, "SummaryBlock", (PyObject *)&__pyx_type_2bx_3bbi_8bbi_file_SummaryBlock) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2bx_3bbi_8bbi_file_SummaryBlock) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "SummaryBlock", (PyObject *)&__pyx_type_2bx_3bbi_8bbi_file_SummaryBlock) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_2bx_3bbi_8bbi_file_SummaryBlock = &__pyx_type_2bx_3bbi_8bbi_file_SummaryBlock;
__pyx_vtabptr_2bx_3bbi_8bbi_file_SummarizedData = &__pyx_vtable_2bx_3bbi_8bbi_file_SummarizedData;
__pyx_vtable_2bx_3bbi_8bbi_file_SummarizedData.accumulate_interval_value = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float))__pyx_f_2bx_3bbi_8bbi_file_14SummarizedData_accumulate_interval_value;
- if (PyType_Ready(&__pyx_type_2bx_3bbi_8bbi_file_SummarizedData) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_type_2bx_3bbi_8bbi_file_SummarizedData.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_8bbi_file_SummarizedData.tp_dict, __pyx_vtabptr_2bx_3bbi_8bbi_file_SummarizedData) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "SummarizedData", (PyObject *)&__pyx_type_2bx_3bbi_8bbi_file_SummarizedData) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2bx_3bbi_8bbi_file_SummarizedData) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_8bbi_file_SummarizedData.tp_dict, __pyx_vtabptr_2bx_3bbi_8bbi_file_SummarizedData) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "SummarizedData", (PyObject *)&__pyx_type_2bx_3bbi_8bbi_file_SummarizedData) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_2bx_3bbi_8bbi_file_SummarizedData = &__pyx_type_2bx_3bbi_8bbi_file_SummarizedData;
__pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile = &__pyx_vtable_2bx_3bbi_8bbi_file_BBIFile;
__pyx_vtable_2bx_3bbi_8bbi_file_BBIFile.visit_blocks_in_region = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler *))__pyx_f_2bx_3bbi_8bbi_file_7BBIFile_visit_blocks_in_region;
@@ -12791,25 +12639,22 @@ PyMODINIT_FUNC PyInit_bbi_file(void)
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__pyx_vtable_2bx_3bbi_8bbi_file_BBIFile.query = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int, int __pyx_skip_dispatch))__pyx_f_2bx_3bbi_8bbi_file_7BBIFile_query;
__pyx_vtable_2bx_3bbi_8bbi_file_BBIFile._summarize_from_full = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int))__pyx_f_2bx_3bbi_8bbi_file_7BBIFile__summarize_from_full;
- if (PyType_Ready(&__pyx_type_2bx_3bbi_8bbi_file_BBIFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_type_2bx_3bbi_8bbi_file_BBIFile.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_8bbi_file_BBIFile.tp_dict, __pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "BBIFile", (PyObject *)&__pyx_type_2bx_3bbi_8bbi_file_BBIFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2bx_3bbi_8bbi_file_BBIFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_8bbi_file_BBIFile.tp_dict, __pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "BBIFile", (PyObject *)&__pyx_type_2bx_3bbi_8bbi_file_BBIFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile = &__pyx_type_2bx_3bbi_8bbi_file_BBIFile;
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@@ -12822,10 +12667,10 @@ PyMODINIT_FUNC PyInit_bbi_file(void)
#endif
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/*--- Variable import code ---*/
/*--- Function import code ---*/
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@@ -12839,15 +12684,19 @@ PyMODINIT_FUNC PyInit_bbi_file(void)
*/
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@@ -12856,84 +12705,80 @@ PyMODINIT_FUNC PyInit_bbi_file(void)
*
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* # Signatures for bbi related file types
*
* cdef public int big_wig_sig = 0x888FFC26 # <<<<<<<<<<<<<<
@@ -12942,7 +12787,7 @@ PyMODINIT_FUNC PyInit_bbi_file(void)
*/
big_wig_sig = 0x888FFC26;
- /* "bx/bbi/bbi_file.pyx":31
+ /* "bx/bbi/bbi_file.pyx":29
*
* cdef public int big_wig_sig = 0x888FFC26
* cdef public int big_bed_sig = 0x8789F2EB # <<<<<<<<<<<<<<
@@ -12957,28 +12802,23 @@ PyMODINIT_FUNC PyInit_bbi_file(void)
* """
*/
__pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":979
+ /* "numpy.pxd":975
* arr.base = baseptr
*
* cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<<
* if arr.base is NULL:
* return None
*/
-
- /*--- Wrapped vars code ---*/
-
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
if (__pyx_m) {
- if (__pyx_d) {
- __Pyx_AddTraceback("init bx.bbi.bbi_file", __pyx_clineno, __pyx_lineno, __pyx_filename);
- }
+ __Pyx_AddTraceback("init bx.bbi.bbi_file", __pyx_clineno, __pyx_lineno, __pyx_filename);
Py_DECREF(__pyx_m); __pyx_m = 0;
} else if (!PyErr_Occurred()) {
PyErr_SetString(PyExc_ImportError, "init bx.bbi.bbi_file");
@@ -12992,7 +12832,7 @@ PyMODINIT_FUNC PyInit_bbi_file(void)
#endif
}
-/* --- Runtime support code --- */
+/* Runtime support code */
#if CYTHON_REFNANNY
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
PyObject *m = NULL, *p = NULL;
@@ -13007,17 +12847,19 @@ end:
Py_XDECREF(m);
return (__Pyx_RefNannyAPIStruct *)r;
}
-#endif
+#endif /* CYTHON_REFNANNY */
-static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
- PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name);
- if (unlikely(!result)) {
- PyErr_Format(PyExc_NameError,
-#if PY_MAJOR_VERSION >= 3
- "name '%U' is not defined", name);
-#else
- "name '%.200s' is not defined", PyString_AS_STRING(name));
-#endif
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
+ PyObject *result;
+ result = PyObject_GetAttr(dict, name);
+ if (!result) {
+ if (dict != __pyx_b) {
+ PyErr_Clear();
+ result = PyObject_GetAttr(__pyx_b, name);
+ }
+ if (!result) {
+ PyErr_SetObject(PyExc_NameError, name);
+ }
}
return result;
}
@@ -13042,7 +12884,7 @@ static void __Pyx_RaiseArgtupleInvalid(
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
+ "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
@@ -13146,12 +12988,12 @@ arg_passed_twice:
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
- "%.200s() keywords must be strings", function_name);
+ "%s() keywords must be strings", function_name);
goto bad;
invalid_keyword:
PyErr_Format(PyExc_TypeError,
#if PY_MAJOR_VERSION < 3
- "%.200s() got an unexpected keyword argument '%.200s'",
+ "%s() got an unexpected keyword argument '%s'",
function_name, PyString_AsString(key));
#else
"%s() got an unexpected keyword argument '%U'",
@@ -13161,45 +13003,9 @@ bad:
return -1;
}
-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
- PyObject *result;
-#if CYTHON_COMPILING_IN_CPYTHON
- result = PyDict_GetItem(__pyx_d, name);
- if (likely(result)) {
- Py_INCREF(result);
- } else {
-#else
- result = PyObject_GetItem(__pyx_d, name);
- if (!result) {
- PyErr_Clear();
-#endif
- result = __Pyx_GetBuiltinName(name);
- }
- return result;
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- PyObject *result;
- ternaryfunc call = func->ob_type->tp_call;
- if (unlikely(!call))
- return PyObject_Call(func, arg, kw);
- if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
- return NULL;
- result = (*call)(func, arg, kw);
- Py_LeaveRecursiveCall();
- if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
- PyErr_SetString(
- PyExc_SystemError,
- "NULL result without error in PyObject_Call");
- }
- return result;
-}
-#endif
-
static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
if (unlikely(!type)) {
- PyErr_SetString(PyExc_SystemError, "Missing type object");
+ PyErr_Format(PyExc_SystemError, "Missing type object");
return 0;
}
if (likely(PyObject_TypeCheck(obj, type)))
@@ -13257,7 +13063,7 @@ static int __Pyx_BufFmt_ParseNumber(const char** ts) {
}
static int __Pyx_BufFmt_ExpectNumber(const char **ts) {
int number = __Pyx_BufFmt_ParseNumber(ts);
- if (number == -1)
+ if (number == -1) /* First char was not a digit */
PyErr_Format(PyExc_ValueError,\
"Does not understand character buffer dtype format string ('%c')", **ts);
return number;
@@ -13502,7 +13308,7 @@ static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) {
ctx->fmt_offset += size;
if (arraysize)
ctx->fmt_offset += (arraysize - 1) * size;
- --ctx->enc_count;
+ --ctx->enc_count; /* Consume from buffer string */
while (1) {
if (field == &ctx->root) {
ctx->head = NULL;
@@ -13510,7 +13316,7 @@ static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) {
__Pyx_BufFmt_RaiseExpected(ctx);
return -1;
}
- break;
+ break; /* breaks both loops as ctx->enc_count == 0 */
}
ctx->head->field = ++field;
if (field->type == NULL) {
@@ -13519,7 +13325,7 @@ static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) {
continue;
} else if (field->type->typegroup == 'S') {
size_t parent_offset = ctx->head->parent_offset + field->offset;
- if (field->type->fields->type == NULL) continue;
+ if (field->type->fields->type == NULL) continue; /* empty struct */
field = field->type->fields;
++ctx->head;
ctx->head->field = field;
@@ -13549,10 +13355,8 @@ __pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp)
}
if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
while (*ts && *ts != ')') {
- switch (*ts) {
- case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue;
- default: break;
- }
+ if (isspace(*ts))
+ continue;
number = __Pyx_BufFmt_ExpectNumber(&ts);
if (number == -1) return NULL;
if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i])
@@ -13592,10 +13396,10 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha
__Pyx_BufFmt_RaiseExpected(ctx);
return NULL;
}
- return ts;
+ return ts;
case ' ':
- case '\r':
- case '\n':
+ case 10:
+ case 13:
++ts;
break;
case '<':
@@ -13620,7 +13424,7 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha
case '^':
ctx->new_packmode = *ts++;
break;
- case 'T':
+ case 'T': /* substruct */
{
const char* ts_after_sub;
size_t i, struct_count = ctx->new_count;
@@ -13632,7 +13436,7 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha
return NULL;
}
if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_type = 0;
+ ctx->enc_type = 0; /* Erase processed last struct element */
ctx->enc_count = 0;
ctx->struct_alignment = 0;
++ts;
@@ -13645,12 +13449,12 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha
if (struct_alignment) ctx->struct_alignment = struct_alignment;
}
break;
- case '}':
+ case '}': /* end of substruct; either repeat or move on */
{
size_t alignment = ctx->struct_alignment;
++ts;
if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_type = 0;
+ ctx->enc_type = 0; /* Erase processed last struct element */
if (alignment && ctx->fmt_offset % alignment) {
ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment);
}
@@ -13671,25 +13475,21 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha
if (*ts != 'f' && *ts != 'd' && *ts != 'g') {
__Pyx_BufFmt_RaiseUnexpectedChar('Z');
return NULL;
- }
+ } /* fall through */
case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I':
case 'l': case 'L': case 'q': case 'Q':
case 'f': case 'd': case 'g':
- case 'O': case 'p':
+ case 'O': case 's': case 'p':
if (ctx->enc_type == *ts && got_Z == ctx->is_complex &&
ctx->enc_packmode == ctx->new_packmode) {
ctx->enc_count += ctx->new_count;
- ctx->new_count = 1;
- got_Z = 0;
- ++ts;
- break;
+ } else {
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ ctx->enc_count = ctx->new_count;
+ ctx->enc_packmode = ctx->new_packmode;
+ ctx->enc_type = *ts;
+ ctx->is_complex = got_Z;
}
- case 's':
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_count = ctx->new_count;
- ctx->enc_packmode = ctx->new_packmode;
- ctx->enc_type = *ts;
- ctx->is_complex = got_Z;
++ts;
ctx->new_count = 1;
got_Z = 0;
@@ -13794,113 +13594,6 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
#endif
}
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) {
- PyObject *self, *result;
- PyCFunction cfunc;
- cfunc = PyCFunction_GET_FUNCTION(func);
- self = PyCFunction_GET_SELF(func);
- if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
- return NULL;
- result = cfunc(self, arg);
- Py_LeaveRecursiveCall();
- if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
- PyErr_SetString(
- PyExc_SystemError,
- "NULL result without error in PyObject_Call");
- }
- return result;
-}
-#endif
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) {
- PyObject *result;
- PyObject *args = PyTuple_New(1);
- if (unlikely(!args)) return NULL;
- Py_INCREF(arg);
- PyTuple_SET_ITEM(args, 0, arg);
- result = __Pyx_PyObject_Call(func, args, NULL);
- Py_DECREF(args);
- return result;
-}
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
-#ifdef __Pyx_CyFunction_USED
- if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) {
-#else
- if (likely(PyCFunction_Check(func))) {
-#endif
- if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) {
- return __Pyx_PyObject_CallMethO(func, arg);
- }
- }
- return __Pyx__PyObject_CallOneArg(func, arg);
-}
-#else
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
- PyObject* args = PyTuple_Pack(1, arg);
- return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL;
-}
-#endif
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) {
-#ifdef __Pyx_CyFunction_USED
- if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) {
-#else
- if (likely(PyCFunction_Check(func))) {
-#endif
- if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) {
- return __Pyx_PyObject_CallMethO(func, NULL);
- }
- }
- return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL);
-}
-#endif
-
-static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) {
- PyObject *method, *result = NULL;
- method = __Pyx_PyObject_GetAttrStr(obj, method_name);
- if (unlikely(!method)) goto bad;
-#if CYTHON_COMPILING_IN_CPYTHON
- if (likely(PyMethod_Check(method))) {
- PyObject *self = PyMethod_GET_SELF(method);
- if (likely(self)) {
- PyObject *args;
- PyObject *function = PyMethod_GET_FUNCTION(method);
- args = PyTuple_New(2);
- if (unlikely(!args)) goto bad;
- Py_INCREF(self);
- PyTuple_SET_ITEM(args, 0, self);
- Py_INCREF(arg);
- PyTuple_SET_ITEM(args, 1, arg);
- Py_INCREF(function);
- Py_DECREF(method); method = NULL;
- result = __Pyx_PyObject_Call(function, args, NULL);
- Py_DECREF(args);
- Py_DECREF(function);
- return result;
- }
- }
-#endif
- result = __Pyx_PyObject_CallOneArg(method, arg);
-bad:
- Py_XDECREF(method);
- return result;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
- if (likely(PyList_CheckExact(L))) {
- if (unlikely(__Pyx_PyList_Append(L, x) < 0)) return -1;
- } else {
- PyObject* retval = __Pyx_PyObject_CallMethod1(L, __pyx_n_s_append, x);
- if (unlikely(!retval))
- return -1;
- Py_DECREF(retval);
- }
- return 0;
-}
-
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
PyErr_Format(PyExc_ValueError,
"too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
@@ -13908,7 +13601,7 @@ static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
- "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack",
+ "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
index, (index == 1) ? "" : "s");
}
@@ -13982,7 +13675,11 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
goto raise_error;
}
}
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyClass_Check(type)) {
+ #else
if (PyType_Check(type)) {
+ #endif
#if CYTHON_COMPILING_IN_PYPY
if (!value) {
Py_INCREF(Py_None);
@@ -13997,13 +13694,26 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
goto raise_error;
}
value = type;
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+ Py_INCREF(type);
+ }
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
+ #else
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ #endif
}
__Pyx_ErrRestore(type, value, tb);
return;
@@ -14013,7 +13723,7 @@ raise_error:
Py_XDECREF(tb);
return;
}
-#else
+#else /* Python 3+ */
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
PyObject* owned_instance = NULL;
if (tb == Py_None) {
@@ -14034,62 +13744,46 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
value = type;
type = (PyObject*) Py_TYPE(value);
} else if (PyExceptionClass_Check(type)) {
- PyObject *instance_class = NULL;
- if (value && PyExceptionInstance_Check(value)) {
- instance_class = (PyObject*) Py_TYPE(value);
- if (instance_class != type) {
- if (PyObject_IsSubclass(instance_class, type)) {
- type = instance_class;
- } else {
- instance_class = NULL;
- }
- }
+ PyObject *args;
+ if (!value)
+ args = PyTuple_New(0);
+ else if (PyTuple_Check(value)) {
+ Py_INCREF(value);
+ args = value;
}
- if (!instance_class) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- } else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyObject_Call(type, args, NULL);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
+ else
+ args = PyTuple_Pack(1, value);
+ if (!args)
+ goto bad;
+ owned_instance = PyEval_CallObject(type, args);
+ Py_DECREF(args);
+ if (!owned_instance)
+ goto bad;
+ value = owned_instance;
+ if (!PyExceptionInstance_Check(value)) {
+ PyErr_Format(PyExc_TypeError,
+ "calling %R should have returned an instance of "
+ "BaseException, not %R",
+ type, Py_TYPE(value));
+ goto bad;
}
} else {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
-#if PY_VERSION_HEX >= 0x03030000
- if (cause) {
-#else
if (cause && cause != Py_None) {
-#endif
PyObject *fixed_cause;
- if (cause == Py_None) {
- fixed_cause = NULL;
- } else if (PyExceptionClass_Check(cause)) {
+ if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
if (fixed_cause == NULL)
goto bad;
- } else if (PyExceptionInstance_Check(cause)) {
+ }
+ else if (PyExceptionInstance_Check(cause)) {
fixed_cause = cause;
Py_INCREF(fixed_cause);
- } else {
+ }
+ else {
PyErr_SetString(PyExc_TypeError,
"exception causes must derive from "
"BaseException");
@@ -14099,13 +13793,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
PyErr_SetObject(type, value);
if (tb) {
-#if CYTHON_COMPILING_IN_PYPY
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyErr_Fetch(tmp_type, tmp_value, tmp_tb);
- Py_INCREF(tb);
- PyErr_Restore(tmp_type, tmp_value, tb);
- Py_XDECREF(tmp_tb);
-#else
PyThreadState *tstate = PyThreadState_GET();
PyObject* tmp_tb = tstate->curexc_traceback;
if (tb != tmp_tb) {
@@ -14113,7 +13800,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
tstate->curexc_traceback = tb;
Py_XDECREF(tmp_tb);
}
-#endif
}
bad:
Py_XDECREF(owned_instance);
@@ -14121,277 +13807,15 @@ bad:
}
#endif
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
- PyObject *r;
- if (!j) return NULL;
- r = PyObject_GetItem(o, j);
- Py_DECREF(j);
- return r;
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (is_list || PyList_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
- PyObject *r = PyList_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- }
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- } else {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- return NULL;
- }
- }
- return m->sq_item(o, i);
- }
- }
-#else
- if (is_list || PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+static void __Pyx_RaiseBufferFallbackError(void) {
+ PyErr_Format(PyExc_ValueError,
+ "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!");
}
static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
}
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
- PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
- if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
- PyErr_Format(PyExc_ImportError,
- #if PY_MAJOR_VERSION < 3
- "cannot import name %.230s", PyString_AS_STRING(name));
- #else
- "cannot import name %S", name);
- #endif
- }
- return value;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0,
- 0,
- 0,
- 0,
- 0,
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line,
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- __pyx_d, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
PyObject *empty_list = 0;
PyObject *module = 0;
@@ -14399,8 +13823,8 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
PyObject *empty_dict = 0;
PyObject *list;
#if PY_VERSION_HEX < 0x03030000
- PyObject *py_import;
- py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
+ PyObject *py_import = 0;
+ py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
if (!py_import)
goto bad;
#endif
@@ -14418,6 +13842,7 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
empty_dict = PyDict_New();
if (!empty_dict)
goto bad;
+ #if PY_VERSION_HEX >= 0x02050000
{
#if PY_MAJOR_VERSION >= 3
if (level == -1) {
@@ -14436,585 +13861,123 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
if (!module) {
if (!PyErr_ExceptionMatches(PyExc_ImportError))
goto bad;
- PyErr_Clear();
- }
- }
- level = 0;
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-#if PY_MAJOR_VERSION < 3
-static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
- if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags);
- if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags);
- PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
- return -1;
-}
-static void __Pyx_ReleaseBuffer(Py_buffer *view) {
- PyObject *obj = view->obj;
- if (!obj) return;
- if (PyObject_CheckBuffer(obj)) {
- PyBuffer_Release(view);
- return;
- }
- if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; }
- Py_DECREF(obj);
- view->obj = NULL;
-}
-#endif
-
-
- #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \
- { \
- func_type value = func_value; \
- if (sizeof(target_type) < sizeof(func_type)) { \
- if (unlikely(value != (func_type) (target_type) value)) { \
- func_type zero = 0; \
- if (is_unsigned && unlikely(value < zero)) \
- goto raise_neg_overflow; \
- else \
- goto raise_overflow; \
- } \
- } \
- return (target_type) value; \
- }
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_As_unsigned_int(PyObject *x) {
- const unsigned int neg_one = (unsigned int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(unsigned int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (unsigned int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned int, digit, ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
- if (sizeof(unsigned int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(unsigned int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long long, PyLong_AsUnsignedLongLong(x))
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned int, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(unsigned int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (sizeof(unsigned int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, long, PyLong_AsLong(x))
- } else if (sizeof(unsigned int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, long long, PyLong_AsLongLong(x))
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- unsigned int val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (unsigned int) -1;
- }
- } else {
- unsigned int val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned int) -1;
- val = __Pyx_PyInt_As_unsigned_int(tmp);
- Py_DECREF(tmp);
- return val;
- }
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to unsigned int");
- return (unsigned int) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned int");
- return (unsigned int) -1;
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
- if (sizeof(int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x))
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x))
- } else if (sizeof(int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x))
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- int val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (int) -1;
- }
- } else {
- int val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (int) -1;
- val = __Pyx_PyInt_As_int(tmp);
- Py_DECREF(tmp);
- return val;
- }
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to int");
- return (int) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_int(unsigned int value) {
- const unsigned int neg_one = (unsigned int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(unsigned int) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(unsigned int) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(unsigned int) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(unsigned int) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(unsigned int) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(unsigned int),
- little, !is_unsigned);
- }
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(int) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ PyErr_Clear();
+ }
+ }
+ level = 0; /* try absolute import on failure */
}
- } else {
- if (sizeof(int) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ #endif
+ if (!module) {
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_level = PyInt_FromLong(level);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, level);
+ #endif
}
}
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(int),
- little, !is_unsigned);
+ #else
+ if (level>0) {
+ PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
+ goto bad;
}
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, NULL);
+ #endif
+bad:
+ #if PY_VERSION_HEX < 0x03030000
+ Py_XDECREF(py_import);
+ #endif
+ Py_XDECREF(empty_list);
+ Py_XDECREF(empty_dict);
+ return module;
}
-static CYTHON_INLINE unsigned short __Pyx_PyInt_As_unsigned_short(PyObject *x) {
- const unsigned short neg_one = (unsigned short) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(unsigned short) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned short, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (unsigned short) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned short, digit, ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
- if (sizeof(unsigned short) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(unsigned short, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(unsigned short) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned short, unsigned long long, PyLong_AsUnsignedLongLong(x))
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned short, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(unsigned short, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (sizeof(unsigned short) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned short, long, PyLong_AsLong(x))
- } else if (sizeof(unsigned short) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned short, long long, PyLong_AsLongLong(x))
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- unsigned short val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (unsigned short) -1;
- }
+static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
+ CYTHON_UNUSED PyObject *getbuffer_cobj;
+ #if PY_VERSION_HEX >= 0x02060000
+ if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags);
+ #endif
+ if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags);
+ #if PY_VERSION_HEX < 0x02060000
+ if (obj->ob_type->tp_dict &&
+ (getbuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
+ "__pyx_getbuffer"))) {
+ getbufferproc func;
+ #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
+ func = (getbufferproc) PyCapsule_GetPointer(getbuffer_cobj, "getbuffer(obj, view, flags)");
+ #else
+ func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj);
+ #endif
+ Py_DECREF(getbuffer_cobj);
+ if (!func)
+ goto fail;
+ return func(obj, view, flags);
} else {
- unsigned short val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned short) -1;
- val = __Pyx_PyInt_As_unsigned_short(tmp);
- Py_DECREF(tmp);
- return val;
+ PyErr_Clear();
}
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to unsigned short");
- return (unsigned short) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned short");
- return (unsigned short) -1;
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_As_unsigned_PY_LONG_LONG(PyObject *x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(unsigned PY_LONG_LONG) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned PY_LONG_LONG, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (unsigned PY_LONG_LONG) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned PY_LONG_LONG, digit, ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
- if (sizeof(unsigned PY_LONG_LONG) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(unsigned PY_LONG_LONG, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(unsigned PY_LONG_LONG) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned PY_LONG_LONG, unsigned long long, PyLong_AsUnsignedLongLong(x))
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned PY_LONG_LONG, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(unsigned PY_LONG_LONG, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (sizeof(unsigned PY_LONG_LONG) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned PY_LONG_LONG, long, PyLong_AsLong(x))
- } else if (sizeof(unsigned PY_LONG_LONG) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned PY_LONG_LONG, long long, PyLong_AsLongLong(x))
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- unsigned PY_LONG_LONG val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
+ #endif
+ PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
+#if PY_VERSION_HEX < 0x02060000
+fail:
#endif
- return (unsigned PY_LONG_LONG) -1;
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG) -1;
- val = __Pyx_PyInt_As_unsigned_PY_LONG_LONG(tmp);
- Py_DECREF(tmp);
- return val;
- }
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG) -1;
+ return -1;
}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_PY_LONG_LONG(unsigned PY_LONG_LONG value) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(unsigned PY_LONG_LONG) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(unsigned PY_LONG_LONG) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(unsigned PY_LONG_LONG) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(unsigned PY_LONG_LONG) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(unsigned PY_LONG_LONG) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(unsigned PY_LONG_LONG),
- little, !is_unsigned);
+static void __Pyx_ReleaseBuffer(Py_buffer *view) {
+ PyObject *obj = view->obj;
+ CYTHON_UNUSED PyObject *releasebuffer_cobj;
+ if (!obj) return;
+ #if PY_VERSION_HEX >= 0x02060000
+ if (PyObject_CheckBuffer(obj)) {
+ PyBuffer_Release(view);
+ return;
}
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(long) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
+ #endif
+ if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; }
+ #if PY_VERSION_HEX < 0x02060000
+ if (obj->ob_type->tp_dict &&
+ (releasebuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
+ "__pyx_releasebuffer"))) {
+ releasebufferproc func;
+ #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
+ func = (releasebufferproc) PyCapsule_GetPointer(releasebuffer_cobj, "releasebuffer(obj, view)");
+ #else
+ func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj);
+ #endif
+ Py_DECREF(releasebuffer_cobj);
+ if (!func)
+ goto fail;
+ func(obj, view);
+ return;
} else {
- if (sizeof(long) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(long),
- little, !is_unsigned);
+ PyErr_Clear();
}
+ #endif
+ goto nofail;
+#if PY_VERSION_HEX < 0x02060000
+fail:
+#endif
+ PyErr_WriteUnraisable(obj);
+nofail:
+ Py_DECREF(obj);
+ view->obj = NULL;
}
+#endif /* PY_MAJOR_VERSION < 3 */
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_short(unsigned short value) {
- const unsigned short neg_one = (unsigned short) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(unsigned short) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(unsigned short) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(unsigned short) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(unsigned short) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(unsigned short) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(unsigned short),
- little, !is_unsigned);
- }
+
+ static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
+#if PY_MAJOR_VERSION < 3
+ PyErr_Format(PyExc_ImportError, "cannot import name %.230s",
+ PyString_AsString(name));
+#else
+ PyErr_Format(PyExc_ImportError, "cannot import name %S", name);
+#endif
}
#if CYTHON_CCOMPLEX
@@ -15257,99 +14220,404 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_short(unsigned short va
#endif
#endif
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
- const long neg_one = (long) -1, const_zero = 0;
+static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
+ const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned char" :
+ "value too large to convert to unsigned char");
+ }
+ return (unsigned char)-1;
+ }
+ return (unsigned char)val;
+ }
+ return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
+ const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned short" :
+ "value too large to convert to unsigned short");
+ }
+ return (unsigned short)-1;
+ }
+ return (unsigned short)val;
+ }
+ return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
+ const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned int" :
+ "value too large to convert to unsigned int");
+ }
+ return (unsigned int)-1;
+ }
+ return (unsigned int)val;
+ }
+ return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
+ const char neg_one = (char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to char" :
+ "value too large to convert to char");
+ }
+ return (char)-1;
+ }
+ return (char)val;
+ }
+ return (char)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
+ const short neg_one = (short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to short" :
+ "value too large to convert to short");
+ }
+ return (short)-1;
+ }
+ return (short)val;
+ }
+ return (short)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
+ const int neg_one = (int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to int" :
+ "value too large to convert to int");
+ }
+ return (int)-1;
+ }
+ return (int)val;
+ }
+ return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
+ const signed char neg_one = (signed char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed char" :
+ "value too large to convert to signed char");
+ }
+ return (signed char)-1;
+ }
+ return (signed char)val;
+ }
+ return (signed char)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
+ const signed short neg_one = (signed short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed short" :
+ "value too large to convert to signed short");
+ }
+ return (signed short)-1;
+ }
+ return (signed short)val;
+ }
+ return (signed short)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
+ const signed int neg_one = (signed int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed int" :
+ "value too large to convert to signed int");
+ }
+ return (signed int)-1;
+ }
+ return (signed int)val;
+ }
+ return (signed int)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
+ const int neg_one = (int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to int" :
+ "value too large to convert to int");
+ }
+ return (int)-1;
+ }
+ return (int)val;
+ }
+ return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
+ const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return (unsigned long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return (unsigned long)PyLong_AsUnsignedLong(x);
+ } else {
+ return (unsigned long)PyLong_AsLong(x);
+ }
+ } else {
+ unsigned long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned long)-1;
+ val = __Pyx_PyInt_AsUnsignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
+ const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return (unsigned PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
+ } else {
+ return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
+ }
+ } else {
+ unsigned PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
+ const long neg_one = (long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long)-1;
+ }
+ return (long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long)-1;
+ }
+ return (long)PyLong_AsUnsignedLong(x);
+ } else {
+ return (long)PyLong_AsLong(x);
+ }
+ } else {
+ long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (long)-1;
+ val = __Pyx_PyInt_AsLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
+ const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
+#if PY_VERSION_HEX < 0x03000000
if (likely(PyInt_Check(x))) {
- if (sizeof(long) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (long) val;
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to PY_LONG_LONG");
+ return (PY_LONG_LONG)-1;
}
+ return (PY_LONG_LONG)val;
} else
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
- if (sizeof(long) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to PY_LONG_LONG");
+ return (PY_LONG_LONG)-1;
}
+ return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
} else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
+ return (PY_LONG_LONG)PyLong_AsLongLong(x);
+ }
+ } else {
+ PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
+ const signed long neg_one = (signed long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed long");
+ return (signed long)-1;
+ }
+ return (signed long)val;
+ } else
#endif
- if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x))
- } else if (sizeof(long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x))
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed long");
+ return (signed long)-1;
}
+ return (signed long)PyLong_AsUnsignedLong(x);
+ } else {
+ return (signed long)PyLong_AsLong(x);
}
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- long val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
+ } else {
+ signed long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (signed long)-1;
+ val = __Pyx_PyInt_AsSignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
+ const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed PY_LONG_LONG");
+ return (signed PY_LONG_LONG)-1;
+ }
+ return (signed PY_LONG_LONG)val;
+ } else
#endif
- return (long) -1;
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed PY_LONG_LONG");
+ return (signed PY_LONG_LONG)-1;
+ }
+ return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
+ } else {
+ return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
}
} else {
- long val;
+ signed PY_LONG_LONG val;
PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long) -1;
- val = __Pyx_PyInt_As_long(tmp);
+ if (!tmp) return (signed PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsSignedLongLong(tmp);
Py_DECREF(tmp);
return val;
}
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to long");
- return (long) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
}
static int __Pyx_check_binary_version(void) {
@@ -15362,11 +14630,32 @@ static int __Pyx_check_binary_version(void) {
"compiletime version %s of module '%.100s' "
"does not match runtime version %s",
ctversion, __Pyx_MODULE_NAME, rtversion);
+ #if PY_VERSION_HEX < 0x02050000
+ return PyErr_Warn(NULL, message);
+ #else
return PyErr_WarnEx(NULL, message, 1);
+ #endif
}
return 0;
}
+static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
+#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
+ PyObject *ob = PyCapsule_New(vtable, 0, 0);
+#else
+ PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
+#endif
+ if (!ob)
+ goto bad;
+ if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
+ goto bad;
+ Py_DECREF(ob);
+ return 0;
+bad:
+ Py_XDECREF(ob);
+ return -1;
+}
+
#ifndef __PYX_HAVE_RT_ImportModule
#define __PYX_HAVE_RT_ImportModule
static PyObject *__Pyx_ImportModule(const char *name) {
@@ -15412,7 +14701,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
goto bad;
if (!PyType_Check(result)) {
PyErr_Format(PyExc_TypeError,
- "%.200s.%.200s is not a type object",
+ "%s.%s is not a type object",
module_name, class_name);
goto bad;
}
@@ -15432,11 +14721,15 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyErr_Warn(NULL, warning) < 0) goto bad;
+ #else
if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
+ #endif
}
else if ((size_t)basicsize != size) {
PyErr_Format(PyExc_ValueError,
- "%.200s.%.200s has the wrong size, try recompiling",
+ "%s.%s has the wrong size, try recompiling",
module_name, class_name);
goto bad;
}
@@ -15448,6 +14741,168 @@ bad:
}
#endif
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
+ int start = 0, mid = 0, end = count - 1;
+ if (end >= 0 && code_line > entries[end].code_line) {
+ return count;
+ }
+ while (start < end) {
+ mid = (start + end) / 2;
+ if (code_line < entries[mid].code_line) {
+ end = mid;
+ } else if (code_line > entries[mid].code_line) {
+ start = mid + 1;
+ } else {
+ return mid;
+ }
+ }
+ if (code_line <= entries[mid].code_line) {
+ return mid;
+ } else {
+ return mid + 1;
+ }
+}
+static PyCodeObject *__pyx_find_code_object(int code_line) {
+ PyCodeObject* code_object;
+ int pos;
+ if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
+ return NULL;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
+ return NULL;
+ }
+ code_object = __pyx_code_cache.entries[pos].code_object;
+ Py_INCREF(code_object);
+ return code_object;
+}
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
+ int pos, i;
+ __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
+ if (unlikely(!code_line)) {
+ return;
+ }
+ if (unlikely(!entries)) {
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (likely(entries)) {
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = 64;
+ __pyx_code_cache.count = 1;
+ entries[0].code_line = code_line;
+ entries[0].code_object = code_object;
+ Py_INCREF(code_object);
+ }
+ return;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
+ PyCodeObject* tmp = entries[pos].code_object;
+ entries[pos].code_object = code_object;
+ Py_DECREF(tmp);
+ return;
+ }
+ if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
+ int new_max = __pyx_code_cache.max_count + 64;
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
+ __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (unlikely(!entries)) {
+ return;
+ }
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = new_max;
+ }
+ for (i=__pyx_code_cache.count; i>pos; i--) {
+ entries[i] = entries[i-1];
+ }
+ entries[pos].code_line = code_line;
+ entries[pos].code_object = code_object;
+ __pyx_code_cache.count++;
+ Py_INCREF(code_object);
+}
+
+#include "compile.h"
+#include "frameobject.h"
+#include "traceback.h"
+static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
+ const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
+ PyObject *py_srcfile = 0;
+ PyObject *py_funcname = 0;
+ #if PY_MAJOR_VERSION < 3
+ py_srcfile = PyString_FromString(filename);
+ #else
+ py_srcfile = PyUnicode_FromString(filename);
+ #endif
+ if (!py_srcfile) goto bad;
+ if (c_line) {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ #else
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ #endif
+ }
+ else {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromString(funcname);
+ #else
+ py_funcname = PyUnicode_FromString(funcname);
+ #endif
+ }
+ if (!py_funcname) goto bad;
+ py_code = __Pyx_PyCode_New(
+ 0, /*int argcount,*/
+ 0, /*int kwonlyargcount,*/
+ 0, /*int nlocals,*/
+ 0, /*int stacksize,*/
+ 0, /*int flags,*/
+ __pyx_empty_bytes, /*PyObject *code,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
+ py_srcfile, /*PyObject *filename,*/
+ py_funcname, /*PyObject *name,*/
+ py_line, /*int firstlineno,*/
+ __pyx_empty_bytes /*PyObject *lnotab*/
+ );
+ Py_DECREF(py_srcfile);
+ Py_DECREF(py_funcname);
+ return py_code;
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ return NULL;
+}
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
+ PyObject *py_globals = 0;
+ PyFrameObject *py_frame = 0;
+ py_code = __pyx_find_code_object(c_line ? c_line : py_line);
+ if (!py_code) {
+ py_code = __Pyx_CreateCodeObjectForTraceback(
+ funcname, c_line, py_line, filename);
+ if (!py_code) goto bad;
+ __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
+ }
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
+ py_frame = PyFrame_New(
+ PyThreadState_GET(), /*PyThreadState *tstate,*/
+ py_code, /*PyCodeObject *code,*/
+ py_globals, /*PyObject *globals,*/
+ 0 /*PyObject *locals*/
+ );
+ if (!py_frame) goto bad;
+ py_frame->f_lineno = py_line;
+ PyTraceBack_Here(py_frame);
+bad:
+ Py_XDECREF(py_code);
+ Py_XDECREF(py_frame);
+}
+
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
while (t->p) {
#if PY_MAJOR_VERSION < 3
@@ -15458,7 +14913,7 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
} else {
*t->p = PyString_FromStringAndSize(t->s, t->n - 1);
}
- #else
+ #else /* Python 3+ has unicode identifiers */
if (t->is_unicode | t->is_str) {
if (t->intern) {
*t->p = PyUnicode_InternFromString(t->s);
@@ -15478,71 +14933,6 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
return 0;
}
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
- return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
- Py_ssize_t ignore;
- return __Pyx_PyObject_AsStringAndSize(o, &ignore);
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
- if (
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- __Pyx_sys_getdefaultencoding_not_ascii &&
-#endif
- PyUnicode_Check(o)) {
-#if PY_VERSION_HEX < 0x03030000
- char* defenc_c;
- PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
- if (!defenc) return NULL;
- defenc_c = PyBytes_AS_STRING(defenc);
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- {
- char* end = defenc_c + PyBytes_GET_SIZE(defenc);
- char* c;
- for (c = defenc_c; c < end; c++) {
- if ((unsigned char) (*c) >= 128) {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
- }
- }
-#endif
- *length = PyBytes_GET_SIZE(defenc);
- return defenc_c;
-#else
- if (__Pyx_PyUnicode_READY(o) == -1) return NULL;
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- if (PyUnicode_IS_ASCII(o)) {
- *length = PyUnicode_GET_LENGTH(o);
- return PyUnicode_AsUTF8(o);
- } else {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
-#else
- return PyUnicode_AsUTF8AndSize(o, length);
-#endif
-#endif
- } else
-#endif
-#if !CYTHON_COMPILING_IN_PYPY
- if (PyByteArray_Check(o)) {
- *length = PyByteArray_GET_SIZE(o);
- return PyByteArray_AS_STRING(o);
- } else
-#endif
- {
- char* result;
- int r = PyBytes_AsStringAndSize(o, &result, length);
- if (unlikely(r < 0)) {
- return NULL;
- } else {
- return result;
- }
- }
-}
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
int is_true = x == Py_True;
if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
@@ -15552,14 +14942,14 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
PyNumberMethods *m;
const char *name = NULL;
PyObject *res = NULL;
-#if PY_MAJOR_VERSION < 3
+#if PY_VERSION_HEX < 0x03000000
if (PyInt_Check(x) || PyLong_Check(x))
#else
if (PyLong_Check(x))
#endif
return Py_INCREF(x), x;
m = Py_TYPE(x)->tp_as_number;
-#if PY_MAJOR_VERSION < 3
+#if PY_VERSION_HEX < 0x03000000
if (m && m->nb_int) {
name = "int";
res = PyNumber_Int(x);
@@ -15575,13 +14965,13 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
}
#endif
if (res) {
-#if PY_MAJOR_VERSION < 3
+#if PY_VERSION_HEX < 0x03000000
if (!PyInt_Check(res) && !PyLong_Check(res)) {
#else
if (!PyLong_Check(res)) {
#endif
PyErr_Format(PyExc_TypeError,
- "__%.4s__ returned non-%.4s (type %.200s)",
+ "__%s__ returned non-%s (type %.200s)",
name, name, Py_TYPE(res)->tp_name);
Py_DECREF(res);
return NULL;
@@ -15595,31 +14985,35 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
}
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_ssize_t ival;
- PyObject *x;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_CheckExact(b)))
- return PyInt_AS_LONG(b);
-#endif
- if (likely(PyLong_CheckExact(b))) {
- #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(b)) {
- case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0];
- case 0: return 0;
- case 1: return ((PyLongObject*)b)->ob_digit[0];
- }
- #endif
- #endif
- return PyLong_AsSsize_t(b);
- }
- x = PyNumber_Index(b);
+ PyObject* x = PyNumber_Index(b);
if (!x) return -1;
ival = PyInt_AsSsize_t(x);
Py_DECREF(x);
return ival;
}
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
- return PyInt_FromSize_t(ival);
+#if PY_VERSION_HEX < 0x02050000
+ if (ival <= LONG_MAX)
+ return PyInt_FromLong((long)ival);
+ else {
+ unsigned char *bytes = (unsigned char *) &ival;
+ int one = 1; int little = (int)*(unsigned char*)&one;
+ return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
+ }
+#else
+ return PyInt_FromSize_t(ival);
+#endif
+}
+static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
+ unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
+ if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
+ return (size_t)-1;
+ } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to size_t");
+ return (size_t)-1;
+ }
+ return (size_t)val;
}
diff --git a/lib/bx/bbi/bbi_file.pyx b/lib/bx/bbi/bbi_file.pyx
index 1b8424e..d8f3d84 100644
--- a/lib/bx/bbi/bbi_file.pyx
+++ b/lib/bx/bbi/bbi_file.pyx
@@ -18,8 +18,6 @@ from libc cimport limits
import numpy
cimport numpy
-cimport numpy as np
-import numpy as np
from bx.misc.binary_file import BinaryFileReader
from cStringIO import StringIO
@@ -298,16 +296,6 @@ cdef class ZoomLevel:
reader.seek( self.index_offset )
ctf = CIRTreeFile( reader.file )
block_list = ctf.find_overlapping_blocks( chrom_id, start, end )
-
- sum_dtype = np.dtype([('chrom_id', np.uint32),
- ('start', np.uint32),
- ('end', np.uint32),
- ('valid_count', np.uint32),
- ('min_val', np.float32),
- ('max_val', np.float32),
- ('sum_data', np.float32),
- ('sum_squares', np.float32)])
-
for offset, size in block_list:
# Seek to and read all data for the block
reader.seek( offset )
@@ -320,14 +308,7 @@ cdef class ZoomLevel:
# The block should be a bunch of summaries.
assert block_size % summary_on_disk_size == 0
item_count = block_size / summary_on_disk_size
-
- arr = np.fromstring(block_data, sum_dtype, item_count)
- # covert to dict to match old implementation:
- d = [dict(zip(arr.dtype.names, x)) for x in arr]
- rval.extend(d)
-
-
- """
+ # Create another reader just for the block, shouldn't be too expensive
block_reader = BinaryFileReader( StringIO( block_data ), is_little_endian=reader.is_little_endian )
for i from 0 <= i < item_count:
## NOTE: Look carefully at bbiRead again to be sure the endian
@@ -351,7 +332,7 @@ cdef class ZoomLevel:
summary.sum_squares = block_reader.read_float()
rval.append( summary )
- """
+
return rval
cdef _get_summary_slice( self, bits32 base_start, bits32 base_end, summaries ):
@@ -365,29 +346,70 @@ cdef class ZoomLevel:
if summaries:
- # TODO: if we keep this a an array from summary_blocks in region,
- # this will be much faster.
