@@ -256,6 +256,7 @@ gmql_take <- function(input_data, rows)

     sampleList <- lapply(list, function(x){

         x <- x[-1]

         names(x) <- seq_name

+        x$start = x$start +1

         g <- GenomicRanges::makeGRangesFromDataFrame(x,

                                     keep.extra.columns = TRUE,

                                     start.field = "start",

@@ -174,9 +174,7 @@ read_GRangesList <- function(samples)

     df <- data.frame(samples)

     df <- df[-2] #delete group_name

     len_df <- dim(df)[1] # number of rows

-    region_matrix <- as.matrix(vapply(df, as.character,character(len_df)))

-    region_matrix[is.na(region_matrix)] <- "NA"

-    region_matrix <- region_matrix[,setdiff(colnames(region_matrix),"width")]

+

     col_types <- vapply(df,class,character(1))

     col_names <- names(col_types)

     #re order the schema?

@@ -193,9 +191,13 @@ read_GRangesList <- function(samples)

         col_names <- plyr::revalue(col_names,c(start = "left", 

                                         end = "right", seqnames = "chr"))

         schema_matrix <- cbind(col_names,toupper(col_types))

+        df$start = df$start - 1

         schema_matrix<- schema_matrix[setdiff(rownames(schema_matrix),

                                         c("group","width")),]

     }

+    region_matrix <- as.matrix(vapply(df, as.character,character(len_df)))

+    region_matrix[is.na(region_matrix)] <- "NA"

+    region_matrix <- region_matrix[,setdiff(colnames(region_matrix),"width")]

     rownames(schema_matrix) <- NULL

     colnames(schema_matrix) <- NULL