v1.5.1 - install fix

Ensures mergeCavemanResults from CaVEMan is deployed.

v1.5.0 - bugfixed caveman and support for BED based unmatched normal

v1.5.0: Pulls bugfixed version of CaVEMan 1.6.1
Supports BED version of caveman unmatched normal files.

v1.4.1 - correct limit based processing

Number of required threads when using limit was not being set correctly. Generally results in needless thrashing of disk doing file checks but in some cases corrupt data or race conditions were occurring.

v1.4.0 - pulldown flagging functional

Additional command-line options required to make pulldown (WXS) flagging work are added, should be used in conjunction with cgpCaVEManPostProcessing v1.1.0 or better

v1.3.1 - as v1.3.0 with correct version reported

No other real changes, see v1.3.0

CaVEMan 1.5.2 and species/assembly behaviour altered

Bad version number, please use v1.3.1

v1.2.0 - CaVEMan 1.5.1

Upgraded to CaVEMan 1.5.1 which uses htslib access methods to improve split step.

Minor code changes to handle incompatible fasta indexing between pre 1.0 samtools and htslib samtools.

v1.1.3 - Updated underlying CaVEMan version

Other minor modifications are to allow certain dependancies to only be required when specific step is requested when '-p' is in use.

v1.1.2 - Stable release

Uses CaVEMan v1.4.2, allows http/ftp based normal panels and germline bed file is only required at the flag step when -process is specified.

Stable version, from dev branch, pre release - 1.1.1

Fixes #2 #5 #6
Updates to order of code in option setup to fix bug where job limit checking was throwing an error.