- min_val = summaries[0]['min_val']
- max_val = summaries[0]['max_val']
+ min_val = summaries[0].min_val
+ max_val = summaries[0].max_val
for summary in summaries:
- if summary['start'] >= base_end:
+ if summary.start >= base_end:
break
- overlap = range_intersection( base_start, base_end, summary['start'], summary['end'] )
+ overlap = range_intersection( base_start, base_end, summary.start, summary.end )
if overlap > 0:
- overlap_factor = <double> overlap / (summary['end'] - summary['start'])
+ overlap_factor = <double> overlap / (summary.end - summary.start)
- valid_count += summary['valid_count'] * overlap_factor
- sum_data += summary['sum_data'] * overlap_factor
- sum_squares += summary['sum_squares'] * overlap_factor
+ valid_count += summary.valid_count * overlap_factor
+ sum_data += summary.sum_data * overlap_factor
+ sum_squares += summary.sum_squares * overlap_factor
- if max_val < summary['max_val']:
- max_val = summary['max_val']
- if min_val > summary['min_val']:
- min_val = summary['min_val']
+ if max_val < summary.max_val:
+ max_val = summary.max_val
+ if min_val > summary.min_val:
+ min_val = summary.min_val
return valid_count, sum_data, sum_squares, min_val, max_val
cdef _summarize( self, bits32 chrom_id, bits32 start, bits32 end, int summary_size ):
- return SummarizedData( start, end, summary_size )
+ """
+ Summarize directly from file.
+
+ Looking at Jim's code, it appears that
+ - bbiSummariesInRegion returns all summaries that span start-end in
+ sorted order
+ - bbiSummarySlice is then used to aggregate over the subset of those
+ summaries that overlap a single summary element
+ """
+ cdef bits32 base_start, base_end, base_step
+
+ # We locally cdef the arrays so all indexing will be at C speeds
+ cdef numpy.ndarray[numpy.float64_t] valid_count
+ cdef numpy.ndarray[numpy.float64_t] min_val
+ cdef numpy.ndarray[numpy.float64_t] max_val
+ cdef numpy.ndarray[numpy.float64_t] sum_data
+ cdef numpy.ndarray[numpy.float64_t] sum_squares
+
+ # What we will load into
+ rval = SummarizedData( start, end, summary_size )
+ valid_count = rval.valid_count
+ min_val = rval.min_val
+ max_val = rval.max_val
+ sum_data = rval.sum_data
+ sum_squares = rval.sum_squares
+ # First, load up summaries
+ reader = self.bbi_file.reader
+ reader.seek( self.index_offset )
+ summaries = self._summary_blocks_in_region(chrom_id, start, end)
+
+ base_step = (end - start) / summary_size
+ base_start = start
+ base_end = start
+
+ for i in range(summary_size):
+ base_end += base_step
+
+ while summaries and summaries[0].end <= base_start:
+ summaries.popleft()
+
+ valid_count[i], sum_data[i], sum_squares[i], min_val[i], max_val[i] = self._get_summary_slice(base_start, base_end, summaries)
+ base_start = base_end
+
+ return rval
diff --git a/lib/bx/bbi/bigbed_file.c b/lib/bx/bbi/bigbed_file.c
index 2797459..f4016b7 100644
--- a/lib/bx/bbi/bigbed_file.c
+++ b/lib/bx/bbi/bigbed_file.c
@@ -1,26 +1,13 @@
-/* Generated by Cython 0.22 */
+/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
#define PY_SSIZE_T_CLEAN
-#ifndef CYTHON_USE_PYLONG_INTERNALS
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#else
-#include "pyconfig.h"
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 1
-#else
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#endif
-#endif
-#endif
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000)
- #error Cython requires Python 2.6+ or Python 3.2+.
+#elif PY_VERSION_HEX < 0x02040000
+ #error Cython requires Python 2.4+.
#else
-#define CYTHON_ABI "0_22"
-#include <stddef.h>
+#include <stddef.h> /* For offsetof */
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
@@ -54,29 +41,80 @@
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
-#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag)
-#define Py_OptimizeFlag 0
+#if PY_VERSION_HEX < 0x02050000
+ typedef int Py_ssize_t;
+ #define PY_SSIZE_T_MAX INT_MAX
+ #define PY_SSIZE_T_MIN INT_MIN
+ #define PY_FORMAT_SIZE_T ""
+ #define CYTHON_FORMAT_SSIZE_T ""
+ #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
+ #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
+ #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
+ (PyErr_Format(PyExc_TypeError, \
+ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
+ (PyObject*)0))
+ #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
+ !PyComplex_Check(o))
+ #define PyIndex_Check __Pyx_PyIndex_Check
+ #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
+ #define __PYX_BUILD_PY_SSIZE_T "i"
+#else
+ #define __PYX_BUILD_PY_SSIZE_T "n"
+ #define CYTHON_FORMAT_SSIZE_T "z"
+ #define __Pyx_PyIndex_Check PyIndex_Check
+#endif
+#if PY_VERSION_HEX < 0x02060000
+ #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
+ #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
+ #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
+ #define PyVarObject_HEAD_INIT(type, size) \
+ PyObject_HEAD_INIT(type) size,
+ #define PyType_Modified(t)
+ typedef struct {
+ void *buf;
+ PyObject *obj;
+ Py_ssize_t len;
+ Py_ssize_t itemsize;
+ int readonly;
+ int ndim;
+ char *format;
+ Py_ssize_t *shape;
+ Py_ssize_t *strides;
+ Py_ssize_t *suboffsets;
+ void *internal;
+ } Py_buffer;
+ #define PyBUF_SIMPLE 0
+ #define PyBUF_WRITABLE 0x0001
+ #define PyBUF_FORMAT 0x0004
+ #define PyBUF_ND 0x0008
+ #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
+ #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
+ #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
+ #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
+ #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
+ #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
+ #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
+ typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
+ typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
-#define __PYX_BUILD_PY_SSIZE_T "n"
-#define CYTHON_FORMAT_SSIZE_T "z"
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
- #define __Pyx_DefaultClassType PyClass_Type
+ PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
- #define __Pyx_DefaultClassType PyType_Type
+#endif
+#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
+ #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
- #define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE)
- #define Py_TPFLAGS_HAVE_FINALIZE 0
+#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
+ #define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
#define CYTHON_PEP393_ENABLED 1
@@ -84,34 +122,13 @@
0 : _PyUnicode_Ready((PyObject *)(op)))
#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u)
- #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
#define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
#else
#define CYTHON_PEP393_ENABLED 0
#define __Pyx_PyUnicode_READY(op) (0)
#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE))
- #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
- #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if CYTHON_COMPILING_IN_PYPY
- #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b)
- #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b)
- #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s)
-#else
- #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b)
- #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \
- PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
- #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s)
-#endif
-#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
-#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b)
-#else
- #define __Pyx_PyString_Format(a, b) PyString_Format(a, b)
+ #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#endif
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
@@ -120,12 +137,27 @@
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
- #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
-#else
- #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj))
- #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
+#if PY_VERSION_HEX < 0x02060000
+ #define PyBytesObject PyStringObject
+ #define PyBytes_Type PyString_Type
+ #define PyBytes_Check PyString_Check
+ #define PyBytes_CheckExact PyString_CheckExact
+ #define PyBytes_FromString PyString_FromString
+ #define PyBytes_FromStringAndSize PyString_FromStringAndSize
+ #define PyBytes_FromFormat PyString_FromFormat
+ #define PyBytes_DecodeEscape PyString_DecodeEscape
+ #define PyBytes_AsString PyString_AsString
+ #define PyBytes_AsStringAndSize PyString_AsStringAndSize
+ #define PyBytes_Size PyString_Size
+ #define PyBytes_AS_STRING PyString_AS_STRING
+ #define PyBytes_GET_SIZE PyString_GET_SIZE
+ #define PyBytes_Repr PyString_Repr
+ #define PyBytes_Concat PyString_Concat
+ #define PyBytes_ConcatAndDel PyString_ConcatAndDel
+#endif
+#if PY_VERSION_HEX < 0x02060000
+ #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
+ #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#endif
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
@@ -146,17 +178,11 @@
#define PyInt_AsSsize_t PyLong_AsSsize_t
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
- #define PyNumber_Int PyNumber_Long
#endif
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
-#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY
- #ifndef PyUnicode_InternFromString
- #define PyUnicode_InternFromString(s) PyUnicode_FromString(s)
- #endif
-#endif
-#if PY_VERSION_HEX < 0x030200A4
+#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
#define __Pyx_PyInt_AsHash_t PyInt_AsLong
@@ -164,61 +190,42 @@
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
+#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
+ #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
+ #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
#else
- #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
-#endif
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
- #elif defined(_MSC_VER)
- #define CYTHON_INLINE __inline
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
+ #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
+ #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
-#ifndef CYTHON_RESTRICT
- #if defined(__GNUC__)
- #define CYTHON_RESTRICT __restrict__
- #elif defined(_MSC_VER) && _MSC_VER >= 1400
- #define CYTHON_RESTRICT __restrict
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_RESTRICT restrict
- #else
- #define CYTHON_RESTRICT
- #endif
+#if PY_MAJOR_VERSION >= 3
+ #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
-#ifdef NAN
-#define __PYX_NAN() ((float) NAN)
+#if PY_VERSION_HEX < 0x02050000
+ #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
+ #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
+ #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
#else
-static CYTHON_INLINE float __PYX_NAN() {
- /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
- a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
- a quiet NaN. */
- float value;
- memset(&value, 0xFF, sizeof(value));
- return value;
-}
+ #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
+ #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
+ #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
-#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None)
-#ifdef __cplusplus
-template<typename T>
-void __Pyx_call_destructor(T* x) {
- x->~T();
-}
-template<typename T>
-class __Pyx_FakeReference {
- public:
- __Pyx_FakeReference() : ptr(NULL) { }
- __Pyx_FakeReference(T& ref) : ptr(&ref) { }
- T *operator->() { return ptr; }
- operator T&() { return *ptr; }
- private:
- T *ptr;
-};
+#if PY_VERSION_HEX < 0x02050000
+ #define __Pyx_NAMESTR(n) ((char *)(n))
+ #define __Pyx_DOCSTR(n) ((char *)(n))
+#else
+ #define __Pyx_NAMESTR(n) (n)
+ #define __Pyx_DOCSTR(n) (n)
#endif
@@ -257,6 +264,17 @@ class __Pyx_FakeReference {
#define CYTHON_WITHOUT_ASSERTIONS
#endif
+#ifndef CYTHON_INLINE
+ #if defined(__GNUC__)
+ #define CYTHON_INLINE __inline__
+ #elif defined(_MSC_VER)
+ #define CYTHON_INLINE __inline
+ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define CYTHON_INLINE inline
+ #else
+ #define CYTHON_INLINE
+ #endif
+#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
@@ -270,157 +288,40 @@ class __Pyx_FakeReference {
# define CYTHON_UNUSED
# endif
#endif
-typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
- const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
-
-#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
-#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
-#define __PYX_DEFAULT_STRING_ENCODING ""
-#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
-#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \
- (sizeof(type) < sizeof(Py_ssize_t)) || \
- (sizeof(type) > sizeof(Py_ssize_t) && \
- likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX) && \
- (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \
- v == (type)PY_SSIZE_T_MIN))) || \
- (sizeof(type) == sizeof(Py_ssize_t) && \
- (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX))) )
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
-#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
-#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
-#define __Pyx_PyBytes_FromString PyBytes_FromString
-#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#else
- #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
-#endif
-#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s)
-#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s)
-#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s)
-#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s)
-#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
-#if PY_MAJOR_VERSION < 3
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
-{
- const Py_UNICODE *u_end = u;
- while (*u_end++) ;
- return (size_t)(u_end - u - 1);
-}
-#else
-#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
-#endif
-#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
-#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
-#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
+typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
+
+#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
+#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
+static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
#else
#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
-static int __Pyx_sys_getdefaultencoding_not_ascii;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys;
- PyObject* default_encoding = NULL;
- PyObject* ascii_chars_u = NULL;
- PyObject* ascii_chars_b = NULL;
- const char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (!sys) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
- Py_DECREF(sys);
- if (!default_encoding) goto bad;
- default_encoding_c = PyBytes_AsString(default_encoding);
- if (!default_encoding_c) goto bad;
- if (strcmp(default_encoding_c, "ascii") == 0) {
- __Pyx_sys_getdefaultencoding_not_ascii = 0;
- } else {
- char ascii_chars[128];
- int c;
- for (c = 0; c < 128; c++) {
- ascii_chars[c] = c;
- }
- __Pyx_sys_getdefaultencoding_not_ascii = 1;
- ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
- if (!ascii_chars_u) goto bad;
- ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
- if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
- PyErr_Format(
- PyExc_ValueError,
- "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
- default_encoding_c);
- goto bad;
- }
- Py_DECREF(ascii_chars_u);
- Py_DECREF(ascii_chars_b);
- }
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return -1;
-}
-#endif
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
-#else
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
-static char* __PYX_DEFAULT_STRING_ENCODING;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys;
- PyObject* default_encoding = NULL;
- char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (!sys) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- Py_DECREF(sys);
- if (!default_encoding) goto bad;
- default_encoding_c = PyBytes_AsString(default_encoding);
- if (!default_encoding_c) goto bad;
- __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
- if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
- strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(default_encoding);
- return -1;
-}
-#endif
-#endif
-/* Test for GCC > 2.95 */
-#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))
- #define likely(x) __builtin_expect(!!(x), 1)
- #define unlikely(x) __builtin_expect(!!(x), 0)
-#else /* !__GNUC__ or GCC < 2.95 */
+#ifdef __GNUC__
+ /* Test for GCC > 2.95 */
+ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
+ #define likely(x) __builtin_expect(!!(x), 1)
+ #define unlikely(x) __builtin_expect(!!(x), 0)
+ #else /* __GNUC__ > 2 ... */
+ #define likely(x) (x)
+ #define unlikely(x) (x)
+ #endif /* __GNUC__ > 2 ... */
+#else /* __GNUC__ */
#define likely(x) (x)
#define unlikely(x) (x)
#endif /* __GNUC__ */
-
+
static PyObject *__pyx_m;
-static PyObject *__pyx_d;
static PyObject *__pyx_b;
static PyObject *__pyx_empty_tuple;
static PyObject *__pyx_empty_bytes;
@@ -452,12 +353,12 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
- "bx/bbi/bigbed_file.pyx",
- "__init__.pxd",
- "bx/bbi/bpt_file.pxd",
- "bx/bbi/cirtree_file.pxd",
+ "bigbed_file.pyx",
+ "numpy.pxd",
+ "bpt_file.pxd",
+ "cirtree_file.pxd",
"type.pxd",
- "bx/bbi/bbi_file.pxd",
+ "bbi_file.pxd",
};
/* "types.pxd":1
@@ -546,7 +447,7 @@ typedef int __pyx_t_2bx_3bbi_5types_signed32;
*/
typedef int __pyx_t_2bx_3bbi_5types_boolean;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":726
+/* "numpy.pxd":723
* # in Cython to enable them only on the right systems.
*
* ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
@@ -555,7 +456,7 @@ typedef int __pyx_t_2bx_3bbi_5types_boolean;
*/
typedef npy_int8 __pyx_t_5numpy_int8_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":727
+/* "numpy.pxd":724
*
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
@@ -564,7 +465,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t;
*/
typedef npy_int16 __pyx_t_5numpy_int16_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":728
+/* "numpy.pxd":725
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
@@ -573,7 +474,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t;
*/
typedef npy_int32 __pyx_t_5numpy_int32_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":729
+/* "numpy.pxd":726
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
@@ -582,7 +483,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t;
*/
typedef npy_int64 __pyx_t_5numpy_int64_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":733
+/* "numpy.pxd":730
* #ctypedef npy_int128 int128_t
*
* ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
@@ -591,7 +492,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t;
*/
typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":734
+/* "numpy.pxd":731
*
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
@@ -600,7 +501,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t;
*/
typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":735
+/* "numpy.pxd":732
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
@@ -609,7 +510,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t;
*/
typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":736
+/* "numpy.pxd":733
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
@@ -618,7 +519,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t;
*/
typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":740
+/* "numpy.pxd":737
* #ctypedef npy_uint128 uint128_t
*
* ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
@@ -627,7 +528,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t;
*/
typedef npy_float32 __pyx_t_5numpy_float32_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":741
+/* "numpy.pxd":738
*
* ctypedef npy_float32 float32_t
* ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
@@ -636,7 +537,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t;
*/
typedef npy_float64 __pyx_t_5numpy_float64_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":750
+/* "numpy.pxd":747
* # The int types are mapped a bit surprising --
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t # <<<<<<<<<<<<<<
@@ -645,7 +546,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t;
*/
typedef npy_long __pyx_t_5numpy_int_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":751
+/* "numpy.pxd":748
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
@@ -654,7 +555,7 @@ typedef npy_long __pyx_t_5numpy_int_t;
*/
typedef npy_longlong __pyx_t_5numpy_long_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":752
+/* "numpy.pxd":749
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
@@ -663,7 +564,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t;
*/
typedef npy_longlong __pyx_t_5numpy_longlong_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":754
+/* "numpy.pxd":751
* ctypedef npy_longlong longlong_t
*
* ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
@@ -672,7 +573,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t;
*/
typedef npy_ulong __pyx_t_5numpy_uint_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":755
+/* "numpy.pxd":752
*
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
@@ -681,7 +582,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":756
+/* "numpy.pxd":753
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
@@ -690,7 +591,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":758
+/* "numpy.pxd":755
* ctypedef npy_ulonglong ulonglong_t
*
* ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
@@ -699,7 +600,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
*/
typedef npy_intp __pyx_t_5numpy_intp_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":759
+/* "numpy.pxd":756
*
* ctypedef npy_intp intp_t
* ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
@@ -708,7 +609,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t;
*/
typedef npy_uintp __pyx_t_5numpy_uintp_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":761
+/* "numpy.pxd":758
* ctypedef npy_uintp uintp_t
*
* ctypedef npy_double float_t # <<<<<<<<<<<<<<
@@ -717,7 +618,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t;
*/
typedef npy_double __pyx_t_5numpy_float_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":762
+/* "numpy.pxd":759
*
* ctypedef npy_double float_t
* ctypedef npy_double double_t # <<<<<<<<<<<<<<
@@ -726,7 +627,7 @@ typedef npy_double __pyx_t_5numpy_float_t;
*/
typedef npy_double __pyx_t_5numpy_double_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":763
+/* "numpy.pxd":760
* ctypedef npy_double float_t
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
@@ -756,18 +657,18 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
/*--- Type declarations ---*/
-struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile;
-struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile;
struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock;
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData;
-struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler;
struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile;
+struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile;
+struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler;
struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler;
+struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile;
+struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData;
struct __pyx_obj_2bx_3bbi_11bigbed_file_SummarizingBlockHandler;
struct __pyx_obj_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler;
-struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile;
+struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":765
+/* "numpy.pxd":762
* ctypedef npy_longdouble longdouble_t
*
* ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
@@ -776,7 +677,7 @@ struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile;
*/
typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":766
+/* "numpy.pxd":763
*
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
@@ -785,7 +686,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
*/
typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":767
+/* "numpy.pxd":764
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
@@ -794,7 +695,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
*/
typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":769
+/* "numpy.pxd":766
* ctypedef npy_clongdouble clongdouble_t
*
* ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
@@ -803,50 +704,6 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
*/
typedef npy_cdouble __pyx_t_5numpy_complex_t;
-/* "bpt_file.pxd":5
- * from types cimport *
- *
- * cdef class BPTFile: # <<<<<<<<<<<<<<
- * """
- * On disk B+ tree compatible with Jim Kent's bPlusTree.c
- */
-struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile {
- PyObject_HEAD
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- __pyx_t_2bx_3bbi_5types_bits32 block_size;
- __pyx_t_2bx_3bbi_5types_bits32 key_size;
- __pyx_t_2bx_3bbi_5types_bits32 value_size;
- __pyx_t_2bx_3bbi_5types_bits64 item_count;
- __pyx_t_2bx_3bbi_5types_bits64 root_offset;
-};
-
-
-/* "cirtree_file.pxd":3
- * from types cimport *
- *
- * cdef class CIRTreeFile: # <<<<<<<<<<<<<<
- * cdef object file
- * cdef object reader
- */
-struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile {
- PyObject_HEAD
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- __pyx_t_2bx_3bbi_5types_bits64 root_offset;
- __pyx_t_2bx_3bbi_5types_bits32 block_size;
- __pyx_t_2bx_3bbi_5types_bits64 item_count;
- __pyx_t_2bx_3bbi_5types_bits32 start_chrom_ix;
- __pyx_t_2bx_3bbi_5types_bits32 start_base;
- __pyx_t_2bx_3bbi_5types_bits32 end_chrom_ix;
- __pyx_t_2bx_3bbi_5types_bits32 end_base;
- __pyx_t_2bx_3bbi_5types_bits64 file_size;
- __pyx_t_2bx_3bbi_5types_bits32 items_per_slot;
-};
-
-
/* "bbi_file.pxd":8
* cimport numpy
*
@@ -867,40 +724,6 @@ struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock {
};
-/* "bbi_file.pxd":21
- * cdef public double sum_squares
- *
- * cdef class SummarizedData: # <<<<<<<<<<<<<<
- * """
- * The result of using SummaryBlocks read from the file to produce a
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtab;
- __pyx_t_2bx_3bbi_5types_bits32 start;
- __pyx_t_2bx_3bbi_5types_bits32 end;
- int size;
- PyArrayObject *valid_count;
- PyArrayObject *min_val;
- PyArrayObject *max_val;
- PyArrayObject *sum_data;
- PyArrayObject *sum_squares;
-};
-
-
-/* "bbi_file.pxd":39
- * cdef class BBIFile
- *
- * cdef class BlockHandler: # <<<<<<<<<<<<<<
- * """
- * Callback for `BBIFile.visit_blocks_in_region`
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtab;
-};
-
-
/* "bbi_file.pxd":37
* cdef accumulate_interval_value( self, bits32 s, bits32 e, float val )
*
@@ -930,8 +753,33 @@ struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile {
};
-/* "bx/bbi/bigbed_file.pyx":44
- * return "".join(read) if len(read) > 1 else read[0]
+/* "bx/bbi/bigbed_file.pyx":85
+ * self.intervals.append( ( s, e, rest ) )
+ *
+ * cdef class BigBedFile( BBIFile ): # <<<<<<<<<<<<<<
+ * """
+ * A "big binary indexed" file whose raw data is in BED format.
+ */
+struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile {
+ struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile __pyx_base;
+};
+
+
+/* "bbi_file.pxd":39
+ * cdef class BBIFile
+ *
+ * cdef class BlockHandler: # <<<<<<<<<<<<<<
+ * """
+ * Callback for `BBIFile.visit_blocks_in_region`
+ */
+struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtab;
+};
+
+
+/* "bx/bbi/bigbed_file.pyx":20
+ * return min( end1, end2 ) - max( start1, start2 )
*
* cdef class BigBedBlockHandler( BlockHandler ): # <<<<<<<<<<<<<<
* """
@@ -945,7 +793,52 @@ struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler {
};
-/* "bx/bbi/bigbed_file.pyx":76
+/* "cirtree_file.pxd":3
+ * from types cimport *
+ *
+ * cdef class CIRTreeFile: # <<<<<<<<<<<<<<
+ * cdef object file
+ * cdef object reader
+ */
+struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile {
+ PyObject_HEAD
+ PyObject *file;
+ PyObject *reader;
+ __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
+ __pyx_t_2bx_3bbi_5types_bits64 root_offset;
+ __pyx_t_2bx_3bbi_5types_bits32 block_size;
+ __pyx_t_2bx_3bbi_5types_bits64 item_count;
+ __pyx_t_2bx_3bbi_5types_bits32 start_chrom_ix;
+ __pyx_t_2bx_3bbi_5types_bits32 start_base;
+ __pyx_t_2bx_3bbi_5types_bits32 end_chrom_ix;
+ __pyx_t_2bx_3bbi_5types_bits32 end_base;
+ __pyx_t_2bx_3bbi_5types_bits64 file_size;
+ __pyx_t_2bx_3bbi_5types_bits32 items_per_slot;
+};
+
+
+/* "bbi_file.pxd":21
+ * cdef public double sum_squares
+ *
+ * cdef class SummarizedData: # <<<<<<<<<<<<<<
+ * """
+ * The result of using SummaryBlocks read from the file to produce a
+ */
+struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtab;
+ __pyx_t_2bx_3bbi_5types_bits32 start;
+ __pyx_t_2bx_3bbi_5types_bits32 end;
+ int size;
+ PyArrayObject *valid_count;
+ PyArrayObject *min_val;
+ PyArrayObject *max_val;
+ PyArrayObject *sum_data;
+ PyArrayObject *sum_squares;
+};
+
+
+/* "bx/bbi/bigbed_file.pyx":54
* pass
*
* cdef class SummarizingBlockHandler( BigBedBlockHandler ): # <<<<<<<<<<<<<<
@@ -958,7 +851,7 @@ struct __pyx_obj_2bx_3bbi_11bigbed_file_SummarizingBlockHandler {
};
-/* "bx/bbi/bigbed_file.pyx":95
+/* "bx/bbi/bigbed_file.pyx":73
* self.sd.accumulate_interval_value( s, e, 1 )
*
* cdef class IntervalAccumulatingBlockHandler( BigBedBlockHandler ): # <<<<<<<<<<<<<<
@@ -971,31 +864,25 @@ struct __pyx_obj_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler {
};
-/* "bx/bbi/bigbed_file.pyx":107
- * self.intervals.append( ( s, e, rest ) )
+/* "bpt_file.pxd":5
+ * from types cimport *
*
- * cdef class BigBedFile( BBIFile ): # <<<<<<<<<<<<<<
+ * cdef class BPTFile: # <<<<<<<<<<<<<<
* """
- * A "big binary indexed" file whose raw data is in BED format.
+ * On disk B+ tree compatible with Jim Kent's bPlusTree.c
*/
-struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile {
- struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile __pyx_base;
-};
-
-
-
-/* "bbi_file.pxd":21
- * cdef public double sum_squares
- *
- * cdef class SummarizedData: # <<<<<<<<<<<<<<
- * """
- * The result of using SummaryBlocks read from the file to produce a
- */
-
-struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData {
- PyObject *(*accumulate_interval_value)(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float);
+struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile {
+ PyObject_HEAD
+ PyObject *file;
+ PyObject *reader;
+ __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
+ __pyx_t_2bx_3bbi_5types_bits32 block_size;
+ __pyx_t_2bx_3bbi_5types_bits32 key_size;
+ __pyx_t_2bx_3bbi_5types_bits32 value_size;
+ __pyx_t_2bx_3bbi_5types_bits64 item_count;
+ __pyx_t_2bx_3bbi_5types_bits64 root_offset;
};
-static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtabptr_2bx_3bbi_8bbi_file_SummarizedData;
+
/* "bbi_file.pxd":37
@@ -1018,6 +905,21 @@ struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile {
static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile *__pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile;
+/* "bx/bbi/bigbed_file.pyx":85
+ * self.intervals.append( ( s, e, rest ) )
+ *
+ * cdef class BigBedFile( BBIFile ): # <<<<<<<<<<<<<<
+ * """
+ * A "big binary indexed" file whose raw data is in BED format.
+ */
+
+struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_BigBedFile {
+ struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile __pyx_base;
+ PyObject *(*get)(struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int __pyx_skip_dispatch);
+};
+static struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_BigBedFile *__pyx_vtabptr_2bx_3bbi_11bigbed_file_BigBedFile;
+
+
/* "bbi_file.pxd":39
* cdef class BBIFile
*
@@ -1032,8 +934,8 @@ struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler {
static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtabptr_2bx_3bbi_8bbi_file_BlockHandler;
-/* "bx/bbi/bigbed_file.pyx":44
- * return "".join(read) if len(read) > 1 else read[0]
+/* "bx/bbi/bigbed_file.pyx":20
+ * return min( end1, end2 ) - max( start1, start2 )
*
* cdef class BigBedBlockHandler( BlockHandler ): # <<<<<<<<<<<<<<
* """
@@ -1047,49 +949,46 @@ struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_BigBedBlockHandler {
static struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_BigBedBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigbed_file_BigBedBlockHandler;
-/* "bx/bbi/bigbed_file.pyx":76
- * pass
+/* "bx/bbi/bigbed_file.pyx":73
+ * self.sd.accumulate_interval_value( s, e, 1 )
*
- * cdef class SummarizingBlockHandler( BigBedBlockHandler ): # <<<<<<<<<<<<<<
+ * cdef class IntervalAccumulatingBlockHandler( BigBedBlockHandler ): # <<<<<<<<<<<<<<
+ * cdef list intervals
* """
- * Accumulates intervals into a SummarizedData
*/
-struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_SummarizingBlockHandler {
+struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler {
struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_BigBedBlockHandler __pyx_base;
};
-static struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_SummarizingBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigbed_file_SummarizingBlockHandler;
+static struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler;
-/* "bx/bbi/bigbed_file.pyx":95
- * self.sd.accumulate_interval_value( s, e, 1 )
+/* "bbi_file.pxd":21
+ * cdef public double sum_squares
*
- * cdef class IntervalAccumulatingBlockHandler( BigBedBlockHandler ): # <<<<<<<<<<<<<<
- * cdef list intervals
+ * cdef class SummarizedData: # <<<<<<<<<<<<<<
* """
+ * The result of using SummaryBlocks read from the file to produce a
*/
-struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler {
- struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_BigBedBlockHandler __pyx_base;
+struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData {
+ PyObject *(*accumulate_interval_value)(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float);
};
-static struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler;
+static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtabptr_2bx_3bbi_8bbi_file_SummarizedData;
-/* "bx/bbi/bigbed_file.pyx":107
- * self.intervals.append( ( s, e, rest ) )
+/* "bx/bbi/bigbed_file.pyx":54
+ * pass
*
- * cdef class BigBedFile( BBIFile ): # <<<<<<<<<<<<<<
+ * cdef class SummarizingBlockHandler( BigBedBlockHandler ): # <<<<<<<<<<<<<<
* """
- * A "big binary indexed" file whose raw data is in BED format.
