added functionality to start mapping from existing chunks. And changed all absolute path to relative (so that path stay /home/share instead of /data )
Revert "added functionality to start mapping from existing chunks. And changed all absolute path to relative (so that path stay /home/share instead of /data )"

This reverts commit 00fa2375c6b4ab396ae5ec5c49063b8399725d12.
added functionality to start mapping from existing chunks dir for ilumina PE
added -M options to BWA mem mapping job to make output compatible with Picard (mark shorter split hits as secondary hits)