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