working on doc updates
new random site generator
Merge branch 'master' of github.com:adamewing/bamsurgeon
option to keep secondary alignments, bwa mem tweaks
aux script updates
add check for bam index
add aux script
need int
Merge remote branch 'upstream/master'

Conflicts:
	etc/makevcf_indels.py
Fixed double outut of indels
Merge branch 'master' of github.com:CSB5/bamsurgeon