Merge pull request #42 from wtsi-npg/devel

merge from devel for release 0.08
Merge branch 'dkj-devel' into devel
removed the incorrect "level=0" from the final bamrecompress
removed the superfluous sortorder flag from the final bamrecompress
Merge pull request #44 from dozy/bamreccompress_fix

removed the incorrect "level=0" and sortorder flag from the final bamrecompress
install action should not remove lib directory at target; added compilation test; enabled warnings in scripts
Merge branch 'mgcam-devel' into devel
allow specification of (biobambam) markduplicates executable as a subst_param, with a default of bammarkduplicates2 until questions about bammarkstreamingduplicates are resolved
Merge pull request #46 from dozy/bammarkduplicates_change

allow specification of markduplicates executable as parameter
change default markduplicates to bammarkduplicates2 for vtlib template set
Merge pull request #48 from dozy/bmd_change_vtlib

bammarkduplicates2 for vtlib
Added bwa executable substitution parameter
Moving from bamcheck to samtools stats; adjusted output fileformat accordingly
Merge pull request #47 from wtsi-npg/devel

release 0.09
Replaced whitespaces by tabs, fixed indentation
Replaced whitespaces with tabs
Merge pull request #49 from stepf/devel

Added bwa substitution; Moved from bamcheck to samtools stats
Added bamseqchecksum to output files
Merge pull request #50 from stepf/whitespace

Replaced whitespaces with tabs, fixed indentation
Merge branch 'bamseqchecksum' of https://github.com/stepf/p4 into stepf-bamseqchecksum