don't override -f behaviour in subtract so that -r and -F play nicely with -f. Thanks to @ajank

remove in_header() cruft

account for overlapping pairs

warn about -g when using BAM input in genomecov

cleanup groupby

Merge pull request #549 from jmarshall/warnings

Use std::vector's default constructor

Fixed typo and resulting clang compiler warning

Use hex character constants for char values

Merge pull request #539 from cviner/master

Merge pull request #540 from iansealy/master

Merge pull request #547 from udincer/patch-1

Clarify homebrew installation under OSX

Merge pull request #544 from jmarshall/dos-files

Ignore CR characters at the ends of lines