+ * Accumulates intervals into a SummarizedData
*/
-struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_BigBedFile {
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile __pyx_base;
- PyObject *(*get)(struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int __pyx_skip_dispatch);
+struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_SummarizingBlockHandler {
+ struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_BigBedBlockHandler __pyx_base;
};
-static struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_BigBedFile *__pyx_vtabptr_2bx_3bbi_11bigbed_file_BigBedFile;
-
-/* --- Runtime support code (head) --- */
+static struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_SummarizingBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigbed_file_SummarizingBlockHandler;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
@@ -1103,7 +1002,7 @@ static struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_BigBedFile *__pyx_vtabptr_
void (*FinishContext)(void**);
} __Pyx_RefNannyAPIStruct;
static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
- static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname);
+ static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); /*proto*/
#define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
#ifdef WITH_THREAD
#define __Pyx_RefNannySetupContext(name, acquire_gil) \
@@ -1140,173 +1039,167 @@ static struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_BigBedFile *__pyx_vtabptr_
#define __Pyx_XDECREF(r) Py_XDECREF(r)
#define __Pyx_XGOTREF(r)
#define __Pyx_XGIVEREF(r)
-#endif
-#define __Pyx_XDECREF_SET(r, v) do { \
- PyObject *tmp = (PyObject *) r; \
- r = v; __Pyx_XDECREF(tmp); \
- } while (0)
-#define __Pyx_DECREF_SET(r, v) do { \
- PyObject *tmp = (PyObject *) r; \
- r = v; __Pyx_DECREF(tmp); \
- } while (0)
+#endif /* CYTHON_REFNANNY */
#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
- PyTypeObject* tp = Py_TYPE(obj);
- if (likely(tp->tp_getattro))
- return tp->tp_getattro(obj, attr_name);
-#if PY_MAJOR_VERSION < 3
- if (likely(tp->tp_getattr))
- return tp->tp_getattr(obj, PyString_AS_STRING(attr_name));
-#endif
- return PyObject_GetAttr(obj, attr_name);
-}
-#else
-#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
-#endif
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
-static PyObject *__Pyx_GetBuiltinName(PyObject *name);
+static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
+ Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
-#else
-#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
-#endif
+static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
-#endif
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
+ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
+ const char* function_name); /*proto*/
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);
-
-#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
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- __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \
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-#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
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-#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
- (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck);
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck);
-
-static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
- int result = PySequence_Contains(seq, item);
- return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
+#define __Pyx_SetItemInt(o, i, v, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_SetItemInt_Fast(o, i, v) : \
+ __Pyx_SetItemInt_Generic(o, to_py_func(i), v))
+static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) {
+ int r;
+ if (!j) return -1;
+ r = PyObject_SetItem(o, j, v);
+ Py_DECREF(j);
+ return r;
}
-
+static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) {
#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
- PyListObject* L = (PyListObject*) list;
- Py_ssize_t len = Py_SIZE(list);
- if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) {
- Py_INCREF(x);
- PyList_SET_ITEM(list, len, x);
- Py_SIZE(list) = len+1;
- return 0;
+ if (PyList_CheckExact(o)) {
+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
+ PyObject* old = PyList_GET_ITEM(o, n);
+ Py_INCREF(v);
+ PyList_SET_ITEM(o, n, v);
+ Py_DECREF(old);
+ return 1;
+ }
+ } else { /* inlined PySequence_SetItem() */
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_ass_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return -1;
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+ }
+ return m->sq_ass_item(o, i, v);
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}
- return PyList_Append(list, x);
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-#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
+#if CYTHON_COMPILING_IN_PYPY
+ if (PySequence_Check(o) && !PyDict_Check(o)) {
+#else
+ if (PySequence_Check(o)) {
#endif
+ return PySequence_SetItem(o, i, v);
+ }
+#endif
+ return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
+}
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- PyObject** py_start, PyObject** py_stop, PyObject** py_slice,
- int has_cstart, int has_cstop, int wraparound);
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-#define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
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-#define __Pyx_PyBaseString_Join(s, v) (PyUnicode_CheckExact(s) ? PyUnicode_Join(s, v) : __Pyx_PyBytes_Join(s, v))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
+ PyObject *r;
+ if (!j) return NULL;
+ r = PyObject_GetItem(o, j);
+ Py_DECREF(j);
+ return r;
+}
+#define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_List_Fast(o, i) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
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+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
#else
-#define __Pyx_PyString_Join PyUnicode_Join
-#define __Pyx_PyBaseString_Join PyUnicode_Join
+ return PySequence_GetItem(o, i);
#endif
+}
+#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_Tuple_Fast(o, i) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
#if CYTHON_COMPILING_IN_CPYTHON
- #if PY_MAJOR_VERSION < 3
- #define __Pyx_PyBytes_Join _PyString_Join
- #else
- #define __Pyx_PyBytes_Join _PyBytes_Join
- #endif
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
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+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
#else
-static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values);
+ return PySequence_GetItem(o, i);
#endif
-
-static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
- Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found);
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-static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);
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-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
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-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name);
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+}
+#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_Fast(o, i) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
+ if (PyList_CheckExact(o)) {
+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ }
+ else if (PyTuple_CheckExact(o)) {
+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ } else { /* inlined PySequence_GetItem() */
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return NULL;
+ i += l;
+ }
+ return m->sq_item(o, i);
+ }
+ }
#else
-#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL)
+ if (PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
+ }
#endif
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+}
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE int __Pyx_IterFinish(void);
+static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected);
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb);
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb);
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause);
-
-#if PY_MAJOR_VERSION >= 3
-static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
- PyObject *value;
- value = PyDict_GetItemWithError(d, key);
- if (unlikely(!value)) {
- if (!PyErr_Occurred()) {
- PyObject* args = PyTuple_Pack(1, key);
- if (likely(args))
- PyErr_SetObject(PyExc_KeyError, args);
- Py_XDECREF(args);
- }
- return NULL;
- }
- Py_INCREF(value);
- return value;
-}
-#else
- #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
-#endif
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/
static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
-static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type);
+static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc);
@@ -1314,40 +1207,9 @@ static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, trav
static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc);
-static void* __Pyx_GetVtable(PyObject *dict);
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable);
-
-static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name);
-
-typedef struct {
- int code_line;
- PyCodeObject* code_object;
-} __Pyx_CodeObjectCacheEntry;
-struct __Pyx_CodeObjectCache {
- int count;
- int max_count;
- __Pyx_CodeObjectCacheEntry* entries;
-};
-static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
-static PyCodeObject *__pyx_find_code_object(int code_line);
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
-
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename);
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_As_unsigned_int(PyObject *);
-
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_int(unsigned int value);
+static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name);
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
@@ -1361,7 +1223,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_int(unsigned int value)
#define __Pyx_CREAL(z) ((z).real)
#define __Pyx_CIMAG(z) ((z).imag)
#endif
-#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX
+#if defined(_WIN32) && defined(__cplusplus) && CYTHON_CCOMPLEX
#define __Pyx_SET_CREAL(z,x) ((z).real(x))
#define __Pyx_SET_CIMAG(z,y) ((z).imag(y))
#else
@@ -1447,7 +1309,37 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
#endif
#endif
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
+static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
+
+static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
+
+static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *);
+
+static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *);
+
+static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *);
+
+static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *);
+
+static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *);
+
+static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *);
+
+static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *);
+
+static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *);
+
+static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *);
+
+static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *);
+
+static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *);
+
+static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *);
+
+static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);
+
+static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
static int __Pyx_check_binary_version(void);
@@ -1459,18 +1351,33 @@ static int __Pyx_check_binary_version(void);
#endif
#endif
-static PyObject *__Pyx_ImportModule(const char *name);
+static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict);
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t);
+static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
+
+typedef struct {
+ int code_line;
+ PyCodeObject* code_object;
+} __Pyx_CodeObjectCacheEntry;
+struct __Pyx_CodeObjectCache {
+ int count;
+ int max_count;
+ __Pyx_CodeObjectCacheEntry* entries;
+};
+static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
+static PyCodeObject *__pyx_find_code_object(int code_line);
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
+
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename); /*proto*/
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-static PyObject *__pyx_f_2bx_3bbi_11bigbed_file_18BigBedBlockHandler_handle_block(struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler *__pyx_v_self, PyObject *__pyx_v_block_data, struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_bbi_file); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_11bigbed_file_18BigBedBlockHandler_handle_interval_value(CYTHON_UNUSED struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler *__pyx_v_self, CYTHON_UNUSED __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_s, CYTHON_UNUSED __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_e, CYTHON_UNUSED PyObject *__pyx_v_rest); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_11bigbed_file_23SummarizingBlockHandler_handle_interval_value(struct __pyx_obj_2bx_3bbi_11bigbed_file_SummarizingBlockHandler *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_s, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_e, CYTHON_UNUSED PyObject *__pyx_v_rest); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_11bigbed_file_32IntervalAccumulatingBlockHandler_handle_interval_value(struct __pyx_obj_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_s, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_e, PyObject *__pyx_v_rest); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_11bigbed_file_10BigBedFile__summarize_from_full(struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_chrom_id, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_v_summary_size); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_11bigbed_file_10BigBedFile_get(struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile *__pyx_v_self, char *__pyx_v_chrom, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_skip_dispatch); /* proto*/
/* Module declarations from 'bx.bbi.types' */
@@ -1518,12 +1425,12 @@ static PyTypeObject *__pyx_ptype_2bx_3bbi_11bigbed_file_BigBedBlockHandler = 0;
static PyTypeObject *__pyx_ptype_2bx_3bbi_11bigbed_file_SummarizingBlockHandler = 0;
static PyTypeObject *__pyx_ptype_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler = 0;
static PyTypeObject *__pyx_ptype_2bx_3bbi_11bigbed_file_BigBedFile = 0;
-static PyObject *__pyx_f_2bx_3bbi_11bigbed_file_read_c_string(PyObject *); /*proto*/
#define __Pyx_MODULE_NAME "bx.bbi.bigbed_file"
int __pyx_module_is_main_bx__bbi__bigbed_file = 0;
/* Implementation of 'bx.bbi.bigbed_file' */
static PyObject *__pyx_builtin_range;
+static PyObject *__pyx_builtin_round;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_RuntimeError;
static int __pyx_pf_2bx_3bbi_11bigbed_file_18BigBedBlockHandler___init__(struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_chrom_id, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end); /* proto */
@@ -1533,140 +1440,113 @@ static int __pyx_pf_2bx_3bbi_11bigbed_file_10BigBedFile___init__(struct __pyx_ob
static PyObject *__pyx_pf_2bx_3bbi_11bigbed_file_10BigBedFile_2get(struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile *__pyx_v_self, char *__pyx_v_chrom, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end); /* proto */
static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
-static PyObject *__pyx_tp_new_2bx_3bbi_11bigbed_file_BigBedBlockHandler(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_2bx_3bbi_11bigbed_file_SummarizingBlockHandler(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_2bx_3bbi_11bigbed_file_BigBedFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static char __pyx_k_[] = "\000";
-static char __pyx_k_B[] = "B";
-static char __pyx_k_H[] = "H";
-static char __pyx_k_I[] = "I";
-static char __pyx_k_L[] = "L";
-static char __pyx_k_O[] = "O";
-static char __pyx_k_Q[] = "Q";
-static char __pyx_k_b[] = "b";
-static char __pyx_k_d[] = "d";
-static char __pyx_k_f[] = "f";
-static char __pyx_k_g[] = "g";
-static char __pyx_k_h[] = "h";
-static char __pyx_k_i[] = "i";
-static char __pyx_k_l[] = "l";
-static char __pyx_k_q[] = "q";
-static char __pyx_k_Zd[] = "Zd";
-static char __pyx_k_Zf[] = "Zf";
-static char __pyx_k_Zg[] = "Zg";
-static char __pyx_k__3[] = "";
-static char __pyx_k__5[] = "\t";
-static char __pyx_k__7[] = "+";
-static char __pyx_k_np[] = "np";
-static char __pyx_k_LLL[] = "LLL";
-static char __pyx_k_end[] = "end";
-static char __pyx_k_get[] = "get";
-static char __pyx_k_inf[] = "inf";
-static char __pyx_k_out[] = "out";
-static char __pyx_k_file[] = "file";
-static char __pyx_k_find[] = "find";
-static char __pyx_k_init[] = "__init__";
-static char __pyx_k_join[] = "join";
-static char __pyx_k_main[] = "__main__";
-static char __pyx_k_read[] = "read";
-static char __pyx_k_seek[] = "seek";
-static char __pyx_k_tell[] = "tell";
-static char __pyx_k_test[] = "__test__";
-static char __pyx_k_zlib[] = "zlib";
-static char __pyx_k_chrom[] = "chrom";
-static char __pyx_k_numpy[] = "numpy";
-static char __pyx_k_range[] = "range";
-static char __pyx_k_round[] = "round";
-static char __pyx_k_split[] = "split";
-static char __pyx_k_start[] = "start";
-static char __pyx_k_bigbed[] = "bigbed";
-static char __pyx_k_import[] = "__import__";
-static char __pyx_k_StringIO[] = "StringIO";
-static char __pyx_k_chrom_id[] = "chrom_id";
-static char __pyx_k_cStringIO[] = "cStringIO";
-static char __pyx_k_ValueError[] = "ValueError";
-static char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
-static char __pyx_k_BigBed_file[] = "\nBigBed file.\n";
-static char __pyx_k_RuntimeError[] = "RuntimeError";
-static char __pyx_k_summary_size[] = "summary_size";
-static char __pyx_k_GenomicInterval[] = "GenomicInterval";
-static char __pyx_k_bx_intervals_io[] = "bx.intervals.io";
-static char __pyx_k_read_and_unpack[] = "read_and_unpack";
-static char __pyx_k_BinaryFileReader[] = "BinaryFileReader";
-static char __pyx_k_is_little_endian[] = "is_little_endian";
-static char __pyx_k_bx_misc_binary_file[] = "bx.misc.binary_file";
-static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous";
-static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
-static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd";
-static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported";
-static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous";
-static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short.";
-static PyObject *__pyx_kp_s_;
-static PyObject *__pyx_n_s_BinaryFileReader;
-static PyObject *__pyx_kp_u_Format_string_allocated_too_shor;
-static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2;
-static PyObject *__pyx_n_s_GenomicInterval;
-static PyObject *__pyx_n_s_LLL;
-static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor;
-static PyObject *__pyx_n_s_RuntimeError;
-static PyObject *__pyx_n_s_StringIO;
-static PyObject *__pyx_n_s_ValueError;
-static PyObject *__pyx_kp_s__3;
-static PyObject *__pyx_kp_s__5;
-static PyObject *__pyx_kp_s__7;
-static PyObject *__pyx_n_s_bigbed;
-static PyObject *__pyx_n_s_bx_intervals_io;
-static PyObject *__pyx_n_s_bx_misc_binary_file;
-static PyObject *__pyx_n_s_cStringIO;
-static PyObject *__pyx_n_s_chrom;
-static PyObject *__pyx_n_s_chrom_id;
-static PyObject *__pyx_n_s_end;
-static PyObject *__pyx_n_s_file;
-static PyObject *__pyx_n_s_find;
-static PyObject *__pyx_n_s_get;
-static PyObject *__pyx_n_s_import;
-static PyObject *__pyx_n_s_inf;
-static PyObject *__pyx_n_s_init;
-static PyObject *__pyx_n_s_is_little_endian;
-static PyObject *__pyx_n_s_join;
-static PyObject *__pyx_n_s_main;
-static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous;
-static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou;
-static PyObject *__pyx_n_s_np;
-static PyObject *__pyx_n_s_numpy;
-static PyObject *__pyx_n_s_out;
-static PyObject *__pyx_n_s_pyx_vtable;
-static PyObject *__pyx_n_s_range;
-static PyObject *__pyx_n_s_read;
-static PyObject *__pyx_n_s_read_and_unpack;
-static PyObject *__pyx_n_s_round;
-static PyObject *__pyx_n_s_seek;
-static PyObject *__pyx_n_s_split;
-static PyObject *__pyx_n_s_start;
-static PyObject *__pyx_n_s_summary_size;
-static PyObject *__pyx_n_s_tell;
-static PyObject *__pyx_n_s_test;
-static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd;
-static PyObject *__pyx_n_s_zlib;
+static char __pyx_k_1[] = "\t";
+static char __pyx_k_3[] = "+";
+static char __pyx_k_4[] = "ndarray is not C contiguous";
+static char __pyx_k_6[] = "ndarray is not Fortran contiguous";
+static char __pyx_k_8[] = "Non-native byte order not supported";
+static char __pyx_k_10[] = "unknown dtype code in numpy.pxd (%d)";
+static char __pyx_k_11[] = "Format string allocated too short, see comment in numpy.pxd";
+static char __pyx_k_14[] = "Format string allocated too short.";
+static char __pyx_k_16[] = "\nBigBed file.\n";
+static char __pyx_k_17[] = "bx.intervals.io";
+static char __pyx_k_18[] = "bx.misc.binary_file";
+static char __pyx_k__B[] = "B";
+static char __pyx_k__H[] = "H";
+static char __pyx_k__I[] = "I";
+static char __pyx_k__L[] = "L";
+static char __pyx_k__O[] = "O";
+static char __pyx_k__Q[] = "Q";
+static char __pyx_k__b[] = "b";
+static char __pyx_k__d[] = "d";
+static char __pyx_k__f[] = "f";
+static char __pyx_k__g[] = "g";
+static char __pyx_k__h[] = "h";
+static char __pyx_k__i[] = "i";
+static char __pyx_k__l[] = "l";
+static char __pyx_k__q[] = "q";
+static char __pyx_k__Zd[] = "Zd";
+static char __pyx_k__Zf[] = "Zf";
+static char __pyx_k__Zg[] = "Zg";
+static char __pyx_k__end[] = "end";
+static char __pyx_k__get[] = "get";
+static char __pyx_k__inf[] = "inf";
+static char __pyx_k__file[] = "file";
+static char __pyx_k__tell[] = "tell";
+static char __pyx_k__zlib[] = "zlib";
+static char __pyx_k__chrom[] = "chrom";
+static char __pyx_k__numpy[] = "numpy";
+static char __pyx_k__range[] = "range";
+static char __pyx_k__round[] = "round";
+static char __pyx_k__split[] = "split";
+static char __pyx_k__start[] = "start";
+static char __pyx_k__bigbed[] = "bigbed";
+static char __pyx_k__StringIO[] = "StringIO";
+static char __pyx_k____init__[] = "__init__";
+static char __pyx_k____main__[] = "__main__";
+static char __pyx_k____test__[] = "__test__";
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-
- /* function exit code */
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__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
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__Pyx_AddTraceback("numpy._util_dtypestring", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__pyx_t_1 = (__pyx_v_base == Py_None);
- __pyx_t_2 = (__pyx_t_1 != 0);
- if (__pyx_t_2) {
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/*else*/ {
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Py_INCREF(__pyx_v_base);
- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":975
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Py_XDECREF(__pyx_v_arr->base);
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*/
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__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
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+ goto __pyx_L3;
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struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler *p;
PyObject *o = __pyx_ptype_2bx_3bbi_8bbi_file_BlockHandler->tp_new(t, a, k);
- if (unlikely(!o)) return 0;
+ if (!o) return 0;
p = ((struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler *)o);
p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler*)__pyx_vtabptr_2bx_3bbi_11bigbed_file_BigBedBlockHandler;
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}
static void __pyx_tp_dealloc_2bx_3bbi_11bigbed_file_BigBedBlockHandler(PyObject *o) {
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- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
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}
@@ -6064,9 +5290,107 @@ static PyMethodDef __pyx_methods_2bx_3bbi_11bigbed_file_BigBedBlockHandler[] = {
{0, 0, 0, 0}
};
+static PyNumberMethods __pyx_tp_as_number_BigBedBlockHandler = {
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+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
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+ 0, /*reserved*/
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+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
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+ 0, /*nb_inplace_add*/
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+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
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+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_BigBedBlockHandler = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_BigBedBlockHandler = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_BigBedBlockHandler = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
static PyTypeObject __pyx_type_2bx_3bbi_11bigbed_file_BigBedBlockHandler = {
PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bigbed_file.BigBedBlockHandler", /*tp_name*/
+ __Pyx_NAMESTR("bx.bbi.bigbed_file.BigBedBlockHandler"), /*tp_name*/
sizeof(struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_2bx_3bbi_11bigbed_file_BigBedBlockHandler, /*tp_dealloc*/
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0, /*reserved*/
#endif
0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ &__pyx_tp_as_number_BigBedBlockHandler, /*tp_as_number*/
+ &__pyx_tp_as_sequence_BigBedBlockHandler, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_BigBedBlockHandler, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
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+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("\n BlockHandler that parses the block into a series of BED records\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
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0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
#endif
};
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static PyObject *__pyx_tp_new_2bx_3bbi_11bigbed_file_SummarizingBlockHandler(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_2bx_3bbi_11bigbed_file_SummarizingBlockHandler *p;
PyObject *o = __pyx_tp_new_2bx_3bbi_11bigbed_file_BigBedBlockHandler(t, a, k);
- if (unlikely(!o)) return 0;
+ if (!o) return 0;
p = ((struct __pyx_obj_2bx_3bbi_11bigbed_file_SummarizingBlockHandler *)o);
p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler*)__pyx_vtabptr_2bx_3bbi_11bigbed_file_SummarizingBlockHandler;
p->sd = ((struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *)Py_None); Py_INCREF(Py_None);
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static void __pyx_tp_dealloc_2bx_3bbi_11bigbed_file_SummarizingBlockHandler(PyObject *o) {
struct __pyx_obj_2bx_3bbi_11bigbed_file_SummarizingBlockHandler *p = (struct __pyx_obj_2bx_3bbi_11bigbed_file_SummarizingBlockHandler *)o;
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
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PyObject_GC_UnTrack(o);
Py_CLEAR(p->sd);
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PyObject_GC_Track(o);
__pyx_tp_dealloc_2bx_3bbi_11bigbed_file_BigBedBlockHandler(o);
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}
static int __pyx_tp_clear_2bx_3bbi_11bigbed_file_SummarizingBlockHandler(PyObject *o) {
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struct __pyx_obj_2bx_3bbi_11bigbed_file_SummarizingBlockHandler *p = (struct __pyx_obj_2bx_3bbi_11bigbed_file_SummarizingBlockHandler *)o;
+ PyObject* tmp;
if (likely(__pyx_ptype_2bx_3bbi_11bigbed_file_BigBedBlockHandler)) { if (__pyx_ptype_2bx_3bbi_11bigbed_file_BigBedBlockHandler->tp_clear) __pyx_ptype_2bx_3bbi_11bigbed_file_BigBedBlockHandler->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_2bx_3bbi_11bigbed_file_SummarizingBlockHandler);
tmp = ((PyObject*)p->sd);
p->sd = ((struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *)Py_None); Py_INCREF(Py_None);
@@ -6172,9 +5487,107 @@ static PyMethodDef __pyx_methods_2bx_3bbi_11bigbed_file_SummarizingBlockHandler[
{0, 0, 0, 0}
};
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+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_SummarizingBlockHandler = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_SummarizingBlockHandler = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_SummarizingBlockHandler = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
static PyTypeObject __pyx_type_2bx_3bbi_11bigbed_file_SummarizingBlockHandler = {
PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bigbed_file.SummarizingBlockHandler", /*tp_name*/
+ __Pyx_NAMESTR("bx.bbi.bigbed_file.SummarizingBlockHandler"), /*tp_name*/
sizeof(struct __pyx_obj_2bx_3bbi_11bigbed_file_SummarizingBlockHandler), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_2bx_3bbi_11bigbed_file_SummarizingBlockHandler, /*tp_dealloc*/
@@ -6187,17 +5600,17 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigbed_file_SummarizingBlockHandler =
0, /*reserved*/
#endif
0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ &__pyx_tp_as_number_SummarizingBlockHandler, /*tp_as_number*/
+ &__pyx_tp_as_sequence_SummarizingBlockHandler, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_SummarizingBlockHandler, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- "\n Accumulates intervals into a SummarizedData\n ", /*tp_doc*/
+ &__pyx_tp_as_buffer_SummarizingBlockHandler, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("\n Accumulates intervals into a SummarizedData\n "), /*tp_doc*/
__pyx_tp_traverse_2bx_3bbi_11bigbed_file_SummarizingBlockHandler, /*tp_traverse*/
__pyx_tp_clear_2bx_3bbi_11bigbed_file_SummarizingBlockHandler, /*tp_clear*/
0, /*tp_richcompare*/
@@ -6223,9 +5636,8 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigbed_file_SummarizingBlockHandler =
0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
#endif
};
static struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler __pyx_vtable_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler;
@@ -6233,7 +5645,7 @@ static struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockH
static PyObject *__pyx_tp_new_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler *p;
PyObject *o = __pyx_tp_new_2bx_3bbi_11bigbed_file_BigBedBlockHandler(t, a, k);
- if (unlikely(!o)) return 0;
+ if (!o) return 0;
p = ((struct __pyx_obj_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler *)o);
p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler*)__pyx_vtabptr_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler;
p->intervals = ((PyObject*)Py_None); Py_INCREF(Py_None);
@@ -6242,16 +5654,8 @@ static PyObject *__pyx_tp_new_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHa
static void __pyx_tp_dealloc_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler(PyObject *o) {
struct __pyx_obj_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler *p = (struct __pyx_obj_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler *)o;
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
PyObject_GC_UnTrack(o);
Py_CLEAR(p->intervals);
- #if CYTHON_COMPILING_IN_CPYTHON
- if (PyType_IS_GC(Py_TYPE(o)->tp_base))
- #endif
PyObject_GC_Track(o);
__pyx_tp_dealloc_2bx_3bbi_11bigbed_file_BigBedBlockHandler(o);
}
@@ -6267,8 +5671,8 @@ static int __pyx_tp_traverse_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHan
}
static int __pyx_tp_clear_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler(PyObject *o) {
- PyObject* tmp;
struct __pyx_obj_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler *p = (struct __pyx_obj_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler *)o;
+ PyObject* tmp;
if (likely(__pyx_ptype_2bx_3bbi_11bigbed_file_BigBedBlockHandler)) { if (__pyx_ptype_2bx_3bbi_11bigbed_file_BigBedBlockHandler->tp_clear) __pyx_ptype_2bx_3bbi_11bigbed_file_BigBedBlockHandler->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler);
tmp = ((PyObject*)p->intervals);
p->intervals = ((PyObject*)Py_None); Py_INCREF(Py_None);
@@ -6280,9 +5684,107 @@ static PyMethodDef __pyx_methods_2bx_3bbi_11bigbed_file_IntervalAccumulatingBloc
{0, 0, 0, 0}
};
+static PyNumberMethods __pyx_tp_as_number_IntervalAccumulatingBlockHandler = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_IntervalAccumulatingBlockHandler = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_IntervalAccumulatingBlockHandler = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_IntervalAccumulatingBlockHandler = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
static PyTypeObject __pyx_type_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler = {
PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bigbed_file.IntervalAccumulatingBlockHandler", /*tp_name*/
+ __Pyx_NAMESTR("bx.bbi.bigbed_file.IntervalAccumulatingBlockHandler"), /*tp_name*/
sizeof(struct __pyx_obj_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler, /*tp_dealloc*/
@@ -6295,16 +5797,16 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockH
0, /*reserved*/
#endif
0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IntervalAccumulatingBlockHandler, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IntervalAccumulatingBlockHandler, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IntervalAccumulatingBlockHandler, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ &__pyx_tp_as_buffer_IntervalAccumulatingBlockHandler, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
__pyx_tp_traverse_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler, /*tp_traverse*/
__pyx_tp_clear_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler, /*tp_clear*/
@@ -6331,9 +5833,8 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockH
0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
#endif
};
static struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_BigBedFile __pyx_vtable_2bx_3bbi_11bigbed_file_BigBedFile;
@@ -6341,42 +5842,135 @@ static struct __pyx_vtabstruct_2bx_3bbi_11bigbed_file_BigBedFile __pyx_vtable_2b
static PyObject *__pyx_tp_new_2bx_3bbi_11bigbed_file_BigBedFile(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile *p;
PyObject *o = __pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_new(t, a, k);
- if (unlikely(!o)) return 0;
+ if (!o) return 0;
p = ((struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile *)o);
p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile*)__pyx_vtabptr_2bx_3bbi_11bigbed_file_BigBedFile;
return o;
}
static void __pyx_tp_dealloc_2bx_3bbi_11bigbed_file_BigBedFile(PyObject *o) {
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
PyObject_GC_UnTrack(o);
PyObject_GC_Track(o);
if (likely(__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile)) __pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_dealloc(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_2bx_3bbi_11bigbed_file_BigBedFile);
}
-static int __pyx_tp_traverse_2bx_3bbi_11bigbed_file_BigBedFile(PyObject *o, visitproc v, void *a) {
- int e;
- e = ((likely(__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile)) ? ((__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_traverse) ? __pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_2bx_3bbi_11bigbed_file_BigBedFile)); if (e) return e;
- return 0;
-}
+static int __pyx_tp_traverse_2bx_3bbi_11bigbed_file_BigBedFile(PyObject *o, visitproc v, void *a) {
+ int e;
+ e = ((likely(__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile)) ? ((__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_traverse) ? __pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_2bx_3bbi_11bigbed_file_BigBedFile)); if (e) return e;
+ return 0;
+}
+
+static int __pyx_tp_clear_2bx_3bbi_11bigbed_file_BigBedFile(PyObject *o) {
+ if (likely(__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile)) { if (__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_clear) __pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_2bx_3bbi_11bigbed_file_BigBedFile);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_2bx_3bbi_11bigbed_file_BigBedFile[] = {
+ {__Pyx_NAMESTR("get"), (PyCFunction)__pyx_pw_2bx_3bbi_11bigbed_file_10BigBedFile_3get, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_3bbi_11bigbed_file_10BigBedFile_2get)},
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_BigBedFile = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_BigBedFile = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
-static int __pyx_tp_clear_2bx_3bbi_11bigbed_file_BigBedFile(PyObject *o) {
- if (likely(__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile)) { if (__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_clear) __pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_2bx_3bbi_11bigbed_file_BigBedFile);
- return 0;
-}
+static PyMappingMethods __pyx_tp_as_mapping_BigBedFile = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
-static PyMethodDef __pyx_methods_2bx_3bbi_11bigbed_file_BigBedFile[] = {
- {"get", (PyCFunction)__pyx_pw_2bx_3bbi_11bigbed_file_10BigBedFile_3get, METH_VARARGS|METH_KEYWORDS, __pyx_doc_2bx_3bbi_11bigbed_file_10BigBedFile_2get},
- {0, 0, 0, 0}
+static PyBufferProcs __pyx_tp_as_buffer_BigBedFile = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
};
static PyTypeObject __pyx_type_2bx_3bbi_11bigbed_file_BigBedFile = {
PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bigbed_file.BigBedFile", /*tp_name*/
+ __Pyx_NAMESTR("bx.bbi.bigbed_file.BigBedFile"), /*tp_name*/
sizeof(struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_2bx_3bbi_11bigbed_file_BigBedFile, /*tp_dealloc*/
@@ -6389,17 +5983,17 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigbed_file_BigBedFile = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ &__pyx_tp_as_number_BigBedFile, /*tp_as_number*/
+ &__pyx_tp_as_sequence_BigBedFile, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_BigBedFile, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- "\n A \"big binary indexed\" file whose raw data is in BED format.\n ", /*tp_doc*/
+ &__pyx_tp_as_buffer_BigBedFile, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("\n A \"big binary indexed\" file whose raw data is in BED format.\n "), /*tp_doc*/
__pyx_tp_traverse_2bx_3bbi_11bigbed_file_BigBedFile, /*tp_traverse*/
__pyx_tp_clear_2bx_3bbi_11bigbed_file_BigBedFile, /*tp_clear*/
0, /*tp_richcompare*/
@@ -6425,9 +6019,8 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigbed_file_BigBedFile = {
0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
#endif
};
@@ -6442,8 +6035,8 @@ static struct PyModuleDef __pyx_moduledef = {
#else
PyModuleDef_HEAD_INIT,
#endif
- "bigbed_file",
- __pyx_k_BigBed_file, /* m_doc */
+ __Pyx_NAMESTR("bigbed_file"),
+ __Pyx_DOCSTR(__pyx_k_16), /* m_doc */
-1, /* m_size */
__pyx_methods /* m_methods */,
NULL, /* m_reload */
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+ __pyx_k_tuple_15 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_u_14)); if (unlikely(!__pyx_k_tuple_15)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_15);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_15));
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -6623,13 +6185,12 @@ static int __Pyx_InitCachedConstants(void) {
static int __Pyx_InitGlobals(void) {
if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_int_2 = PyInt_FromLong(2); if (unlikely(!__pyx_int_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_int_5 = PyInt_FromLong(5); if (unlikely(!__pyx_int_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_int_8 = PyInt_FromLong(8); if (unlikely(!__pyx_int_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_int_12 = PyInt_FromLong(12); if (unlikely(!__pyx_int_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_int_2273964779 = PyInt_FromString((char *)"2273964779", 0, 0); if (unlikely(!__pyx_int_2273964779)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_2 = PyInt_FromLong(2); if (unlikely(!__pyx_int_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_5 = PyInt_FromLong(5); if (unlikely(!__pyx_int_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_15 = PyInt_FromLong(15); if (unlikely(!__pyx_int_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_2273964779 = PyInt_FromString((char *)"2273964779", 0, 0); if (unlikely(!__pyx_int_2273964779)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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return -1;
@@ -6645,9 +6206,6 @@ PyMODINIT_FUNC PyInit_bigbed_file(void)
{
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
__Pyx_RefNannyDeclarations
#if CYTHON_REFNANNY
__Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
@@ -6680,26 +6238,11 @@ PyMODINIT_FUNC PyInit_bigbed_file(void)
#endif
/*--- Module creation code ---*/
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4("bigbed_file", __pyx_methods, __pyx_k_BigBed_file, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("bigbed_file"), __pyx_methods, __Pyx_DOCSTR(__pyx_k_16), 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- Py_INCREF(__pyx_d);
- __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_PYPY
- Py_INCREF(__pyx_b);
- #endif
- if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- /*--- Initialize various global constants etc. ---*/
- if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
- if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- if (__pyx_module_is_main_bx__bbi__bigbed_file) {
- if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- }
#if PY_MAJOR_VERSION >= 3
{
PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -6708,6 +6251,16 @@ PyMODINIT_FUNC PyInit_bigbed_file(void)
}
}
#endif
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_PYPY
+ Py_INCREF(__pyx_b);
+ #endif
+ if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ /*--- Initialize various global constants etc. ---*/
+ if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_module_is_main_bx__bbi__bigbed_file) {
+ if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ }
/*--- Builtin init code ---*/
if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Constants init code ---*/
@@ -6723,28 +6276,25 @@ PyMODINIT_FUNC PyInit_bigbed_file(void)
__pyx_vtable_2bx_3bbi_11bigbed_file_BigBedBlockHandler.__pyx_base.handle_block = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler *, PyObject *, struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *))__pyx_f_2bx_3bbi_11bigbed_file_18BigBedBlockHandler_handle_block;
__pyx_vtable_2bx_3bbi_11bigbed_file_BigBedBlockHandler.handle_interval_value = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, PyObject *))__pyx_f_2bx_3bbi_11bigbed_file_18BigBedBlockHandler_handle_interval_value;
__pyx_type_2bx_3bbi_11bigbed_file_BigBedBlockHandler.tp_base = __pyx_ptype_2bx_3bbi_8bbi_file_BlockHandler;
- if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigbed_file_BigBedBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_type_2bx_3bbi_11bigbed_file_BigBedBlockHandler.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigbed_file_BigBedBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigbed_file_BigBedBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "BigBedBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigbed_file_BigBedBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigbed_file_BigBedBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigbed_file_BigBedBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigbed_file_BigBedBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "BigBedBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigbed_file_BigBedBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_2bx_3bbi_11bigbed_file_BigBedBlockHandler = &__pyx_type_2bx_3bbi_11bigbed_file_BigBedBlockHandler;
__pyx_vtabptr_2bx_3bbi_11bigbed_file_SummarizingBlockHandler = &__pyx_vtable_2bx_3bbi_11bigbed_file_SummarizingBlockHandler;
__pyx_vtable_2bx_3bbi_11bigbed_file_SummarizingBlockHandler.__pyx_base = *__pyx_vtabptr_2bx_3bbi_11bigbed_file_BigBedBlockHandler;
__pyx_vtable_2bx_3bbi_11bigbed_file_SummarizingBlockHandler.__pyx_base.handle_interval_value = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, PyObject *))__pyx_f_2bx_3bbi_11bigbed_file_23SummarizingBlockHandler_handle_interval_value;
__pyx_type_2bx_3bbi_11bigbed_file_SummarizingBlockHandler.tp_base = __pyx_ptype_2bx_3bbi_11bigbed_file_BigBedBlockHandler;
- if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigbed_file_SummarizingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_type_2bx_3bbi_11bigbed_file_SummarizingBlockHandler.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigbed_file_SummarizingBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigbed_file_SummarizingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "SummarizingBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigbed_file_SummarizingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigbed_file_SummarizingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigbed_file_SummarizingBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigbed_file_SummarizingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "SummarizingBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigbed_file_SummarizingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_2bx_3bbi_11bigbed_file_SummarizingBlockHandler = &__pyx_type_2bx_3bbi_11bigbed_file_SummarizingBlockHandler;
__pyx_vtabptr_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler = &__pyx_vtable_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler;
__pyx_vtable_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler.__pyx_base = *__pyx_vtabptr_2bx_3bbi_11bigbed_file_BigBedBlockHandler;
__pyx_vtable_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler.__pyx_base.handle_interval_value = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, PyObject *))__pyx_f_2bx_3bbi_11bigbed_file_32IntervalAccumulatingBlockHandler_handle_interval_value;
__pyx_type_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler.tp_base = __pyx_ptype_2bx_3bbi_11bigbed_file_BigBedBlockHandler;
- if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_type_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "IntervalAccumulatingBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IntervalAccumulatingBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler = &__pyx_type_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler;
__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile = __Pyx_ImportType("bx.bbi.bbi_file", "BBIFile", sizeof(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile), 1); if (unlikely(!__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile = (struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile*)__Pyx_GetVtable(__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_dict); if (unlikely(!__pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -6753,10 +6303,9 @@ PyMODINIT_FUNC PyInit_bigbed_file(void)
__pyx_vtable_2bx_3bbi_11bigbed_file_BigBedFile.__pyx_base._summarize_from_full = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int))__pyx_f_2bx_3bbi_11bigbed_file_10BigBedFile__summarize_from_full;
__pyx_vtable_2bx_3bbi_11bigbed_file_BigBedFile.get = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int __pyx_skip_dispatch))__pyx_f_2bx_3bbi_11bigbed_file_10BigBedFile_get;
__pyx_type_2bx_3bbi_11bigbed_file_BigBedFile.tp_base = __pyx_ptype_2bx_3bbi_8bbi_file_BBIFile;
- if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigbed_file_BigBedFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_type_2bx_3bbi_11bigbed_file_BigBedFile.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigbed_file_BigBedFile.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigbed_file_BigBedFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "BigBedFile", (PyObject *)&__pyx_type_2bx_3bbi_11bigbed_file_BigBedFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigbed_file_BigBedFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigbed_file_BigBedFile.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigbed_file_BigBedFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "BigBedFile", (PyObject *)&__pyx_type_2bx_3bbi_11bigbed_file_BigBedFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_2bx_3bbi_11bigbed_file_BigBedFile = &__pyx_type_2bx_3bbi_11bigbed_file_BigBedFile;
/*--- Type import code ---*/
__pyx_ptype_2bx_3bbi_8bpt_file_BPTFile = __Pyx_ImportType("bx.bbi.bpt_file", "BPTFile", sizeof(struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile), 1); if (unlikely(!__pyx_ptype_2bx_3bbi_8bpt_file_BPTFile)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -6769,10 +6318,10 @@ PyMODINIT_FUNC PyInit_bigbed_file(void)
#endif
0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (is_list || PyList_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
- PyObject *r = PyList_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- }
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- } else {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- return NULL;
- }
- }
- return m->sq_item(o, i);
- }
- }
-#else
- if (is_list || PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
- PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
- PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
- int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyMappingMethods* mp;
-#if PY_MAJOR_VERSION < 3
- PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence;
- if (likely(ms && ms->sq_slice)) {
- if (!has_cstart) {
- if (_py_start && (*_py_start != Py_None)) {
- cstart = __Pyx_PyIndex_AsSsize_t(*_py_start);
- if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
- } else
- cstart = 0;
- }
- if (!has_cstop) {
- if (_py_stop && (*_py_stop != Py_None)) {
- cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop);
- if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
- } else
- cstop = PY_SSIZE_T_MAX;
- }
- if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) {
- Py_ssize_t l = ms->sq_length(obj);
- if (likely(l >= 0)) {
- if (cstop < 0) {
- cstop += l;
- if (cstop < 0) cstop = 0;
- }
- if (cstart < 0) {
- cstart += l;
- if (cstart < 0) cstart = 0;
- }
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- goto bad;
- }
- }
- return ms->sq_slice(obj, cstart, cstop);
- }
-#endif
- mp = Py_TYPE(obj)->tp_as_mapping;
- if (likely(mp && mp->mp_subscript))
-#endif
- {
- PyObject* result;
- PyObject *py_slice, *py_start, *py_stop;
- if (_py_slice) {
- py_slice = *_py_slice;
- } else {
- PyObject* owned_start = NULL;
- PyObject* owned_stop = NULL;
- if (_py_start) {
- py_start = *_py_start;
- } else {
- if (has_cstart) {
