51.11.0

• added support for RNA analysis/quantification using STAR and salmon
• removed unneeded coordinate sort and duplicate marking when there is no alignment to a target reference

51.10.2

• use bwa aln for human split with tophat target alignment

51.10.1

• Modified qc run function list, removed copy_interop and switched archive_to_irods to samplesheet

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

51.6

• test and code fixes to ensure problem-free tests under Perl 5.22.2
• tweak to qc_report_dir in bsub command for one library per lane case
• fix convert-low-quality flag in bambi decode command; set bid_implementation always to bambi

release 51.4

do not run alignment_filter_metrics qc check on spike tag

no p4 processing for phix

47.2

release 47.2