bamnostic
1.1.8

Contents:

  • Installation
  • Getting Started
  • Module documentation
  • Citation and Support
bamnostic
  • »
  • Welcome to bamnostic’s documentation!
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Welcome to bamnostic’s documentation!¶

This documentation site is a work in progress as I continue to hone my reStructuredText skills. All of the module documentation is here, but a more detailed “Getting Started” should be available soon.

Note

CRAM format is not supported at this time.

Contents:

  • Installation
    • Through the conda package manager (Anaconda Cloud)
    • Through the Python Package Index (PyPI)
    • Through pip+Github
    • Traditional GitHub clone
  • Getting Started
    • Importing bamnostic
    • Loading your BAM file
    • Get the header
    • Data validation through head()
    • Getting the next read
    • Exploring a read
      • Read Name
      • 0-based Start Position (raw, aligned, reference)
      • CIGAR & QUAL Strings
      • Sequence Length (raw, aligned, reference)
      • Nucleotide Sequence
      • Read Flag and Decoded Flag
    • Serial Access
    • Random Access
  • Module documentation
    • Core Module (bamnostic.core)
    • Bgzip BAM Format (BGZF) file handlers (bamnostic.bgzf)
    • Binary Alignment Map (BAM) file handlers (bamnostic.bam)
    • BAM Index (BAI) file handler (bamnostic.bai)
    • Coordinate-Sorted Index (CSI) file handler (bamnostic.csi)
    • BAMnostic Utilities (bamnostic.utils)
  • Citation and Support
    • Citation
    • Support for BAMnostic

Indices and tables¶

  • Index

  • Module Index

  • Search Page

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© Copyright 2018, Marcus D. Sherman.

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