- owned_start = py_start = PyInt_FromSsize_t(cstart);
- if (unlikely(!py_start)) goto bad;
- } else
- py_start = Py_None;
- }
- if (_py_stop) {
- py_stop = *_py_stop;
- } else {
- if (has_cstop) {
- owned_stop = py_stop = PyInt_FromSsize_t(cstop);
- if (unlikely(!py_stop)) {
- Py_XDECREF(owned_start);
- goto bad;
- }
- } else
- py_stop = Py_None;
- }
- py_slice = PySlice_New(py_start, py_stop, Py_None);
- Py_XDECREF(owned_start);
- Py_XDECREF(owned_stop);
- if (unlikely(!py_slice)) goto bad;
- }
-#if CYTHON_COMPILING_IN_CPYTHON
- result = mp->mp_subscript(obj, py_slice);
-#else
- result = PyObject_GetItem(obj, py_slice);
-#endif
- if (!_py_slice) {
- Py_DECREF(py_slice);
- }
- return result;
- }
- PyErr_Format(PyExc_TypeError,
- "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name);
-bad:
- return NULL;
-}
-
-static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) {
- int r;
- if (!j) return -1;
- r = PyObject_SetItem(o, j, v);
- Py_DECREF(j);
- return r;
-}
-static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
- int is_list, int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (is_list || PyList_CheckExact(o)) {
- Py_ssize_t n = (!wraparound) ? i : ((likely(i >= 0)) ? i : i + PyList_GET_SIZE(o));
- if ((!boundscheck) || likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
- PyObject* old = PyList_GET_ITEM(o, n);
- Py_INCREF(v);
- PyList_SET_ITEM(o, n, v);
- Py_DECREF(old);
- return 1;
+ result = PyObject_GetAttr(dict, name);
+ if (!result) {
+ if (dict != __pyx_b) {
+ PyErr_Clear();
+ result = PyObject_GetAttr(__pyx_b, name);
}
- } else {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_ass_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- return -1;
- }
- }
- return m->sq_ass_item(o, i, v);
+ if (!result) {
+ PyErr_SetObject(PyExc_NameError, name);
}
}
-#else
-#if CYTHON_COMPILING_IN_PYPY
- if (is_list || (PySequence_Check(o) && !PyDict_Check(o))) {
-#else
- if (is_list || PySequence_Check(o)) {
-#endif
- return PySequence_SetItem(o, i, v);
- }
-#endif
- return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
-}
-
-#if !CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values) {
- return PyObject_CallMethodObjArgs(sep, __pyx_n_s_join, values, NULL);
+ return result;
}
-#endif
static void __Pyx_RaiseArgtupleInvalid(
const char* func_name,
@@ -7255,7 +6516,7 @@ static void __Pyx_RaiseArgtupleInvalid(
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
+ "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
@@ -7359,52 +6620,20 @@ arg_passed_twice:
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
- "%.200s() keywords must be strings", function_name);
+ "%s() keywords must be strings", function_name);
goto bad;
invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%.200s() got an unexpected keyword argument '%.200s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
- PyObject *result;
-#if CYTHON_COMPILING_IN_CPYTHON
- result = PyDict_GetItem(__pyx_d, name);
- if (likely(result)) {
- Py_INCREF(result);
- } else {
-#else
- result = PyObject_GetItem(__pyx_d, name);
- if (!result) {
- PyErr_Clear();
-#endif
- result = __Pyx_GetBuiltinName(name);
- }
- return result;
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) {
-#ifdef __Pyx_CyFunction_USED
- if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) {
-#else
- if (likely(PyCFunction_Check(func))) {
-#endif
- if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) {
- return __Pyx_PyObject_CallMethO(func, NULL);
- }
- }
- return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL);
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION < 3
+ "%s() got an unexpected keyword argument '%s'",
+ function_name, PyString_AsString(key));
+ #else
+ "%s() got an unexpected keyword argument '%U'",
+ function_name, key);
+ #endif
+bad:
+ return -1;
}
-#endif
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
PyErr_Format(PyExc_ValueError,
@@ -7413,7 +6642,7 @@ static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
- "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack",
+ "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
index, (index == 1) ? "" : "s");
}
@@ -7511,7 +6740,11 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
goto raise_error;
}
}
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyClass_Check(type)) {
+ #else
if (PyType_Check(type)) {
+ #endif
#if CYTHON_COMPILING_IN_PYPY
if (!value) {
Py_INCREF(Py_None);
@@ -7526,13 +6759,26 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
goto raise_error;
}
value = type;
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+ Py_INCREF(type);
+ }
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
+ #else
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ #endif
}
__Pyx_ErrRestore(type, value, tb);
return;
@@ -7542,7 +6788,7 @@ raise_error:
Py_XDECREF(tb);
return;
}
-#else
+#else /* Python 3+ */
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
PyObject* owned_instance = NULL;
if (tb == Py_None) {
@@ -7563,62 +6809,46 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
value = type;
type = (PyObject*) Py_TYPE(value);
} else if (PyExceptionClass_Check(type)) {
- PyObject *instance_class = NULL;
- if (value && PyExceptionInstance_Check(value)) {
- instance_class = (PyObject*) Py_TYPE(value);
- if (instance_class != type) {
- if (PyObject_IsSubclass(instance_class, type)) {
- type = instance_class;
- } else {
- instance_class = NULL;
- }
- }
+ PyObject *args;
+ if (!value)
+ args = PyTuple_New(0);
+ else if (PyTuple_Check(value)) {
+ Py_INCREF(value);
+ args = value;
}
- if (!instance_class) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- } else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyObject_Call(type, args, NULL);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
+ else
+ args = PyTuple_Pack(1, value);
+ if (!args)
+ goto bad;
+ owned_instance = PyEval_CallObject(type, args);
+ Py_DECREF(args);
+ if (!owned_instance)
+ goto bad;
+ value = owned_instance;
+ if (!PyExceptionInstance_Check(value)) {
+ PyErr_Format(PyExc_TypeError,
+ "calling %R should have returned an instance of "
+ "BaseException, not %R",
+ type, Py_TYPE(value));
+ goto bad;
}
} else {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
-#if PY_VERSION_HEX >= 0x03030000
- if (cause) {
-#else
if (cause && cause != Py_None) {
-#endif
PyObject *fixed_cause;
- if (cause == Py_None) {
- fixed_cause = NULL;
- } else if (PyExceptionClass_Check(cause)) {
+ if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
if (fixed_cause == NULL)
goto bad;
- } else if (PyExceptionInstance_Check(cause)) {
+ }
+ else if (PyExceptionInstance_Check(cause)) {
fixed_cause = cause;
Py_INCREF(fixed_cause);
- } else {
+ }
+ else {
PyErr_SetString(PyExc_TypeError,
"exception causes must derive from "
"BaseException");
@@ -7628,13 +6858,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
PyErr_SetObject(type, value);
if (tb) {
-#if CYTHON_COMPILING_IN_PYPY
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyErr_Fetch(tmp_type, tmp_value, tmp_tb);
- Py_INCREF(tb);
- PyErr_Restore(tmp_type, tmp_value, tb);
- Py_XDECREF(tmp_tb);
-#else
PyThreadState *tstate = PyThreadState_GET();
PyObject* tmp_tb = tstate->curexc_traceback;
if (tb != tmp_tb) {
@@ -7642,7 +6865,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
tstate->curexc_traceback = tb;
Py_XDECREF(tmp_tb);
}
-#endif
}
bad:
Py_XDECREF(owned_instance);
@@ -7656,7 +6878,7 @@ static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
if (unlikely(!type)) {
- PyErr_SetString(PyExc_SystemError, "Missing type object");
+ PyErr_Format(PyExc_SystemError, "Missing type object");
return 0;
}
if (likely(PyObject_TypeCheck(obj, type)))
@@ -7669,240 +6891,32 @@ static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) {
PyTypeObject* type = Py_TYPE(obj);
while (type && type->tp_dealloc != current_tp_dealloc)
- type = type->tp_base;
- while (type && type->tp_dealloc == current_tp_dealloc)
- type = type->tp_base;
- if (type)
- type->tp_dealloc(obj);
-}
-
-static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_traverse != current_tp_traverse)
- type = type->tp_base;
- while (type && type->tp_traverse == current_tp_traverse)
- type = type->tp_base;
- if (type && type->tp_traverse)
- return type->tp_traverse(obj, v, a);
- return 0;
-}
-
-static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_clear != current_tp_clear)
- type = type->tp_base;
- while (type && type->tp_clear == current_tp_clear)
- type = type->tp_base;
- if (type && type->tp_clear)
- type->tp_clear(obj);
-}
-
-static void* __Pyx_GetVtable(PyObject *dict) {
- void* ptr;
- PyObject *ob = PyObject_GetItem(dict, __pyx_n_s_pyx_vtable);
- if (!ob)
- goto bad;
-#if PY_VERSION_HEX >= 0x02070000
- ptr = PyCapsule_GetPointer(ob, 0);
-#else
- ptr = PyCObject_AsVoidPtr(ob);
-#endif
- if (!ptr && !PyErr_Occurred())
- PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
- Py_DECREF(ob);
- return ptr;
-bad:
- Py_XDECREF(ob);
- return NULL;
-}
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
- PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
- if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
- PyErr_Format(PyExc_ImportError,
- #if PY_MAJOR_VERSION < 3
- "cannot import name %.230s", PyString_AS_STRING(name));
- #else
- "cannot import name %S", name);
- #endif
- }
- return value;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0,
- 0,
- 0,
- 0,
- 0,
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line,
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- __pyx_d, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
+ type = type->tp_base;
+ while (type && type->tp_dealloc == current_tp_dealloc)
+ type = type->tp_base;
+ if (type)
+ type->tp_dealloc(obj);
+}
+
+static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
+ PyTypeObject* type = Py_TYPE(obj);
+ while (type && type->tp_traverse != current_tp_traverse)
+ type = type->tp_base;
+ while (type && type->tp_traverse == current_tp_traverse)
+ type = type->tp_base;
+ if (type && type->tp_traverse)
+ return type->tp_traverse(obj, v, a);
+ return 0;
+}
+
+static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
+ PyTypeObject* type = Py_TYPE(obj);
+ while (type && type->tp_clear != current_tp_clear)
+ type = type->tp_base;
+ while (type && type->tp_clear == current_tp_clear)
+ type = type->tp_base;
+ if (type && type->tp_clear)
+ type->tp_clear(obj);
}
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
@@ -7912,8 +6926,8 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
PyObject *empty_dict = 0;
PyObject *list;
#if PY_VERSION_HEX < 0x03030000
- PyObject *py_import;
- py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
+ PyObject *py_import = 0;
+ py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
if (!py_import)
goto bad;
#endif
@@ -7931,6 +6945,7 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
empty_dict = PyDict_New();
if (!empty_dict)
goto bad;
+ #if PY_VERSION_HEX >= 0x02050000
{
#if PY_MAJOR_VERSION >= 3
if (level == -1) {
@@ -7952,7 +6967,7 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
PyErr_Clear();
}
}
- level = 0;
+ level = 0; /* try absolute import on failure */
}
#endif
if (!module) {
@@ -7969,6 +6984,14 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
#endif
}
}
+ #else
+ if (level>0) {
+ PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
+ goto bad;
+ }
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, NULL);
+ #endif
bad:
#if PY_VERSION_HEX < 0x03030000
Py_XDECREF(py_import);
@@ -7978,293 +7001,13 @@ bad:
return module;
}
-#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \
- { \
- func_type value = func_value; \
- if (sizeof(target_type) < sizeof(func_type)) { \
- if (unlikely(value != (func_type) (target_type) value)) { \
- func_type zero = 0; \
- if (is_unsigned && unlikely(value < zero)) \
- goto raise_neg_overflow; \
- else \
- goto raise_overflow; \
- } \
- } \
- return (target_type) value; \
- }
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_As_unsigned_int(PyObject *x) {
- const unsigned int neg_one = (unsigned int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(unsigned int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (unsigned int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned int, digit, ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
- if (sizeof(unsigned int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(unsigned int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long long, PyLong_AsUnsignedLongLong(x))
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned int, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(unsigned int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (sizeof(unsigned int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, long, PyLong_AsLong(x))
- } else if (sizeof(unsigned int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, long long, PyLong_AsLongLong(x))
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- unsigned int val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (unsigned int) -1;
- }
- } else {
- unsigned int val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned int) -1;
- val = __Pyx_PyInt_As_unsigned_int(tmp);
- Py_DECREF(tmp);
- return val;
- }
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to unsigned int");
- return (unsigned int) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned int");
- return (unsigned int) -1;
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
+static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
- if (sizeof(int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x))
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x))
- } else if (sizeof(int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x))
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+ PyErr_Format(PyExc_ImportError, "cannot import name %.230s",
+ PyString_AsString(name));
#else
- int val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
+ PyErr_Format(PyExc_ImportError, "cannot import name %S", name);
#endif
- return (int) -1;
- }
- } else {
- int val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (int) -1;
- val = __Pyx_PyInt_As_int(tmp);
- Py_DECREF(tmp);
- return val;
- }
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to int");
- return (int) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(long) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(long) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(long),
- little, !is_unsigned);
- }
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(int) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(int) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(int),
- little, !is_unsigned);
- }
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_int(unsigned int value) {
- const unsigned int neg_one = (unsigned int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(unsigned int) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(unsigned int) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(unsigned int) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(unsigned int) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(unsigned int) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(unsigned int),
- little, !is_unsigned);
- }
}
#if CYTHON_CCOMPLEX
@@ -8507,99 +7250,404 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_int(unsigned int value)
#endif
#endif
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
- const long neg_one = (long) -1, const_zero = 0;
+static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
+ const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned char" :
+ "value too large to convert to unsigned char");
+ }
+ return (unsigned char)-1;
+ }
+ return (unsigned char)val;
+ }
+ return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
+ const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned short" :
+ "value too large to convert to unsigned short");
+ }
+ return (unsigned short)-1;
+ }
+ return (unsigned short)val;
+ }
+ return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
+ const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned int" :
+ "value too large to convert to unsigned int");
+ }
+ return (unsigned int)-1;
+ }
+ return (unsigned int)val;
+ }
+ return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
+ const char neg_one = (char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to char" :
+ "value too large to convert to char");
+ }
+ return (char)-1;
+ }
+ return (char)val;
+ }
+ return (char)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
+ const short neg_one = (short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to short" :
+ "value too large to convert to short");
+ }
+ return (short)-1;
+ }
+ return (short)val;
+ }
+ return (short)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
+ const int neg_one = (int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to int" :
+ "value too large to convert to int");
+ }
+ return (int)-1;
+ }
+ return (int)val;
+ }
+ return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
+ const signed char neg_one = (signed char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed char" :
+ "value too large to convert to signed char");
+ }
+ return (signed char)-1;
+ }
+ return (signed char)val;
+ }
+ return (signed char)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
+ const signed short neg_one = (signed short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed short" :
+ "value too large to convert to signed short");
+ }
+ return (signed short)-1;
+ }
+ return (signed short)val;
+ }
+ return (signed short)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
+ const signed int neg_one = (signed int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed int" :
+ "value too large to convert to signed int");
+ }
+ return (signed int)-1;
+ }
+ return (signed int)val;
+ }
+ return (signed int)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
+ const int neg_one = (int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to int" :
+ "value too large to convert to int");
+ }
+ return (int)-1;
+ }
+ return (int)val;
+ }
+ return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
+ const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return (unsigned long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return (unsigned long)PyLong_AsUnsignedLong(x);
+ } else {
+ return (unsigned long)PyLong_AsLong(x);
+ }
+ } else {
+ unsigned long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned long)-1;
+ val = __Pyx_PyInt_AsUnsignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
+ const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return (unsigned PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
+ } else {
+ return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
+ }
+ } else {
+ unsigned PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
+ const long neg_one = (long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long)-1;
+ }
+ return (long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long)-1;
+ }
+ return (long)PyLong_AsUnsignedLong(x);
+ } else {
+ return (long)PyLong_AsLong(x);
+ }
+ } else {
+ long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (long)-1;
+ val = __Pyx_PyInt_AsLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
+ const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to PY_LONG_LONG");
+ return (PY_LONG_LONG)-1;
+ }
+ return (PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to PY_LONG_LONG");
+ return (PY_LONG_LONG)-1;
+ }
+ return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
+ } else {
+ return (PY_LONG_LONG)PyLong_AsLongLong(x);
+ }
+ } else {
+ PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
+ const signed long neg_one = (signed long)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
+#if PY_VERSION_HEX < 0x03000000
if (likely(PyInt_Check(x))) {
- if (sizeof(long) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (long) val;
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed long");
+ return (signed long)-1;
}
+ return (signed long)val;
} else
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
- if (sizeof(long) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed long");
+ return (signed long)-1;
}
+ return (signed long)PyLong_AsUnsignedLong(x);
} else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x))
- } else if (sizeof(long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x))
- }
+ return (signed long)PyLong_AsLong(x);
}
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- long val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
+ } else {
+ signed long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (signed long)-1;
+ val = __Pyx_PyInt_AsSignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
+ const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed PY_LONG_LONG");
+ return (signed PY_LONG_LONG)-1;
+ }
+ return (signed PY_LONG_LONG)val;
+ } else
#endif
- return (long) -1;
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed PY_LONG_LONG");
+ return (signed PY_LONG_LONG)-1;
+ }
+ return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
+ } else {
+ return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
}
} else {
- long val;
+ signed PY_LONG_LONG val;
PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long) -1;
- val = __Pyx_PyInt_As_long(tmp);
+ if (!tmp) return (signed PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsSignedLongLong(tmp);
Py_DECREF(tmp);
return val;
}
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to long");
- return (long) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
}
static int __Pyx_check_binary_version(void) {
@@ -8612,7 +7660,11 @@ static int __Pyx_check_binary_version(void) {
"compiletime version %s of module '%.100s' "
"does not match runtime version %s",
ctversion, __Pyx_MODULE_NAME, rtversion);
+ #if PY_VERSION_HEX < 0x02050000
+ return PyErr_Warn(NULL, message);
+ #else
return PyErr_WarnEx(NULL, message, 1);
+ #endif
}
return 0;
}
@@ -8662,7 +7714,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
goto bad;
if (!PyType_Check(result)) {
PyErr_Format(PyExc_TypeError,
- "%.200s.%.200s is not a type object",
+ "%s.%s is not a type object",
module_name, class_name);
goto bad;
}
@@ -8682,11 +7734,15 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyErr_Warn(NULL, warning) < 0) goto bad;
+ #else
if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
+ #endif
}
else if ((size_t)basicsize != size) {
PyErr_Format(PyExc_ValueError,
- "%.200s.%.200s has the wrong size, try recompiling",
+ "%s.%s has the wrong size, try recompiling",
module_name, class_name);
goto bad;
}
@@ -8698,6 +7754,204 @@ bad:
}
#endif
+static void* __Pyx_GetVtable(PyObject *dict) {
+ void* ptr;
+ PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
+ if (!ob)
+ goto bad;
+#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
+ ptr = PyCapsule_GetPointer(ob, 0);
+#else
+ ptr = PyCObject_AsVoidPtr(ob);
+#endif
+ if (!ptr && !PyErr_Occurred())
+ PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
+ Py_DECREF(ob);
+ return ptr;
+bad:
+ Py_XDECREF(ob);
+ return NULL;
+}
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
+#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
+ PyObject *ob = PyCapsule_New(vtable, 0, 0);
+#else
+ PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
+#endif
+ if (!ob)
+ goto bad;
+ if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
+ goto bad;
+ Py_DECREF(ob);
+ return 0;
+bad:
+ Py_XDECREF(ob);
+ return -1;
+}
+
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
+ int start = 0, mid = 0, end = count - 1;
+ if (end >= 0 && code_line > entries[end].code_line) {
+ return count;
+ }
+ while (start < end) {
+ mid = (start + end) / 2;
+ if (code_line < entries[mid].code_line) {
+ end = mid;
+ } else if (code_line > entries[mid].code_line) {
+ start = mid + 1;
+ } else {
+ return mid;
+ }
+ }
+ if (code_line <= entries[mid].code_line) {
+ return mid;
+ } else {
+ return mid + 1;
+ }
+}
+static PyCodeObject *__pyx_find_code_object(int code_line) {
+ PyCodeObject* code_object;
+ int pos;
+ if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
+ return NULL;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
+ return NULL;
+ }
+ code_object = __pyx_code_cache.entries[pos].code_object;
+ Py_INCREF(code_object);
+ return code_object;
+}
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
+ int pos, i;
+ __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
+ if (unlikely(!code_line)) {
+ return;
+ }
+ if (unlikely(!entries)) {
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (likely(entries)) {
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = 64;
+ __pyx_code_cache.count = 1;
+ entries[0].code_line = code_line;
+ entries[0].code_object = code_object;
+ Py_INCREF(code_object);
+ }
+ return;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
+ PyCodeObject* tmp = entries[pos].code_object;
+ entries[pos].code_object = code_object;
+ Py_DECREF(tmp);
+ return;
+ }
+ if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
+ int new_max = __pyx_code_cache.max_count + 64;
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
+ __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (unlikely(!entries)) {
+ return;
+ }
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = new_max;
+ }
+ for (i=__pyx_code_cache.count; i>pos; i--) {
+ entries[i] = entries[i-1];
+ }
+ entries[pos].code_line = code_line;
+ entries[pos].code_object = code_object;
+ __pyx_code_cache.count++;
+ Py_INCREF(code_object);
+}
+
+#include "compile.h"
+#include "frameobject.h"
+#include "traceback.h"
+static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
+ const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
+ PyObject *py_srcfile = 0;
+ PyObject *py_funcname = 0;
+ #if PY_MAJOR_VERSION < 3
+ py_srcfile = PyString_FromString(filename);
+ #else
+ py_srcfile = PyUnicode_FromString(filename);
+ #endif
+ if (!py_srcfile) goto bad;
+ if (c_line) {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ #else
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ #endif
+ }
+ else {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromString(funcname);
+ #else
+ py_funcname = PyUnicode_FromString(funcname);
+ #endif
+ }
+ if (!py_funcname) goto bad;
+ py_code = __Pyx_PyCode_New(
+ 0, /*int argcount,*/
+ 0, /*int kwonlyargcount,*/
+ 0, /*int nlocals,*/
+ 0, /*int stacksize,*/
+ 0, /*int flags,*/
+ __pyx_empty_bytes, /*PyObject *code,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
+ py_srcfile, /*PyObject *filename,*/
+ py_funcname, /*PyObject *name,*/
+ py_line, /*int firstlineno,*/
+ __pyx_empty_bytes /*PyObject *lnotab*/
+ );
+ Py_DECREF(py_srcfile);
+ Py_DECREF(py_funcname);
+ return py_code;
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ return NULL;
+}
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
+ PyObject *py_globals = 0;
+ PyFrameObject *py_frame = 0;
+ py_code = __pyx_find_code_object(c_line ? c_line : py_line);
+ if (!py_code) {
+ py_code = __Pyx_CreateCodeObjectForTraceback(
+ funcname, c_line, py_line, filename);
+ if (!py_code) goto bad;
+ __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
+ }
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
+ py_frame = PyFrame_New(
+ PyThreadState_GET(), /*PyThreadState *tstate,*/
+ py_code, /*PyCodeObject *code,*/
+ py_globals, /*PyObject *globals,*/
+ 0 /*PyObject *locals*/
+ );
+ if (!py_frame) goto bad;
+ py_frame->f_lineno = py_line;
+ PyTraceBack_Here(py_frame);
+bad:
+ Py_XDECREF(py_code);
+ Py_XDECREF(py_frame);
+}
+
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
while (t->p) {
#if PY_MAJOR_VERSION < 3
@@ -8708,7 +7962,7 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
} else {
*t->p = PyString_FromStringAndSize(t->s, t->n - 1);
}
- #else
+ #else /* Python 3+ has unicode identifiers */
if (t->is_unicode | t->is_str) {
if (t->intern) {
*t->p = PyUnicode_InternFromString(t->s);
@@ -8728,71 +7982,6 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
return 0;
}
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
- return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
- Py_ssize_t ignore;
- return __Pyx_PyObject_AsStringAndSize(o, &ignore);
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
- if (
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- __Pyx_sys_getdefaultencoding_not_ascii &&
-#endif
- PyUnicode_Check(o)) {
-#if PY_VERSION_HEX < 0x03030000
- char* defenc_c;
- PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
- if (!defenc) return NULL;
- defenc_c = PyBytes_AS_STRING(defenc);
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- {
- char* end = defenc_c + PyBytes_GET_SIZE(defenc);
- char* c;
- for (c = defenc_c; c < end; c++) {
- if ((unsigned char) (*c) >= 128) {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
- }
- }
-#endif
- *length = PyBytes_GET_SIZE(defenc);
- return defenc_c;
-#else
- if (__Pyx_PyUnicode_READY(o) == -1) return NULL;
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- if (PyUnicode_IS_ASCII(o)) {
- *length = PyUnicode_GET_LENGTH(o);
- return PyUnicode_AsUTF8(o);
- } else {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
-#else
- return PyUnicode_AsUTF8AndSize(o, length);
-#endif
-#endif
- } else
-#endif
-#if !CYTHON_COMPILING_IN_PYPY
- if (PyByteArray_Check(o)) {
- *length = PyByteArray_GET_SIZE(o);
- return PyByteArray_AS_STRING(o);
- } else
-#endif
- {
- char* result;
- int r = PyBytes_AsStringAndSize(o, &result, length);
- if (unlikely(r < 0)) {
- return NULL;
- } else {
- return result;
- }
- }
-}
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
int is_true = x == Py_True;
if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
@@ -8802,14 +7991,14 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
PyNumberMethods *m;
const char *name = NULL;
PyObject *res = NULL;
-#if PY_MAJOR_VERSION < 3
+#if PY_VERSION_HEX < 0x03000000
if (PyInt_Check(x) || PyLong_Check(x))
#else
if (PyLong_Check(x))
#endif
return Py_INCREF(x), x;
m = Py_TYPE(x)->tp_as_number;
-#if PY_MAJOR_VERSION < 3
+#if PY_VERSION_HEX < 0x03000000
if (m && m->nb_int) {
name = "int";
res = PyNumber_Int(x);
@@ -8825,13 +8014,13 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
}
#endif
if (res) {
-#if PY_MAJOR_VERSION < 3
+#if PY_VERSION_HEX < 0x03000000
if (!PyInt_Check(res) && !PyLong_Check(res)) {
#else
if (!PyLong_Check(res)) {
#endif
PyErr_Format(PyExc_TypeError,
- "__%.4s__ returned non-%.4s (type %.200s)",
+ "__%s__ returned non-%s (type %.200s)",
name, name, Py_TYPE(res)->tp_name);
Py_DECREF(res);
return NULL;
@@ -8845,31 +8034,35 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
}
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_ssize_t ival;
- PyObject *x;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_CheckExact(b)))
- return PyInt_AS_LONG(b);
-#endif
- if (likely(PyLong_CheckExact(b))) {
- #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(b)) {
- case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0];
- case 0: return 0;
- case 1: return ((PyLongObject*)b)->ob_digit[0];
- }
- #endif
- #endif
- return PyLong_AsSsize_t(b);
- }
- x = PyNumber_Index(b);
+ PyObject* x = PyNumber_Index(b);
if (!x) return -1;
ival = PyInt_AsSsize_t(x);
Py_DECREF(x);
return ival;
}
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
- return PyInt_FromSize_t(ival);
+#if PY_VERSION_HEX < 0x02050000
+ if (ival <= LONG_MAX)
+ return PyInt_FromLong((long)ival);
+ else {
+ unsigned char *bytes = (unsigned char *) &ival;
+ int one = 1; int little = (int)*(unsigned char*)&one;
+ return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
+ }
+#else
+ return PyInt_FromSize_t(ival);
+#endif
+}
+static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
+ unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
+ if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
+ return (size_t)-1;
+ } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to size_t");
+ return (size_t)-1;
+ }
+ return (size_t)val;
}
diff --git a/lib/bx/bbi/bigbed_file.pyx b/lib/bx/bbi/bigbed_file.pyx
index 9674770..420d934 100644
--- a/lib/bx/bbi/bigbed_file.pyx
+++ b/lib/bx/bbi/bigbed_file.pyx
@@ -1,12 +1,11 @@
-#cython: profile=False
"""
BigBed file.
"""
from bbi_file cimport *
from cirtree_file cimport CIRTreeFile
-import numpy as np
-cimport numpy as np
+import numpy
+cimport numpy
from types cimport *
from bx.intervals.io import GenomicInterval
from bx.misc.binary_file import BinaryFileReader
@@ -18,29 +17,6 @@ DEF big_bed_sig = 0x8789F2EB
cdef inline int range_intersection( int start1, int end1, int start2, int end2 ):
return min( end1, end2 ) - max( start1, start2 )
-cdef str read_c_string(fh):
- """
- Read a zero terminated (C style) string
- Read in chunks of 8 bytes to minimize calls to read.
- If we read to much then seek back to the correct place.
- """
- chunksize = 8
- read = [fh.read(chunksize)]
- while not '\0' in read[-1]:
- r = fh.read(chunksize)
- read.append(r)
- if len(r) != chunksize:
- break
-
- pos = read[-1].find('\0')
- l = len(read[-1])
- if l == chunksize:
- fh.seek(-(chunksize - pos) + 1, 1)
- if l != chunksize:
- read[-1] = read[-1][:pos]
-
- return "".join(read) if len(read) > 1 else read[0]
-
cdef class BigBedBlockHandler( BlockHandler ):
"""
BlockHandler that parses the block into a series of BED records
@@ -63,13 +39,15 @@ cdef class BigBedBlockHandler( BlockHandler ):
block_reader = BinaryFileReader( string_io, is_little_endian=bbi_file.reader.is_little_endian )
length = len( block_data )
while string_io.tell() < length:
- chrom_id, s, e = block_reader.read_and_unpack("LLL", 12)
- rest = read_c_string(string_io)
-
+ chrom_id = block_reader.read_uint32()
+ s = block_reader.read_uint32()
+ e = block_reader.read_uint32()
+ rest = block_reader.read_c_string()
if chrom_id != self.chrom_id:
continue
if s < self.end and e > self.start:
self.handle_interval_value( s, e, rest )
+
cdef handle_interval_value( self, bits32 s, bits32 e, str rest ):
pass
@@ -83,9 +61,9 @@ cdef class SummarizingBlockHandler( BigBedBlockHandler ):
# What we will load into
self.sd = SummarizedData( start, end, summary_size )
for i in range(summary_size):
- self.sd.min_val[i] = +np.inf
+ self.sd.min_val[i] = +numpy.inf
for i in range(summary_size):
- self.sd.max_val[i] = -np.inf
+ self.sd.max_val[i] = -numpy.inf
cdef handle_interval_value( self, bits32 s, bits32 e, str rest ):
# FIXME: Does this really obvious thing actually do what we want?
@@ -117,7 +95,9 @@ cdef class BigBedFile( BBIFile ):
"""
v = SummarizingBlockHandler( chrom_id, start, end, summary_size )
self.visit_blocks_in_region( chrom_id, start, end, v )
- np.round(v.sd.valid_count, out=v.sd.valid_count)
+ # Round valid count, in place
+ for i from 0 <= i < summary_size:
+ v.sd.valid_count[i] = round( v.sd.valid_count[i] )
return v.sd
cpdef get( self, char * chrom, bits32 start, bits32 end ):
diff --git a/lib/bx/bbi/bigwig_file.c b/lib/bx/bbi/bigwig_file.c
index 832e80a..1fd18d3 100644
--- a/lib/bx/bbi/bigwig_file.c
+++ b/lib/bx/bbi/bigwig_file.c
@@ -1,26 +1,13 @@
-/* Generated by Cython 0.22 */
+/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
#define PY_SSIZE_T_CLEAN
-#ifndef CYTHON_USE_PYLONG_INTERNALS
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#else
-#include "pyconfig.h"
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 1
-#else
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#endif
-#endif
-#endif
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000)
- #error Cython requires Python 2.6+ or Python 3.2+.
+#elif PY_VERSION_HEX < 0x02040000
+ #error Cython requires Python 2.4+.
#else
-#define CYTHON_ABI "0_22"
-#include <stddef.h>
+#include <stddef.h> /* For offsetof */
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
@@ -54,29 +41,80 @@
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
-#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag)
-#define Py_OptimizeFlag 0
+#if PY_VERSION_HEX < 0x02050000
+ typedef int Py_ssize_t;
+ #define PY_SSIZE_T_MAX INT_MAX
+ #define PY_SSIZE_T_MIN INT_MIN
+ #define PY_FORMAT_SIZE_T ""
+ #define CYTHON_FORMAT_SSIZE_T ""
+ #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
+ #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
+ #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
+ (PyErr_Format(PyExc_TypeError, \
+ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
+ (PyObject*)0))
+ #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
+ !PyComplex_Check(o))
+ #define PyIndex_Check __Pyx_PyIndex_Check
+ #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
+ #define __PYX_BUILD_PY_SSIZE_T "i"
+#else
+ #define __PYX_BUILD_PY_SSIZE_T "n"
+ #define CYTHON_FORMAT_SSIZE_T "z"
+ #define __Pyx_PyIndex_Check PyIndex_Check
+#endif
+#if PY_VERSION_HEX < 0x02060000
+ #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
+ #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
+ #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
+ #define PyVarObject_HEAD_INIT(type, size) \
+ PyObject_HEAD_INIT(type) size,
+ #define PyType_Modified(t)
+ typedef struct {
+ void *buf;
+ PyObject *obj;
+ Py_ssize_t len;
+ Py_ssize_t itemsize;
+ int readonly;
+ int ndim;
+ char *format;
+ Py_ssize_t *shape;
+ Py_ssize_t *strides;
+ Py_ssize_t *suboffsets;
+ void *internal;
+ } Py_buffer;
+ #define PyBUF_SIMPLE 0
+ #define PyBUF_WRITABLE 0x0001
+ #define PyBUF_FORMAT 0x0004
+ #define PyBUF_ND 0x0008
+ #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
+ #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
+ #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
+ #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
+ #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
+ #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
+ #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
+ typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
+ typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
-#define __PYX_BUILD_PY_SSIZE_T "n"
-#define CYTHON_FORMAT_SSIZE_T "z"
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
- #define __Pyx_DefaultClassType PyClass_Type
+ PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
- #define __Pyx_DefaultClassType PyType_Type
+#endif
+#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
+ #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
- #define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE)
- #define Py_TPFLAGS_HAVE_FINALIZE 0
+#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
+ #define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
#define CYTHON_PEP393_ENABLED 1
@@ -84,34 +122,13 @@
0 : _PyUnicode_Ready((PyObject *)(op)))
#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u)
- #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
#define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
#else
#define CYTHON_PEP393_ENABLED 0
#define __Pyx_PyUnicode_READY(op) (0)
#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE))
- #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
- #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if CYTHON_COMPILING_IN_PYPY
- #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b)
- #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b)
- #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s)
-#else
- #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b)
- #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \
- PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
- #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s)
-#endif
-#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
-#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b)
-#else
- #define __Pyx_PyString_Format(a, b) PyString_Format(a, b)
+ #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#endif
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
@@ -120,12 +137,27 @@
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
- #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
-#else
- #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj))
- #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
+#if PY_VERSION_HEX < 0x02060000
+ #define PyBytesObject PyStringObject
+ #define PyBytes_Type PyString_Type
+ #define PyBytes_Check PyString_Check
+ #define PyBytes_CheckExact PyString_CheckExact
+ #define PyBytes_FromString PyString_FromString
+ #define PyBytes_FromStringAndSize PyString_FromStringAndSize
+ #define PyBytes_FromFormat PyString_FromFormat
+ #define PyBytes_DecodeEscape PyString_DecodeEscape
+ #define PyBytes_AsString PyString_AsString
+ #define PyBytes_AsStringAndSize PyString_AsStringAndSize
+ #define PyBytes_Size PyString_Size
+ #define PyBytes_AS_STRING PyString_AS_STRING
+ #define PyBytes_GET_SIZE PyString_GET_SIZE
+ #define PyBytes_Repr PyString_Repr
+ #define PyBytes_Concat PyString_Concat
+ #define PyBytes_ConcatAndDel PyString_ConcatAndDel
+#endif
+#if PY_VERSION_HEX < 0x02060000
+ #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
+ #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#endif
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
@@ -146,17 +178,11 @@
#define PyInt_AsSsize_t PyLong_AsSsize_t
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
- #define PyNumber_Int PyNumber_Long
#endif
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
-#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY
- #ifndef PyUnicode_InternFromString
- #define PyUnicode_InternFromString(s) PyUnicode_FromString(s)
- #endif
-#endif
-#if PY_VERSION_HEX < 0x030200A4
+#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
#define __Pyx_PyInt_AsHash_t PyInt_AsLong
@@ -164,61 +190,42 @@
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
+#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
+ #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
+ #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
#else
- #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
-#endif
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
- #elif defined(_MSC_VER)
- #define CYTHON_INLINE __inline
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
+ #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
+ #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
-#ifndef CYTHON_RESTRICT
- #if defined(__GNUC__)
- #define CYTHON_RESTRICT __restrict__
- #elif defined(_MSC_VER) && _MSC_VER >= 1400
- #define CYTHON_RESTRICT __restrict
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_RESTRICT restrict
- #else
- #define CYTHON_RESTRICT
- #endif
+#if PY_MAJOR_VERSION >= 3
+ #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
-#ifdef NAN
-#define __PYX_NAN() ((float) NAN)
+#if PY_VERSION_HEX < 0x02050000
+ #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
+ #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
+ #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
#else
-static CYTHON_INLINE float __PYX_NAN() {
- /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
- a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
- a quiet NaN. */
- float value;
- memset(&value, 0xFF, sizeof(value));
- return value;
-}
+ #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
+ #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
+ #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
-#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None)
-#ifdef __cplusplus
-template<typename T>
-void __Pyx_call_destructor(T* x) {
- x->~T();
-}
-template<typename T>
-class __Pyx_FakeReference {
- public:
- __Pyx_FakeReference() : ptr(NULL) { }
- __Pyx_FakeReference(T& ref) : ptr(&ref) { }
- T *operator->() { return ptr; }
- operator T&() { return *ptr; }
- private:
- T *ptr;
-};
+#if PY_VERSION_HEX < 0x02050000
+ #define __Pyx_NAMESTR(n) ((char *)(n))
+ #define __Pyx_DOCSTR(n) ((char *)(n))
+#else
+ #define __Pyx_NAMESTR(n) (n)
+ #define __Pyx_DOCSTR(n) (n)
#endif
@@ -257,6 +264,17 @@ class __Pyx_FakeReference {
#define CYTHON_WITHOUT_ASSERTIONS
#endif
+#ifndef CYTHON_INLINE
+ #if defined(__GNUC__)
+ #define CYTHON_INLINE __inline__
+ #elif defined(_MSC_VER)
+ #define CYTHON_INLINE __inline
+ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define CYTHON_INLINE inline
+ #else
+ #define CYTHON_INLINE
+ #endif
+#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
@@ -270,157 +288,40 @@ class __Pyx_FakeReference {
# define CYTHON_UNUSED
# endif
#endif
-typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
- const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
-
-#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
-#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
-#define __PYX_DEFAULT_STRING_ENCODING ""
-#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
-#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \
- (sizeof(type) < sizeof(Py_ssize_t)) || \
- (sizeof(type) > sizeof(Py_ssize_t) && \
- likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX) && \
- (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \
- v == (type)PY_SSIZE_T_MIN))) || \
- (sizeof(type) == sizeof(Py_ssize_t) && \
- (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX))) )
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
-#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
-#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
-#define __Pyx_PyBytes_FromString PyBytes_FromString
-#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#else
- #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
-#endif
-#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s)
-#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s)
-#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s)
-#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s)
-#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
-#if PY_MAJOR_VERSION < 3
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
-{
- const Py_UNICODE *u_end = u;
- while (*u_end++) ;
- return (size_t)(u_end - u - 1);
-}
-#else
-#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
-#endif
-#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
-#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
-#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
+typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
+
+#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
+#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
+static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
#else
#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
-static int __Pyx_sys_getdefaultencoding_not_ascii;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys;
- PyObject* default_encoding = NULL;
- PyObject* ascii_chars_u = NULL;
- PyObject* ascii_chars_b = NULL;
- const char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (!sys) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
- Py_DECREF(sys);
- if (!default_encoding) goto bad;
- default_encoding_c = PyBytes_AsString(default_encoding);
- if (!default_encoding_c) goto bad;
- if (strcmp(default_encoding_c, "ascii") == 0) {
- __Pyx_sys_getdefaultencoding_not_ascii = 0;
- } else {
- char ascii_chars[128];
- int c;
- for (c = 0; c < 128; c++) {
- ascii_chars[c] = c;
- }
- __Pyx_sys_getdefaultencoding_not_ascii = 1;
- ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
- if (!ascii_chars_u) goto bad;
- ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
- if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
- PyErr_Format(
- PyExc_ValueError,
- "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
- default_encoding_c);
- goto bad;
- }
- Py_DECREF(ascii_chars_u);
- Py_DECREF(ascii_chars_b);
- }
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return -1;
-}
-#endif
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
-#else
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
-static char* __PYX_DEFAULT_STRING_ENCODING;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys;
- PyObject* default_encoding = NULL;
- char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (!sys) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- Py_DECREF(sys);
- if (!default_encoding) goto bad;
- default_encoding_c = PyBytes_AsString(default_encoding);
- if (!default_encoding_c) goto bad;
- __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
- if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
- strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(default_encoding);
- return -1;
-}
-#endif
-#endif
-/* Test for GCC > 2.95 */
-#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))
- #define likely(x) __builtin_expect(!!(x), 1)
- #define unlikely(x) __builtin_expect(!!(x), 0)
-#else /* !__GNUC__ or GCC < 2.95 */
+#ifdef __GNUC__
+ /* Test for GCC > 2.95 */
+ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
+ #define likely(x) __builtin_expect(!!(x), 1)
+ #define unlikely(x) __builtin_expect(!!(x), 0)
+ #else /* __GNUC__ > 2 ... */
+ #define likely(x) (x)
+ #define unlikely(x) (x)
+ #endif /* __GNUC__ > 2 ... */
+#else /* __GNUC__ */
#define likely(x) (x)
#define unlikely(x) (x)
#endif /* __GNUC__ */
-
+
static PyObject *__pyx_m;
-static PyObject *__pyx_d;
static PyObject *__pyx_b;
static PyObject *__pyx_empty_tuple;
static PyObject *__pyx_empty_bytes;
@@ -452,13 +353,48 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
- "bx/bbi/bigwig_file.pyx",
- "__init__.pxd",
- "bx/bbi/bpt_file.pxd",
- "bx/bbi/cirtree_file.pxd",
+ "bigwig_file.pyx",
+ "numpy.pxd",
+ "bpt_file.pxd",
+ "cirtree_file.pxd",
"type.pxd",
- "bx/bbi/bbi_file.pxd",
+ "bbi_file.pxd",
};
+#define IS_UNSIGNED(type) (((type) -1) > 0)
+struct __Pyx_StructField_;
+#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0)
+typedef struct {
+ const char* name; /* for error messages only */
+ struct __Pyx_StructField_* fields;
+ size_t size; /* sizeof(type) */
+ size_t arraysize[8]; /* length of array in each dimension */
+ int ndim;
+ char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject, c_H_ar */
+ char is_unsigned;
+ int flags;
+} __Pyx_TypeInfo;
+typedef struct __Pyx_StructField_ {
+ __Pyx_TypeInfo* type;
+ const char* name;
+ size_t offset;
+} __Pyx_StructField;
+typedef struct {
+ __Pyx_StructField* field;
+ size_t parent_offset;
+} __Pyx_BufFmt_StackElem;
+typedef struct {
+ __Pyx_StructField root;
+ __Pyx_BufFmt_StackElem* head;
+ size_t fmt_offset;
+ size_t new_count, enc_count;
+ size_t struct_alignment;
+ int is_complex;
+ char enc_type;
+ char new_packmode;
+ char enc_packmode;
+ char is_valid_array;
+} __Pyx_BufFmt_Context;
+
/* "types.pxd":1
* ctypedef unsigned char UBYTE # <<<<<<<<<<<<<<
@@ -546,7 +482,7 @@ typedef int __pyx_t_2bx_3bbi_5types_signed32;
*/
typedef int __pyx_t_2bx_3bbi_5types_boolean;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":726
+/* "numpy.pxd":723
* # in Cython to enable them only on the right systems.
