Metadata-Version: 1.1
Name: readtagger
Version: 0.3.3
Summary: Tags reads in a BAM file based on other BAM files.
Home-page: https://github.com/bardin-lab/readtagger
Author: Marius van den Beek
Author-email: m.vandenbeek@gmail.com
License: MIT
Description: Readtagger
        ----------
        .. image:: https://travis-ci.org/bardin-lab/readtagger.svg?branch=master
            :target: https://travis-ci.org/bardin-lab/readtagger
        
        .. image:: https://coveralls.io/repos/github/bardin-lab/readtagger/badge.svg?branch=master
            :target: https://coveralls.io/github/bardin-lab/readtagger?branch=master
        
        .. image:: https://badge.fury.io/py/readtagger.svg
            :target: https://badge.fury.io/py/readtagger
        
        .. image:: https://anaconda.org/mvdbeek/readtagger/badges/version.svg
            :target: https://anaconda.org/mvdbeek/readtagger
        
        Tags reads in a BAM file based on other BAM files.
        
        Installation
        ------------
        
        ::
        
            pip install readtagger
        
        Usage
        ------
        
        To tag reads in file ``a.bam`` with file ``b.bam`` and output to path
        output.bam, type
        
        ::
        
            readtagger --tag_file a.bam --annotate_with b.bam ----output_file output.bam
        
        This will by default tag reads with the AD, AR, BD and BR tags, where
        the AD tag has detail mapping information for the current read, while
        the BD tag has the information for the mate. AR and BR contain the
        aligned reference (i.e chromosome). The first letter can be changed on a
        per-file basis by appending ":first\_letter\_read:first\_letter\_mate"
        to the file path. To change the above example into X for the read and Y
        for the mate, run:
        
        ::
        
            readtagger --tag_file a.bam --annotate_with b.bam:X:Z ----output_file output.bam
        
        To tag one bam file using multiple alignment files, run:
        
        ::
        
            readtagger --tag_file a.bam --annotate_with b.bam:A:B c.bam:C:D ----output_file output.bam
        
        Now reads that align in file ``b.bam`` will be tagged with AR, AD and
        BR, BD, while reads aligned in file ``c.bam`` are marked with CR, CD and
        DR, DD.
        
        Advanced usage
        --------------
        
        To see the advanced options, type:
        
        ::
        
            readtagger -h
        
        Testing
        -------
        
        If you modify readtagger, you can run all tests by running tox:
        
        ::
        
            pip install tox
            tox
        
        
        
        
        
        History
        -------
        
        .. to_doc
        
        ---------------------
        0.3.3 (2017-03-02)
        ---------------------
        * Fix a crash when writing GFF for a cluster of hardclipped reads
        * Change confusing variable names and copypasted docstring
        
        ---------------------
        0.3.2 (2017-03-02)
        ---------------------
        * Fix another crash when tuple starts with 1,2,7 or 8
        
        ---------------------
        0.3.1 (2017-03-02)
        ---------------------
        * Fix a crash when a mismatch is the last item in a cigartuple
        
        ---------------------
        0.3.0 (2017-03-02)
        ---------------------
        
        * Add a galaxy tool for the findcluster script
        * Add new script that finds clusters of reads and outputs GFF or BAM files with these clusters.
        * Implement writing clusters as GFF files
        * Implement writing out reads with cluster number annotated in CD tag.
        * Implement merging of clusters based on whether reads contribute to common contigs
        * Use cached-property where it makes sense
        * Add module to find, join and annotate clusters of reads
        * Represent cigartuple as namedtuple
        * Add a Roadmap file
        * Add more logic for finding ends of insertions and
        * Manipulate cluster of reads to find TSDs
        * Add module for cap3 assembly and manipulation of assembled reads
        * Fix conda recipe script entrypoints
        
        ---------------------
        0.2.0 (2017-02-21)
        ---------------------
        * Reformat help text in galaxy wrappers
        * Add add_matesequence script to add the sequence of the mate of the current read as a tag
        * Add option to discard alternative tag if read is a proper pair
        * Stitch cigars that are separated by I or D events
        * Add a tag tuple that knows how to format itself
        * Update README.rst example with current default tag prefix
        * Test with and without discarding verified reads
        * Symlink test-files that are shared with the galaxy test, add testcase for allow_dovetailing script
        * Fix HISTORY.rst formatting
        
        ---------------------
        0.1.13(2017-02-17)
        ---------------------
        * Add instructions for development
        * Install planemo in deployment step
        
        ---------------------
        0.1.12(2017-02-17)
        ---------------------
        * Test deployment again
        
        ---------------------
        0.1.11 (2017-02-17)
        ---------------------
        * Test deployment
        
        ---------------------
        0.1.10 (2017-02-17)
        ---------------------
        * Fix toolshed deployment
        
        ---------------------
        0.1.9 (2017-02-17)
        ---------------------
        * Add automated deployment to Galaxy Toolshed
        * Add instructions for development and release process
        
        ---------------------
        0.1.8 (2017-02-17)
        ---------------------
        * Minor release to test release process
        
        ---------------------
        0.1.7 (2017-02-17)
        ---------------------
        * Extend testing with coverage testing
        * Automate deployment to pypi and conda
        * Register project with pyup.io
        
        ---------------------
        0.1.6 (2017-02-16)
        ---------------------
        * Rename to readtagger
        * Fix bug with stdin closing file descriptor too early, leading to corrupt
          BAM files
        * Extend testing
        
        ---------------------
        0.1.5 (2017-02-12)
        ---------------------
        * Add option (-wd) to write suboptimal tag into separate BAM file
        * Add option (-wv) to write verified tags into separate BAM file
        * Performance improvments by letting sambamba handle BAM reading
          and writing. Also elimininate regualr expression to parse cigarstring
        
        ---------------------
        0.1.4 (2017-02-10)
        ---------------------
        * Add option (-k) to keep alternative tags if they do not
          explain the softclipped read any better.
          Default is to discard them.
        
        ---------------------
        0.1.3.2 (2017-02-08)
        ---------------------
        * Fix dovetailing script
        
        ---------------------
        0.1.3 (2017-02-07)
        ---------------------
        * Add option to allow dovetailing in alignment files when tagging reads
        * Add separate entrypoint for standalone script
        
        ---------------------
        0.1.2 (2017-02-05)
        ---------------------
        * Add conda recipe
        * Python3 string fix
        
        ---------------------
        0.1.0 (2017-02-05)
        ---------------------
        * Initial version
        
        
Keywords: Bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Environment :: Console
Classifier: Operating System :: POSIX
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
