Upgrade BWA so that aln is now availiable iunder same version as mem
Merge pull request #45 from ICGC-TCGA-PanCancer/bwa-upgrade

Tests were fine, merging to dev, but no release for now.
minor correction to upgrade path
minor conflict
Updated to shard input when running BWA-mem, BWA-aln functionallity should be maintained
Updated version and release files following merge
Merge branch 'master' of https://github.com/ICGC-TCGA-PanCancer/PCAP-core