*
* ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
@@ -555,7 +491,7 @@ typedef int __pyx_t_2bx_3bbi_5types_boolean;
*/
typedef npy_int8 __pyx_t_5numpy_int8_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":727
+/* "numpy.pxd":724
*
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
@@ -564,7 +500,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t;
*/
typedef npy_int16 __pyx_t_5numpy_int16_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":728
+/* "numpy.pxd":725
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
@@ -573,7 +509,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t;
*/
typedef npy_int32 __pyx_t_5numpy_int32_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":729
+/* "numpy.pxd":726
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
@@ -582,7 +518,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t;
*/
typedef npy_int64 __pyx_t_5numpy_int64_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":733
+/* "numpy.pxd":730
* #ctypedef npy_int128 int128_t
*
* ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
@@ -591,7 +527,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t;
*/
typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":734
+/* "numpy.pxd":731
*
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
@@ -600,7 +536,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t;
*/
typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":735
+/* "numpy.pxd":732
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
@@ -609,7 +545,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t;
*/
typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":736
+/* "numpy.pxd":733
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
@@ -618,7 +554,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t;
*/
typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":740
+/* "numpy.pxd":737
* #ctypedef npy_uint128 uint128_t
*
* ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
@@ -627,7 +563,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t;
*/
typedef npy_float32 __pyx_t_5numpy_float32_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":741
+/* "numpy.pxd":738
*
* ctypedef npy_float32 float32_t
* ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
@@ -636,7 +572,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t;
*/
typedef npy_float64 __pyx_t_5numpy_float64_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":750
+/* "numpy.pxd":747
* # The int types are mapped a bit surprising --
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t # <<<<<<<<<<<<<<
@@ -645,7 +581,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t;
*/
typedef npy_long __pyx_t_5numpy_int_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":751
+/* "numpy.pxd":748
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
@@ -654,7 +590,7 @@ typedef npy_long __pyx_t_5numpy_int_t;
*/
typedef npy_longlong __pyx_t_5numpy_long_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":752
+/* "numpy.pxd":749
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
@@ -663,7 +599,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t;
*/
typedef npy_longlong __pyx_t_5numpy_longlong_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":754
+/* "numpy.pxd":751
* ctypedef npy_longlong longlong_t
*
* ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
@@ -672,7 +608,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t;
*/
typedef npy_ulong __pyx_t_5numpy_uint_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":755
+/* "numpy.pxd":752
*
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
@@ -681,7 +617,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":756
+/* "numpy.pxd":753
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
@@ -690,7 +626,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":758
+/* "numpy.pxd":755
* ctypedef npy_ulonglong ulonglong_t
*
* ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
@@ -699,7 +635,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
*/
typedef npy_intp __pyx_t_5numpy_intp_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":759
+/* "numpy.pxd":756
*
* ctypedef npy_intp intp_t
* ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
@@ -708,7 +644,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t;
*/
typedef npy_uintp __pyx_t_5numpy_uintp_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":761
+/* "numpy.pxd":758
* ctypedef npy_uintp uintp_t
*
* ctypedef npy_double float_t # <<<<<<<<<<<<<<
@@ -717,7 +653,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t;
*/
typedef npy_double __pyx_t_5numpy_float_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":762
+/* "numpy.pxd":759
*
* ctypedef npy_double float_t
* ctypedef npy_double double_t # <<<<<<<<<<<<<<
@@ -726,7 +662,7 @@ typedef npy_double __pyx_t_5numpy_float_t;
*/
typedef npy_double __pyx_t_5numpy_double_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":763
+/* "numpy.pxd":760
* ctypedef npy_double float_t
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
@@ -756,19 +692,19 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
/*--- Type declarations ---*/
-struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile;
-struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile;
struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock;
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData;
-struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler;
struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile;
+struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile;
+struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler;
struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler;
-struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler;
struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler;
struct __pyx_obj_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler;
-struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile;
+struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile;
+struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData;
+struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler;
+struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":765
+/* "numpy.pxd":762
* ctypedef npy_longdouble longdouble_t
*
* ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
@@ -777,7 +713,7 @@ struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile;
*/
typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":766
+/* "numpy.pxd":763
*
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
@@ -786,7 +722,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
*/
typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":767
+/* "numpy.pxd":764
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
@@ -795,7 +731,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
*/
typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-/* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":769
+/* "numpy.pxd":766
* ctypedef npy_clongdouble clongdouble_t
*
* ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
@@ -804,50 +740,6 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
*/
typedef npy_cdouble __pyx_t_5numpy_complex_t;
-/* "bpt_file.pxd":5
- * from types cimport *
- *
- * cdef class BPTFile: # <<<<<<<<<<<<<<
- * """
- * On disk B+ tree compatible with Jim Kent's bPlusTree.c
- */
-struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile {
- PyObject_HEAD
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- __pyx_t_2bx_3bbi_5types_bits32 block_size;
- __pyx_t_2bx_3bbi_5types_bits32 key_size;
- __pyx_t_2bx_3bbi_5types_bits32 value_size;
- __pyx_t_2bx_3bbi_5types_bits64 item_count;
- __pyx_t_2bx_3bbi_5types_bits64 root_offset;
-};
-
-
-/* "cirtree_file.pxd":3
- * from types cimport *
- *
- * cdef class CIRTreeFile: # <<<<<<<<<<<<<<
- * cdef object file
- * cdef object reader
- */
-struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile {
- PyObject_HEAD
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- __pyx_t_2bx_3bbi_5types_bits64 root_offset;
- __pyx_t_2bx_3bbi_5types_bits32 block_size;
- __pyx_t_2bx_3bbi_5types_bits64 item_count;
- __pyx_t_2bx_3bbi_5types_bits32 start_chrom_ix;
- __pyx_t_2bx_3bbi_5types_bits32 start_base;
- __pyx_t_2bx_3bbi_5types_bits32 end_chrom_ix;
- __pyx_t_2bx_3bbi_5types_bits32 end_base;
- __pyx_t_2bx_3bbi_5types_bits64 file_size;
- __pyx_t_2bx_3bbi_5types_bits32 items_per_slot;
-};
-
-
/* "bbi_file.pxd":8
* cimport numpy
*
@@ -868,40 +760,6 @@ struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock {
};
-/* "bbi_file.pxd":21
- * cdef public double sum_squares
- *
- * cdef class SummarizedData: # <<<<<<<<<<<<<<
- * """
- * The result of using SummaryBlocks read from the file to produce a
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtab;
- __pyx_t_2bx_3bbi_5types_bits32 start;
- __pyx_t_2bx_3bbi_5types_bits32 end;
- int size;
- PyArrayObject *valid_count;
- PyArrayObject *min_val;
- PyArrayObject *max_val;
- PyArrayObject *sum_data;
- PyArrayObject *sum_squares;
-};
-
-
-/* "bbi_file.pxd":39
- * cdef class BBIFile
- *
- * cdef class BlockHandler: # <<<<<<<<<<<<<<
- * """
- * Callback for `BBIFile.visit_blocks_in_region`
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtab;
-};
-
-
/* "bbi_file.pxd":37
* cdef accumulate_interval_value( self, bits32 s, bits32 e, float val )
*
@@ -931,34 +789,46 @@ struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile {
};
-/* "bx/bbi/bigwig_file.pyx":28
- * return [l[i:i + n] for i in range(0, len(l), n)]
+/* "bx/bbi/bigwig_file.pyx":122
+ * array[ i ] = val
*
- * cdef class BigWigBlockHandler( BlockHandler ): # <<<<<<<<<<<<<<
+ * cdef class BigWigFile( BBIFile ): # <<<<<<<<<<<<<<
* """
- * BlockHandler that parses the block into a series of wiggle records, and calls `handle_interval_value` for each.
+ * A "big binary indexed" file whose raw data is in wiggle format.
*/
-struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler {
- struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler __pyx_base;
- __pyx_t_2bx_3bbi_5types_bits32 start;
- __pyx_t_2bx_3bbi_5types_bits32 end;
+struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile {
+ struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile __pyx_base;
};
-/* "bx/bbi/bigwig_file.pyx":74
- * pass
+/* "bbi_file.pxd":39
+ * cdef class BBIFile
*
- * cdef class SummarizingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
+ * cdef class BlockHandler: # <<<<<<<<<<<<<<
* """
- * Accumulates intervals into a SummarizedData
+ * Callback for `BBIFile.visit_blocks_in_region`
*/
-struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler {
- struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler __pyx_base;
- struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *sd;
+struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtab;
+};
+
+
+/* "bx/bbi/bigwig_file.pyx":23
+ * return min( end1, end2 ) - max( start1, start2 )
+ *
+ * cdef class BigWigBlockHandler( BlockHandler ): # <<<<<<<<<<<<<<
+ * """
+ * BlockHandler that parses the block into a series of wiggle records, and calls `handle_interval_value` for each.
+ */
+struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler {
+ struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler __pyx_base;
+ __pyx_t_2bx_3bbi_5types_bits32 start;
+ __pyx_t_2bx_3bbi_5types_bits32 end;
};
-/* "bx/bbi/bigwig_file.pyx":89
+/* "bx/bbi/bigwig_file.pyx":93
* self.sd.accumulate_interval_value( s, e, val )
*
* cdef class IntervalAccumulatingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
@@ -971,7 +841,7 @@ struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler {
};
-/* "bx/bbi/bigwig_file.pyx":101
+/* "bx/bbi/bigwig_file.pyx":105
* self.intervals.append( ( s, e, val ) )
*
* cdef class ArrayAccumulatingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
@@ -984,19 +854,30 @@ struct __pyx_obj_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler {
};
-/* "bx/bbi/bigwig_file.pyx":116
- * self.array[s - self.start:e - self.start] = val
+/* "cirtree_file.pxd":3
+ * from types cimport *
*
- * cdef class BigWigFile( BBIFile ): # <<<<<<<<<<<<<<
- * """
- * A "big binary indexed" file whose raw data is in wiggle format.
+ * cdef class CIRTreeFile: # <<<<<<<<<<<<<<
+ * cdef object file
+ * cdef object reader
*/
-struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile {
- struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile __pyx_base;
+struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile {
+ PyObject_HEAD
+ PyObject *file;
+ PyObject *reader;
+ __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
+ __pyx_t_2bx_3bbi_5types_bits64 root_offset;
+ __pyx_t_2bx_3bbi_5types_bits32 block_size;
+ __pyx_t_2bx_3bbi_5types_bits64 item_count;
+ __pyx_t_2bx_3bbi_5types_bits32 start_chrom_ix;
+ __pyx_t_2bx_3bbi_5types_bits32 start_base;
+ __pyx_t_2bx_3bbi_5types_bits32 end_chrom_ix;
+ __pyx_t_2bx_3bbi_5types_bits32 end_base;
+ __pyx_t_2bx_3bbi_5types_bits64 file_size;
+ __pyx_t_2bx_3bbi_5types_bits32 items_per_slot;
};
-
/* "bbi_file.pxd":21
* cdef public double sum_squares
*
@@ -1004,31 +885,52 @@ struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile {
* """
* The result of using SummaryBlocks read from the file to produce a
*/
-
-struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData {
- PyObject *(*accumulate_interval_value)(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float);
+struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtab;
+ __pyx_t_2bx_3bbi_5types_bits32 start;
+ __pyx_t_2bx_3bbi_5types_bits32 end;
+ int size;
+ PyArrayObject *valid_count;
+ PyArrayObject *min_val;
+ PyArrayObject *max_val;
+ PyArrayObject *sum_data;
+ PyArrayObject *sum_squares;
};
-static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtabptr_2bx_3bbi_8bbi_file_SummarizedData;
-/* "bbi_file.pxd":37
- * cdef accumulate_interval_value( self, bits32 s, bits32 e, float val )
- *
- * cdef class BBIFile # <<<<<<<<<<<<<<
+/* "bx/bbi/bigwig_file.pyx":76
+ * pass
*
- * cdef class BlockHandler:
- */
-
-struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile {
- PyObject *(*visit_blocks_in_region)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler *);
- PyObject *(*_get_chrom_id_and_size)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *);
- PyObject *(*_best_zoom_level)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, int);
- PyObject *(*summarize)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int, int __pyx_skip_dispatch);
- PyObject *(*summarize_from_full)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int, int __pyx_skip_dispatch);
- PyObject *(*query)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int, int __pyx_skip_dispatch);
- PyObject *(*_summarize_from_full)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int);
+ * cdef class SummarizingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
+ * """
+ * Accumulates intervals into a SummarizedData
+ */
+struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler {
+ struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler __pyx_base;
+ struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *sd;
+};
+
+
+/* "bpt_file.pxd":5
+ * from types cimport *
+ *
+ * cdef class BPTFile: # <<<<<<<<<<<<<<
+ * """
+ * On disk B+ tree compatible with Jim Kent's bPlusTree.c
+ */
+struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile {
+ PyObject_HEAD
+ PyObject *file;
+ PyObject *reader;
+ __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
+ __pyx_t_2bx_3bbi_5types_bits32 block_size;
+ __pyx_t_2bx_3bbi_5types_bits32 key_size;
+ __pyx_t_2bx_3bbi_5types_bits32 value_size;
+ __pyx_t_2bx_3bbi_5types_bits64 item_count;
+ __pyx_t_2bx_3bbi_5types_bits64 root_offset;
};
-static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile *__pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile;
+
/* "bbi_file.pxd":39
@@ -1045,8 +947,8 @@ struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler {
static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtabptr_2bx_3bbi_8bbi_file_BlockHandler;
-/* "bx/bbi/bigwig_file.pyx":28
- * return [l[i:i + n] for i in range(0, len(l), n)]
+/* "bx/bbi/bigwig_file.pyx":23
+ * return min( end1, end2 ) - max( start1, start2 )
*
* cdef class BigWigBlockHandler( BlockHandler ): # <<<<<<<<<<<<<<
* """
@@ -1060,50 +962,56 @@ struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigBlockHandler {
static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigwig_file_BigWigBlockHandler;
-/* "bx/bbi/bigwig_file.pyx":74
- * pass
+/* "bx/bbi/bigwig_file.pyx":105
+ * self.intervals.append( ( s, e, val ) )
*
- * cdef class SummarizingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
+ * cdef class ArrayAccumulatingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
* """
- * Accumulates intervals into a SummarizedData
+ * Accumulates intervals into a list of intervals with values
*/
-struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_SummarizingBlockHandler {
+struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler {
struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigBlockHandler __pyx_base;
};
-static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_SummarizingBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigwig_file_SummarizingBlockHandler;
+static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler;
-/* "bx/bbi/bigwig_file.pyx":89
- * self.sd.accumulate_interval_value( s, e, val )
+/* "bbi_file.pxd":21
+ * cdef public double sum_squares
*
- * cdef class IntervalAccumulatingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
- * cdef list intervals
+ * cdef class SummarizedData: # <<<<<<<<<<<<<<
* """
+ * The result of using SummaryBlocks read from the file to produce a
*/
-struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler {
- struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigBlockHandler __pyx_base;
+struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData {
+ PyObject *(*accumulate_interval_value)(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float);
};
-static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler;
+static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtabptr_2bx_3bbi_8bbi_file_SummarizedData;
-/* "bx/bbi/bigwig_file.pyx":101
- * self.intervals.append( ( s, e, val ) )
+/* "bbi_file.pxd":37
+ * cdef accumulate_interval_value( self, bits32 s, bits32 e, float val )
*
- * cdef class ArrayAccumulatingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
- * """
- * Accumulates intervals into a list of intervals with values
+ * cdef class BBIFile # <<<<<<<<<<<<<<
+ *
+ * cdef class BlockHandler:
*/
-struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler {
- struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigBlockHandler __pyx_base;
+struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile {
+ PyObject *(*visit_blocks_in_region)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler *);
+ PyObject *(*_get_chrom_id_and_size)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *);
+ PyObject *(*_best_zoom_level)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, int);
+ PyObject *(*summarize)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int, int __pyx_skip_dispatch);
+ PyObject *(*summarize_from_full)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int, int __pyx_skip_dispatch);
+ PyObject *(*query)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int, int __pyx_skip_dispatch);
+ PyObject *(*_summarize_from_full)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int);
};
-static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler;
+static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile *__pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile;
-/* "bx/bbi/bigwig_file.pyx":116
- * self.array[s - self.start:e - self.start] = val
+/* "bx/bbi/bigwig_file.pyx":122
+ * array[ i ] = val
*
* cdef class BigWigFile( BBIFile ): # <<<<<<<<<<<<<<
* """
@@ -1117,7 +1025,33 @@ struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigFile {
};
static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigFile *__pyx_vtabptr_2bx_3bbi_11bigwig_file_BigWigFile;
-/* --- Runtime support code (head) --- */
+
+/* "bx/bbi/bigwig_file.pyx":93
+ * self.sd.accumulate_interval_value( s, e, val )
+ *
+ * cdef class IntervalAccumulatingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
+ * cdef list intervals
+ * """
+ */
+
+struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler {
+ struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigBlockHandler __pyx_base;
+};
+static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler;
+
+
+/* "bx/bbi/bigwig_file.pyx":76
+ * pass
+ *
+ * cdef class SummarizingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
+ * """
+ * Accumulates intervals into a SummarizedData
+ */
+
+struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_SummarizingBlockHandler {
+ struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigBlockHandler __pyx_base;
+};
+static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_SummarizingBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigwig_file_SummarizingBlockHandler;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
@@ -1131,7 +1065,7 @@ static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigFile *__pyx_vtabptr_
void (*FinishContext)(void**);
} __Pyx_RefNannyAPIStruct;
static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
- static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname);
+ static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); /*proto*/
#define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
#ifdef WITH_THREAD
#define __Pyx_RefNannySetupContext(name, acquire_gil) \
@@ -1168,217 +1102,209 @@ static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigFile *__pyx_vtabptr_
#define __Pyx_XDECREF(r) Py_XDECREF(r)
#define __Pyx_XGOTREF(r)
#define __Pyx_XGIVEREF(r)
-#endif
-#define __Pyx_XDECREF_SET(r, v) do { \
- PyObject *tmp = (PyObject *) r; \
- r = v; __Pyx_XDECREF(tmp); \
- } while (0)
-#define __Pyx_DECREF_SET(r, v) do { \
- PyObject *tmp = (PyObject *) r; \
- r = v; __Pyx_DECREF(tmp); \
- } while (0)
+#endif /* CYTHON_REFNANNY */
#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
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- PyTypeObject* tp = Py_TYPE(obj);
- if (likely(tp->tp_getattro))
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-#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
-#endif
-
-static PyObject *__Pyx_GetBuiltinName(PyObject *name);
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
- Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found);
+ Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
-static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);
+static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
- const char* function_name);
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
-#else
-#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
-#endif
+ const char* function_name); /*proto*/
+#define __Pyx_SetItemInt(o, i, v, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_SetItemInt_Fast(o, i, v) : \
+ __Pyx_SetItemInt_Generic(o, to_py_func(i), v))
+static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) {
+ int r;
+ if (!j) return -1;
+ r = PyObject_SetItem(o, j, v);
+ Py_DECREF(j);
+ return r;
+}
+static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) {
#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) {
- PyListObject* L = (PyListObject*) list;
- Py_ssize_t len = Py_SIZE(list);
- if (likely(L->allocated > len)) {
- Py_INCREF(x);
- PyList_SET_ITEM(list, len, x);
- Py_SIZE(list) = len+1;
- return 0;
+ if (PyList_CheckExact(o)) {
+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
+ PyObject* old = PyList_GET_ITEM(o, n);
+ Py_INCREF(v);
+ PyList_SET_ITEM(o, n, v);
+ Py_DECREF(old);
+ return 1;
+ }
+ } else { /* inlined PySequence_SetItem() */
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_ass_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return -1;
+ i += l;
+ }
+ return m->sq_ass_item(o, i, v);
+ }
}
- return PyList_Append(list, x);
-}
#else
-#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x)
+#if CYTHON_COMPILING_IN_PYPY
+ if (PySequence_Check(o) && !PyDict_Check(o)) {
+#else
+ if (PySequence_Check(o)) {
#endif
-
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
- PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
- PyObject** py_start, PyObject** py_stop, PyObject** py_slice,
- int has_cstart, int has_cstop, int wraparound);
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
+ return PySequence_SetItem(o, i, v);
+ }
#endif
+ return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
+}
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);
-
-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name);
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
-
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-
-static CYTHON_INLINE int __Pyx_IterFinish(void);
+static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected);
+static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj,
+ __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack);
+static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info);
-static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);
+static void __Pyx_RaiseBufferIndexError(int axis); /*proto*/
-#define __Pyx_PyObject_DelSlice(obj, cstart, cstop, py_start, py_stop, py_slice, has_cstart, has_cstop, wraparound) \
- __Pyx_PyObject_SetSlice(obj, (PyObject*)NULL, cstart, cstop, py_start, py_stop, py_slice, has_cstart, has_cstop, wraparound)
-static CYTHON_INLINE int __Pyx_PyObject_SetSlice(
- PyObject* obj, PyObject* value, Py_ssize_t cstart, Py_ssize_t cstop,
- PyObject** py_start, PyObject** py_stop, PyObject** py_slice,
- int has_cstart, int has_cstop, int wraparound);
+#define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0)
+ static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
+ PyObject *r;
+ if (!j) return NULL;
+ r = PyObject_GetItem(o, j);
+ Py_DECREF(j);
+ return r;
+}
+#define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_List_Fast(o, i) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
- PyListObject* L = (PyListObject*) list;
- Py_ssize_t len = Py_SIZE(list);
- if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) {
- Py_INCREF(x);
- PyList_SET_ITEM(list, len, x);
- Py_SIZE(list) = len+1;
- return 0;
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
- return PyList_Append(list, x);
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
+#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_Tuple_Fast(o, i) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
#else
-#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
+ return PySequence_GetItem(o, i);
#endif
-
-static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type);
-
-#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \
- (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \
- __Pyx_GetItemInt_Generic(o, to_py_func(i))))
-#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
- (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck);
-#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
- (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck);
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck);
-
-#define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) : \
- (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) : \
- __Pyx_SetItemInt_Generic(o, to_py_func(i), v)))
-static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v);
-static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
- int is_list, int wraparound, int boundscheck);
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb);
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb);
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause);
-
-#if PY_MAJOR_VERSION >= 3
-static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
- PyObject *value;
- value = PyDict_GetItemWithError(d, key);
- if (unlikely(!value)) {
- if (!PyErr_Occurred()) {
- PyObject* args = PyTuple_Pack(1, key);
- if (likely(args))
- PyErr_SetObject(PyExc_KeyError, args);
- Py_XDECREF(args);
+}
+#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_Fast(o, i) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (PyList_CheckExact(o)) {
+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ }
+ else if (PyTuple_CheckExact(o)) {
+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ } else { /* inlined PySequence_GetItem() */
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return NULL;
+ i += l;
+ }
+ return m->sq_item(o, i);
}
- return NULL;
}
- Py_INCREF(value);
- return value;
-}
#else
- #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
+ if (PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
+ }
#endif
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+}
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
-
-static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc);
-
-static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse);
-
-static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc);
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
-static void* __Pyx_GetVtable(PyObject *dict);
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static int __Pyx_SetVtable(PyObject *dict, void *vtable);
+static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
-static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name);
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
-typedef struct {
- int code_line;
- PyCodeObject* code_object;
-} __Pyx_CodeObjectCacheEntry;
-struct __Pyx_CodeObjectCache {
- int count;
- int max_count;
- __Pyx_CodeObjectCacheEntry* entries;
-};
-static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
-static PyCodeObject *__pyx_find_code_object(int code_line);
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename);
+static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
+static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc);
-static CYTHON_INLINE unsigned int __Pyx_PyInt_As_unsigned_int(PyObject *);
+static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse);
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
+static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc);
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
+typedef struct {
+ Py_ssize_t shape, strides, suboffsets;
+} __Pyx_Buf_DimInfo;
+typedef struct {
+ size_t refcount;
+ Py_buffer pybuffer;
+} __Pyx_Buffer;
+typedef struct {
+ __Pyx_Buffer *rcbuffer;
+ char *data;
+ __Pyx_Buf_DimInfo diminfo[8];
+} __Pyx_LocalBuf_ND;
-static CYTHON_INLINE unsigned char __Pyx_PyInt_As_unsigned_char(PyObject *);
+#if PY_MAJOR_VERSION < 3
+ static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags);
+ static void __Pyx_ReleaseBuffer(Py_buffer *view);
+#else
+ #define __Pyx_GetBuffer PyObject_GetBuffer
+ #define __Pyx_ReleaseBuffer PyBuffer_Release
+#endif
-static CYTHON_INLINE unsigned short __Pyx_PyInt_As_unsigned_short(PyObject *);
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_short(unsigned short value);
+ static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0};
+static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1};
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_int(unsigned int value);
+static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name);
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
@@ -1392,7 +1318,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_int(unsigned int value)
#define __Pyx_CREAL(z) ((z).real)
#define __Pyx_CIMAG(z) ((z).imag)
#endif
-#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX
+#if defined(_WIN32) && defined(__cplusplus) && CYTHON_CCOMPLEX
#define __Pyx_SET_CREAL(z,x) ((z).real(x))
#define __Pyx_SET_CIMAG(z,y) ((z).imag(y))
#else
@@ -1478,42 +1404,85 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
#endif
#endif
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
+static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
-static int __Pyx_check_binary_version(void);
+static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
-#if !defined(__Pyx_PyIdentifier_FromString)
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
-#else
- #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
-#endif
-#endif
+static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *);
-static PyObject *__Pyx_ImportModule(const char *name);
+static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *);
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict);
+static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *);
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t);
+static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *);
-static PyObject *__pyx_f_2bx_3bbi_11bigwig_file_18BigWigBlockHandler_handle_block(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler *__pyx_v_self, PyObject *__pyx_v_block_data, struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_bbi_file); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_11bigwig_file_18BigWigBlockHandler_handle_interval_value(CYTHON_UNUSED struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler *__pyx_v_self, CYTHON_UNUSED __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_s, CYTHON_UNUSED __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_e, CYTHON_UNUSED float __pyx_v_val); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_11bigwig_file_23SummarizingBlockHandler_handle_interval_value(struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_s, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_e, float __pyx_v_val); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_11bigwig_file_32IntervalAccumulatingBlockHandler_handle_interval_value(struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_s, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_e, float __pyx_v_val); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_11bigwig_file_29ArrayAccumulatingBlockHandler_handle_interval_value(struct __pyx_obj_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_s, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_e, float __pyx_v_val); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_11bigwig_file_10BigWigFile__summarize_from_full(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_chrom_id, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_v_summary_size); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_11bigwig_file_10BigWigFile_get(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile *__pyx_v_self, char *__pyx_v_chrom, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_skip_dispatch); /* proto*/
-static PyObject *__pyx_f_2bx_3bbi_11bigwig_file_10BigWigFile_get_as_array(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile *__pyx_v_self, char *__pyx_v_chrom, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_skip_dispatch); /* proto*/
+static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *);
-/* Module declarations from 'bx.bbi.types' */
+static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *);
-/* Module declarations from 'bx.bbi.bpt_file' */
-static PyTypeObject *__pyx_ptype_2bx_3bbi_8bpt_file_BPTFile = 0;
+static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *);
-/* Module declarations from 'bx.bbi.cirtree_file' */
-static PyTypeObject *__pyx_ptype_2bx_3bbi_12cirtree_file_CIRTreeFile = 0;
+static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *);
-/* Module declarations from 'cpython.buffer' */
+static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *);
+
+static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *);
+
+static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *);
+
+static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *);
+
+static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);
+
+static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
+
+static int __Pyx_check_binary_version(void);
+
+#if !defined(__Pyx_PyIdentifier_FromString)
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
+#else
+ #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
+#endif
+#endif
+
+static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+
+static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
+
+typedef struct {
+ int code_line;
+ PyCodeObject* code_object;
+} __Pyx_CodeObjectCacheEntry;
+struct __Pyx_CodeObjectCache {
+ int count;
+ int max_count;
+ __Pyx_CodeObjectCacheEntry* entries;
+};
+static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
+static PyCodeObject *__pyx_find_code_object(int code_line);
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
+
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename); /*proto*/
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
+
+
+/* Module declarations from 'bx.bbi.types' */
+
+/* Module declarations from 'bx.bbi.bpt_file' */
+static PyTypeObject *__pyx_ptype_2bx_3bbi_8bpt_file_BPTFile = 0;
+
+/* Module declarations from 'bx.bbi.cirtree_file' */
+static PyTypeObject *__pyx_ptype_2bx_3bbi_12cirtree_file_CIRTreeFile = 0;
+
+/* Module declarations from 'cpython.buffer' */
/* Module declarations from 'cpython.ref' */
@@ -1552,16 +1521,15 @@ static PyTypeObject *__pyx_ptype_2bx_3bbi_11bigwig_file_SummarizingBlockHandler
static PyTypeObject *__pyx_ptype_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler = 0;
static PyTypeObject *__pyx_ptype_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler = 0;
static PyTypeObject *__pyx_ptype_2bx_3bbi_11bigwig_file_BigWigFile = 0;
+static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t = { "float32_t", NULL, sizeof(__pyx_t_5numpy_float32_t), { 0 }, 0, 'R', 0, 0 };
#define __Pyx_MODULE_NAME "bx.bbi.bigwig_file"
int __pyx_module_is_main_bx__bbi__bigwig_file = 0;
/* Implementation of 'bx.bbi.bigwig_file' */
static PyObject *__pyx_builtin_range;
-static PyObject *__pyx_builtin_enumerate;
static PyObject *__pyx_builtin_round;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_RuntimeError;
-static PyObject *__pyx_pf_2bx_3bbi_11bigwig_file_chunks(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_l, PyObject *__pyx_v_n); /* proto */
static int __pyx_pf_2bx_3bbi_11bigwig_file_18BigWigBlockHandler___init__(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end); /* proto */
static int __pyx_pf_2bx_3bbi_11bigwig_file_23SummarizingBlockHandler___init__(struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_v_summary_size); /* proto */
static int __pyx_pf_2bx_3bbi_11bigwig_file_32IntervalAccumulatingBlockHandler___init__(struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end); /* proto */
@@ -1571,143 +1539,116 @@ static PyObject *__pyx_pf_2bx_3bbi_11bigwig_file_10BigWigFile_2get(struct __pyx_
static PyObject *__pyx_pf_2bx_3bbi_11bigwig_file_10BigWigFile_4get_as_array(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile *__pyx_v_self, char *__pyx_v_chrom, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end); /* proto */
static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
-static PyObject *__pyx_tp_new_2bx_3bbi_11bigwig_file_BigWigBlockHandler(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_2bx_3bbi_11bigwig_file_SummarizingBlockHandler(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_2bx_3bbi_11bigwig_file_BigWigFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static char __pyx_k_B[] = "B";
-static char __pyx_k_H[] = "H";
-static char __pyx_k_I[] = "I";
-static char __pyx_k_L[] = "L";
-static char __pyx_k_O[] = "O";
-static char __pyx_k_Q[] = "Q";
-static char __pyx_k_b[] = "b";
-static char __pyx_k_d[] = "d";
-static char __pyx_k_f[] = "f";
-static char __pyx_k_g[] = "g";
-static char __pyx_k_h[] = "h";
-static char __pyx_k_i[] = "i";
-static char __pyx_k_l[] = "l";
-static char __pyx_k_n[] = "n";
-static char __pyx_k_q[] = "q";
-static char __pyx_k_Lf[] = "Lf";
-static char __pyx_k_Zd[] = "Zd";
-static char __pyx_k_Zf[] = "Zf";
-static char __pyx_k_Zg[] = "Zg";
-static char __pyx_k_LLf[] = "LLf";
-static char __pyx_k_end[] = "end";
-static char __pyx_k_get[] = "get";
-static char __pyx_k_inf[] = "inf";
-static char __pyx_k_nan[] = "nan";
-static char __pyx_k_file[] = "file";
-static char __pyx_k_init[] = "__init__";
-static char __pyx_k_main[] = "__main__";
-static char __pyx_k_test[] = "__test__";
-static char __pyx_k_zlib[] = "zlib";
-static char __pyx_k_chrom[] = "chrom";
-static char __pyx_k_deque[] = "deque";
-static char __pyx_k_dtype[] = "dtype";
-static char __pyx_k_numpy[] = "numpy";
-static char __pyx_k_range[] = "range";
-static char __pyx_k_round[] = "round";
-static char __pyx_k_start[] = "start";
-static char __pyx_k_zeros[] = "zeros";
-static char __pyx_k_bigwig[] = "bigwig";
-static char __pyx_k_chunks[] = "chunks";
-static char __pyx_k_import[] = "__import__";
-static char __pyx_k_float32[] = "float32";
-static char __pyx_k_LLLLLBBH[] = "LLLLLBBH";
-static char __pyx_k_StringIO[] = "StringIO";
-static char __pyx_k_cStringIO[] = "cStringIO";
-static char __pyx_k_enumerate[] = "enumerate";
