Merge pull request #12 from wtsi-npg/devel

Devel
Merge pull request #13 from wtsi-npg/master

srl changes
Merge pull request #64 from wtsi-npg/devel

wtsi devel -> master pull request to create v10.8
Merge pull request #65 from wtsi-npg/master

pull tag from master to devel
cache cycle calibration tables when the tile changes rather than doing a lookup for every read
Merge remote branch 'wtsi-npg/devel' into devel
bug fix, cycle_cts now reset when the tile changes
code for error analysis, enable by #define ST_STRUCTURE in calibration_pu.c
bug fix
Merge pull request #66 from srl147/devel

Devel
Merge pull request #67 from wtsi-npg/devel

Devel
added tile_sort() routine for qsort
removed some unused variable warnings
dropped explict skip of purity=0.25 bin for subst and context
No longer require tile size, dropped intensity_dir and tile width/height CMD line
options. Region tables for each tile stored in a hash keyed on x/y region index.
Filter file and reports now ordered by tile
dropped intensity_dir from pb_align, no longer needed by spatial filter
dropped magic number from calibration_pu.c and some tidiying up
restored but deprecated -intensity_dir in pb_align script
Merge pull request #68 from srl147/devel

Devel
Merge pull request #69 from wtsi-npg/devel

Devel
added homopolymer to error analysis
Merge pull request #14 from wtsi-npg/devel

Devel