speed up a little, closeend
	// check speed here!
    /*
	if (bamCore->flag & BAM_CINS) return true;
	if (bamCore->flag & BAM_CDEL) return true;
	if (bamCore->flag & BAM_CREF_SKIP) return true;
	if (bamCore->flag & BAM_CSOFT_CLIP) return true;
	if (bamCore->flag & BAM_CHARD_CLIP) return true;
	if (bamCore->flag & BAM_CPAD) return true;
     */
use op to calculate BAM_CIN and so on. decreased about 10% sensitivity but speed is no longer a problem
prefer long option names in scripts
remove Makefile.local

This is an intermediate step towards vendoring samtools.
remove "dependency file" generation

The way this was done causes "building" to happen even when trying to
make non-build targets, e.g. config and clean.  The "dependency files"
don't appear to be required to successfully build.
add missing file to clean target
vendor samtools
remove phony config target from pindel and pindel-debug targets
add .travis.yml
install cppcheck dependency
install gcovr depdendency
disable functional-tests for now since they are currently broken