Further tweaks

magnusdv · May 16, 2023 · de37557 · de37557
1 parent aead14d
commit de37557
Showing 1 changed file with 8 additions and 8 deletions.
diff --git a/R/readFam.R b/R/readFam.R
@@ -250,8 +250,8 @@ readFam = function(famfile, useDVI = NA, Xchrom = FALSE, prefixAdded = "added_",
     frqs = as.numeric(x[als.lines + 1])
 
     if("0" %in% als) {
-      warning(sprintf("Illegal allele '0' at locus %s. Changed to '00'.", loc.name), call. = FALSE)
-      als[als == "0"] = "00"
+      warning(sprintf("Database error, locus %s: Illegal allele '0'. Changed to 'z'.", loc.name), call. = FALSE)
+      als[als == "0"] = "z"
     }
 
     # Check for illegal alleles, including "Rest allele", with stepwise models
@@ -260,20 +260,20 @@ readFam = function(famfile, useDVI = NA, Xchrom = FALSE, prefixAdded = "added_",
       alsNum = suppressWarnings(as.numeric(als))
       if(any(is.na(alsNum))) {
         change = TRUE
-        warning(sprintf("Non-numerical allele '%s' at locus %s incompatible with stepwise model. Changed to 'proportional.",
-                         als[is.na(alsNum)][1], loc.name), call. = FALSE)
+        warning(sprintf("Database error, locus %s: Non-numerical allele '%s' incompatible with stepwise model. Changed to proportional model.",
+                        loc.name, als[is.na(alsNum)][1]), call. = FALSE)
       }
       else if(any(alsNum < 1)) {
         change = TRUE
-        warning(sprintf("Database error: Allele '%s' at locus %s is incompatible with stepwise model. Changed to 'proportional'.",
-                        als[alsNum < 1][1], loc.name), call. = FALSE)
+        warning(sprintf("Database error, locus %s: Allele '%s' incompatible with stepwise model. Changed to proportional model.",
+                        loc.name, als[alsNum < 1][1]), call. = FALSE)
       }
       else {
         badMicro = round(alsNum, 1) != alsNum
         if(any(badMicro)) {
           change = TRUE
-          warning(sprintf("Database error: Illegal microvariant '%s' at locus %s. Changed mutation model to 'proportional'.",
-                          als[badMicro][1], loc.name), call. = FALSE)
+          warning(sprintf("Database error, locus %s: Illegal microvariant '%s'. Changed to proportional model.",
+                          loc.name, als[badMicro][1]), call. = FALSE)
         }
       }
       if(change) {