check_tradis

Attempt at encorporating a step to check if the BAMs are from a TraDIS
analysis before putting in the database.
reverting change
Tradis step added
Remove bamcheck files after adding tags

Forces re-check of bam
Small fix

Fixes problem constructing bamcheck file path
Increase memory

Increase to 8GB. Fails on 2GB.
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
Merge pull request #220 from andrewjpage/pipeline

fix bam parser compile error
Turned off safe

@ line 101
Merge pull request #221 from carlacummins/pipeline

Turned off safe
Merge branch 'vr_tradistags' into pipeline

Conflicts:
	modules/VertRes/Pipelines/Import_iRODS_fastq.pm
Merge pull request #222 from andrewjpage/pipeline

Pipeline
GPL
Merge pull request #223 from andrewjpage/pipeline

GPL
check if lane already stored but db not updated
Merge pull request #224 from andrewjpage/stored_fix

check if lane already stored but db not updated