Metadata-Version: 2.1
Name: bripy
Version: 0.0.1a2
Summary: Bam read index in python.
Home-page: https://github.com/nanoporetech/bripy
Author: ont-research
License: UNKNOWN
Description: ﻿
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        Bripy
        ======
        
        Bripy is a python library for extracting reads from a bam by read name. It
        uses the [bri](https://github.com/jts/bri) library from Jared Simpson.
        
        © 2019 Oxford Nanopore Technologies Ltd.
        
        Installation
        ------------
        
        `bripy` can be installed using pip:
        
            pip install bripy
        
        For python3.5 and python3.6 under linux this will download precompiled
        binaries, in other environments a source distribution will be downloaded
        and compiled. Compilation from source requires the same libraries as
        [htslib](https://github.com/samtools/htslib):
        
            'm', 'z', 'lzma', 'bz2', 'pthread', 'curl', 'crypto'
        
        since htslib is built from source as part of the process.
        
        Usage
        -----
        
        The library contains a single class interface and two example programs. To
        index a bam file for later retrieval of reads run:
        
            bripy index <bamfile>
        
        This program is analogous to the `bri index <bamfile`. The second program
        will retrieve reads from a bam by name:
        
            bripy get <bamfile> <read name>
        
        Again this program is analogous to running `bri get <bamfile> <read name>`.
        
        The `bripy` API is simple, the following will return a string containing
        sam formatted alignments:
        
            bri = BamReadIndex(bam_file)
            sam_data = bri.get_alignments(read_name)
        
        This API is likely to change in future to provide a more useful data structure
        akin to a `pysam.AlignedSegment`.
        
        
        License
        -------
        
        **Licence and Copyright**
        
        © 2019 Oxford Nanopore Technologies Ltd.
        
        `bripy` is distributed under the terms of the Mozilla Public License 2.0.
        
        **Research Release**
        
        Research releases are provided as technology demonstrators to provide early
        access to features or stimulate Community development of tools. Support for
        this software will be minimal and is only provided directly by the developers.
        Feature requests, improvements, and discussions are welcome and can be
        implemented by forking and pull requests. However much as we would
        like to rectify every issue and piece of feedback users may have, the
        developers may have limited resource for support of this software. Research
        releases may be unstable and subject to rapid iteration by Oxford Nanopore
        Technologies.
        
Platform: UNKNOWN
Requires-Python: >=3.5.*,<3.7
Description-Content-Type: text/markdown
