1. NanoMethViz
  2. R
  3. assertions.R
Browse code

Removed support for CSI files because Rsamtools does not support it

shians authored on 05/03/2024 03:43:24
Showing 1 changed files
R/assertions.R
History View file @ 503f05d
... ... 
@@ -15,16 +15,15 @@ assert_readable <- function(x) {
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 #' @importFrom purrr map_lgl
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 assert_has_index <- function(x) {
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-    has_index <- purrr::map_lgl(paste0(x, ".bai"), fs::file_exists) |
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-                 purrr::map_lgl(paste0(x, ".csi"), fs::file_exists)
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+    has_index <- purrr::map_lgl(paste0(x, ".bai"), fs::file_exists)
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     if (any(!has_index)) {
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         no_index <- x[!has_index]
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         if (length(no_index) == 1) {
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-            stop(glue::glue("files '{no_index}' does not have bam index, this can be fixed by running `samtools index` in the command line."))
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+            stop(glue::glue("file '{no_index}' does not have bam index (.bai), this can be fixed by running `samtools index` in the command line."))
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         } else {
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             no_index <- paste(glue::glue("'{no_index}'"), collapse = ", ")
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-            stop(glue::glue("files {no_index} do not have bam index, this can be fixed by running `samtools index` in the command line."))
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+            stop(glue::glue("files {no_index} do not have bam index (.bai), this can be fixed by running `samtools index` in the command line."))
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         }
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     }
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 }
Browse code

Added handling of csi indices for BAM files

shians authored on 04/03/2024 23:51:25
Showing 1 changed files
R/assertions.R
History View file @ 3e4687a
... ... 
@@ -15,7 +15,8 @@ assert_readable <- function(x) {
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 #' @importFrom purrr map_lgl
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 assert_has_index <- function(x) {
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-    has_index <- purrr::map_lgl(paste0(x, ".bai"), fs::file_exists)
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+    has_index <- purrr::map_lgl(paste0(x, ".bai"), fs::file_exists) |
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+                 purrr::map_lgl(paste0(x, ".csi"), fs::file_exists)
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     if (any(!has_index)) {
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         no_index <- x[!has_index]
Browse code

Updated assertions

Shians authored on 05/06/2023 05:00:37
Showing 1 changed files
R/assertions.R
History View file @ 24bb51b
... ... 
@@ -8,7 +8,7 @@ assert_readable <- function(x) {
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             stop(glue::glue("Path '{unreadables}' does not exist"))
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         } else {
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             unreadables <- paste(glue::glue("'{unreadables}'"), collapse = ", ")
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-            stop(glue::glue("Paths {unreadables} do not exist"))
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+            stop(glue::glue("paths {unreadables} do not exist"))
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         }
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     }
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 }
... ... 
@@ -20,10 +20,10 @@ assert_has_index <- function(x) {
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     if (any(!has_index)) {
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         no_index <- x[!has_index]
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         if (length(no_index) == 1) {
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-            stop(glue::glue("files '{no_index}' does not have bam index"))
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+            stop(glue::glue("files '{no_index}' does not have bam index, this can be fixed by running `samtools index` in the command line."))
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         } else {
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             no_index <- paste(glue::glue("'{no_index}'"), collapse = ", ")
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-            stop(glue::glue("files {no_index} do not have bam index"))
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+            stop(glue::glue("files {no_index} do not have bam index, this can be fixed by running `samtools index` in the command line."))
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         }
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     }
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 }
Browse code

Added check for BAM indices

Shians authored on 31/05/2023 03:09:33
Showing 1 changed files
R/assertions.R
History View file @ 15074e8
... ... 
@@ -12,3 +12,18 @@ assert_readable <- function(x) {
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         }
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     }
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 }
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+
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+#' @importFrom purrr map_lgl
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+assert_has_index <- function(x) {
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+    has_index <- purrr::map_lgl(paste0(x, ".bai"), fs::file_exists)
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+
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+    if (any(!has_index)) {
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+        no_index <- x[!has_index]
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+        if (length(no_index) == 1) {
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+            stop(glue::glue("files '{no_index}' does not have bam index"))
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+        } else {
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+            no_index <- paste(glue::glue("'{no_index}'"), collapse = ", ")
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+            stop(glue::glue("files {no_index} do not have bam index"))
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+        }
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+    }
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+}
Browse code

Fixed readability assertions

Shians authored on 11/04/2023 01:17:24
Showing 1 changed files
R/assertions.R
History View file @ 7b648a5
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,14 @@
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+#' @importFrom purrr map_lgl
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+assert_readable <- function(x) {
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+    readable <- purrr::map_lgl(x, fs::file_exists)
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+
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+    if (any(!readable)) {
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+        unreadables <- x[!readable]
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+        if (length(unreadables) == 1) {
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+            stop(glue::glue("Path '{unreadables}' does not exist"))
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+        } else {
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+            unreadables <- paste(glue::glue("'{unreadables}'"), collapse = ", ")
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+            stop(glue::glue("Paths {unreadables} do not exist"))
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+        }
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+    }
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+}