Welcome to parabam

Author:Henry Farmery Date:August 16, 2017 Version:0.1

parabam is a python package that allows users to quickly and easily conduct analysis on BAM files. parabam is designed to allow the user to make maximum useage of the processing power available to their machines.

Running an analysis on a BAM file can be as easy as specifiying a single function and then typing a command into on your terminal. More advanced users may incorporate parabam into their own code or expand parabam by making using of OOP inheritence.

Contents:

• Preface - Quickstart
• Introduction
  • Installing parabam
  • Running parabam on a cluster
• Fundamentals of parabam
  • The subset and stat operations
  • Ways of interacting with parabam
  • Engines and constants
  • Output Files
  • Pysam classes: read and master
• The subset interface
  • What is the subset interface for?
  • Producing a single subset
  • Producing multiple subsets
  • Subset Specification
• Examples subset
  • From the command line
  • From within python
• The stat Interface
  • What is the stat interface for?
• Examples: stat
  • From the command line
  • From within python
• Technical Details
  • How does parabam actually work?

Useful Document Links

• Index
• Module Index
• Search Page