add SortingBufferedOutput class
add generic external memory sorting and test program
add test program for measuring BAM collation speed compared to uncollated input speed
- make readFile method in AutoArray read fixed size blocks (instead of the whole chunk at once)
- add FastQ reader for gziped streams
fix scope
add CheckedInputStreamAtOffsetWrapper class
add CheckedInputStreamAtOffset.hpp in src/Makefile.am
add option to disable byte count checking in FastQ decoding
add FastInterval pass through for StreamFastQReaderWrapper
disable byte counting for decoding FastQ from gzip compressed streams
update testing code for gzip compressed FastQ decoding
add GzipFileFastQReader
add missing include
avoid flush operations in FastQ output
implement output stream based on BgzfDeflate class
add writeSyncedCount method in BgzfDeflateParallel class
refactor GzipHeader class and add GzipHeaderSimple class storing less detailed data
make GzipSingleStream class resettable
make Inflate class resettable
simplify GzipStream class (do not repeatedly instantiate GzipSingleStream class)