Metadata-Version: 2.1
Name: ngsindex
Version: 0.1.4
Summary: Utilities for working with NGS index formats.
Home-page: https://github.com/jdidion/ngsindex
Author: John Didion
Author-email: github@didion.net
License: MIT
Description: # ngsindex
        
        Support for reading various NGS-related index formats:
        
        * [BAI](https://samtools.github.io/hts-specs/SAMv1.pdf)
        * [TBI](https://samtools.github.io/hts-specs/tabix.pdf)
        * [CSI](https://samtools.github.io/hts-specs/CSIv2.pdf)
        
        # Installation
        
        ```bash
        pip install ngsindex
        ```
        
        # Usage
        
        ```python
        from ngsindex import IndexType, resolve_index_file, parse_index
        from pathlib import Path
        
        bam_file = Path('/path/to/reads.bam')
        
        # Resolve the location of the BAM index file.
        index_file = resolve_index_file(bam_file, IndexType.BAI)
        
        # Load the index
        index = parse_index(index_file)
        
        # Loop through chromosome indexes
        for refidx in index.ref_indexes:
            ...
        ```
        
        # Limitations
        
        * CRAM files are not yet supported (neither .crai nor .bai index files).
        
        # Todo
        
        * Add support for splitting BAI:
          * https://github.com/samtools/hts-specs/pull/321
          * https://github.com/tomwhite/hts-specs/blob/sbi/SAMv1.tex
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: License :: OSI Approved :: MIT License
Classifier: License :: Public Domain
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.6
Description-Content-Type: text/markdown
