Metadata-Version: 2.1
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
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
Requires-Dist: pysam (==0.15.4)
Requires-Dist: pybedtools (==0.8.1)
Requires-Dist: pyfaidx (==0.5.8)
Requires-Dist: pytest (==5.4.2)
Requires-Dist: click (==7.1.2)
Requires-Dist: pysamstats (==1.1.2)
Requires-Dist: pandas (==1.0.3)

===========
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.


