Metadata-Version: 2.4
Name: cbs
Version: 1.0.0
Summary: List coverage blind spots
Home-page: https://github.com/christofsteel/cbs
Download-URL: https://github.com/christofsteel/cbs/tarball/1.0
Author: Christoph Stahl
Author-email: christoph.stahl@uni-dortmund.de
License: MIT
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
License-File: LICENSE.txt
Requires-Dist: h5py
Requires-Dist: numpy
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: download-url
Dynamic: home-page
Dynamic: license
Dynamic: license-file
Dynamic: requires-dist
Dynamic: summary

Coverage Blind Spots
====================

This software lists all positions in given bam files, that have no or only 
very limited coverage and stores the result in a hdf5 file.

Usage
-----

::

    cbs [-h] [--min-cov MIN_COV] files [files ...] output

If multiple files are given, a position is designated a blind spot, if no file
contains a coverage of at least MIN_COV at this position.

Output
------

The output is a hdf5 file with the following structure. For every chromosome a 
group is created, that contains a dataset called `missing_cov`. The dataset 
contains rows of tuples of 32bit integer, representing the first blind spot and
the first position having enough coverage.

Install
-------

This software requires python3, samtools, hdf5, numpy and h5py. All python 
dependencies can be installed by installing cbs via pip::

    pip install git+https://github.com/christofsteel/cbs.git
