Merge pull request #49 from wtsi-npg/devel

Devel
Merge pull request #53 from wtsi-npg/devel

pull from Devel for release 10.4
Merge pull request #55 from wtsi-npg/devel

Devel
Merge pull request #56 from srl147/devel

Devel - bug fix in bam_header_add_pg()
Merge pull request #57 from wtsi-npg/devel

Devel
allow jar for BAM joining to be specified on command line
prefix/output bam should be able to include directory path
option to pass arguments to bwa sam{se,pe} command
Merge pull request #58 from dkj/devel

passing arguments for bwa sam{se,pe}, specifying BAM join jar location, allow output to include directory path
refactor get_real_path_name
refactor get_command_line
use bam_header_dup from samtools
Merge pull request #59 from dkj/devel

Refactoring and code removal
Merge pull request #60 from wtsi-npg/devel

Devel
Merge pull request #61 from wtsi-npg/master

v10.7
use Perl from PATH
Merge pull request #62 from dkj/devel

use Perl from PATH
Merge pull request #64 from wtsi-npg/devel

wtsi devel -> master pull request to create v10.8
Merge pull request #65 from wtsi-npg/master

pull tag from master to devel
Merge remote branch 'wtsi-npg/devel' into devel