-static char __pyx_k_ValueError[] = "ValueError";
-static char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
-static char __pyx_k_BigWig_file[] = "\nBigWig file.\n";
-static char __pyx_k_collections[] = "collections";
-static char __pyx_k_RuntimeError[] = "RuntimeError";
-static char __pyx_k_get_as_array[] = "get_as_array";
-static char __pyx_k_summary_size[] = "summary_size";
-static char __pyx_k_read_and_unpack[] = "read_and_unpack";
-static char __pyx_k_BinaryFileReader[] = "BinaryFileReader";
-static char __pyx_k_is_little_endian[] = "is_little_endian";
-static char __pyx_k_bx_bbi_bigwig_file[] = "bx.bbi.bigwig_file";
-static char __pyx_k_bx_misc_binary_file[] = "bx.misc.binary_file";
-static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous";
-static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
-static char __pyx_k_usr_local_src_bx_python_mod_lib[] = "/usr/local/src/bx-python-mod/lib/bx/bbi/bigwig_file.pyx";
-static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd";
-static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported";
-static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous";
-static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short.";
-static PyObject *__pyx_n_s_BinaryFileReader;
-static PyObject *__pyx_kp_u_Format_string_allocated_too_shor;
-static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2;
-static PyObject *__pyx_n_s_LLLLLBBH;
-static PyObject *__pyx_n_s_LLf;
-static PyObject *__pyx_n_s_Lf;
-static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor;
-static PyObject *__pyx_n_s_RuntimeError;
-static PyObject *__pyx_n_s_StringIO;
-static PyObject *__pyx_n_s_ValueError;
-static PyObject *__pyx_n_s_bigwig;
-static PyObject *__pyx_n_s_bx_bbi_bigwig_file;
-static PyObject *__pyx_n_s_bx_misc_binary_file;
-static PyObject *__pyx_n_s_cStringIO;
-static PyObject *__pyx_n_s_chrom;
-static PyObject *__pyx_n_s_chunks;
-static PyObject *__pyx_n_s_collections;
-static PyObject *__pyx_n_s_deque;
-static PyObject *__pyx_n_s_dtype;
-static PyObject *__pyx_n_s_end;
-static PyObject *__pyx_n_s_enumerate;
-static PyObject *__pyx_n_s_f;
-static PyObject *__pyx_n_s_file;
-static PyObject *__pyx_n_s_float32;
-static PyObject *__pyx_n_s_get;
-static PyObject *__pyx_n_s_get_as_array;
-static PyObject *__pyx_n_s_i;
-static PyObject *__pyx_n_s_import;
-static PyObject *__pyx_n_s_inf;
-static PyObject *__pyx_n_s_init;
-static PyObject *__pyx_n_s_is_little_endian;
-static PyObject *__pyx_n_s_l;
-static PyObject *__pyx_n_s_main;
-static PyObject *__pyx_n_s_n;
-static PyObject *__pyx_n_s_nan;
-static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous;
-static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou;
-static PyObject *__pyx_n_s_numpy;
-static PyObject *__pyx_n_s_pyx_vtable;
-static PyObject *__pyx_n_s_range;
-static PyObject *__pyx_n_s_read_and_unpack;
-static PyObject *__pyx_n_s_round;
-static PyObject *__pyx_n_s_start;
-static PyObject *__pyx_n_s_summary_size;
-static PyObject *__pyx_n_s_test;
-static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd;
-static PyObject *__pyx_kp_s_usr_local_src_bx_python_mod_lib;
-static PyObject *__pyx_n_s_zeros;
-static PyObject *__pyx_n_s_zlib;
-static PyObject *__pyx_int_0;
+static char __pyx_k_2[] = "ndarray is not C contiguous";
+static char __pyx_k_4[] = "ndarray is not Fortran contiguous";
+static char __pyx_k_6[] = "Non-native byte order not supported";
+static char __pyx_k_8[] = "unknown dtype code in numpy.pxd (%d)";
+static char __pyx_k_9[] = "Format string allocated too short, see comment in numpy.pxd";
+static char __pyx_k_12[] = "Format string allocated too short.";
+static char __pyx_k_14[] = "\nBigWig file.\n";
+static char __pyx_k_15[] = "bx.misc.binary_file";
+static char __pyx_k__B[] = "B";
+static char __pyx_k__H[] = "H";
+static char __pyx_k__I[] = "I";
+static char __pyx_k__L[] = "L";
+static char __pyx_k__O[] = "O";
+static char __pyx_k__Q[] = "Q";
+static char __pyx_k__b[] = "b";
+static char __pyx_k__d[] = "d";
+static char __pyx_k__f[] = "f";
+static char __pyx_k__g[] = "g";
+static char __pyx_k__h[] = "h";
+static char __pyx_k__i[] = "i";
+static char __pyx_k__l[] = "l";
+static char __pyx_k__q[] = "q";
+static char __pyx_k__Zd[] = "Zd";
+static char __pyx_k__Zf[] = "Zf";
+static char __pyx_k__Zg[] = "Zg";
+static char __pyx_k__end[] = "end";
+static char __pyx_k__get[] = "get";
+static char __pyx_k__inf[] = "inf";
+static char __pyx_k__nan[] = "nan";
+static char __pyx_k__file[] = "file";
+static char __pyx_k__skip[] = "skip";
+static char __pyx_k__zlib[] = "zlib";
+static char __pyx_k__chrom[] = "chrom";
+static char __pyx_k__deque[] = "deque";
+static char __pyx_k__dtype[] = "dtype";
+static char __pyx_k__numpy[] = "numpy";
+static char __pyx_k__range[] = "range";
+static char __pyx_k__round[] = "round";
+static char __pyx_k__start[] = "start";
+static char __pyx_k__zeros[] = "zeros";
+static char __pyx_k__bigwig[] = "bigwig";
+static char __pyx_k__float32[] = "float32";
+static char __pyx_k__StringIO[] = "StringIO";
+static char __pyx_k____init__[] = "__init__";
+static char __pyx_k____main__[] = "__main__";
+static char __pyx_k____test__[] = "__test__";
+static char __pyx_k__cStringIO[] = "cStringIO";
+static char __pyx_k__ValueError[] = "ValueError";
+static char __pyx_k__read_float[] = "read_float";
+static char __pyx_k__read_uint8[] = "read_uint8";
+static char __pyx_k__collections[] = "collections";
+static char __pyx_k__read_uint16[] = "read_uint16";
+static char __pyx_k__read_uint32[] = "read_uint32";
+static char __pyx_k__RuntimeError[] = "RuntimeError";
+static char __pyx_k__get_as_array[] = "get_as_array";
+static char __pyx_k__summary_size[] = "summary_size";
+static char __pyx_k__BinaryFileReader[] = "BinaryFileReader";
+static char __pyx_k__is_little_endian[] = "is_little_endian";
+static PyObject *__pyx_kp_u_12;
+static PyObject *__pyx_n_s_15;
+static PyObject *__pyx_kp_u_2;
+static PyObject *__pyx_kp_u_4;
+static PyObject *__pyx_kp_u_6;
+static PyObject *__pyx_kp_u_8;
+static PyObject *__pyx_kp_u_9;
+static PyObject *__pyx_n_s__BinaryFileReader;
+static PyObject *__pyx_n_s__RuntimeError;
+static PyObject *__pyx_n_s__StringIO;
+static PyObject *__pyx_n_s__ValueError;
+static PyObject *__pyx_n_s____init__;
+static PyObject *__pyx_n_s____main__;
+static PyObject *__pyx_n_s____test__;
+static PyObject *__pyx_n_s__bigwig;
+static PyObject *__pyx_n_s__cStringIO;
+static PyObject *__pyx_n_s__chrom;
+static PyObject *__pyx_n_s__collections;
+static PyObject *__pyx_n_s__deque;
+static PyObject *__pyx_n_s__dtype;
+static PyObject *__pyx_n_s__end;
+static PyObject *__pyx_n_s__file;
+static PyObject *__pyx_n_s__float32;
+static PyObject *__pyx_n_s__get;
+static PyObject *__pyx_n_s__get_as_array;
+static PyObject *__pyx_n_s__inf;
+static PyObject *__pyx_n_s__is_little_endian;
+static PyObject *__pyx_n_s__nan;
+static PyObject *__pyx_n_s__numpy;
+static PyObject *__pyx_n_s__range;
+static PyObject *__pyx_n_s__read_float;
+static PyObject *__pyx_n_s__read_uint16;
+static PyObject *__pyx_n_s__read_uint32;
+static PyObject *__pyx_n_s__read_uint8;
+static PyObject *__pyx_n_s__round;
+static PyObject *__pyx_n_s__skip;
+static PyObject *__pyx_n_s__start;
+static PyObject *__pyx_n_s__summary_size;
+static PyObject *__pyx_n_s__zeros;
+static PyObject *__pyx_n_s__zlib;
static PyObject *__pyx_int_1;
-static PyObject *__pyx_int_2;
-static PyObject *__pyx_int_3;
-static PyObject *__pyx_int_24;
+static PyObject *__pyx_int_15;
static PyObject *__pyx_int_2291137574;
-static PyObject *__pyx_tuple_;
-static PyObject *__pyx_slice__2;
-static PyObject *__pyx_slice__3;
-static PyObject *__pyx_tuple__4;
-static PyObject *__pyx_tuple__5;
-static PyObject *__pyx_tuple__6;
-static PyObject *__pyx_tuple__7;
-static PyObject *__pyx_tuple__8;
-static PyObject *__pyx_tuple__9;
-static PyObject *__pyx_tuple__10;
-static PyObject *__pyx_codeobj__11;
-
-/* "bx/bbi/bigwig_file.pyx":21
+static PyObject *__pyx_k_tuple_1;
+static PyObject *__pyx_k_tuple_3;
+static PyObject *__pyx_k_tuple_5;
+static PyObject *__pyx_k_tuple_7;
+static PyObject *__pyx_k_tuple_10;
+static PyObject *__pyx_k_tuple_11;
+static PyObject *__pyx_k_tuple_13;
+
+/* "bx/bbi/bigwig_file.pyx":20
* DEF bwg_fixed_step = 3
*
* cdef inline int range_intersection( int start1, int end1, int start2, int end2 ): # <<<<<<<<<<<<<<
@@ -1724,23 +1665,23 @@ static CYTHON_INLINE int __pyx_f_2bx_3bbi_11bigwig_file_range_intersection(int _
int __pyx_t_4;
__Pyx_RefNannySetupContext("range_intersection", 0);
- /* "bx/bbi/bigwig_file.pyx":22
+ /* "bx/bbi/bigwig_file.pyx":21
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* cdef inline int range_intersection( int start1, int end1, int start2, int end2 ):
* return min( end1, end2 ) - max( start1, start2 ) # <<<<<<<<<<<<<<
*
- * def chunks(l, n):
+ * cdef class BigWigBlockHandler( BlockHandler ):
*/
__pyx_t_1 = __pyx_v_end2;
__pyx_t_2 = __pyx_v_end1;
- if (((__pyx_t_1 < __pyx_t_2) != 0)) {
+ if ((__pyx_t_1 < __pyx_t_2)) {
__pyx_t_3 = __pyx_t_1;
} else {
__pyx_t_3 = __pyx_t_2;
}
__pyx_t_1 = __pyx_v_start2;
__pyx_t_2 = __pyx_v_start1;
- if (((__pyx_t_1 > __pyx_t_2) != 0)) {
+ if ((__pyx_t_1 > __pyx_t_2)) {
__pyx_t_4 = __pyx_t_1;
} else {
__pyx_t_4 = __pyx_t_2;
@@ -1748,265 +1689,22 @@ static CYTHON_INLINE int __pyx_f_2bx_3bbi_11bigwig_file_range_intersection(int _
__pyx_r = (__pyx_t_3 - __pyx_t_4);
goto __pyx_L0;
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- *
- * cdef inline int range_intersection( int start1, int end1, int start2, int end2 ): # <<<<<<<<<<<<<<
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-
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__pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start;
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{0, 0, 0, 0}
};
+static PyNumberMethods __pyx_tp_as_number_BigWigBlockHandler = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_BigWigBlockHandler = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_BigWigBlockHandler = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_BigWigBlockHandler = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_BigWigBlockHandler = {
PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bigwig_file.BigWigBlockHandler", /*tp_name*/
+ __Pyx_NAMESTR("bx.bbi.bigwig_file.BigWigBlockHandler"), /*tp_name*/
sizeof(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_2bx_3bbi_11bigwig_file_BigWigBlockHandler, /*tp_dealloc*/
@@ -6927,17 +6125,17 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_BigWigBlockHandler = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ &__pyx_tp_as_number_BigWigBlockHandler, /*tp_as_number*/
+ &__pyx_tp_as_sequence_BigWigBlockHandler, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_BigWigBlockHandler, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- "\n BlockHandler that parses the block into a series of wiggle records, and calls `handle_interval_value` for each.\n ", /*tp_doc*/
+ &__pyx_tp_as_buffer_BigWigBlockHandler, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("\n BlockHandler that parses the block into a series of wiggle records, and calls `handle_interval_value` for each.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
@@ -6963,9 +6161,8 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_BigWigBlockHandler = {
0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
#endif
};
static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_SummarizingBlockHandler __pyx_vtable_2bx_3bbi_11bigwig_file_SummarizingBlockHandler;
@@ -6973,7 +6170,7 @@ static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_SummarizingBlockHandler __
static PyObject *__pyx_tp_new_2bx_3bbi_11bigwig_file_SummarizingBlockHandler(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler *p;
PyObject *o = __pyx_tp_new_2bx_3bbi_11bigwig_file_BigWigBlockHandler(t, a, k);
- if (unlikely(!o)) return 0;
+ if (!o) return 0;
p = ((struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler *)o);
p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler*)__pyx_vtabptr_2bx_3bbi_11bigwig_file_SummarizingBlockHandler;
p->sd = ((struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *)Py_None); Py_INCREF(Py_None);
@@ -6982,16 +6179,8 @@ static PyObject *__pyx_tp_new_2bx_3bbi_11bigwig_file_SummarizingBlockHandler(PyT
static void __pyx_tp_dealloc_2bx_3bbi_11bigwig_file_SummarizingBlockHandler(PyObject *o) {
struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler *p = (struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler *)o;
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
PyObject_GC_UnTrack(o);
Py_CLEAR(p->sd);
- #if CYTHON_COMPILING_IN_CPYTHON
- if (PyType_IS_GC(Py_TYPE(o)->tp_base))
- #endif
PyObject_GC_Track(o);
__pyx_tp_dealloc_2bx_3bbi_11bigwig_file_BigWigBlockHandler(o);
}
@@ -7007,8 +6196,8 @@ static int __pyx_tp_traverse_2bx_3bbi_11bigwig_file_SummarizingBlockHandler(PyOb
}
static int __pyx_tp_clear_2bx_3bbi_11bigwig_file_SummarizingBlockHandler(PyObject *o) {
- PyObject* tmp;
struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler *p = (struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler *)o;
+ PyObject* tmp;
if (likely(__pyx_ptype_2bx_3bbi_11bigwig_file_BigWigBlockHandler)) { if (__pyx_ptype_2bx_3bbi_11bigwig_file_BigWigBlockHandler->tp_clear) __pyx_ptype_2bx_3bbi_11bigwig_file_BigWigBlockHandler->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_2bx_3bbi_11bigwig_file_SummarizingBlockHandler);
tmp = ((PyObject*)p->sd);
p->sd = ((struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *)Py_None); Py_INCREF(Py_None);
@@ -7020,9 +6209,107 @@ static PyMethodDef __pyx_methods_2bx_3bbi_11bigwig_file_SummarizingBlockHandler[
{0, 0, 0, 0}
};
+static PyNumberMethods __pyx_tp_as_number_SummarizingBlockHandler = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_SummarizingBlockHandler = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_SummarizingBlockHandler = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_SummarizingBlockHandler = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_SummarizingBlockHandler = {
PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bigwig_file.SummarizingBlockHandler", /*tp_name*/
+ __Pyx_NAMESTR("bx.bbi.bigwig_file.SummarizingBlockHandler"), /*tp_name*/
sizeof(struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_2bx_3bbi_11bigwig_file_SummarizingBlockHandler, /*tp_dealloc*/
@@ -7035,17 +6322,17 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_SummarizingBlockHandler =
0, /*reserved*/
#endif
0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ &__pyx_tp_as_number_SummarizingBlockHandler, /*tp_as_number*/
+ &__pyx_tp_as_sequence_SummarizingBlockHandler, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_SummarizingBlockHandler, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- "\n Accumulates intervals into a SummarizedData\n ", /*tp_doc*/
+ &__pyx_tp_as_buffer_SummarizingBlockHandler, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("\n Accumulates intervals into a SummarizedData\n "), /*tp_doc*/
__pyx_tp_traverse_2bx_3bbi_11bigwig_file_SummarizingBlockHandler, /*tp_traverse*/
__pyx_tp_clear_2bx_3bbi_11bigwig_file_SummarizingBlockHandler, /*tp_clear*/
0, /*tp_richcompare*/
@@ -7071,9 +6358,8 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_SummarizingBlockHandler =
0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
#endif
};
static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler __pyx_vtable_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler;
@@ -7081,7 +6367,7 @@ static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockH
static PyObject *__pyx_tp_new_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler *p;
PyObject *o = __pyx_tp_new_2bx_3bbi_11bigwig_file_BigWigBlockHandler(t, a, k);
- if (unlikely(!o)) return 0;
+ if (!o) return 0;
p = ((struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler *)o);
p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler*)__pyx_vtabptr_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler;
p->intervals = ((PyObject*)Py_None); Py_INCREF(Py_None);
@@ -7090,16 +6376,8 @@ static PyObject *__pyx_tp_new_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHa
static void __pyx_tp_dealloc_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler(PyObject *o) {
struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler *p = (struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler *)o;
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
PyObject_GC_UnTrack(o);
Py_CLEAR(p->intervals);
- #if CYTHON_COMPILING_IN_CPYTHON
- if (PyType_IS_GC(Py_TYPE(o)->tp_base))
- #endif
PyObject_GC_Track(o);
__pyx_tp_dealloc_2bx_3bbi_11bigwig_file_BigWigBlockHandler(o);
}
@@ -7115,8 +6393,8 @@ static int __pyx_tp_traverse_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHan
}
static int __pyx_tp_clear_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler(PyObject *o) {
- PyObject* tmp;
struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler *p = (struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler *)o;
+ PyObject* tmp;
if (likely(__pyx_ptype_2bx_3bbi_11bigwig_file_BigWigBlockHandler)) { if (__pyx_ptype_2bx_3bbi_11bigwig_file_BigWigBlockHandler->tp_clear) __pyx_ptype_2bx_3bbi_11bigwig_file_BigWigBlockHandler->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler);
tmp = ((PyObject*)p->intervals);
p->intervals = ((PyObject*)Py_None); Py_INCREF(Py_None);
@@ -7128,31 +6406,129 @@ static PyMethodDef __pyx_methods_2bx_3bbi_11bigwig_file_IntervalAccumulatingBloc
{0, 0, 0, 0}
};
-static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler = {
- PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bigwig_file.IntervalAccumulatingBlockHandler", /*tp_name*/
- sizeof(struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
+static PyNumberMethods __pyx_tp_as_number_IntervalAccumulatingBlockHandler = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
#if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
+ 0, /*nb_divide*/
#endif
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_IntervalAccumulatingBlockHandler = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_IntervalAccumulatingBlockHandler = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_IntervalAccumulatingBlockHandler = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("bx.bbi.bigwig_file.IntervalAccumulatingBlockHandler"), /*tp_name*/
+ sizeof(struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_IntervalAccumulatingBlockHandler, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IntervalAccumulatingBlockHandler, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IntervalAccumulatingBlockHandler, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ &__pyx_tp_as_buffer_IntervalAccumulatingBlockHandler, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
__pyx_tp_traverse_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler, /*tp_traverse*/
__pyx_tp_clear_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler, /*tp_clear*/
@@ -7179,9 +6555,8 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockH
0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
#endif
};
static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler __pyx_vtable_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler;
@@ -7189,7 +6564,7 @@ static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHand
static PyObject *__pyx_tp_new_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler *p;
PyObject *o = __pyx_tp_new_2bx_3bbi_11bigwig_file_BigWigBlockHandler(t, a, k);
- if (unlikely(!o)) return 0;
+ if (!o) return 0;
p = ((struct __pyx_obj_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler *)o);
p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler*)__pyx_vtabptr_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler;
p->array = ((PyArrayObject *)Py_None); Py_INCREF(Py_None);
@@ -7198,16 +6573,8 @@ static PyObject *__pyx_tp_new_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandl
static void __pyx_tp_dealloc_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler(PyObject *o) {
struct __pyx_obj_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler *p = (struct __pyx_obj_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler *)o;
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
PyObject_GC_UnTrack(o);
Py_CLEAR(p->array);
- #if CYTHON_COMPILING_IN_CPYTHON
- if (PyType_IS_GC(Py_TYPE(o)->tp_base))
- #endif
PyObject_GC_Track(o);
__pyx_tp_dealloc_2bx_3bbi_11bigwig_file_BigWigBlockHandler(o);
}
@@ -7223,8 +6590,8 @@ static int __pyx_tp_traverse_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandle
}
static int __pyx_tp_clear_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler(PyObject *o) {
- PyObject* tmp;
struct __pyx_obj_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler *p = (struct __pyx_obj_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler *)o;
+ PyObject* tmp;
if (likely(__pyx_ptype_2bx_3bbi_11bigwig_file_BigWigBlockHandler)) { if (__pyx_ptype_2bx_3bbi_11bigwig_file_BigWigBlockHandler->tp_clear) __pyx_ptype_2bx_3bbi_11bigwig_file_BigWigBlockHandler->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler);
tmp = ((PyObject*)p->array);
p->array = ((PyArrayObject *)Py_None); Py_INCREF(Py_None);
@@ -7236,9 +6603,107 @@ static PyMethodDef __pyx_methods_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHa
{0, 0, 0, 0}
};
+static PyNumberMethods __pyx_tp_as_number_ArrayAccumulatingBlockHandler = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_ArrayAccumulatingBlockHandler = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_ArrayAccumulatingBlockHandler = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_ArrayAccumulatingBlockHandler = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler = {
PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bigwig_file.ArrayAccumulatingBlockHandler", /*tp_name*/
+ __Pyx_NAMESTR("bx.bbi.bigwig_file.ArrayAccumulatingBlockHandler"), /*tp_name*/
sizeof(struct __pyx_obj_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler, /*tp_dealloc*/
@@ -7251,17 +6716,17 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHand
0, /*reserved*/
#endif
0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ &__pyx_tp_as_number_ArrayAccumulatingBlockHandler, /*tp_as_number*/
+ &__pyx_tp_as_sequence_ArrayAccumulatingBlockHandler, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_ArrayAccumulatingBlockHandler, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- "\n Accumulates intervals into a list of intervals with values\n ", /*tp_doc*/
+ &__pyx_tp_as_buffer_ArrayAccumulatingBlockHandler, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("\n Accumulates intervals into a list of intervals with values\n "), /*tp_doc*/
__pyx_tp_traverse_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler, /*tp_traverse*/
__pyx_tp_clear_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler, /*tp_clear*/
0, /*tp_richcompare*/
@@ -7287,9 +6752,8 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHand
0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
#endif
};
static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigFile __pyx_vtable_2bx_3bbi_11bigwig_file_BigWigFile;
@@ -7297,18 +6761,13 @@ static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigFile __pyx_vtable_2b
static PyObject *__pyx_tp_new_2bx_3bbi_11bigwig_file_BigWigFile(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile *p;
PyObject *o = __pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_new(t, a, k);
- if (unlikely(!o)) return 0;
+ if (!o) return 0;
p = ((struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile *)o);
p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile*)__pyx_vtabptr_2bx_3bbi_11bigwig_file_BigWigFile;
return o;
}
static void __pyx_tp_dealloc_2bx_3bbi_11bigwig_file_BigWigFile(PyObject *o) {
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
PyObject_GC_UnTrack(o);
PyObject_GC_Track(o);
if (likely(__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile)) __pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_dealloc(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_2bx_3bbi_11bigwig_file_BigWigFile);
@@ -7326,14 +6785,112 @@ static int __pyx_tp_clear_2bx_3bbi_11bigwig_file_BigWigFile(PyObject *o) {
}
static PyMethodDef __pyx_methods_2bx_3bbi_11bigwig_file_BigWigFile[] = {
- {"get", (PyCFunction)__pyx_pw_2bx_3bbi_11bigwig_file_10BigWigFile_3get, METH_VARARGS|METH_KEYWORDS, __pyx_doc_2bx_3bbi_11bigwig_file_10BigWigFile_2get},
- {"get_as_array", (PyCFunction)__pyx_pw_2bx_3bbi_11bigwig_file_10BigWigFile_5get_as_array, METH_VARARGS|METH_KEYWORDS, __pyx_doc_2bx_3bbi_11bigwig_file_10BigWigFile_4get_as_array},
+ {__Pyx_NAMESTR("get"), (PyCFunction)__pyx_pw_2bx_3bbi_11bigwig_file_10BigWigFile_3get, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_3bbi_11bigwig_file_10BigWigFile_2get)},
+ {__Pyx_NAMESTR("get_as_array"), (PyCFunction)__pyx_pw_2bx_3bbi_11bigwig_file_10BigWigFile_5get_as_array, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_3bbi_11bigwig_file_10BigWigFile_4get_as_array)},
{0, 0, 0, 0}
};
+static PyNumberMethods __pyx_tp_as_number_BigWigFile = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_BigWigFile = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_BigWigFile = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_BigWigFile = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_BigWigFile = {
PyVarObject_HEAD_INIT(0, 0)
- "bx.bbi.bigwig_file.BigWigFile", /*tp_name*/
+ __Pyx_NAMESTR("bx.bbi.bigwig_file.BigWigFile"), /*tp_name*/
sizeof(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_2bx_3bbi_11bigwig_file_BigWigFile, /*tp_dealloc*/
@@ -7346,17 +6903,17 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_BigWigFile = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
+ &__pyx_tp_as_number_BigWigFile, /*tp_as_number*/
+ &__pyx_tp_as_sequence_BigWigFile, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_BigWigFile, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- "\n A \"big binary indexed\" file whose raw data is in wiggle format.\n ", /*tp_doc*/
+ &__pyx_tp_as_buffer_BigWigFile, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("\n A \"big binary indexed\" file whose raw data is in wiggle format.\n "), /*tp_doc*/
__pyx_tp_traverse_2bx_3bbi_11bigwig_file_BigWigFile, /*tp_traverse*/
__pyx_tp_clear_2bx_3bbi_11bigwig_file_BigWigFile, /*tp_clear*/
0, /*tp_richcompare*/
@@ -7382,9 +6939,8 @@ static PyTypeObject __pyx_type_2bx_3bbi_11bigwig_file_BigWigFile = {
0, /*tp_subclasses*/
0, /*tp_weaklist*/
0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
#endif
};
@@ -7399,8 +6955,8 @@ static struct PyModuleDef __pyx_moduledef = {
#else
PyModuleDef_HEAD_INIT,
#endif
- "bigwig_file",
- __pyx_k_BigWig_file, /* m_doc */
+ __Pyx_NAMESTR("bigwig_file"),
+ __Pyx_DOCSTR(__pyx_k_14), /* m_doc */
-1, /* m_size */
__pyx_methods /* m_methods */,
NULL, /* m_reload */
@@ -7411,63 +6967,53 @@ static struct PyModuleDef __pyx_moduledef = {
#endif
static __Pyx_StringTabEntry __pyx_string_tab[] = {
- {&__pyx_n_s_BinaryFileReader, __pyx_k_BinaryFileReader, sizeof(__pyx_k_BinaryFileReader), 0, 0, 1, 1},
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- {&__pyx_kp_u_Format_string_allocated_too_shor_2, __pyx_k_Format_string_allocated_too_shor_2, sizeof(__pyx_k_Format_string_allocated_too_shor_2), 0, 1, 0, 0},
- {&__pyx_n_s_LLLLLBBH, __pyx_k_LLLLLBBH, sizeof(__pyx_k_LLLLLBBH), 0, 0, 1, 1},
- {&__pyx_n_s_LLf, __pyx_k_LLf, sizeof(__pyx_k_LLf), 0, 0, 1, 1},
- {&__pyx_n_s_Lf, __pyx_k_Lf, sizeof(__pyx_k_Lf), 0, 0, 1, 1},
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- {&__pyx_n_s_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 0, 0, 1, 1},
- {&__pyx_n_s_StringIO, __pyx_k_StringIO, sizeof(__pyx_k_StringIO), 0, 0, 1, 1},
- {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1},
- {&__pyx_n_s_bigwig, __pyx_k_bigwig, sizeof(__pyx_k_bigwig), 0, 0, 1, 1},
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- {&__pyx_n_s_bx_misc_binary_file, __pyx_k_bx_misc_binary_file, sizeof(__pyx_k_bx_misc_binary_file), 0, 0, 1, 1},
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- {&__pyx_n_s_float32, __pyx_k_float32, sizeof(__pyx_k_float32), 0, 0, 1, 1},
- {&__pyx_n_s_get, __pyx_k_get, sizeof(__pyx_k_get), 0, 0, 1, 1},
- {&__pyx_n_s_get_as_array, __pyx_k_get_as_array, sizeof(__pyx_k_get_as_array), 0, 0, 1, 1},
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- {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1},
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- {&__pyx_n_s_init, __pyx_k_init, sizeof(__pyx_k_init), 0, 0, 1, 1},
- {&__pyx_n_s_is_little_endian, __pyx_k_is_little_endian, sizeof(__pyx_k_is_little_endian), 0, 0, 1, 1},
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- {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
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- {&__pyx_n_s_nan, __pyx_k_nan, sizeof(__pyx_k_nan), 0, 0, 1, 1},
- {&__pyx_kp_u_ndarray_is_not_C_contiguous, __pyx_k_ndarray_is_not_C_contiguous, sizeof(__pyx_k_ndarray_is_not_C_contiguous), 0, 1, 0, 0},
- {&__pyx_kp_u_ndarray_is_not_Fortran_contiguou, __pyx_k_ndarray_is_not_Fortran_contiguou, sizeof(__pyx_k_ndarray_is_not_Fortran_contiguou), 0, 1, 0, 0},
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return -1;
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- int __pyx_clineno = 0;
__Pyx_RefNannyDeclarations
#if CYTHON_REFNANNY
__Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
@@ -7652,26 +7158,11 @@ PyMODINIT_FUNC PyInit_bigwig_file(void)
#endif
/*--- Module creation code ---*/
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4("bigwig_file", __pyx_methods, __pyx_k_BigWig_file, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("bigwig_file"), __pyx_methods, __Pyx_DOCSTR(__pyx_k_14), 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- Py_INCREF(__pyx_d);
- __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_PYPY
- Py_INCREF(__pyx_b);
- #endif
- if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- /*--- Initialize various global constants etc. ---*/
- if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
- if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- if (__pyx_module_is_main_bx__bbi__bigwig_file) {
- if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- }
#if PY_MAJOR_VERSION >= 3
{
PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -7680,6 +7171,16 @@ PyMODINIT_FUNC PyInit_bigwig_file(void)
}
}
#endif
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_PYPY
+ Py_INCREF(__pyx_b);
+ #endif
+ if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ /*--- Initialize various global constants etc. ---*/
+ if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_module_is_main_bx__bbi__bigwig_file) {
+ if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ }
/*--- Builtin init code ---*/
if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Constants init code ---*/
@@ -7695,37 +7196,33 @@ PyMODINIT_FUNC PyInit_bigwig_file(void)
__pyx_vtable_2bx_3bbi_11bigwig_file_BigWigBlockHandler.__pyx_base.handle_block = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler *, PyObject *, struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *))__pyx_f_2bx_3bbi_11bigwig_file_18BigWigBlockHandler_handle_block;
__pyx_vtable_2bx_3bbi_11bigwig_file_BigWigBlockHandler.handle_interval_value = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float))__pyx_f_2bx_3bbi_11bigwig_file_18BigWigBlockHandler_handle_interval_value;
__pyx_type_2bx_3bbi_11bigwig_file_BigWigBlockHandler.tp_base = __pyx_ptype_2bx_3bbi_8bbi_file_BlockHandler;
- if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigwig_file_BigWigBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_type_2bx_3bbi_11bigwig_file_BigWigBlockHandler.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigwig_file_BigWigBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigwig_file_BigWigBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "BigWigBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigwig_file_BigWigBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigwig_file_BigWigBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigwig_file_BigWigBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigwig_file_BigWigBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "BigWigBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigwig_file_BigWigBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_2bx_3bbi_11bigwig_file_BigWigBlockHandler = &__pyx_type_2bx_3bbi_11bigwig_file_BigWigBlockHandler;
__pyx_vtabptr_2bx_3bbi_11bigwig_file_SummarizingBlockHandler = &__pyx_vtable_2bx_3bbi_11bigwig_file_SummarizingBlockHandler;
__pyx_vtable_2bx_3bbi_11bigwig_file_SummarizingBlockHandler.__pyx_base = *__pyx_vtabptr_2bx_3bbi_11bigwig_file_BigWigBlockHandler;
__pyx_vtable_2bx_3bbi_11bigwig_file_SummarizingBlockHandler.__pyx_base.handle_interval_value = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float))__pyx_f_2bx_3bbi_11bigwig_file_23SummarizingBlockHandler_handle_interval_value;
__pyx_type_2bx_3bbi_11bigwig_file_SummarizingBlockHandler.tp_base = __pyx_ptype_2bx_3bbi_11bigwig_file_BigWigBlockHandler;
- if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigwig_file_SummarizingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_type_2bx_3bbi_11bigwig_file_SummarizingBlockHandler.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigwig_file_SummarizingBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigwig_file_SummarizingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "SummarizingBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigwig_file_SummarizingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigwig_file_SummarizingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigwig_file_SummarizingBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigwig_file_SummarizingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "SummarizingBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigwig_file_SummarizingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_2bx_3bbi_11bigwig_file_SummarizingBlockHandler = &__pyx_type_2bx_3bbi_11bigwig_file_SummarizingBlockHandler;
__pyx_vtabptr_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler = &__pyx_vtable_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler;
__pyx_vtable_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler.__pyx_base = *__pyx_vtabptr_2bx_3bbi_11bigwig_file_BigWigBlockHandler;
__pyx_vtable_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler.__pyx_base.handle_interval_value = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float))__pyx_f_2bx_3bbi_11bigwig_file_32IntervalAccumulatingBlockHandler_handle_interval_value;
__pyx_type_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler.tp_base = __pyx_ptype_2bx_3bbi_11bigwig_file_BigWigBlockHandler;
- if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_type_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "IntervalAccumulatingBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IntervalAccumulatingBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler = &__pyx_type_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler;
__pyx_vtabptr_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler = &__pyx_vtable_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler;
__pyx_vtable_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler.__pyx_base = *__pyx_vtabptr_2bx_3bbi_11bigwig_file_BigWigBlockHandler;
__pyx_vtable_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler.__pyx_base.handle_interval_value = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float))__pyx_f_2bx_3bbi_11bigwig_file_29ArrayAccumulatingBlockHandler_handle_interval_value;
__pyx_type_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler.tp_base = __pyx_ptype_2bx_3bbi_11bigwig_file_BigWigBlockHandler;
- if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_type_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "ArrayAccumulatingBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "ArrayAccumulatingBlockHandler", (PyObject *)&__pyx_type_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler = &__pyx_type_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler;
__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile = __Pyx_ImportType("bx.bbi.bbi_file", "BBIFile", sizeof(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile), 1); if (unlikely(!__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile = (struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile*)__Pyx_GetVtable(__pyx_ptype_2bx_3bbi_8bbi_file_BBIFile->tp_dict); if (unlikely(!__pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -7735,10 +7232,9 @@ PyMODINIT_FUNC PyInit_bigwig_file(void)
__pyx_vtable_2bx_3bbi_11bigwig_file_BigWigFile.get = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int __pyx_skip_dispatch))__pyx_f_2bx_3bbi_11bigwig_file_10BigWigFile_get;
__pyx_vtable_2bx_3bbi_11bigwig_file_BigWigFile.get_as_array = (PyObject *(*)(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int __pyx_skip_dispatch))__pyx_f_2bx_3bbi_11bigwig_file_10BigWigFile_get_as_array;
__pyx_type_2bx_3bbi_11bigwig_file_BigWigFile.tp_base = __pyx_ptype_2bx_3bbi_8bbi_file_BBIFile;
- if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigwig_file_BigWigFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_type_2bx_3bbi_11bigwig_file_BigWigFile.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigwig_file_BigWigFile.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigwig_file_BigWigFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "BigWigFile", (PyObject *)&__pyx_type_2bx_3bbi_11bigwig_file_BigWigFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2bx_3bbi_11bigwig_file_BigWigFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_2bx_3bbi_11bigwig_file_BigWigFile.tp_dict, __pyx_vtabptr_2bx_3bbi_11bigwig_file_BigWigFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "BigWigFile", (PyObject *)&__pyx_type_2bx_3bbi_11bigwig_file_BigWigFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_2bx_3bbi_11bigwig_file_BigWigFile = &__pyx_type_2bx_3bbi_11bigwig_file_BigWigFile;
/*--- Type import code ---*/
__pyx_ptype_2bx_3bbi_8bpt_file_BPTFile = __Pyx_ImportType("bx.bbi.bpt_file", "BPTFile", sizeof(struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile), 1); if (unlikely(!__pyx_ptype_2bx_3bbi_8bpt_file_BPTFile)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -7751,10 +7247,10 @@ PyMODINIT_FUNC PyInit_bigwig_file(void)
#endif
0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -7762,133 +7258,128 @@ PyMODINIT_FUNC PyInit_bigwig_file(void)
/*--- Function import code ---*/
/*--- Execution code ---*/
- /* "bx/bbi/bigwig_file.pyx":6
+ /* "bx/bbi/bigwig_file.pyx":5
* """
*
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*/
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+ PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__deque));
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+ /* "bx/bbi/bigwig_file.pyx":8
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* from types cimport *
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- if (PyDict_SetItem(__pyx_d, __pyx_n_s_numpy, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__numpy, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "bx/bbi/bigwig_file.pyx":12
+ /* "bx/bbi/bigwig_file.pyx":11
* cimport numpy
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* from bx.misc.binary_file import BinaryFileReader # <<<<<<<<<<<<<<
* from cStringIO import StringIO
* import zlib
*/
- __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_n_s_BinaryFileReader);
- PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_BinaryFileReader);
- __Pyx_GIVEREF(__pyx_n_s_BinaryFileReader);
- __pyx_t_1 = __Pyx_Import(__pyx_n_s_bx_misc_binary_file, __pyx_t_2, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_n_s__BinaryFileReader));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__BinaryFileReader));
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- if (PyDict_SetItem(__pyx_d, __pyx_n_s_BinaryFileReader, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ /* "bx/bbi/bigwig_file.pyx":12
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* from bx.misc.binary_file import BinaryFileReader
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*
*/
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+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__StringIO);
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- /* "bx/bbi/bigwig_file.pyx":14
+ /* "bx/bbi/bigwig_file.pyx":13
* from bx.misc.binary_file import BinaryFileReader
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* import zlib # <<<<<<<<<<<<<<
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* DEF big_wig_sig = 0x888FFC26
*/
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/* "bx/bbi/bigwig_file.pyx":1
- * #cython: profile=False # <<<<<<<<<<<<<<
- * """
+ * """ # <<<<<<<<<<<<<<
* BigWig file.
