NAME

getReadsInUnique.pl

SYNOPSIS


  getReadsInUnique.pl 
                      -iRead  <454Contigs.ace.1.pairs>    
                      -cName  <contig name>
                      -cPos   <left|right>
                      -bStart <unique boundry start>
                      -bEnd   <unique boundry end>
                      -oRead  <path to read pair output file>
                      -help

DESCRIPTION

This script takes read pair file, contig name, position ( left or right of gap ), unique boundary start, unique 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 reads in boundaries specified are examined. Unpaired reads are output if a read or portion of the read falls within the boundaries. Additionally, paired reads are output the read or portion of the read falls within the boundary and it is oriented in such a way that its mate lies in the direction of the gap.

VERSION

$Revision: 1.6 $

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

HISTORY