working on support for foreign bams
modifying chrY test reference to have complete map file
updating foreignbam option
updating makefile with new small chrY reference
make allelotype take foreign bams, and deal with all STRs spanned by each read
improving method to get STR allele for multiple strs in same read
more tests and tweaks for ExtractCigar
using interval trees to get spanned intervals
using interval trees
removing unused param in ParseRead
getting rid of -j default option for make scripts since it kills my desktop
get rid of obsolete --dont-include-flank option
Merge branch 'foreignbam'
fixing merge conflict in ReadContainer.cpp