+ * """
*/
__pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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- /* "../../lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":979
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goto __pyx_L0;
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__Pyx_XDECREF(__pyx_t_2);
if (__pyx_m) {
- if (__pyx_d) {
- __Pyx_AddTraceback("init bx.bbi.bigwig_file", __pyx_clineno, __pyx_lineno, __pyx_filename);
- }
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Py_DECREF(__pyx_m); __pyx_m = 0;
} else if (!PyErr_Occurred()) {
PyErr_SetString(PyExc_ImportError, "init bx.bbi.bigwig_file");
@@ -7902,7 +7393,7 @@ PyMODINIT_FUNC PyInit_bigwig_file(void)
#endif
}
-/* --- Runtime support code --- */
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#if CYTHON_REFNANNY
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
PyObject *m = NULL, *p = NULL;
@@ -7917,17 +7408,19 @@ end:
Py_XDECREF(m);
return (__Pyx_RefNannyAPIStruct *)r;
}
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-static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
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- if (unlikely(!result)) {
- PyErr_Format(PyExc_NameError,
-#if PY_MAJOR_VERSION >= 3
- "name '%U' is not defined", name);
-#else
- "name '%.200s' is not defined", PyString_AS_STRING(name));
-#endif
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
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+ result = PyObject_GetAttr(dict, name);
+ if (!result) {
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+ PyErr_Clear();
+ result = PyObject_GetAttr(__pyx_b, name);
+ }
+ if (!result) {
+ PyErr_SetObject(PyExc_NameError, name);
+ }
}
return result;
}
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more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
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goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
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goto bad;
invalid_keyword:
PyErr_Format(PyExc_TypeError,
#if PY_MAJOR_VERSION < 3
- "%.200s() got an unexpected keyword argument '%.200s'",
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function_name, PyString_AsString(key));
#else
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- }
- if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) {
- Py_ssize_t l = ms->sq_length(obj);
- if (likely(l >= 0)) {
- if (cstop < 0) {
- cstop += l;
- if (cstop < 0) cstop = 0;
- }
- if (cstart < 0) {
- cstart += l;
- if (cstart < 0) cstart = 0;
- }
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- goto bad;
- }
+static CYTHON_INLINE int __Pyx_IsLittleEndian(void) {
+ unsigned int n = 1;
+ return *(unsigned char*)(&n) != 0;
+}
+static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx,
+ __Pyx_BufFmt_StackElem* stack,
+ __Pyx_TypeInfo* type) {
+ stack[0].field = &ctx->root;
+ stack[0].parent_offset = 0;
+ ctx->root.type = type;
+ ctx->root.name = "buffer dtype";
+ ctx->root.offset = 0;
+ ctx->head = stack;
+ ctx->head->field = &ctx->root;
+ ctx->fmt_offset = 0;
+ ctx->head->parent_offset = 0;
+ ctx->new_packmode = '@';
+ ctx->enc_packmode = '@';
+ ctx->new_count = 1;
+ ctx->enc_count = 0;
+ ctx->enc_type = 0;
+ ctx->is_complex = 0;
+ ctx->is_valid_array = 0;
+ ctx->struct_alignment = 0;
+ while (type->typegroup == 'S') {
+ ++ctx->head;
+ ctx->head->field = type->fields;
+ ctx->head->parent_offset = 0;
+ type = type->fields->type;
+ }
+}
+static int __Pyx_BufFmt_ParseNumber(const char** ts) {
+ int count;
+ const char* t = *ts;
+ if (*t < '0' || *t > '9') {
+ return -1;
+ } else {
+ count = *t++ - '0';
+ while (*t >= '0' && *t < '9') {
+ count *= 10;
+ count += *t++ - '0';
}
- return ms->sq_slice(obj, cstart, cstop);
}
-#endif
- mp = Py_TYPE(obj)->tp_as_mapping;
- if (likely(mp && mp->mp_subscript))
-#endif
- {
- PyObject* result;
- PyObject *py_slice, *py_start, *py_stop;
- if (_py_slice) {
- py_slice = *_py_slice;
- } else {
- PyObject* owned_start = NULL;
- PyObject* owned_stop = NULL;
- if (_py_start) {
- py_start = *_py_start;
- } else {
- if (has_cstart) {
- owned_start = py_start = PyInt_FromSsize_t(cstart);
- if (unlikely(!py_start)) goto bad;
- } else
- py_start = Py_None;
- }
- if (_py_stop) {
- py_stop = *_py_stop;
- } else {
- if (has_cstop) {
- owned_stop = py_stop = PyInt_FromSsize_t(cstop);
- if (unlikely(!py_stop)) {
- Py_XDECREF(owned_start);
- goto bad;
- }
- } else
- py_stop = Py_None;
- }
- py_slice = PySlice_New(py_start, py_stop, Py_None);
- Py_XDECREF(owned_start);
- Py_XDECREF(owned_stop);
- if (unlikely(!py_slice)) goto bad;
- }
-#if CYTHON_COMPILING_IN_CPYTHON
- result = mp->mp_subscript(obj, py_slice);
-#else
- result = PyObject_GetItem(obj, py_slice);
-#endif
- if (!_py_slice) {
- Py_DECREF(py_slice);
- }
- return result;
+ *ts = t;
+ return count;
+}
+static int __Pyx_BufFmt_ExpectNumber(const char **ts) {
+ int number = __Pyx_BufFmt_ParseNumber(ts);
+ if (number == -1) /* First char was not a digit */
+ PyErr_Format(PyExc_ValueError,\
+ "Does not understand character buffer dtype format string ('%c')", **ts);
+ return number;
+}
+static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) {
+ PyErr_Format(PyExc_ValueError,
+ "Unexpected format string character: '%c'", ch);
+}
+static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) {
+ switch (ch) {
+ case 'c': return "'char'";
+ case 'b': return "'signed char'";
+ case 'B': return "'unsigned char'";
+ case 'h': return "'short'";
+ case 'H': return "'unsigned short'";
+ case 'i': return "'int'";
+ case 'I': return "'unsigned int'";
+ case 'l': return "'long'";
+ case 'L': return "'unsigned long'";
+ case 'q': return "'long long'";
+ case 'Q': return "'unsigned long long'";
+ case 'f': return (is_complex ? "'complex float'" : "'float'");
+ case 'd': return (is_complex ? "'complex double'" : "'double'");
+ case 'g': return (is_complex ? "'complex long double'" : "'long double'");
+ case 'T': return "a struct";
+ case 'O': return "Python object";
+ case 'P': return "a pointer";
+ case 's': case 'p': return "a string";
+ case 0: return "end";
+ default: return "unparseable format string";
+ }
+}
+static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) {
+ switch (ch) {
+ case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
+ case 'h': case 'H': return 2;
+ case 'i': case 'I': case 'l': case 'L': return 4;
+ case 'q': case 'Q': return 8;
+ case 'f': return (is_complex ? 8 : 4);
+ case 'd': return (is_complex ? 16 : 8);
+ case 'g': {
+ PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g')..");
+ return 0;
+ }
+ case 'O': case 'P': return sizeof(void*);
+ default:
+ __Pyx_BufFmt_RaiseUnexpectedChar(ch);
+ return 0;
+ }
+}
+static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) {
+ switch (ch) {
+ case 'c': case 'b': case 'B': case 's': case 'p': return 1;
+ case 'h': case 'H': return sizeof(short);
+ case 'i': case 'I': return sizeof(int);
+ case 'l': case 'L': return sizeof(long);
+ #ifdef HAVE_LONG_LONG
+ case 'q': case 'Q': return sizeof(PY_LONG_LONG);
+ #endif
+ case 'f': return sizeof(float) * (is_complex ? 2 : 1);
+ case 'd': return sizeof(double) * (is_complex ? 2 : 1);
+ case 'g': return sizeof(long double) * (is_complex ? 2 : 1);
+ case 'O': case 'P': return sizeof(void*);
+ default: {
+ __Pyx_BufFmt_RaiseUnexpectedChar(ch);
+ return 0;
}
- PyErr_Format(PyExc_TypeError,
- "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name);
-bad:
- return NULL;
+ }
}
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) {
- PyObject *self, *result;
- PyCFunction cfunc;
- cfunc = PyCFunction_GET_FUNCTION(func);
- self = PyCFunction_GET_SELF(func);
- if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
- return NULL;
- result = cfunc(self, arg);
- Py_LeaveRecursiveCall();
- if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
- PyErr_SetString(
- PyExc_SystemError,
- "NULL result without error in PyObject_Call");
+typedef struct { char c; short x; } __Pyx_st_short;
+typedef struct { char c; int x; } __Pyx_st_int;
+typedef struct { char c; long x; } __Pyx_st_long;
+typedef struct { char c; float x; } __Pyx_st_float;
+typedef struct { char c; double x; } __Pyx_st_double;
+typedef struct { char c; long double x; } __Pyx_st_longdouble;
+typedef struct { char c; void *x; } __Pyx_st_void_p;
+#ifdef HAVE_LONG_LONG
+typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong;
+#endif
+static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) {
+ switch (ch) {
+ case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
+ case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short);
+ case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int);
+ case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long);
+#ifdef HAVE_LONG_LONG
+ case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG);
+#endif
+ case 'f': return sizeof(__Pyx_st_float) - sizeof(float);
+ case 'd': return sizeof(__Pyx_st_double) - sizeof(double);
+ case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double);
+ case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*);
+ default:
+ __Pyx_BufFmt_RaiseUnexpectedChar(ch);
+ return 0;
+ }
+}
+/* These are for computing the padding at the end of the struct to align
+ on the first member of the struct. This will probably the same as above,
+ but we don't have any guarantees.
+ */
+typedef struct { short x; char c; } __Pyx_pad_short;
+typedef struct { int x; char c; } __Pyx_pad_int;
+typedef struct { long x; char c; } __Pyx_pad_long;
+typedef struct { float x; char c; } __Pyx_pad_float;
+typedef struct { double x; char c; } __Pyx_pad_double;
+typedef struct { long double x; char c; } __Pyx_pad_longdouble;
+typedef struct { void *x; char c; } __Pyx_pad_void_p;
+#ifdef HAVE_LONG_LONG
+typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong;
+#endif
+static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) {
+ switch (ch) {
+ case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
+ case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short);
+ case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int);
+ case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long);
+#ifdef HAVE_LONG_LONG
+ case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG);
+#endif
+ case 'f': return sizeof(__Pyx_pad_float) - sizeof(float);
+ case 'd': return sizeof(__Pyx_pad_double) - sizeof(double);
+ case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double);
+ case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*);
+ default:
+ __Pyx_BufFmt_RaiseUnexpectedChar(ch);
+ return 0;
+ }
+}
+static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) {
+ switch (ch) {
+ case 'c':
+ return 'H';
+ case 'b': case 'h': case 'i':
+ case 'l': case 'q': case 's': case 'p':
+ return 'I';
+ case 'B': case 'H': case 'I': case 'L': case 'Q':
+ return 'U';
+ case 'f': case 'd': case 'g':
+ return (is_complex ? 'C' : 'R');
+ case 'O':
+ return 'O';
+ case 'P':
+ return 'P';
+ default: {
+ __Pyx_BufFmt_RaiseUnexpectedChar(ch);
+ return 0;
}
- return result;
+ }
}
-#endif
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) {
- PyObject *result;
- PyObject *args = PyTuple_New(1);
- if (unlikely(!args)) return NULL;
- Py_INCREF(arg);
- PyTuple_SET_ITEM(args, 0, arg);
- result = __Pyx_PyObject_Call(func, args, NULL);
- Py_DECREF(args);
- return result;
+static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) {
+ if (ctx->head == NULL || ctx->head->field == &ctx->root) {
+ const char* expected;
+ const char* quote;
+ if (ctx->head == NULL) {
+ expected = "end";
+ quote = "";
+ } else {
+ expected = ctx->head->field->type->name;
+ quote = "'";
+ }
+ PyErr_Format(PyExc_ValueError,
+ "Buffer dtype mismatch, expected %s%s%s but got %s",
+ quote, expected, quote,
+ __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex));
+ } else {
+ __Pyx_StructField* field = ctx->head->field;
+ __Pyx_StructField* parent = (ctx->head - 1)->field;
+ PyErr_Format(PyExc_ValueError,
+ "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'",
+ field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex),
+ parent->type->name, field->name);
+ }
}
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
-#ifdef __Pyx_CyFunction_USED
- if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) {
-#else
- if (likely(PyCFunction_Check(func))) {
-#endif
- if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) {
- return __Pyx_PyObject_CallMethO(func, arg);
+static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) {
+ char group;
+ size_t size, offset, arraysize = 1;
+ if (ctx->enc_type == 0) return 0;
+ if (ctx->head->field->type->arraysize[0]) {
+ int i, ndim = 0;
+ if (ctx->enc_type == 's' || ctx->enc_type == 'p') {
+ ctx->is_valid_array = ctx->head->field->type->ndim == 1;
+ ndim = 1;
+ if (ctx->enc_count != ctx->head->field->type->arraysize[0]) {
+ PyErr_Format(PyExc_ValueError,
+ "Expected a dimension of size %zu, got %zu",
+ ctx->head->field->type->arraysize[0], ctx->enc_count);
+ return -1;
}
}
- return __Pyx__PyObject_CallOneArg(func, arg);
-}
-#else
-static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
- PyObject* args = PyTuple_Pack(1, arg);
- return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL;
-}
-#endif
-
-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
- PyObject *result;
-#if CYTHON_COMPILING_IN_CPYTHON
- result = PyDict_GetItem(__pyx_d, name);
- if (likely(result)) {
- Py_INCREF(result);
- } else {
-#else
- result = PyObject_GetItem(__pyx_d, name);
- if (!result) {
- PyErr_Clear();
-#endif
- result = __Pyx_GetBuiltinName(name);
+ if (!ctx->is_valid_array) {
+ PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d",
+ ctx->head->field->type->ndim, ndim);
+ return -1;
}
- return result;
-}
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
- PyErr_Format(PyExc_ValueError,
- "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack",
- index, (index == 1) ? "" : "s");
-}
-
-static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* exc_type = tstate->curexc_type;
- if (unlikely(exc_type)) {
- if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
- PyObject *exc_value, *exc_tb;
- exc_value = tstate->curexc_value;
- exc_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- Py_DECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_tb);
- return 0;
- } else {
- return -1;
- }
+ for (i = 0; i < ctx->head->field->type->ndim; i++) {
+ arraysize *= ctx->head->field->type->arraysize[i];
}
- return 0;
-#else
- if (unlikely(PyErr_Occurred())) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
- return 0;
- } else {
- return -1;
+ ctx->is_valid_array = 0;
+ ctx->enc_count = 1;
+ }
+ group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex);
+ do {
+ __Pyx_StructField* field = ctx->head->field;
+ __Pyx_TypeInfo* type = field->type;
+ if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') {
+ size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex);
+ } else {
+ size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex);
+ }
+ if (ctx->enc_packmode == '@') {
+ size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex);
+ size_t align_mod_offset;
+ if (align_at == 0) return -1;
+ align_mod_offset = ctx->fmt_offset % align_at;
+ if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset;
+ if (ctx->struct_alignment == 0)
+ ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type,
+ ctx->is_complex);
+ }
+ if (type->size != size || type->typegroup != group) {
+ if (type->typegroup == 'C' && type->fields != NULL) {
+ size_t parent_offset = ctx->head->parent_offset + field->offset;
+ ++ctx->head;
+ ctx->head->field = type->fields;
+ ctx->head->parent_offset = parent_offset;
+ continue;
+ }
+ if ((type->typegroup == 'H' || group == 'H') && type->size == size) {
+ } else {
+ __Pyx_BufFmt_RaiseExpected(ctx);
+ return -1;
+ }
+ }
+ offset = ctx->head->parent_offset + field->offset;
+ if (ctx->fmt_offset != offset) {
+ PyErr_Format(PyExc_ValueError,
+ "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected",
+ (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset);
+ return -1;
+ }
+ ctx->fmt_offset += size;
+ if (arraysize)
+ ctx->fmt_offset += (arraysize - 1) * size;
+ --ctx->enc_count; /* Consume from buffer string */
+ while (1) {
+ if (field == &ctx->root) {
+ ctx->head = NULL;
+ if (ctx->enc_count != 0) {
+ __Pyx_BufFmt_RaiseExpected(ctx);
+ return -1;
}
+ break; /* breaks both loops as ctx->enc_count == 0 */
+ }
+ ctx->head->field = ++field;
+ if (field->type == NULL) {
+ --ctx->head;
+ field = ctx->head->field;
+ continue;
+ } else if (field->type->typegroup == 'S') {
+ size_t parent_offset = ctx->head->parent_offset + field->offset;
+ if (field->type->fields->type == NULL) continue; /* empty struct */
+ field = field->type->fields;
+ ++ctx->head;
+ ctx->head->field = field;
+ ctx->head->parent_offset = parent_offset;
+ break;
+ } else {
+ break;
+ }
}
- return 0;
-#endif
+ } while (ctx->enc_count);
+ ctx->enc_type = 0;
+ ctx->is_complex = 0;
+ return 0;
}
-
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else {
- return __Pyx_IterFinish();
+static CYTHON_INLINE PyObject *
+__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp)
+{
+ const char *ts = *tsp;
+ int i = 0, number;
+ int ndim = ctx->head->field->type->ndim;
+;
+ ++ts;
+ if (ctx->new_count != 1) {
+ PyErr_SetString(PyExc_ValueError,
+ "Cannot handle repeated arrays in format string");
+ return NULL;
}
- return 0;
-}
-
-static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
- PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_SetSlice(
- PyObject* obj, PyObject* value, Py_ssize_t cstart, Py_ssize_t cstop,
- PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
- int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyMappingMethods* mp;
-#if PY_MAJOR_VERSION < 3
- PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence;
- if (likely(ms && ms->sq_ass_slice)) {
- if (!has_cstart) {
- if (_py_start && (*_py_start != Py_None)) {
- cstart = __Pyx_PyIndex_AsSsize_t(*_py_start);
- if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
- } else
- cstart = 0;
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ while (*ts && *ts != ')') {
+ if (isspace(*ts))
+ continue;
+ number = __Pyx_BufFmt_ExpectNumber(&ts);
+ if (number == -1) return NULL;
+ if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i])
+ return PyErr_Format(PyExc_ValueError,
+ "Expected a dimension of size %zu, got %d",
+ ctx->head->field->type->arraysize[i], number);
+ if (*ts != ',' && *ts != ')')
+ return PyErr_Format(PyExc_ValueError,
+ "Expected a comma in format string, got '%c'", *ts);
+ if (*ts == ',') ts++;
+ i++;
+ }
+ if (i != ndim)
+ return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d",
+ ctx->head->field->type->ndim, i);
+ if (!*ts) {
+ PyErr_SetString(PyExc_ValueError,
+ "Unexpected end of format string, expected ')'");
+ return NULL;
+ }
+ ctx->is_valid_array = 1;
+ ctx->new_count = 1;
+ *tsp = ++ts;
+ return Py_None;
+}
+static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) {
+ int got_Z = 0;
+ while (1) {
+ switch(*ts) {
+ case 0:
+ if (ctx->enc_type != 0 && ctx->head == NULL) {
+ __Pyx_BufFmt_RaiseExpected(ctx);
+ return NULL;
}
- if (!has_cstop) {
- if (_py_stop && (*_py_stop != Py_None)) {
- cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop);
- if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
- } else
- cstop = PY_SSIZE_T_MAX;
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ if (ctx->head != NULL) {
+ __Pyx_BufFmt_RaiseExpected(ctx);
+ return NULL;
}
- if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) {
- Py_ssize_t l = ms->sq_length(obj);
- if (likely(l >= 0)) {
- if (cstop < 0) {
- cstop += l;
- if (cstop < 0) cstop = 0;
- }
- if (cstart < 0) {
- cstart += l;
- if (cstart < 0) cstart = 0;
- }
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- goto bad;
- }
+ return ts;
+ case ' ':
+ case 10:
+ case 13:
+ ++ts;
+ break;
+ case '<':
+ if (!__Pyx_IsLittleEndian()) {
+ PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler");
+ return NULL;
}
- return ms->sq_ass_slice(obj, cstart, cstop, value);
- }
-#endif
- mp = Py_TYPE(obj)->tp_as_mapping;
- if (likely(mp && mp->mp_ass_subscript))
-#endif
- {
- int result;
- PyObject *py_slice, *py_start, *py_stop;
- if (_py_slice) {
- py_slice = *_py_slice;
+ ctx->new_packmode = '=';
+ ++ts;
+ break;
+ case '>':
+ case '!':
+ if (__Pyx_IsLittleEndian()) {
+ PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler");
+ return NULL;
+ }
+ ctx->new_packmode = '=';
+ ++ts;
+ break;
+ case '=':
+ case '@':
+ case '^':
+ ctx->new_packmode = *ts++;
+ break;
+ case 'T': /* substruct */
+ {
+ const char* ts_after_sub;
+ size_t i, struct_count = ctx->new_count;
+ size_t struct_alignment = ctx->struct_alignment;
+ ctx->new_count = 1;
+ ++ts;
+ if (*ts != '{') {
+ PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'");
+ return NULL;
+ }
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ ctx->enc_type = 0; /* Erase processed last struct element */
+ ctx->enc_count = 0;
+ ctx->struct_alignment = 0;
+ ++ts;
+ ts_after_sub = ts;
+ for (i = 0; i != struct_count; ++i) {
+ ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts);
+ if (!ts_after_sub) return NULL;
+ }
+ ts = ts_after_sub;
+ if (struct_alignment) ctx->struct_alignment = struct_alignment;
+ }
+ break;
+ case '}': /* end of substruct; either repeat or move on */
+ {
+ size_t alignment = ctx->struct_alignment;
+ ++ts;
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ ctx->enc_type = 0; /* Erase processed last struct element */
+ if (alignment && ctx->fmt_offset % alignment) {
+ ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment);
+ }
+ }
+ return ts;
+ case 'x':
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ ctx->fmt_offset += ctx->new_count;
+ ctx->new_count = 1;
+ ctx->enc_count = 0;
+ ctx->enc_type = 0;
+ ctx->enc_packmode = ctx->new_packmode;
+ ++ts;
+ break;
+ case 'Z':
+ got_Z = 1;
+ ++ts;
+ if (*ts != 'f' && *ts != 'd' && *ts != 'g') {
+ __Pyx_BufFmt_RaiseUnexpectedChar('Z');
+ return NULL;
+ } /* fall through */
+ case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I':
+ case 'l': case 'L': case 'q': case 'Q':
+ case 'f': case 'd': case 'g':
+ case 'O': case 's': case 'p':
+ if (ctx->enc_type == *ts && got_Z == ctx->is_complex &&
+ ctx->enc_packmode == ctx->new_packmode) {
+ ctx->enc_count += ctx->new_count;
} else {
- PyObject* owned_start = NULL;
- PyObject* owned_stop = NULL;
- if (_py_start) {
- py_start = *_py_start;
- } else {
- if (has_cstart) {
- owned_start = py_start = PyInt_FromSsize_t(cstart);
- if (unlikely(!py_start)) goto bad;
- } else
- py_start = Py_None;
- }
- if (_py_stop) {
- py_stop = *_py_stop;
- } else {
- if (has_cstop) {
- owned_stop = py_stop = PyInt_FromSsize_t(cstop);
- if (unlikely(!py_stop)) {
- Py_XDECREF(owned_start);
- goto bad;
- }
- } else
- py_stop = Py_None;
- }
- py_slice = PySlice_New(py_start, py_stop, Py_None);
- Py_XDECREF(owned_start);
- Py_XDECREF(owned_stop);
- if (unlikely(!py_slice)) goto bad;
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ ctx->enc_count = ctx->new_count;
+ ctx->enc_packmode = ctx->new_packmode;
+ ctx->enc_type = *ts;
+ ctx->is_complex = got_Z;
}
-#if CYTHON_COMPILING_IN_CPYTHON
- result = mp->mp_ass_subscript(obj, py_slice, value);
-#else
- result = value ? PyObject_SetItem(obj, py_slice, value) : PyObject_DelItem(obj, py_slice);
-#endif
- if (!_py_slice) {
- Py_DECREF(py_slice);
+ ++ts;
+ ctx->new_count = 1;
+ got_Z = 0;
+ break;
+ case ':':
+ ++ts;
+ while(*ts != ':') ++ts;
+ ++ts;
+ break;
+ case '(':
+ if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL;
+ break;
+ default:
+ {
+ int number = __Pyx_BufFmt_ExpectNumber(&ts);
+ if (number == -1) return NULL;
+ ctx->new_count = (size_t)number;
}
- return result;
- }
- PyErr_Format(PyExc_TypeError,
- "'%.200s' object does not support slice %.10s",
- Py_TYPE(obj)->tp_name, value ? "assignment" : "deletion");
-bad:
- return -1;
-}
-
-static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
- if (unlikely(!type)) {
- PyErr_SetString(PyExc_SystemError, "Missing type object");
- return 0;
}
- if (likely(PyObject_TypeCheck(obj, type)))
- return 1;
- PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
- Py_TYPE(obj)->tp_name, type->tp_name);
- return 0;
-}
-
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
- PyObject *r;
- if (!j) return NULL;
- r = PyObject_GetItem(o, j);
- Py_DECREF(j);
- return r;
+ }
}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
+static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) {
+ buf->buf = NULL;
+ buf->obj = NULL;
+ buf->strides = __Pyx_zeros;
+ buf->shape = __Pyx_zeros;
+ buf->suboffsets = __Pyx_minusones;
}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
+static CYTHON_INLINE int __Pyx_GetBufferAndValidate(
+ Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags,
+ int nd, int cast, __Pyx_BufFmt_StackElem* stack)
+{
+ if (obj == Py_None || obj == NULL) {
+ __Pyx_ZeroBuffer(buf);
+ return 0;
+ }
+ buf->buf = NULL;
+ if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail;
+ if (buf->ndim != nd) {
+ PyErr_Format(PyExc_ValueError,
+ "Buffer has wrong number of dimensions (expected %d, got %d)",
+ nd, buf->ndim);
+ goto fail;
+ }
+ if (!cast) {
+ __Pyx_BufFmt_Context ctx;
+ __Pyx_BufFmt_Init(&ctx, stack, dtype);
+ if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail;
+ }
+ if ((unsigned)buf->itemsize != dtype->size) {
+ PyErr_Format(PyExc_ValueError,
+ "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)",
+ buf->itemsize, (buf->itemsize > 1) ? "s" : "",
+ dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : "");
+ goto fail;
+ }
+ if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
+ return 0;
+fail:;
+ __Pyx_ZeroBuffer(buf);
+ return -1;
}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (is_list || PyList_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
- PyObject *r = PyList_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- }
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- } else {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- return NULL;
- }
- }
- return m->sq_item(o, i);
- }
- }
-#else
- if (is_list || PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) {
+ if (info->buf == NULL) return;
+ if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL;
+ __Pyx_ReleaseBuffer(info);
}
-static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) {
- int r;
- if (!j) return -1;
- r = PyObject_SetItem(o, j, v);
- Py_DECREF(j);
- return r;
-}
-static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
- int is_list, int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (is_list || PyList_CheckExact(o)) {
- Py_ssize_t n = (!wraparound) ? i : ((likely(i >= 0)) ? i : i + PyList_GET_SIZE(o));
- if ((!boundscheck) || likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
- PyObject* old = PyList_GET_ITEM(o, n);
- Py_INCREF(v);
- PyList_SET_ITEM(o, n, v);
- Py_DECREF(old);
- return 1;
- }
- } else {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_ass_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- return -1;
- }
- }
- return m->sq_ass_item(o, i, v);
- }
- }
-#else
-#if CYTHON_COMPILING_IN_PYPY
- if (is_list || (PySequence_Check(o) && !PyDict_Check(o))) {
-#else
- if (is_list || PySequence_Check(o)) {
-#endif
- return PySequence_SetItem(o, i, v);
- }
-#endif
- return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
+static void __Pyx_RaiseBufferIndexError(int axis) {
+ PyErr_Format(PyExc_IndexError,
+ "Out of bounds on buffer access (axis %d)", axis);
}
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
@@ -8574,988 +8149,415 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
*tb = tstate->curexc_traceback;
tstate->curexc_type = 0;
tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
-}
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
- Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
- Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- }
- if (PyType_Check(type)) {
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- value = type;
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *instance_class = NULL;
- if (value && PyExceptionInstance_Check(value)) {
- instance_class = (PyObject*) Py_TYPE(value);
- if (instance_class != type) {
- if (PyObject_IsSubclass(instance_class, type)) {
- type = instance_class;
- } else {
- instance_class = NULL;
- }
- }
- }
- if (!instance_class) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- } else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyObject_Call(type, args, NULL);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- }
- } else {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
-#if PY_VERSION_HEX >= 0x03030000
- if (cause) {
-#else
- if (cause && cause != Py_None) {
-#endif
- PyObject *fixed_cause;
- if (cause == Py_None) {
- fixed_cause = NULL;
- } else if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- } else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- } else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
-#if CYTHON_COMPILING_IN_PYPY
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyErr_Fetch(tmp_type, tmp_value, tmp_tb);
- Py_INCREF(tb);
- PyErr_Restore(tmp_type, tmp_value, tb);
- Py_XDECREF(tmp_tb);
-#else
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
-#endif
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-}
-
-static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_dealloc != current_tp_dealloc)
- type = type->tp_base;
- while (type && type->tp_dealloc == current_tp_dealloc)
- type = type->tp_base;
- if (type)
- type->tp_dealloc(obj);
-}
-
-static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_traverse != current_tp_traverse)
- type = type->tp_base;
- while (type && type->tp_traverse == current_tp_traverse)
- type = type->tp_base;
- if (type && type->tp_traverse)
- return type->tp_traverse(obj, v, a);
- return 0;
-}
-
-static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_clear != current_tp_clear)
- type = type->tp_base;
- while (type && type->tp_clear == current_tp_clear)
- type = type->tp_base;
- if (type && type->tp_clear)
- type->tp_clear(obj);
-}
-
-static void* __Pyx_GetVtable(PyObject *dict) {
- void* ptr;
- PyObject *ob = PyObject_GetItem(dict, __pyx_n_s_pyx_vtable);
- if (!ob)
- goto bad;
-#if PY_VERSION_HEX >= 0x02070000
- ptr = PyCapsule_GetPointer(ob, 0);
-#else
- ptr = PyCObject_AsVoidPtr(ob);
-#endif
- if (!ptr && !PyErr_Occurred())
- PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
- Py_DECREF(ob);
- return ptr;
-bad:
- Py_XDECREF(ob);
- return NULL;
-}
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
- PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
- if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
- PyErr_Format(PyExc_ImportError,
- #if PY_MAJOR_VERSION < 3
- "cannot import name %.230s", PyString_AS_STRING(name));
- #else
- "cannot import name %S", name);
- #endif
- }
- return value;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0,
- 0,
- 0,
- 0,
- 0,
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line,
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- __pyx_d, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import;
- py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0;
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \
- { \
- func_type value = func_value; \
- if (sizeof(target_type) < sizeof(func_type)) { \
- if (unlikely(value != (func_type) (target_type) value)) { \
- func_type zero = 0; \
- if (is_unsigned && unlikely(value < zero)) \
- goto raise_neg_overflow; \
- else \
- goto raise_overflow; \
- } \
- } \
- return (target_type) value; \
- }
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_As_unsigned_int(PyObject *x) {
- const unsigned int neg_one = (unsigned int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(unsigned int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (unsigned int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned int, digit, ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
- if (sizeof(unsigned int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(unsigned int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long long, PyLong_AsUnsignedLongLong(x))
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned int, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(unsigned int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (sizeof(unsigned int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, long, PyLong_AsLong(x))
- } else if (sizeof(unsigned int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned int, long long, PyLong_AsLongLong(x))
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+ tstate->curexc_traceback = 0;
#else
- unsigned int val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
+ PyErr_Fetch(type, value, tb);
#endif
- return (unsigned int) -1;
- }
- } else {
- unsigned int val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned int) -1;
- val = __Pyx_PyInt_As_unsigned_int(tmp);
- Py_DECREF(tmp);
- return val;
- }
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to unsigned int");
- return (unsigned int) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned int");
- return (unsigned int) -1;
}
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
- if (sizeof(int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x))
- }
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
+}
+
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+ PyErr_Format(PyExc_ValueError,
+ "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
+ index, (index == 1) ? "" : "s");
+}
+
+static CYTHON_INLINE int __Pyx_IterFinish(void) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* exc_type = tstate->curexc_type;
+ if (unlikely(exc_type)) {
+ if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
+ PyObject *exc_value, *exc_tb;
+ exc_value = tstate->curexc_value;
+ exc_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+ Py_DECREF(exc_type);
+ Py_XDECREF(exc_value);
+ Py_XDECREF(exc_tb);
+ return 0;
} else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x))
- } else if (sizeof(int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x))
- }
+ return -1;
}
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+ }
+ return 0;
#else
- int val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (int) -1;
+ if (unlikely(PyErr_Occurred())) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
+ PyErr_Clear();
+ return 0;
+ } else {
+ return -1;
}
- } else {
- int val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (int) -1;
- val = __Pyx_PyInt_As_int(tmp);
- Py_DECREF(tmp);
- return val;
}
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to int");
- return (int) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
+ return 0;
+#endif
}
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(long) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
+ if (unlikely(retval)) {
+ Py_DECREF(retval);
+ __Pyx_RaiseTooManyValuesError(expected);
+ return -1;
} else {
- if (sizeof(long) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(long),
- little, !is_unsigned);
+ return __Pyx_IterFinish();
}
+ return 0;
}
-static CYTHON_INLINE unsigned char __Pyx_PyInt_As_unsigned_char(PyObject *x) {
- const unsigned char neg_one = (unsigned char) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(unsigned char) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned char, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (unsigned char) val;
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
+ CYTHON_UNUSED PyObject *cause) {
+ Py_XINCREF(type);
+ if (!value || value == Py_None)
+ value = NULL;
+ else
+ Py_INCREF(value);
+ if (!tb || tb == Py_None)
+ tb = NULL;
+ else {
+ Py_INCREF(tb);
+ if (!PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ }
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyClass_Check(type)) {
+ #else
+ if (PyType_Check(type)) {
+ #endif
+#if CYTHON_COMPILING_IN_PYPY
+ if (!value) {
+ Py_INCREF(Py_None);
+ value = Py_None;
}
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned char, digit, ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
- if (sizeof(unsigned char) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(unsigned char, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(unsigned char) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned char, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ PyErr_NormalizeException(&type, &value, &tb);
+ } else {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ value = type;
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+ Py_INCREF(type);
}
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned char, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(unsigned char, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
}
- #endif
-#endif
- if (sizeof(unsigned char) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned char, long, PyLong_AsLong(x))
- } else if (sizeof(unsigned char) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned char, long long, PyLong_AsLongLong(x))
+ #else
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
}
+ #endif
+ }
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+#else /* Python 3+ */
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+ PyObject* owned_instance = NULL;
+ if (tb == Py_None) {
+ tb = 0;
+ } else if (tb && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto bad;
+ }
+ if (value == Py_None)
+ value = 0;
+ if (PyExceptionInstance_Check(type)) {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto bad;
}
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- unsigned char val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (unsigned char) -1;
+ value = type;
+ type = (PyObject*) Py_TYPE(value);
+ } else if (PyExceptionClass_Check(type)) {
+ PyObject *args;
+ if (!value)
+ args = PyTuple_New(0);
+ else if (PyTuple_Check(value)) {
+ Py_INCREF(value);
+ args = value;
+ }
+ else
+ args = PyTuple_Pack(1, value);
+ if (!args)
+ goto bad;
+ owned_instance = PyEval_CallObject(type, args);
+ Py_DECREF(args);
+ if (!owned_instance)
+ goto bad;
+ value = owned_instance;
+ if (!PyExceptionInstance_Check(value)) {
+ PyErr_Format(PyExc_TypeError,
+ "calling %R should have returned an instance of "
+ "BaseException, not %R",
+ type, Py_TYPE(value));
+ goto bad;
}
} else {
- unsigned char val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned char) -1;
- val = __Pyx_PyInt_As_unsigned_char(tmp);
- Py_DECREF(tmp);
- return val;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto bad;
}
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to unsigned char");
- return (unsigned char) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned char");
- return (unsigned char) -1;
-}
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_As_unsigned_short(PyObject *x) {
- const unsigned short neg_one = (unsigned short) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(unsigned short) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned short, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (unsigned short) val;
+ if (cause && cause != Py_None) {
+ PyObject *fixed_cause;
+ if (PyExceptionClass_Check(cause)) {
+ fixed_cause = PyObject_CallObject(cause, NULL);
+ if (fixed_cause == NULL)
+ goto bad;
}
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned short, digit, ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
- if (sizeof(unsigned short) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(unsigned short, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(unsigned short) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned short, unsigned long long, PyLong_AsUnsignedLongLong(x))
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned short, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(unsigned short, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (sizeof(unsigned short) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned short, long, PyLong_AsLong(x))
