51.10

• redirect stderr output to a log (from all NPG and CPAN modules)
• deletion of unused code (illumina2bam,GCLP,OLB,recalibration)
• fix: warn rather than croak in seq_alignment if multiple references for tag 0
• allow p4 stage 1 to analyse runs with different length reads
• sequencescape warehouse loader update (samplesheet LIMS driver for analysis, ml_warehouse_fc_cache for archive)
• RNA-SeQC check added to seq_alignment(RNA-Seq libraries only)
• removed unused force_p4 attribute (and flag)
• p4 stage 2 (seq_alignment) Y-split uses bambi chrsplit instead of SplitBamByChromosomes.jar