deprecating s3 options. more coverage tests for main.cpp
adding test for different number of paired end input files and fixing bug in checking for that
adding additional coverage tests for main.cpp
removing s3 functions from common.h
removing unused quality functions in common.cpp
adding more unit tests
adding some debug statements, plus setting maxflank to correct default (100)
fixing off by one error in ref/alt alleles
adding alignment debug statements and increasing max allowed cigar length
ksort.h: add 'static' to avoid linking errors
MT-Data: check return values of sem/mutex functions
fixing travis build, got rid of tests for cigar string being too long
build: detect Mac-OS-X in 'configure.ac'

Defines USE_MACOS_DISPTACH in 'config.h' if Mac-OS-X is detected.
Multithreading: Adapt MT code for Mac-OS-X
Merge pull request #44 from agordon/mac-fix-2

Mac fix 2
making thomas's allelotype params default
updating tests for thomas's allelotype params set as defaults. adding ability to set alignment speedup params
updating defaults in help messages
fixing compiler warnings (Linux)
making command line tests mktemp not fail on mac