@@ -203,13 +203,13 @@ exportUnivariatePeaks <- function(hmm.list, filename, header=TRUE, separate.file

         # Make score integer

         df$peakScores <- round(df$peakScores)

         numsegments <- nrow(df)

-        df <- cbind(df, thickStart=df$start, thickEnd=df$end)

         # Convert from 1-based closed to 0-based half open

         df$start <- df$start - 1

-        df$thickStart <- df$thickStart - 1

-        # Colors

-        RGB <- t(grDevices::col2rgb(getStateColors('modified')))

-        df$itemRgb <- apply(RGB,1,paste,collapse=",")

+        # df$thickStart <- df$start

+        # df$thickEnd <- df$end

+        # # Colors

+        # RGB <- t(grDevices::col2rgb(getStateColors('modified')))

+        # df$itemRgb <- apply(RGB,1,paste,collapse=",")

         if (nrow(df) == 0) {

             warning('hmm ',imod,' does not contain any \'modified\' calls')

         } else {

@@ -452,11 +452,11 @@ exportMultivariatePeaks <- function(hmm, filename, trackname=NULL, header=TRUE,

         # Convert from 1-based closed to 0-based half open

         df$start <- df$start - 1

-        df$thickStart <- df$start

-        df$thickEnd <- df$end

-        # Colors

-        RGB <- t(grDevices::col2rgb(getStateColors('modified')))

-        df$itemRgb <- apply(RGB,1,paste,collapse=",")

+        # df$thickStart <- df$start

+        # df$thickEnd <- df$end

+        # # Colors

+        # RGB <- t(grDevices::col2rgb(getStateColors('modified')))

+        # df$itemRgb <- apply(RGB,1,paste,collapse=",")

         ## Write to file

         if (separate.files) {

@@ -624,11 +624,11 @@ exportCombinedMultivariatePeaks <- function(hmm, filename, trackname=NULL, heade

         # Convert from 1-based closed to 0-based half open

         df$start <- df$start - 1

-        df$thickStart <- df$start

-        df$thickEnd <- df$end

-        # Colors

-        RGB <- t(grDevices::col2rgb(getStateColors('modified')))

-        df$itemRgb <- apply(RGB,1,paste,collapse=",")

+        # df$thickStart <- df$start

+        # df$thickEnd <- df$end

+        # # Colors

+        # RGB <- t(grDevices::col2rgb(getStateColors('modified')))

+        # df$itemRgb <- apply(RGB,1,paste,collapse=",")

         ## Write to file

         if (separate.files) {