Changed main Makefile to put LDFLAGS after -lbamtools. Fixes customized Bamtools link error when Bamtools already defined in /usr/lib.

ifdef'd out DualQueue and removed usages of it to fix compiler errors wi...

Added sample sub-program with needed changes to main, Makefiles, Context, FileRecordMgr, and RecordOutputMgr.

New unit tests for sort order enforcement, non-existant file. Also added performance test for file input and compression types.

Added 12 new tests to print header for files with large header from uncompressed files, gzip, and bgzip as file, redirect, pipe and fifo.