Metadata-Version: 1.1
Name: cbs
Version: 1.0.0
Summary: List coverage blind spots
Home-page: https://github.com/christofsteel/cbs
Author: Christoph Stahl
Author-email: christoph.stahl@uni-dortmund.de
License: MIT
Download-URL: https://github.com/christofsteel/cbs/tarball/1.0
Description: 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
        
Platform: UNKNOWN
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
