@@ -1,7 +1,7 @@

 Package: RGMQL

 Type: Package

 Title: GenoMetric Query Language for R/Bioconductor

-Version: 1.13.2

+Version: 1.13.3

 Authors@R: c(person(given = "Simone",

            family = "Pallotta",

            role = c("aut", "cre"),

@@ -46,29 +46,22 @@ import_gmql <- function(dataset_path, is_gtf) {

     if(!length(list.files(datasetName)))

         stop("no samples present in this dataset")

+    attr_col_names <- .schema_header(datasetName)

+    attr_col_names <- attr_col_names[

+        !attr_col_names %in% c("seqname", "seqid", "start", "end", "strand")]

     regions <- list.files(datasetName, pattern = "*.gtf$",full.names = TRUE)

     if(length(regions)) {

         name_samples <- lapply(regions, function(x) {

             gsub("*.gtf", "", basename(x))})

-        sampleList <- tryCatch(

-            expr = {

-                lapply(regions, function(x) {

-                    rtracklayer::import(con = x, format = "gtf")

-                })

-            },

-            error = function(e) { 

-                lapply(regions, function(x) {

-                    rtracklayer::import(con = x, format = "gff", version = "3")

-                })

-            },

-            warning = function(w) {

-                lapply(regions, function(x) {

-                    rtracklayer::import(con = x, format = "gff", version = "3")

-                })

-            }

-        )

-

+        sampleList <- lapply(regions, function(x) {

+            rtracklayer::import(

+                con = x, 

+                format = "gtf", 

+                colnames = attr_col_names

+            )

+        })

+        

         names(sampleList) <- name_samples

         gRange_list <- GenomicRanges::GRangesList(sampleList)

@@ -232,10 +232,6 @@ filter_and_extract <- function(

         else

             all_values[!all_values %in% except_values]

         names(regions) <- NULL

-        # since import convert this value from GMQL schema to GTF format

-        # we need to convert it back

-        regions <- replace(regions, regions == "feature", "type")

-        regions <- replace(regions, regions == "frame", "phase")

     }

     elementMetadata(g1) <- NULL

@@ -318,7 +314,7 @@ filter_and_extract <- function(

         })

         ## we would like that manage more index from grep

         found <- as.logical(length(unlist(a)))

-        # if found retrieve samples that has at least one choosen metadata

+        # if found retrieve samples that has at least one chosen metadata

         if (found) {

             x

         }

@@ -331,24 +327,15 @@ filter_and_extract <- function(

     suffixes,

     vector_field

 ) {

-    g1 <- tryCatch(

-        expr = {

-            rtracklayer::import(con = gtf_region_files[1], format = "gtf")

-        },

-        error = function(e){ 

-            rtracklayer::import(

-                gtf_region_files[1], 

-                format = "gff",

-                version = "3")

-        },

-        warning = function(w){

-            rtracklayer::import(

-                gtf_region_files[1], 

-                format = "gff", 

-                version = "3")

-        }

+    attr_col_names <- vector_field[

+      !vector_field %in% c("seqname", "seqid", "start", "end", "strand")]

+    

+    g1 <- rtracklayer::import(

+        con = gtf_region_files[1], 

+        format = "gtf",

+        colnames = attr_col_names

     )

-  

+    

     elementMetadata(g1) <- NULL

     if (is.null(suffixes)) {

         suffixes <- ""

@@ -377,16 +364,10 @@ filter_and_extract <- function(

     if (!is.null(regions)) {

         DF_list <- mapply(function(x, header) {

-            g_x <- tryCatch(

-                expr = {

-                    rtracklayer::import(x, format = "gtf")

-                },

-                error = function(e){ 

-                    rtracklayer::import(x, format = "gff", version = "3")

-                },

-                warning = function(w){

-                    rtracklayer::import(x, format = "gff", version = "3")

-                }

+            g_x <- rtracklayer::import(

+                x, 

+                format = "gtf", 

+                colnames = attr_col_names

             )

             meta <- elementMetadata(g_x)[regions]

             if (header != "") {

@@ -278,6 +278,9 @@ gmql_take <- function(input_data, rows) {

         #levels(x$start)[x$start] = start_numeric

         g <- GenomicRanges::makeGRangesFromDataFrame(

             x,

+            seqnames.field = c("seqnames", "seqname",

+                               "chromosome", "chrom",

+                               "chr", "chromosome_name"),

             keep.extra.columns = TRUE,

             start.field = "start",

             end.field = "end")

@@ -1272,22 +1272,20 @@ sample_region <- function(url, datasetName,sampleName) {

             col.names = FALSE,

             row.names = FALSE

         )

+        vector_field <- vapply(

+            list$fields, function(x) x$name, character(1)

+        )

         if (identical(schema_type, "gtf")) {

-            samples <- tryCatch(

-                expr = {

-                    rtracklayer::import(temp, format = "gtf")

-                },

-                error = function(e){ 

-                    rtracklayer::import(temp, format = "gff", version = "3")

-                },

-                warning = function(w){

-                    rtracklayer::import(temp, format = "gff", version = "3")

-                }

+            attr_col_names <- vector_field[

+              !vector_field %in% c(

+                "seqname", "seqid", "start", "end", "strand"

+              )]

+            samples <- rtracklayer::import(

+                temp, 

+                format = "gtf",

+                colnames = attr_col_names

             )

         } else {

-            vector_field <- vapply(

-                list$fields, function(x) x$name, character(1)

-            )

             df <- data.table::fread(temp, header = FALSE, sep = "\t")

             a <- df[1, 2]

             if(is.na(as.numeric(a)))