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