more robust fix and tests

Author: BradyAJohnston

R/dataframe.R

@@ -23,17 +23,47 @@
   over_origin <- dat$start > dat$end & dat$direction == 1
 
   if (any(over_origin)) {
-    offset <- dat$end[over_origin] + 1
-
     if (is.null(bp)) {
       bp <- max(c(dat$start, dat$end))
     }
-
+    
+    # For origin-spanning features like join(4891..5096,1..751):
+    # - We need to offset the coordinate system so this becomes continuous
+    # - The offset should be chosen so that the feature becomes [new_start..new_end]
+    # - All other features get shifted by the same offset
+    
+    # Find the origin-spanning feature with the smallest end coordinate
+    # This determines our offset
+    min_end <- min(dat$end[over_origin])
+    offset <- min_end
+    
+    # Apply offset to all coordinates
     dat$start <- dat$start - offset
     dat$end <- dat$end - offset
-
-    dat$end[over_origin] <- bp
-
+    
+    # For origin-spanning features, calculate the correct end position
+    # Original: join(4891..5096, 1..751) with bp=5096
+    # After offset by 751: start=4140, end=0
+    # Correct end should be: start + ((5096-4891+1) + 751 - 1) = 4140 + 956 = 5096
+    for (i in which(over_origin)) {
+      original_start <- dat$start[i] + offset  # Restore original start
+      original_end <- dat$end[i] + offset      # Restore original end
+      
+      # Calculate total feature length: (bp - start + 1) + end
+      part1_length <- bp - original_start + 1  # From start to end of plasmid
+      part2_length <- original_end              # From beginning to end position
+      total_length <- part1_length + part2_length
+      
+      # Set the new end position
+      dat$end[i] <- dat$start[i] + total_length - 1
+    }
+    
+    # Handle any negative coordinates by wrapping them around
+    negative_coords <- dat$start < 0 | dat$end < 0
+    dat$start[negative_coords & dat$start < 0] <- 
+      dat$start[negative_coords & dat$start < 0] + bp
+    dat$end[negative_coords & dat$end < 0] <- 
+      dat$end[negative_coords & dat$end < 0] + bp
   }
 
 # only return features where a start was successfully parsed

tests/testthat/test-get_features.R

@@ -77,3 +77,114 @@ test_that("Extract over origin", {
     1
   )
 })
+
+test_that("Origin-spanning feature detection and offset", {
+  # Create test data with origin-spanning feature
+  test_features <- list(
+    list(
+      type = "CDS",
+      name = "TurboID", 
+      start_end = c(4891, 751),
+      direction = 1
+    ),
+    list(
+      type = "gene",
+      name = "normal_gene",
+      start_end = c(1000, 2000), 
+      direction = 1
+    )
+  )
+  
+  # Test with bp = 5096 (plasmid length)
+  df <- .feature_list_to_df(test_features, bp = 5096)
+  
+  # Check that origin-spanning feature is detected
+  expect_true(any(df$start > df$end))
+  
+  # After offset, no feature should have start > end
+  expect_true(all(df$start <= df$end))
+  
+  # Check that the TurboID feature spans correctly
+  turboid <- df[df$name == "TurboID", ]
+  expect_true(nrow(turboid) == 1)
+  expect_true(turboid$start < turboid$end)
+  expect_true(turboid$end > turboid$start)
+})
+
+test_that("Multiple origin-spanning features", {
+  test_features <- list(
+    list(
+      type = "CDS",
+      name = "feature1",
+      start_end = c(4500, 500),
+      direction = 1
+    ),
+    list(
+      type = "CDS", 
+      name = "feature2",
+      start_end = c(4800, 300),
+      direction = 1
+    ),
+    list(
+      type = "gene",
+      name = "normal_feature",
+      start_end = c(1000, 2000),
+      direction = 1
+    )
+  )
+  
+  df <- .feature_list_to_df(test_features, bp = 5000)
+  
+  # All features should have valid coordinates after offset
+  expect_true(all(df$start <= df$end))
+  expect_true(all(df$start >= 0))
+  expect_true(all(df$end >= df$start))
+})
+
+test_that("Complement origin-spanning features", {
+  test_features <- list(
+    list(
+      type = "CDS",
+      name = "complement_feature", 
+      start_end = c(4891, 751),
+      direction = -1  # complement
+    )
+  )
+  
+  df <- .feature_list_to_df(test_features, bp = 5096)
+  
+  # Complement features should not trigger offset logic
+  # (only direction = 1 features should)
+  complement_feat <- df[df$name == "complement_feature", ]
+  expect_true(nrow(complement_feat) == 1)
+})
+
+test_that("Real plasmid file with origin-spanning feature", {
+  # Test the actual problematic file
+  file_path <- system.file("extdata", "559763_pLann.txt", package = "plasmapR")
+  
+  if (file.exists(file_path)) {
+    plasmid <- read_gb(file_path)
+    df <- as.data.frame(plasmid)
+    
+    # Find the TurboID feature
+    turboid <- df[df$name == "TurboID", ]
+    expect_true(nrow(turboid) == 1)
+    
+    # After processing, it should have valid coordinates
+    expect_true(turboid$start < turboid$end)
+    expect_true(turboid$start >= 0)
+    expect_true(turboid$end <= max(df$end))
+    
+    # The feature should span a reasonable length
+    # Original was join(4891..5096,1..751) = (5096-4891) + 751 = 956 bp
+    expected_length <- (5096 - 4891 + 1) + 751  # 957 bp
+    actual_length <- turboid$end - turboid$start + 1
+    
+    # Allow some tolerance for offset calculations
+    expect_true(abs(actual_length - expected_length) <= 10,
+                info = paste("Expected ~", expected_length, "got", actual_length))
+  } else {
+    skip("Test file not found")
+  }
+})