Metadata-Version: 2.1
Name: xsamtools
Version: 0.5.0
Summary: Lightly modified versions of samtools, htslib, and bcftools.
Home-page: https://github.com/xbrianh/xsamtools.git
Author: Brian Hannafious
Author-email: bhannafi@ucsc.edu
License: MIT
Description: # xsamtools
        xsamtools makes the [samtools](https://samtools.github.io/) tooling from [htslib](https://github.com/samtools/htslib)
        and [bcftools](https://github.com/samtools/bcftools) available through pypi packaging. These tools have been lightly
        modified to allow merges on VCF streams without an index.
        
        # Installation
        ```
        pip install xsamtools
        ```
        Installation requires a C toolchain. Typically Ubuntu/Debian systems should have the following packages installed:
          - `libbz2-dev`
          - `liblzma-dev`
          - `libcurl4-openssl-dev`
        
        `libcurl4-openssl-dev` may be omitted at the cost of some cloud support features in htslib.
        
        # Usage
        
        After succesful installation, the following executables are available:
        
        samtools:
          - htsfile
          - bgzip
          - tabix
          - bcftools
        
        xsamtools:
          - merge_vcfs.py
        
        xsamtools also provides Python tooling to create named (FIFO) pipes to Google Storage objects:
        ```
        from xsamtools import pipes
        
        reader = pipes.BlobReaderProcess("bucket-name", "read-key")
        print("reader path", reader.filepath)  # local FIFO filepath
        
        writer_key = pipes.BlobWriterProcess("bucket-name", "writ-key")
        print("writer path", writer.filepath)  # local FIFO filepath
        ```
        These streams appear as either readable or writable files on the filesystem. Such objects are not seekable.
        
        A utility method is also provided to merge VCFs from GS objects:
        ```
        from xsamtools import vcf
        
        vcf.combine("src-bucket-name", ["first-src-vcf-key", "second-src-vcf-key"], "dst-bucket-name", "dst-vcf-key")
        ```
        There is no formal limit on the number of VCF keys. Care should be taken that the VCF objects provided are aligned by
        chromosome or the merge will fail.
        
        # Docker
        
        A Docker image with xsamtools installed is published at
        [https://hub.docker.com/repository/docker/xbrianh/xsamtools](https://hub.docker.com/repository/docker/xbrianh/xsamtools)
        
Platform: MacOS X
Platform: Posix
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
