Added bwa executable substitution parameter
Moving from bamcheck to samtools stats; adjusted output fileformat accordingly
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
Merge branch 'stepf-bamseqchecksum' into devel
Merge pull request #52 from wtsi-npg/master

Merge master back to devel for 0.09
Avoid "_target" in output file names
amend main descriptions
Remove _picard from _dict ids & parameters
Change default mark dup tool back to bamstreamingmarkduplicates
Merge branch 'dkj-devel' into devel
Changed all "mbuffer" and "tee" commands to "teepot" commands
amended some "ioport" names to match preferred naming convention (name should include "IN" or "OUT")
tee exec node fixes following change from mbuffer to teepot
Remove hardcoded paths
Merge pull request #4 from dkj/devel

teepot tweaks
small fix to output file name in examples