check_tradis

Attempt at encorporating a step to check if the BAMs are from a TraDIS
analysis before putting in the database.
If lane is stored, delete the stored path
Get stored lane from symlink instead of database
Now takes in an option to specify is stored path should be deleted or not
Look for files that have a certain word in the name like bam/mpileup and delete entry from fsu file exists table if it exists
Changed logic so that we look for all paths that start with given hierarchy and delete them from file_exists database
Merge pull request #216 from andrewjpage/pipeline

Farm3 updates
corrected wrong variable name
Added a message about delting files from the fsu_file_exists table
removed abs_path when looking for files in fsu_file_exists
Merge pull request #217 from nds/add_option_to_delete_stored_lane

Add option to delete stored lane
Merge branch 'pipeline' of https://github.com/sanger-pathogens/vr-codebase into pipeline

Conflicts:
	modules/VertRes/Pipelines/Import_iRODS_fastq.pm
Merge pull request #218 from carlacummins/pipeline

Merged tradis support
updated list of assembly files
Merge pull request #219 from CraigPorter/vrtracking_tool_fix

updated list of assembly files
fix bam parser compile error