add a function to add in counts to existing reads
refactor to use Region class
fix typo introduced in refactor
add test of increment in merge_roi_counts
Revert "fix typo introduced in refactor"

This reverts commit ebb053a7cfe2e836335335c784fff9b893ffc9e1.
Revert "refactor to use Region class"

This reverts commit ce82ed09e2ff945c6e7ef4942cd986a8a4de23f4.
refactor to use Region class instead of reg_name.
Merge branch 'LS' of github.com:genome/breakdancer into LS