add average and total rows to halSummaraizeMutaitonts
shoulda been in last commit
fix bug in close genome where neighbouring genomes still store a pointer to the closed genome in caches
reinterpret cast of itsCounter breaks vtable of itsCouner.ptr, so we fix by properly casting itsCounter.ptr after
Merge branch 'development' into chains
Merge remote-tracking branch 'origin/development' into chains
Rewrite smart pointer to be cleaner and simpler.  Hopefully this one works
fix assertion out of bounds checks
fix assertion error for zero length range
Complete overhaul of block viz code.  New support of arbitrary queries within a clade, dupes, polling basic alignment stats
use wildcard in makefiles that contain pattern substitutions
attempt to fix ongoing misundersdtaing with myself re inverting subsegments when doing adjacency matches
add simple unit test for block getting code to check coordinate mapping
put thread-locking in blockviz api
fix typo
dug
call pthread_exit at end of main and dont call halclose
Rewrite smart pointer to be cleaner and simpler.  Hopefully this one works
Merge remote-tracking branch 'origin/chains' into lod
add option to halStats to just get numSegments for a genome