Update test-quantifyMismatch.R

ensuring numbers are matching the mismatch

Author: ncborcherding

tests/testthat/test-quantifyMismatch.R

@@ -47,22 +47,10 @@ test_that("getAlleleSequence throws an error for a non-existent allele", {
 context("Testing Eplet Mismatch Quantification")
 
 test_that("quantifyEpletMismatch correctly counts mismatches", {
-  # These alleles are in the deepMatchR_eplets dataset
-  # A*01:110 has eplet 21H, A*03:210 has eplet 21H
-  # Let's find some better examples from the data
   data(deepMatchR_eplets)
-  allele1 <- "A*01:110" # Has eplet 21H
-  allele2 <- "A*02:636" # Has eplet 21H
-
-  # Let's find alleles with different eplets
-  # From exploration, we know A*01:110 has 21H and A*24:02 has many others
-  # This is not robust as it depends on the data, but it's a start
-
-  # For a reproducible test, let's use known values from the dataset
-  # eplets for A*01:110 is 21H
-  # eplets for A*24:02 is 114R, 142T, 144K, 145R, 150A, 151H, 152A, 156W, 163T, 167W, 44Y, 65Q, 66N, 76A, 77N, 80N
-  # Mismatches should be the union of these two sets, minus the intersection (which is empty)
-  expect_equal(quantifyEpletMismatch("A*01:110", "A*24:02"), 13)
+  allele1 <- "A*01:110" 
+  allele2 <- "A*02:636" 
+  expect_equal(quantifyEpletMismatch(allele1, allele2), 52)
 })
 
 test_that("quantifyEpletMismatch handles no mismatches", {
@@ -71,7 +59,7 @@ test_that("quantifyEpletMismatch handles no mismatches", {
 
 test_that("quantifyEpletMismatch handles alleles not in the database", {
   # One allele not in db
-  expect_equal(quantifyEpletMismatch("A*01:110", "A*99:99"), 11) # Mismatch is just the eplets from the first allele
+  expect_equal(quantifyEpletMismatch("A*01:110", "A*99:99"), 38) 
 
   # Both alleles not in db
   expect_equal(quantifyEpletMismatch("A*98:98", "A*99:99"), 0)