Switched pipeline_rnaseqdiffexpression.py over to using featureCounts for producing read counts for use in differential expression.

buildGeneLevelReadCounts and buildTranscriptLevelReadCounts could also possibly be switched over, but I don't know if the output would be equivalent.
merge
Added full test suite for bed2bed.py - cannot guarentee that the bin methods are giving correct output over all cases
Added retries to the commit phase of CSV2DB.py
Changed pipeline so that it now uses featureCounts to quantify exons before running edgeR/DESeq. Currently gtf2table still used for gene/transcript counts, but this should probably be changed.
Removed old coverageBed exon counting and loading code
Code release modifications: Overhauled documentation, made checking for intervals outside chromosome co-ordinates coherent across all methods. Changed logic is that end of interval can now be on the last base of the chromosome
Fixes to the Differential expression report to account for using feautre_counts rather than exon_counts and multiple design fixes
bug fixes, mostly to do with temp file creation on head node and then running on node