NAME

fastQ_brew_Utilities - utilities for fastQ_brew

SYNOPSIS

use base 'Exporter';
use Cwd;
use List::Util qw(min max sum);

DESCRIPTION

This package provides Utility support to fastQ_brew

Support

All contributions are welcome

Reporting Bugs

Report bugs to the fastQ_brew bug tracking system to help keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/dohalloran/fastQ_brew/issues

APPENDIX

The rest of the documentation details each of the object methods.

calcgc

Title   :  calcgc
Usage   :  $Tm = calcgc( $read );
Function:  calculates read GC%
Returns :  GC%

phred_calc

Title   :  phred_calc
Usage   :  $Tm = phred_calc( $read, $lib );
Function:  calculates phred score for each read
Returns :  read phred score

prob_calc

Title   :  prob_calc
Usage   :  prob_calc( $read, $lib );
Function:  calculates error probability for each read
Returns :  probability

adapter_check

Title   :  adapter_check
Usage   :  adapter_check( $read, $adapter, $mismatches );
Function:  searches for matches that permit number of mismatches and removes macthes from reads
Returns :  fastQ file without adapters