Merge pull request #38 from ICGC-TCGA-PanCancer/dev

merge updates for bugfix in biobambam
Merge pull request #41 from ICGC-TCGA-PanCancer/dev

Fix some issues and add xml_to_bas.pl
Merge pull request #44 from ICGC-TCGA-PanCancer/dev

v1.1.1
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