NAME

getReadsInRepeat.pl

SYNOPSIS


  getReadsInRepeat.pl 
                      -iRead  <454Contigs.ace.1.pairs>    
                      -cName  <contig name>
                      -bStart <repeat boundry start>
                      -bEnd   <repeat boundry end>
                      -oRead  <path to read pair output file>
                      -help

DESCRIPTION

This script takes read pair file, contig name, repeat boundary start, repeat boundary end, path to output file of read ids and an optional file name to output a read pair subset file of read pair lines in the target region.

All unpaired reads in boundaries specified are examined. Reads are ouput if the entire read falls within specified boundaries. No overlap.

VERSION

$Revision: 1.4 $

$Date: 2009-08-26 17:18:15 $

HISTORY