Browse code

fixed gdm also. bump version

Simone authored on 19/07/2021 07:04:40
Showing4 changed files

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@@ -1,7 +1,7 @@
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 Package: RGMQL
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 Type: Package
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 Title: GenoMetric Query Language for R/Bioconductor
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-Version: 1.12.3
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+Version: 1.12.4
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 Authors@R: c(person(given = "Simone",
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            family = "Pallotta",
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            role = c("aut", "cre"),
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@@ -104,6 +104,9 @@ import_gmql <- function(dataset_path, is_gtf) {
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                 g <- GenomicRanges::makeGRangesFromDataFrame(
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                     df,
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                     keep.extra.columns = TRUE,
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+                    seqnames.field = c("seqnames", "seqname",
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+                                       "chromosome", "chrom",
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+                                       "chr", "chromosome_name"),
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                     start.field = "left",
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                     end.field = "right")
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             })
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@@ -114,6 +117,9 @@ import_gmql <- function(dataset_path, is_gtf) {
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                 g <- GenomicRanges::makeGRangesFromDataFrame(
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                     df,
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                     keep.extra.columns = TRUE,
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+                    seqnames.field = c("seqnames", "seqname",
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+                                       "chromosome", "chrom",
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+                                       "chr", "chromosome_name"),
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                     start.field = "left",
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                     end.field = "right")
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                 })
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@@ -443,12 +443,18 @@ filter_and_extract <- function(
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         g <- GenomicRanges::makeGRangesFromDataFrame(
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             complete_df,
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             keep.extra.columns = TRUE,
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+            seqnames.field = c("seqnames", "seqname",
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+                               "chromosome", "chrom",
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+                               "chr", "chromosome_name"),
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             start.field = "left",
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             end.field = "right")
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     } else {
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         g <- GenomicRanges::makeGRangesFromDataFrame(
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             df,
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             keep.extra.columns = TRUE,
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+            seqnames.field = c("seqnames", "seqname",
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+                               "chromosome", "chrom",
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+                               "chr", "chromosome_name"),
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             start.field = "left",
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             end.field = "right")
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     }
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@@ -1294,6 +1294,9 @@ sample_region <- function(url, datasetName,sampleName) {
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             samples <- GenomicRanges::makeGRangesFromDataFrame(
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                 df,
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                 keep.extra.columns = TRUE,
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+                seqnames.field = c("seqnames", "seqname",
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+                                   "chromosome", "chrom",
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+                                   "chr", "chromosome_name"),
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                 start.field = "left",
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                 end.field = "right",
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                 strand.field="strand"