Overview

A simple tool for calculating the amount of a gene that is covered by a sample of alignments.

Installation

git clone https://github.com/cdeanj/coveragesampler
cd coveragesampler
make
./csa

Usage

Usage: csa [options]

Options:

-ref_fp    STR/FILE     ref file path (all sequences must be on a single line -- no multi-line FASTAs)
-sam_fp    STR/FILE     sam file path
-min       INT          starting sample level
-max       INT          ending sample level
-skip      INT          amount of sample levels to skip
-t         INT          gene fraction threshold
-samples   INT          iterations per sample level
-out_fp    STR/FILE     output file path

Output

The output is a tab delimited text file with five columns

Level   Iteration   Gene Id Gene Fraction   Hits

• Level: the sampling percent alignments were taken at
• Iteration: the ith iteration of the current sample level
• Gene Id: the reference sequence having a gene fraction greater than the threshold
• Gene Fraction: the number of bases covered by the sample of alignments
• Hits: the number of alignments that had bases cover the reference sequence