Metadata-Version: 1.2
Name: sequence-qc
Version: 0.1.12
Summary: Package for doing various ad-hoc quality control steps from MSK-ACCESS generated FASTQ or BAM files
Home-page: https://github.com/msk-access/sequence_qc
Author: Ian Johnson
Author-email: ionox0@gmail.com
License: Apache Software License 2.0
Description: ===========
        sequence_qc
        ===========
        
        
        .. image:: https://img.shields.io/pypi/v/sequence_qc.svg?
                :target: https://pypi.python.org/pypi/sequence_qc
        
        .. image:: https://travis-ci.com/msk-access/sequence_qc.svg?branch=master
                :target: https://travis-ci.com/github/msk-access/sequence_qc
        
        .. image:: https://readthedocs.org/projects/sequence-qc/badge/?version=latest
                :target: https://sequence-qc.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        
        Package for doing various ad-hoc quality control steps from MSK-ACCESS generated FASTQ or BAM files
        
        
        * Free software: Apache Software License 2.0
        * Documentation: https://msk-access.gitbook.io/sequence_qc/
        
        
        Installation
        ------------
        ``pip install sequence_qc``
        
        Usage
        -----
        
            Usage: calculate_noise [OPTIONS]
        
              Calculate noise level of given bam file, across the given positions in
              `bed_file`.
        
            Options:
              --ref_fasta TEXT           Path to reference fasta, containing all regions
                                         in bed_file  [required]
              --bam_file TEXT            Path to BAM file for calculating noise
                                         [required]
              --bed_file TEXT            Path to BED file containing regions over which to
                                         calculate noise  [required]
              --threshold FLOAT          Alt allele frequency past which to ignore
                                         positions from the calculation
              --truncate INTEGER         Whether to exclude trailing bases from reads that
                                         only partially overlap the bed file (0 or 1)
              --min_mapq INTEGER         Exclude reads with a lower mapping quality
              --min_basq INTEGER         Exclude bases with a lower base quality
              --help                     Show this message and exit.
        
        
        Versioning
        ----------
        To increase the version number use the following command:
        
        ``bumpversion (major|minor|patch) --tag``
        
        
        =======
        History
        =======
        
        0.1.0 (2019-12-06)
        ------------------
        
        * First release on PyPI.
        
Keywords: sequence_qc
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.5
