Merge pull request #102 from pjotrp/master

Makefile: also clean htslib. Important for submodule updates.
faster cram_to_bam
markdup: don't index temporary files
Man page for mpileup
sambamba mpileup: edited man page
man: sambamba-pileup man page
mpileup: when --bcftools was not passed in mpileup would stop on error, rather than
         not call bcftools.