Ensure markdup report for phix does not clash with main markdup report
Merge pull request #9 from dkj/devel

Ensure markdup report for phix does not clash with main markdup report
Add node filtering to samtools flagstat (#406932)
Rename bammarkduplicates output files (#406926)
Corrected filter flag from 0x9ff to 0x900
Rename markdup files
Merge remote-tracking branch 'js10-remote/devel' into devel

Conflicts:
	data/tophat2_sample_template.vtf
Merge remote-tracking branch 'wtsi-npg/devel' into devel
tophat2_sample_template.vtf: changed the naming convention used for bed files (copy target) to <rpt>.<type>.bed (e.g. 12345_2#13.deletions.bed). This should now match the convention expected by the iRODS archiver in data_handling.
vtfp.pl: when multiple instances of a subst_param use the same name in a hash map, the repeated instances now have their attribute names recorded in walk()
Merge pull request #13 from wtsi-npg/devel

fix naming convention for bed files in tophat2 vtf