update qingpeng's citation
fix URLs
PEP8
Merge pull request #677 from ged-lab/fix/qp-citation

update qingpeng's citation
catching up with recent changes
add API checks
include the sandbox
doc doc updates
Merge pull request #580 from ged-lab/fix/release-checklist14Q3

catching up with recent changes
fix broken docs url
add the seqan headers
Fix mismatched include guards, remove deprecated register specification, switch from unnamed to named POSIX semaphore, as unnamed semaphores are deprecated and unsupported on OS X
Add necessary semaphore/fcntl includes to system_sema.h.  Add c++98/c++11 checking to auto/unique ptrs in gff_stream.h
first pass seqan impl
streaming of plain and gzipped FAST[AQ]
restore header order
don't mmap plain FAST[AQ] files
remove extra line from ChangeLog