bio-bam-gindex

README

bio-bam-gindex

Background

A gindex (.gbai) file is an alternate index format for BAM files. The gindex format allows readers to seek into a BAM file more efficiently because the gindex can contain pointers into the BAM file at a finer granularity.

The encoding/bamprovider interface can use a .gbai file as a drop-in replacement for a .bai file.

Usage

Command bio-bam-gindex reads a .bam file and writes a .gbai index file. bio-bam-gindex expects the bam file to arrive on stdin, and writes to stdout. It has a single parameter --shard-size which is the approximate shard size in bytes.

Example usage:

cat foo.bam | bio-bam-gindex --shard-size=65536 > foo.bam.gbai

Documentation

Overview

Command bio-bam-gindex reads a .bam file and writes a .gbai index

file.  bio-bam-gindex expects the bam file to arrive on stdin, and
writes to stdout.  It has a single parameter --shard-size which is
the approximate shard size in bytes.

Usage: cat foo.bam | bio-bam-gindex --shard-size=65536 > foo.bam.gbai