Add pwalign to Suggests, fix unit tests

fmicompbio · May 18, 2024 · 4d4b584 · 4d4b584
1 parent 6aa6c5f
commit 4d4b584
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -54,6 +54,7 @@ Suggests:
     BiocStyle,
     knitr,
     Biostrings,
+    pwalign,
     plotly
 SystemRequirements: GNU make
 biocViews: GeneticVariability, GenomicVariation, Preprocessing

diff --git a/inst/scripts/generateValuesForUnitTestsTrans.R b/inst/scripts/generateValuesForUnitTestsTrans.R
@@ -295,7 +295,7 @@ processReadsTrans <- function(Ldef) {
   if (!all(Ldef$constantForward == "") && Ldef$constantMaxDistForward > (-1)) {
     constForward <- Biostrings::subseq(fq1, start = Ldef$skipForward + Ldef$umiLengthForward + 1, 
                                        width = Ldef$constantLengthForward)
-    dists <- as.matrix(Biostrings::stringDist(
+    dists <- as.matrix(pwalign::stringDist(
       c(DNAStringSet(structure(Ldef$constantForward, 
                                names = paste0("C", length(Ldef$constantForward)))),
         DNAStringSet(constForward)
@@ -307,7 +307,7 @@ processReadsTrans <- function(Ldef) {
   if (!all(Ldef$constantReverse == "") && Ldef$constantMaxDistReverse > (-1)) {
     constReverse <- Biostrings::subseq(fq2, start = Ldef$skipReverse + Ldef$umiLengthReverse + 1, 
                                        width = Ldef$constantLengthReverse)
-    dists <- as.matrix(Biostrings::stringDist(
+    dists <- as.matrix(pwalign::stringDist(
       c(DNAStringSet(structure(Ldef$constantReverse, 
                                names = paste0("C", length(Ldef$constantReverse)))),
         DNAStringSet(constReverse)

diff --git a/tests/testthat/test_calcNearestStringDist.R b/tests/testthat/test_calcNearestStringDist.R
@@ -20,8 +20,8 @@ test_that("calcNearestStringDist works as expected", {
                                                    width = 8),
                       size = 200))
 
-    d0 <- Biostrings::stringDist(x = strs1, method = "hamming")
-    e0 <- Biostrings::stringDist(x = strs2, method = "levenshtein")
+    d0 <- pwalign::stringDist(x = strs1, method = "hamming")
+    e0 <- pwalign::stringDist(x = strs2, method = "levenshtein")
 
     dm <- as.matrix(d0)
     em <- as.matrix(e0)