JAMMv1.0.8

• changed normalization options to either global or chromosome specific, option in peakfinder.r is normAdjust (default is TRUE)

JAMMv1.0.7rev6

Changed input checks for better compatibility with pipeline tools.

JAMMv1.0.7rev5

add -T for custom temporary directoy - streamlined some code and fixd a bug in peakfinder.r

JAMMv1.0.7rev4

changelog; fixed a minor bug with enriched window finding

JAMMv1.0.7rev3

changelog: - fixed bugs in paired-end handling - fixed bugs in automated threshold that slowed it down when input was present

JAMMv1.0.7rev2

Changelog: fixed bugs in paired-end handling-added an option to set pre-scheduling to FALSE for mclapply-some cryptic errors now replaced with warnings or more user-friendly error messages-fixed a bug in peakfinder related to finding one enriched window in a chromosome-added simple depth normalization option to SignalGenerator.sh