Merge pull request #6 from dkj/devel

Refactor PG BAM header record adding
Merge pull request #7 from dkj/devel

bugfix - copy to uninitialised string rather than concat
Merge pull request #51 from srl147/devel

add a count to the ID tag in new @PG lines to ensure ID is unique
remove failed reads when applying spatial filter in pb_align
Merge pull request #54 from srl147/devel

remove failed reads when applying spatial filter in pb_align
bug fix in bam_header_add_pg()
Merge branch 'devel' of github.com:wtsi-npg/pb_calibration into devel
Merge pull request #56 from srl147/devel

Devel - bug fix in bam_header_add_pg()
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