added contrast2(); fixed a bug in haploid mode
added contrast2(); fixed a bug in haploid mode

lh3/samtools,AngieHinrichs/samtabix,AngieHinrichs/samtabix,lh3/samtools,lh3/samtools,AngieHinrichs/samtabix,AngieHinrichs/samtabix,AngieHinrichs/samtabix