Convert build system to non-recursive build.
Build executables in src directory rather than in root directory.
Style changes to sam2mrf.c before working on Issue #1
Fix bug in sam2mrf generateSamEntry where hasSeqs and hasQual parameters are not initially zeroed, resulting in errors processing subsequent SAM entries. Some formatting changes. Build sources as C99.
Convert mrf2sam.c and sam2mrf.c to unix line endings.
Rebase develop on master.