- } else if (sizeof(unsigned short) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned short, long long, PyLong_AsLongLong(x))
- }
+ else if (PyExceptionInstance_Check(cause)) {
+ fixed_cause = cause;
+ Py_INCREF(fixed_cause);
}
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- unsigned short val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (unsigned short) -1;
+ else {
+ PyErr_SetString(PyExc_TypeError,
+ "exception causes must derive from "
+ "BaseException");
+ goto bad;
+ }
+ PyException_SetCause(value, fixed_cause);
+ }
+ PyErr_SetObject(type, value);
+ if (tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* tmp_tb = tstate->curexc_traceback;
+ if (tb != tmp_tb) {
+ Py_INCREF(tb);
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_tb);
}
- } else {
- unsigned short val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned short) -1;
- val = __Pyx_PyInt_As_unsigned_short(tmp);
- Py_DECREF(tmp);
- return val;
}
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to unsigned short");
- return (unsigned short) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned short");
- return (unsigned short) -1;
+bad:
+ Py_XDECREF(owned_instance);
+ return;
+}
+#endif
+
+static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
+}
+
+static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) {
+ PyTypeObject* type = Py_TYPE(obj);
+ while (type && type->tp_dealloc != current_tp_dealloc)
+ type = type->tp_base;
+ while (type && type->tp_dealloc == current_tp_dealloc)
+ type = type->tp_base;
+ if (type)
+ type->tp_dealloc(obj);
}
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_short(unsigned short value) {
- const unsigned short neg_one = (unsigned short) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(unsigned short) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(unsigned short) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(unsigned short) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(unsigned short) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(unsigned short) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(unsigned short),
- little, !is_unsigned);
- }
+static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
+ PyTypeObject* type = Py_TYPE(obj);
+ while (type && type->tp_traverse != current_tp_traverse)
+ type = type->tp_base;
+ while (type && type->tp_traverse == current_tp_traverse)
+ type = type->tp_base;
+ if (type && type->tp_traverse)
+ return type->tp_traverse(obj, v, a);
+ return 0;
}
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(int) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
+static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
+ PyTypeObject* type = Py_TYPE(obj);
+ while (type && type->tp_clear != current_tp_clear)
+ type = type->tp_base;
+ while (type && type->tp_clear == current_tp_clear)
+ type = type->tp_base;
+ if (type && type->tp_clear)
+ type->tp_clear(obj);
+}
+
+#if PY_MAJOR_VERSION < 3
+static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
+ CYTHON_UNUSED PyObject *getbuffer_cobj;
+ #if PY_VERSION_HEX >= 0x02060000
+ if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags);
+ #endif
+ if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags);
+ #if PY_VERSION_HEX < 0x02060000
+ if (obj->ob_type->tp_dict &&
+ (getbuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
+ "__pyx_getbuffer"))) {
+ getbufferproc func;
+ #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
+ func = (getbufferproc) PyCapsule_GetPointer(getbuffer_cobj, "getbuffer(obj, view, flags)");
+ #else
+ func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj);
+ #endif
+ Py_DECREF(getbuffer_cobj);
+ if (!func)
+ goto fail;
+ return func(obj, view, flags);
} else {
- if (sizeof(int) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
+ PyErr_Clear();
}
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(int),
- little, !is_unsigned);
+ #endif
+ PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
+#if PY_VERSION_HEX < 0x02060000
+fail:
+#endif
+ return -1;
+}
+static void __Pyx_ReleaseBuffer(Py_buffer *view) {
+ PyObject *obj = view->obj;
+ CYTHON_UNUSED PyObject *releasebuffer_cobj;
+ if (!obj) return;
+ #if PY_VERSION_HEX >= 0x02060000
+ if (PyObject_CheckBuffer(obj)) {
+ PyBuffer_Release(view);
+ return;
}
+ #endif
+ if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; }
+ #if PY_VERSION_HEX < 0x02060000
+ if (obj->ob_type->tp_dict &&
+ (releasebuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
+ "__pyx_releasebuffer"))) {
+ releasebufferproc func;
+ #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
+ func = (releasebufferproc) PyCapsule_GetPointer(releasebuffer_cobj, "releasebuffer(obj, view)");
+ #else
+ func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj);
+ #endif
+ Py_DECREF(releasebuffer_cobj);
+ if (!func)
+ goto fail;
+ func(obj, view);
+ return;
+ } else {
+ PyErr_Clear();
+ }
+ #endif
+ goto nofail;
+#if PY_VERSION_HEX < 0x02060000
+fail:
+#endif
+ PyErr_WriteUnraisable(obj);
+nofail:
+ Py_DECREF(obj);
+ view->obj = NULL;
}
+#endif /* PY_MAJOR_VERSION < 3 */
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_int(unsigned int value) {
- const unsigned int neg_one = (unsigned int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(unsigned int) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(unsigned int) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(unsigned int) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+
+ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
+ PyObject *empty_list = 0;
+ PyObject *module = 0;
+ PyObject *global_dict = 0;
+ PyObject *empty_dict = 0;
+ PyObject *list;
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_import = 0;
+ py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
+ if (!py_import)
+ goto bad;
+ #endif
+ if (from_list)
+ list = from_list;
+ else {
+ empty_list = PyList_New(0);
+ if (!empty_list)
+ goto bad;
+ list = empty_list;
+ }
+ global_dict = PyModule_GetDict(__pyx_m);
+ if (!global_dict)
+ goto bad;
+ empty_dict = PyDict_New();
+ if (!empty_dict)
+ goto bad;
+ #if PY_VERSION_HEX >= 0x02050000
+ {
+ #if PY_MAJOR_VERSION >= 3
+ if (level == -1) {
+ if (strchr(__Pyx_MODULE_NAME, '.')) {
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_level = PyInt_FromLong(1);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, 1);
+ #endif
+ if (!module) {
+ if (!PyErr_ExceptionMatches(PyExc_ImportError))
+ goto bad;
+ PyErr_Clear();
+ }
+ }
+ level = 0; /* try absolute import on failure */
}
- } else {
- if (sizeof(unsigned int) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(unsigned int) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ #endif
+ if (!module) {
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_level = PyInt_FromLong(level);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, level);
+ #endif
}
}
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(unsigned int),
- little, !is_unsigned);
+ #else
+ if (level>0) {
+ PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
+ goto bad;
}
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, NULL);
+ #endif
+bad:
+ #if PY_VERSION_HEX < 0x03030000
+ Py_XDECREF(py_import);
+ #endif
+ Py_XDECREF(empty_list);
+ Py_XDECREF(empty_dict);
+ return module;
+}
+
+static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
+#if PY_MAJOR_VERSION < 3
+ PyErr_Format(PyExc_ImportError, "cannot import name %.230s",
+ PyString_AsString(name));
+#else
+ PyErr_Format(PyExc_ImportError, "cannot import name %S", name);
+#endif
}
#if CYTHON_CCOMPLEX
@@ -9798,99 +8800,404 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_int(unsigned int value)
#endif
#endif
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
- const long neg_one = (long) -1, const_zero = 0;
+static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
+ const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned char" :
+ "value too large to convert to unsigned char");
+ }
+ return (unsigned char)-1;
+ }
+ return (unsigned char)val;
+ }
+ return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
+ const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned short" :
+ "value too large to convert to unsigned short");
+ }
+ return (unsigned short)-1;
+ }
+ return (unsigned short)val;
+ }
+ return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
+ const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned int" :
+ "value too large to convert to unsigned int");
+ }
+ return (unsigned int)-1;
+ }
+ return (unsigned int)val;
+ }
+ return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
+ const char neg_one = (char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to char" :
+ "value too large to convert to char");
+ }
+ return (char)-1;
+ }
+ return (char)val;
+ }
+ return (char)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
+ const short neg_one = (short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to short" :
+ "value too large to convert to short");
+ }
+ return (short)-1;
+ }
+ return (short)val;
+ }
+ return (short)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
+ const int neg_one = (int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to int" :
+ "value too large to convert to int");
+ }
+ return (int)-1;
+ }
+ return (int)val;
+ }
+ return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
+ const signed char neg_one = (signed char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed char" :
+ "value too large to convert to signed char");
+ }
+ return (signed char)-1;
+ }
+ return (signed char)val;
+ }
+ return (signed char)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
+ const signed short neg_one = (signed short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed short" :
+ "value too large to convert to signed short");
+ }
+ return (signed short)-1;
+ }
+ return (signed short)val;
+ }
+ return (signed short)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
+ const signed int neg_one = (signed int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed int" :
+ "value too large to convert to signed int");
+ }
+ return (signed int)-1;
+ }
+ return (signed int)val;
+ }
+ return (signed int)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
+ const int neg_one = (int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to int" :
+ "value too large to convert to int");
+ }
+ return (int)-1;
+ }
+ return (int)val;
+ }
+ return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
+ const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return (unsigned long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return (unsigned long)PyLong_AsUnsignedLong(x);
+ } else {
+ return (unsigned long)PyLong_AsLong(x);
+ }
+ } else {
+ unsigned long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned long)-1;
+ val = __Pyx_PyInt_AsUnsignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
+ const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return (unsigned PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
+ } else {
+ return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
+ }
+ } else {
+ unsigned PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
+ const long neg_one = (long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long)-1;
+ }
+ return (long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long)-1;
+ }
+ return (long)PyLong_AsUnsignedLong(x);
+ } else {
+ return (long)PyLong_AsLong(x);
+ }
+ } else {
+ long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (long)-1;
+ val = __Pyx_PyInt_AsLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
+ const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to PY_LONG_LONG");
+ return (PY_LONG_LONG)-1;
+ }
+ return (PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to PY_LONG_LONG");
+ return (PY_LONG_LONG)-1;
+ }
+ return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
+ } else {
+ return (PY_LONG_LONG)PyLong_AsLongLong(x);
+ }
+ } else {
+ PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
+ const signed long neg_one = (signed long)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
+#if PY_VERSION_HEX < 0x03000000
if (likely(PyInt_Check(x))) {
- if (sizeof(long) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x))
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- goto raise_neg_overflow;
- }
- return (long) val;
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed long");
+ return (signed long)-1;
}
+ return (signed long)val;
} else
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
if (unlikely(Py_SIZE(x) < 0)) {
- goto raise_neg_overflow;
- }
- if (sizeof(long) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed long");
+ return (signed long)-1;
}
+ return (signed long)PyLong_AsUnsignedLong(x);
} else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
- }
- #endif
-#endif
- if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x))
- } else if (sizeof(long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x))
- }
+ return (signed long)PyLong_AsLong(x);
}
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- long val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
+ } else {
+ signed long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (signed long)-1;
+ val = __Pyx_PyInt_AsSignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
+ const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed PY_LONG_LONG");
+ return (signed PY_LONG_LONG)-1;
+ }
+ return (signed PY_LONG_LONG)val;
+ } else
#endif
- return (long) -1;
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed PY_LONG_LONG");
+ return (signed PY_LONG_LONG)-1;
+ }
+ return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
+ } else {
+ return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
}
} else {
- long val;
+ signed PY_LONG_LONG val;
PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long) -1;
- val = __Pyx_PyInt_As_long(tmp);
+ if (!tmp) return (signed PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsSignedLongLong(tmp);
Py_DECREF(tmp);
return val;
}
-raise_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to long");
- return (long) -1;
-raise_neg_overflow:
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
}
static int __Pyx_check_binary_version(void) {
@@ -9903,7 +9210,11 @@ static int __Pyx_check_binary_version(void) {
"compiletime version %s of module '%.100s' "
"does not match runtime version %s",
ctversion, __Pyx_MODULE_NAME, rtversion);
+ #if PY_VERSION_HEX < 0x02050000
+ return PyErr_Warn(NULL, message);
+ #else
return PyErr_WarnEx(NULL, message, 1);
+ #endif
}
return 0;
}
@@ -9953,7 +9264,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
goto bad;
if (!PyType_Check(result)) {
PyErr_Format(PyExc_TypeError,
- "%.200s.%.200s is not a type object",
+ "%s.%s is not a type object",
module_name, class_name);
goto bad;
}
@@ -9973,11 +9284,15 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyErr_Warn(NULL, warning) < 0) goto bad;
+ #else
if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
+ #endif
}
else if ((size_t)basicsize != size) {
PyErr_Format(PyExc_ValueError,
- "%.200s.%.200s has the wrong size, try recompiling",
+ "%s.%s has the wrong size, try recompiling",
module_name, class_name);
goto bad;
}
@@ -9989,6 +9304,204 @@ bad:
}
#endif
+static void* __Pyx_GetVtable(PyObject *dict) {
+ void* ptr;
+ PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
+ if (!ob)
+ goto bad;
+#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
+ ptr = PyCapsule_GetPointer(ob, 0);
+#else
+ ptr = PyCObject_AsVoidPtr(ob);
+#endif
+ if (!ptr && !PyErr_Occurred())
+ PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
+ Py_DECREF(ob);
+ return ptr;
+bad:
+ Py_XDECREF(ob);
+ return NULL;
+}
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
+#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
+ PyObject *ob = PyCapsule_New(vtable, 0, 0);
+#else
+ PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
+#endif
+ if (!ob)
+ goto bad;
+ if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
+ goto bad;
+ Py_DECREF(ob);
+ return 0;
+bad:
+ Py_XDECREF(ob);
+ return -1;
+}
+
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
+ int start = 0, mid = 0, end = count - 1;
+ if (end >= 0 && code_line > entries[end].code_line) {
+ return count;
+ }
+ while (start < end) {
+ mid = (start + end) / 2;
+ if (code_line < entries[mid].code_line) {
+ end = mid;
+ } else if (code_line > entries[mid].code_line) {
+ start = mid + 1;
+ } else {
+ return mid;
+ }
+ }
+ if (code_line <= entries[mid].code_line) {
+ return mid;
+ } else {
+ return mid + 1;
+ }
+}
+static PyCodeObject *__pyx_find_code_object(int code_line) {
+ PyCodeObject* code_object;
+ int pos;
+ if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
+ return NULL;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
+ return NULL;
+ }
+ code_object = __pyx_code_cache.entries[pos].code_object;
+ Py_INCREF(code_object);
+ return code_object;
+}
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
+ int pos, i;
+ __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
+ if (unlikely(!code_line)) {
+ return;
+ }
+ if (unlikely(!entries)) {
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (likely(entries)) {
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = 64;
+ __pyx_code_cache.count = 1;
+ entries[0].code_line = code_line;
+ entries[0].code_object = code_object;
+ Py_INCREF(code_object);
+ }
+ return;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
+ PyCodeObject* tmp = entries[pos].code_object;
+ entries[pos].code_object = code_object;
+ Py_DECREF(tmp);
+ return;
+ }
+ if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
+ int new_max = __pyx_code_cache.max_count + 64;
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
+ __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (unlikely(!entries)) {
+ return;
+ }
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = new_max;
+ }
+ for (i=__pyx_code_cache.count; i>pos; i--) {
+ entries[i] = entries[i-1];
+ }
+ entries[pos].code_line = code_line;
+ entries[pos].code_object = code_object;
+ __pyx_code_cache.count++;
+ Py_INCREF(code_object);
+}
+
+#include "compile.h"
+#include "frameobject.h"
+#include "traceback.h"
+static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
+ const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
+ PyObject *py_srcfile = 0;
+ PyObject *py_funcname = 0;
+ #if PY_MAJOR_VERSION < 3
+ py_srcfile = PyString_FromString(filename);
+ #else
+ py_srcfile = PyUnicode_FromString(filename);
+ #endif
+ if (!py_srcfile) goto bad;
+ if (c_line) {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ #else
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ #endif
+ }
+ else {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromString(funcname);
+ #else
+ py_funcname = PyUnicode_FromString(funcname);
+ #endif
+ }
+ if (!py_funcname) goto bad;
+ py_code = __Pyx_PyCode_New(
+ 0, /*int argcount,*/
+ 0, /*int kwonlyargcount,*/
+ 0, /*int nlocals,*/
+ 0, /*int stacksize,*/
+ 0, /*int flags,*/
+ __pyx_empty_bytes, /*PyObject *code,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
+ py_srcfile, /*PyObject *filename,*/
+ py_funcname, /*PyObject *name,*/
+ py_line, /*int firstlineno,*/
+ __pyx_empty_bytes /*PyObject *lnotab*/
+ );
+ Py_DECREF(py_srcfile);
+ Py_DECREF(py_funcname);
+ return py_code;
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ return NULL;
+}
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
+ PyObject *py_globals = 0;
+ PyFrameObject *py_frame = 0;
+ py_code = __pyx_find_code_object(c_line ? c_line : py_line);
+ if (!py_code) {
+ py_code = __Pyx_CreateCodeObjectForTraceback(
+ funcname, c_line, py_line, filename);
+ if (!py_code) goto bad;
+ __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
+ }
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
+ py_frame = PyFrame_New(
+ PyThreadState_GET(), /*PyThreadState *tstate,*/
+ py_code, /*PyCodeObject *code,*/
+ py_globals, /*PyObject *globals,*/
+ 0 /*PyObject *locals*/
+ );
+ if (!py_frame) goto bad;
+ py_frame->f_lineno = py_line;
+ PyTraceBack_Here(py_frame);
+bad:
+ Py_XDECREF(py_code);
+ Py_XDECREF(py_frame);
+}
+
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
while (t->p) {
#if PY_MAJOR_VERSION < 3
@@ -9999,7 +9512,7 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
} else {
*t->p = PyString_FromStringAndSize(t->s, t->n - 1);
}
- #else
+ #else /* Python 3+ has unicode identifiers */
if (t->is_unicode | t->is_str) {
if (t->intern) {
*t->p = PyUnicode_InternFromString(t->s);
@@ -10019,71 +9532,6 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
return 0;
}
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
- return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
- Py_ssize_t ignore;
- return __Pyx_PyObject_AsStringAndSize(o, &ignore);
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
- if (
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- __Pyx_sys_getdefaultencoding_not_ascii &&
-#endif
- PyUnicode_Check(o)) {
-#if PY_VERSION_HEX < 0x03030000
- char* defenc_c;
- PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
- if (!defenc) return NULL;
- defenc_c = PyBytes_AS_STRING(defenc);
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- {
- char* end = defenc_c + PyBytes_GET_SIZE(defenc);
- char* c;
- for (c = defenc_c; c < end; c++) {
- if ((unsigned char) (*c) >= 128) {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
- }
- }
-#endif
- *length = PyBytes_GET_SIZE(defenc);
- return defenc_c;
-#else
- if (__Pyx_PyUnicode_READY(o) == -1) return NULL;
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- if (PyUnicode_IS_ASCII(o)) {
- *length = PyUnicode_GET_LENGTH(o);
- return PyUnicode_AsUTF8(o);
- } else {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
-#else
- return PyUnicode_AsUTF8AndSize(o, length);
-#endif
-#endif
- } else
-#endif
-#if !CYTHON_COMPILING_IN_PYPY
- if (PyByteArray_Check(o)) {
- *length = PyByteArray_GET_SIZE(o);
- return PyByteArray_AS_STRING(o);
- } else
-#endif
- {
- char* result;
- int r = PyBytes_AsStringAndSize(o, &result, length);
- if (unlikely(r < 0)) {
- return NULL;
- } else {
- return result;
- }
- }
-}
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
int is_true = x == Py_True;
if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
@@ -10093,14 +9541,14 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
PyNumberMethods *m;
const char *name = NULL;
PyObject *res = NULL;
-#if PY_MAJOR_VERSION < 3
+#if PY_VERSION_HEX < 0x03000000
if (PyInt_Check(x) || PyLong_Check(x))
#else
if (PyLong_Check(x))
#endif
return Py_INCREF(x), x;
m = Py_TYPE(x)->tp_as_number;
-#if PY_MAJOR_VERSION < 3
+#if PY_VERSION_HEX < 0x03000000
if (m && m->nb_int) {
name = "int";
res = PyNumber_Int(x);
@@ -10116,13 +9564,13 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
}
#endif
if (res) {
-#if PY_MAJOR_VERSION < 3
+#if PY_VERSION_HEX < 0x03000000
if (!PyInt_Check(res) && !PyLong_Check(res)) {
#else
if (!PyLong_Check(res)) {
#endif
PyErr_Format(PyExc_TypeError,
- "__%.4s__ returned non-%.4s (type %.200s)",
+ "__%s__ returned non-%s (type %.200s)",
name, name, Py_TYPE(res)->tp_name);
Py_DECREF(res);
return NULL;
@@ -10136,31 +9584,35 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
}
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_ssize_t ival;
- PyObject *x;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_CheckExact(b)))
- return PyInt_AS_LONG(b);
-#endif
- if (likely(PyLong_CheckExact(b))) {
- #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(b)) {
- case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0];
- case 0: return 0;
- case 1: return ((PyLongObject*)b)->ob_digit[0];
- }
- #endif
- #endif
- return PyLong_AsSsize_t(b);
- }
- x = PyNumber_Index(b);
+ PyObject* x = PyNumber_Index(b);
if (!x) return -1;
ival = PyInt_AsSsize_t(x);
Py_DECREF(x);
return ival;
}
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
- return PyInt_FromSize_t(ival);
+#if PY_VERSION_HEX < 0x02050000
+ if (ival <= LONG_MAX)
+ return PyInt_FromLong((long)ival);
+ else {
+ unsigned char *bytes = (unsigned char *) &ival;
+ int one = 1; int little = (int)*(unsigned char*)&one;
+ return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
+ }
+#else
+ return PyInt_FromSize_t(ival);
+#endif
+}
+static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
+ unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
+ if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
+ return (size_t)-1;
+ } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to size_t");
+ return (size_t)-1;
+ }
+ return (size_t)val;
}
diff --git a/lib/bx/bbi/bigwig_file.pyx b/lib/bx/bbi/bigwig_file.pyx
index 73ec601..20c8d82 100644
--- a/lib/bx/bbi/bigwig_file.pyx
+++ b/lib/bx/bbi/bigwig_file.pyx
@@ -1,4 +1,3 @@
-#cython: profile=False
"""
BigWig file.
"""
@@ -21,10 +20,6 @@ DEF bwg_fixed_step = 3
cdef inline int range_intersection( int start1, int end1, int start2, int end2 ):
return min( end1, end2 ) - max( start1, start2 )
-def chunks(l, n):
- n = max(1, n)
- return [l[i:i + n] for i in range(0, len(l), n)]
-
cdef class BigWigBlockHandler( BlockHandler ):
"""
BlockHandler that parses the block into a series of wiggle records, and calls `handle_interval_value` for each.
@@ -44,22 +39,29 @@ cdef class BigWigBlockHandler( BlockHandler ):
cdef float val
# Now we parse the block, first the header
block_reader = BinaryFileReader( StringIO( block_data ), is_little_endian=bbi_file.reader.is_little_endian )
- # _ is skipped byte
- b_chrom_id, b_start, b_end, b_item_step, b_item_span, b_type, _, b_item_count = block_reader.read_and_unpack("LLLLLBBH", 5*4+1+1+2)
-
- if b_type == bwg_bed_graph:
- # [(start, end, val), ...]
- sevs = chunks(block_reader.read_and_unpack("LLf" * b_item_count, (2 * 4 + 4) * b_item_count), 3)
- elif b_type == bwg_variable_step:
- svs = chunks(block_reader.read_and_unpack("Lf" * b_item_count, (4 + 4) * b_item_count), 2)
- sevs = [(s, s + b_item_span, v) for s, v in svs]
- elif b_type == bwg_fixed_step:
- vs = block_reader.read_and_unpack("f" * b_item_count, 4 * b_item_count)
- sevs = [(b_start + (i * b_item_span), b_start + (i * b_item_span) + b_item_span, v) for i, v in enumerate(vs)]
-
- # TODO: change handle_interval to take a numpy array and this will be
- # much faster.
- for s, e, val in sevs:
+ b_chrom_id = block_reader.read_uint32()
+ b_start = block_reader.read_uint32()
+ b_end = block_reader.read_uint32()
+ b_item_step = block_reader.read_uint32()
+ b_item_span = block_reader.read_uint32()
+ b_type = block_reader.read_uint8()
+ block_reader.skip(1)
+ b_item_count = block_reader.read_uint16()
+ for i from 0 <= i < b_item_count:
+ # Depending on the type, s and e are either read or
+ # generate using header, val is always read
+ if b_type == bwg_bed_graph:
+ s = block_reader.read_uint32()
+ e = block_reader.read_uint32()
+ val = block_reader.read_float()
+ elif b_type == bwg_variable_step:
+ s = block_reader.read_uint32()
+ e = s + b_item_span
+ val = block_reader.read_float()
+ elif b_type == bwg_fixed_step:
+ s = b_start + ( i * b_item_span )
+ e = s + b_item_span
+ val = block_reader.read_float()
if s < self.start:
s = self.start
if e > self.end:
@@ -80,10 +82,12 @@ cdef class SummarizingBlockHandler( BigWigBlockHandler ):
BigWigBlockHandler.__init__( self, start, end )
# What we will load into
self.sd = SummarizedData( start, end, summary_size )
- self.sd.min_val[:] = numpy.inf
- self.sd.max_val[:] = -numpy.inf
+ for i in range(summary_size):
+ self.sd.min_val[i] = +numpy.inf
+ for i in range(summary_size):
+ self.sd.max_val[i] = -numpy.inf
- cdef inline handle_interval_value( self, bits32 s, bits32 e, float val ):
+ cdef handle_interval_value( self, bits32 s, bits32 e, float val ):
self.sd.accumulate_interval_value( s, e, val )
cdef class IntervalAccumulatingBlockHandler( BigWigBlockHandler ):
@@ -109,9 +113,11 @@ cdef class ArrayAccumulatingBlockHandler( BigWigBlockHandler ):
self.array[...] = numpy.nan
cdef handle_interval_value( self, bits32 s, bits32 e, float val ):
- #cdef numpy.ndarray[ numpy.float32_t, ndim=1 ] array = self.array
- # Slicing is optimized by Cython
- self.array[s - self.start:e - self.start] = val
+ cdef numpy.ndarray[ numpy.float32_t, ndim=1 ] array = self.array
+ cdef int i
+ # Slicing is not optimized by Cython
+ for i from s - self.start <= i < e - self.start:
+ array[ i ] = val
cdef class BigWigFile( BBIFile ):
"""
diff --git a/lib/bx/bbi/bigwig_tests.py b/lib/bx/bbi/bigwig_tests.py
index 6d4f355..1bb5176 100644
--- a/lib/bx/bbi/bigwig_tests.py
+++ b/lib/bx/bbi/bigwig_tests.py
@@ -1,6 +1,7 @@
import sys, os
import unittest
import numpy
+from functools import partial
try:
sys.path.insert(0, os.path.dirname(os.path.dirname(__file__)))
@@ -24,6 +25,7 @@ class TestBigWig(unittest.TestCase):
def test_get_summary(self):
data = self.bw.query("chr1", 10000, 20000, 10)
means = [ x['mean'] for x in data ]
+ print means
assert numpy.allclose( map(float, means), [-0.17557571594973645, -0.054009292602539061, -0.056892242431640622, -0.03650328826904297, 0.036112907409667966, 0.0064466032981872557, 0.036949024200439454, 0.076638259887695306, 0.043518108367919923, 0.01554749584197998] )
# Summarize variant
@@ -75,8 +77,10 @@ def test_summaries_from_file():
assert allclose( sd.max_val, values )
#elif t == 'std':
# assert numpy.allclose( sd.max_val, values )
- for line in open( "test_data/bbi_tests/test.expectation" ):
- yield check_summary, line
+ for i, line in enumerate( open( "test_data/bbi_tests/test.expectation" ) ):
+ f = partial( check_summary, line )
+ f.description = "Test summaries line %d: %s" % ( i, line[:40] )
+ yield ( f, )
if __name__ == '__main__':
diff --git a/lib/bx/phylo/newick_tests.py b/lib/bx/phylo/newick_tests.py
index 3fca8da..84d86b3 100644
--- a/lib/bx/phylo/newick_tests.py
+++ b/lib/bx/phylo/newick_tests.py
@@ -3,7 +3,7 @@ Tests for `bx.phylo.newick`.
"""
from bx.phylo.newick import *
-import unittest
+from nose.tools import ok_
trees = [ r"(B:6.0,(A:5.0,C:3.0,'Foo ''bar':4.0)Q_X:5.0,D:11.0)label;",
"((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700, seal:12.00300):7.52973,(( monkey:100.85930,cat:47.14069):20.59201, weasel:18.87953):2.09460):3.87382,dog:25.46154);",
@@ -27,7 +27,6 @@ results = [ ( Tree( 'label', [Edge( 6.0, Tree( 'B', None ) ), Edge( 5.0, Tree( '
def tests():
for i in range(len(trees)):
- def _( s, r ):
- assert newick_parser.parse_string( s ) == r
+ _ = lambda: ok_( newick_parser.parse_string( trees[i] ) == results[i] )
_.description = "check tree parsing " + str(i)
- yield _, trees[i], results[i]
+ yield _,
diff --git a/lib/bx/seqmapping_tests.py b/lib/bx/seqmapping_tests.py
index 2f00a61..82c226c 100644
--- a/lib/bx/seqmapping_tests.py
+++ b/lib/bx/seqmapping_tests.py
@@ -11,6 +11,7 @@ from numpy import array, allclose
from StringIO import StringIO
class CharMappingTests( unittest.TestCase ):
+ __test__ = False
def test_DNA( self ):
assert( allclose( bx.seqmapping.DNA.translate( "ACGTacgt-?X" ),
[ 0, 1, 2, 3, 0, 1, 2, 3, 4, -1, -1 ] ) )
@@ -24,6 +25,7 @@ class CharMappingTests( unittest.TestCase ):
assert( allclose( m.translate( "ABCCBA" ), [ 0, 7, -1, -1, 7, 0 ] ) )
class IntMappingTests( unittest.TestCase ):
+ __test__ = False
def test_simple( self ):
m = bx.seqmapping.IntToIntMapping( 4 )
m.set_mapping( 0, 0 )
@@ -75,12 +77,9 @@ rows = [ "AAATTGT-----ATGTCCATCCTTTAAAGGTCATTCCTTTAATGGTCTTTTCTGGACACCACTAGGGGTC
"AAATTCATGATAGTGTCACTCTTAAATAGATGATTC--------TTCACAT---GATGCCAGCAGGGGGC-AGAGCAGGCTGTGAAAT------------------------TTTCCCTTTCTTCAAAG" ]
class AlignmentMappingTests( unittest.TestCase ):
+ __test__ = False
def test_largescale( self ):
- f = StringIO( eight_species_mapping )
- n, m = bx.seqmapping.alignment_mapping_from_file( f )
- t = bx.seqmapping.DNA.translate_list( rows )
- i = m.translate( t )
-
-
-test_classes = [ AlignmentMappingTests, CharMappingTests, IntMappingTests ]
-suite = unittest.TestSuite( [ unittest.makeSuite( c ) for c in test_classes ] )
+ f = StringIO( eight_species_mapping )
+ n, m = bx.seqmapping.alignment_mapping_from_file( f )
+ t = bx.seqmapping.DNA.translate_list( rows )
+ i = m.translate( t )
diff --git a/script_tests/bnMapper_tests.py b/script_tests/bnMapper_tests.py
index 0865a7b..2e685f7 100644
--- a/script_tests/bnMapper_tests.py
+++ b/script_tests/bnMapper_tests.py
@@ -30,5 +30,6 @@ class Test6( base.BaseScriptTest, unittest.TestCase ):
command_line = "./scripts/bnMapper.py ./test_data/epo_tests/hg19_one_peak.bed ./test_data/epo_tests/hg19.mm9.rBest.chain.gz"
output_stdout = base.TestFile( filename="./test_data/epo_tests/hg19_one_peak.mapped.bed" )
-unittest.main()
+if __name__ == "__main__":
+ unittest.main()
diff --git a/script_tests/maf_extract_ranges_indexed_tests.py b/script_tests/maf_extract_ranges_indexed_tests.py
index 2b312ed..e91a016 100644
--- a/script_tests/maf_extract_ranges_indexed_tests.py
+++ b/script_tests/maf_extract_ranges_indexed_tests.py
@@ -2,6 +2,6 @@ import base
import unittest
class Test( base.BaseScriptTest, unittest.TestCase ):
- command_line = "./scripts/maf_extract_ranges_indexed.py ./test_data/maf_tests/mm8_chr7_tiny.maf -c -p mm8. < ${bed}"
+ command_line = "./scripts/maf_extract_ranges_indexed.py ./test_data/maf_tests/mm8_chr7_tiny.maf -c -m 5 -p mm8. < ${bed}"
input_bed = base.TestFile( filename="./test_data/maf_tests/dcking_ghp074.bed" )
output_stdout = base.TestFile( filename="./test_data/maf_tests/dcking_ghp074.maf" )
diff --git a/script_tests/out_to_chain_tests.py b/script_tests/out_to_chain_tests.py
index f05fbef..6169f74 100644
--- a/script_tests/out_to_chain_tests.py
+++ b/script_tests/out_to_chain_tests.py
@@ -5,4 +5,5 @@ class Test( base.BaseScriptTest, unittest.TestCase ):
command_line = "./scripts/out_to_chain.py ./test_data/epo_tests/epo_547_hs_mm_12way_mammals_65.out --chrsizes ./test_data/epo_tests/hg19.chrom.sizes ./test_data/epo_tests/mm9.chrom.sizes"
output_stdout = base.TestFile( filename="./test_data/epo_tests/epo_547_hs_mm_12way_mammals_65.chain" )
-unittest.main()
+if __name__ == "__main__":
+ unittest.main()
diff --git a/scripts/bnMapper.py b/scripts/bnMapper.py
index 54884c1..c0e4d89 100755
--- a/scripts/bnMapper.py
+++ b/scripts/bnMapper.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python -O
+#!/usr/bin/env python
"""Map features from the target species to the query species of a chain alignment file.
This is intended for mapping relatively short features such as Chip-Seq
diff --git a/setup.cfg b/setup.cfg
index ef577b5..3663245 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,15 +1,13 @@
[aliases]
snapshot = egg_info -rb_DEV bdist_egg rotate -m.egg -k1
-test = nosetests
build_docs = build_sphinx build_apidocs
[nosetests]
-#tests=script_tests/
-#tests=lib/bx/
-verbosity=2
-#detailed-errors=0
-#with-doctest=1
-#doctest-extension=pyx
+tests=lib/bx
+#verbosity=2
+#detailed-errors=1
+with-doctest=1
+doctest-extension=pyx
[build_sphinx]
source-dir = doc/source
diff --git a/setup.py b/setup.py
index f5a3c86..28f3584 100644
--- a/setup.py
+++ b/setup.py
@@ -4,30 +4,34 @@ if sys.version_info < (2, 4):
print >> sys.stderr, "ERROR: bx-python requires python 2.4 or greater"
sys.exit()
-# Automatically download setuptools if not available
-from distribute_setup import use_setuptools
-use_setuptools()
+try:
+ from setuptools import setup, find_packages
+except ImportError:
+ from ez_setup import use_setuptools
+ use_setuptools()
from setuptools import *
from glob import glob
-try:
- import numpy
- have_numpy = True
-except:
- have_numpy = False
-
def main():
- setup( name = "bx-python",
- version = "0.7.2",
+
+ numpy = None
+ build_requires = [ 'python-lzo' ]
+ try:
+ import numpy
+ except:
+ build_requires.append( 'numpy' )
+
+ metadata = \
+ dict( name = "bx-python",
+ version = "0.7.4",
+ install_requires=build_requires,
py_modules = [ 'psyco_full' ],
- packages = find_packages( 'lib' ),
package_dir = { '': 'lib' },
package_data = { '': ['*.ps'] },
scripts = glob( "scripts/*.py" ),
- ext_modules = get_extension_modules(),
test_suite = 'nose.collector',
- setup_requires = ['nose>=0.10.4'],
+ tests_require = ['nose'],
author = "James Taylor, Bob Harris, David King, Brent Pedersen, Kanwei Li, and others",
author_email = "james at jamestaylor.org",
description = "Tools for manipulating biological data, particularly multiple sequence alignments",
@@ -46,6 +50,23 @@ def main():
zip_safe = False,
dependency_links = [],
cmdclass=command_classes )
+
+ if len(sys.argv) >= 2 and ('--help' in sys.argv[1:] or
+ sys.argv[1] in ('--help-commands', 'egg_info', '--version', 'clean')):
+ # For these actions, NumPy is not required.
+ #
+ # They are required to succeed without Numpy for example when
+ # pip is used to install when Numpy is not yet present in
+ # the system.
+ pass
+ else:
+ if numpy is None:
+ raise Exception( "numpy must be installed to build" )
+ metadata['packages'] = find_packages( 'lib' )
+ metadata['ext_modules'] = get_extension_modules( numpy_include=numpy.get_include() )
+
+ setup(**metadata)
+
# ---- Commands -------------------------------------------------------------
@@ -109,7 +130,7 @@ except:
# ---- Extension Modules ----------------------------------------------------
-def get_extension_modules():
+def get_extension_modules( numpy_include=None ):
extensions = []
# Bitsets
extensions.append( Extension( "bx.bitset",
@@ -148,21 +169,21 @@ def get_extension_modules():
[ "lib/bx/pwm/_position_weight_matrix.pyx", "src/pwm_utils.c" ],
include_dirs=["src"] ) )
- if have_numpy:
- extensions.append( Extension( "bx.motif._pwm", [ "lib/bx/motif/_pwm.pyx" ],
- include_dirs=[numpy.get_include()] ) )
+ extensions.append( Extension( "bx.motif._pwm", [ "lib/bx/motif/_pwm.pyx" ],
+ include_dirs=[numpy_include] ) )
- # Sparse arrays with summaries organized as trees on disk
- extensions.append( Extension( "bx.arrays.array_tree", [ "lib/bx/arrays/array_tree.pyx" ], include_dirs=[numpy.get_include()] ) )
+ # Sparse arrays with summaries organized as trees on disk
+ extensions.append( Extension( "bx.arrays.array_tree", [ "lib/bx/arrays/array_tree.pyx" ], include_dirs=[numpy_include] ) )
- # Reading UCSC "big binary index" files
- extensions.append( Extension( "bx.bbi.bpt_file", [ "lib/bx/bbi/bpt_file.pyx" ] ) )
- extensions.append( Extension( "bx.bbi.cirtree_file", [ "lib/bx/bbi/cirtree_file.pyx" ] ) )
- extensions.append( Extension( "bx.bbi.bbi_file", [ "lib/bx/bbi/bbi_file.pyx" ], include_dirs=[numpy.get_include()] ) )
- extensions.append( Extension( "bx.bbi.bigwig_file", [ "lib/bx/bbi/bigwig_file.pyx" ], include_dirs=[numpy.get_include()] ) )
- extensions.append( Extension( "bx.bbi.bigbed_file", [ "lib/bx/bbi/bigbed_file.pyx" ], include_dirs=[numpy.get_include()] ) )
- # EPO and Chain arithmetics and IO speedups
- extensions.append( Extension( "bx.align._epo", [ "lib/bx/align/_epo.pyx" ], include_dirs=[numpy.get_include()] ) )
+ # Reading UCSC "big binary index" files
+ extensions.append( Extension( "bx.bbi.bpt_file", [ "lib/bx/bbi/bpt_file.pyx" ] ) )
+ extensions.append( Extension( "bx.bbi.cirtree_file", [ "lib/bx/bbi/cirtree_file.pyx" ] ) )
+ extensions.append( Extension( "bx.bbi.bbi_file", [ "lib/bx/bbi/bbi_file.pyx" ], include_dirs=[numpy_include] ) )
+ extensions.append( Extension( "bx.bbi.bigwig_file", [ "lib/bx/bbi/bigwig_file.pyx" ], include_dirs=[numpy_include] ) )
+ extensions.append( Extension( "bx.bbi.bigbed_file", [ "lib/bx/bbi/bigbed_file.pyx" ], include_dirs=[numpy_include] ) )
+
+ # EPO and Chain arithmetics and IO speedups
+ extensions.append( Extension( "bx.align._epo", [ "lib/bx/align/_epo.pyx" ], include_dirs=[numpy_include] ) )
# Reading UCSC bed and wiggle formats
extensions.append( Extension( "bx.arrays.bed", [ "lib/bx/arrays/bed.pyx" ] ) )
@@ -226,6 +247,5 @@ def monkey_patch_numpy():
if __name__ == "__main__":
monkey_patch_doctest()
- if have_numpy:
- monkey_patch_numpy()
+ monkey_patch_numpy()
main()
--
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