add (incomplete) test for thread pool based bam decoding
extend bam parsing
add simplified thread pool using less alloc/free operations
replace most mutexes in simple thread pool example with spin locks
add posix spin lock class and use it in simple thread pool
refactor
use spin lock instead of mutex in SynchrnousHeap
use spin lock instead of mutex in SynchronousQueue
add virtual getPackageName method
use spin lock instead of mutex in TerminatableSynchronousHeap
refactor parallel stable sorting
note name of current package in SimpleThreadPoolThread
add histogram printing of pending and running package in SimpleThreadPool
adapt example to new API
- use new api
- implement thread pool version of parallel sorting
implement sorted writing in simplethreadpoolbamdecode
read blocks in batches
use posix fd input instead of cin
- add zlib based compressor/decompressor objects/factories
- add block recording in testsimplethreadpoolbamdecode
add option for returning result areas in Hamming distance based searching of BidirectionalDnaIndexTemplate