Correction in analysis.xml example on Feb 3rd missed
ensure SM UUID is converted at first opportunity and lc
Dependencies not in older perl distros
index skip was not included for when using to run in farm like environment
More dependency updates following testing on Ubuntu 12.04 VM
minor output tweek
Fixed #14 as built successfully from scratch on vanilla Ubuntu 12.04 VM new release 0.2 for tagging.
new biobambam with extra features useful for splitting and mn/nm calc
Merge pull request #15 from jwhsanger/master

Divergence Metrics and Executable
Added dependencies for stats code
Modifications for stats that can't be calculated when no mapped data for read group
Updated biobambam version
excluded PCAP::Bam:Stats from new test as requires args
Removed debug
next release will need new biobambam version
Merge pull request #1 from ICGC-TCGA-PanCancer/dev

Bringing changes made by Keiran into this fork