Fixing some typo.
Correct bug in pair_reads with orphaned alignments
fixed vc pipeline prototype
Merge branch 'develop' of ssh://10.3.11.15:7999/gt/gemtools into develop
Fixed stats to work with unpaired reads on a single line
Add support for 0x800 flag for chimeric reads in SAM output.  Turn maps with negative skips into chimeric reads in SAM.  Correct check for duplicate maps in mapq calculation
Change SEGMENT definition so that negative skips will now be printed as chimeras in SAM (necessary) and MAP (un-necessary).  If this is not desriable then we will have to find a clean way to allow SAM and MAP output to have different definitions of SEGMENT.  Fix a scoring bug.
Add support for SA Tags with SAM output and chimeric reads.  Currently only works with gt.scorereads; if it appears OK will add switches to gt.map2sam
Fix bug where SAM CIGAR print mismatches was always set to on.  Get gt.map2sam to use common MAPQ calculation code from gt_map_score.c
Correct bugs with unpaired read input
Added null checks on mmap copy and in gt.filter
Merge branch 'develop' of ssh://fenris.ti00a1.pcb.ub.es:7999/gt/gemtools into develop
Merge branch 'develop' of ssh://10.3.11.15:7999/gt/gemtools into develop
Add support for printing SAM MD tags
Merge branch 'develop' of ssh://fenris.ti00a1.pcb.ub.es:7999/gt/gemtools into develop
Added splitmap and merge step to vc-pipeline
Merge branch 'develop' of ssh://fenris.ti00a1.pcb.ub.es:7999/gt/gemtools into develop
Added plugin loading for GT-99
Merge branch 'develop' of ssh://10.3.11.15:7999/gt/gemtools into develop
Change SAM tag options to use the new --tags option allowing multiple tags to be specified in the form like this:  NH:yes;XT:no;MD;yes. So far only applied to gt.scorereads