Merge pull request #4 from dkj/devel

teepot tweaks
small fix to output file name in examples
added subst_param_name "phix_or_target" to md5 file name produced by bamrecompress
added subst_param_name "phix_or_target" to index file name produced by bamrecompress, and
to calibration_pu
save seqchksum files
use samtools merge instead of bamcat because of deadlock problems
some changes to parmater names to follow new input/output convention
alignment_wtsi_stage2_template.json
  added outputs for new samtools stats reports

final_output_prep.json
  added -F 0x900 filter flag to bamcheck
  added outputs for new samtools stats reports
  added samtools_executable param to allow selection of samtools version

post_alignment.json
  added samtools_executable param to allow selection of samtools version

seqchksum.json
  changed from bamcat to samtools merge to avoid deadlock
  added samtools_executable param to allow selection of samtools version
removed unused edges
dealt with warnings of udefined variables
simplified some logging messages which were using out-of-date attributes
large wait (500 minutes) to avoid unnecessary spill to disk

had previously been an mbuffer