Fix bug in align_stats with missing qualities, and correct a few compile warnings and bugs wiht gcc 4.8.2
Add makefile switch to allow switching off use of inline (necessary for library functions with clang); Change printing of unmapped paired reads in MAP format to use a single line
Fix problems with missing lines from interleaved input in gt.scorereads.c and a bug introduced with the previous commit to allow unmapped pairs to be printed on a single MAP output line
Correct incorrect tests for negative values against unsigned variables
Fix bug with unmapped read pairs and SAM output
Fix bug with pair scoring
Fix bug(s) with single end input

Fix bug(s) with single end input
Fix memory leak when printing SA and MD SAM tags
Fix bug with multiple threads and SAM output in gt.scorereads
Another try to remove threading bug in gt.scorereads and SAM output
Typos correction
New: added the expandBooleans option for non-standard command-line generation
Add extra check got gt_vbof_gprintf so that the safety dump of an output
buffer is only acrried out if the last printed character in the buffer is
an EOL, to avoid lines being split in multi-threaded output
Avoid generating pairs which are much worse than the best pairing
Add maximum limit on no. pair maps printed out in SAM or MAP map files.  In addition, the paired maps are now sorted on quality so if we don't take all, we always take the best maps.
Add limits to no. of orphan maps (where a single end mapping is not included in a pair)
Orphan maps are sorted by quality, and the best are taken if the total number is above the limit
The limits are set by default to 32 paired maps and 16 orphan maps per read, but these can be
changed using command line options in gt.scorereads
Remove extraneous file
pipeline updated
Merge branch 'develop' of ssh://10.3.11.15:7999/gt/gemtools into develop
Merge branch 'develop' of ssh://10.3.11.15:7999/gt/gemtools into develop