Skip to content

Fix size_t subtraction underflow issue #52

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
csoneson merged 3 commits into from
Jan 8, 2025
Merged

Fix size_t subtraction underflow issue #52

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
1985678
Version bump
csoneson Jan 8, 2025
34bad2d
Adjust maxMergedLength/minMergedLength in mergeReadPairPartial if the…
csoneson Jan 8, 2025
d741fa2
Fix indentation for consistency
csoneson Jan 8, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: mutscan
Title: Preprocessing and Analysis of Deep Mutational Scanning Data
Version: 0.3.2
Version: 0.3.3
Authors@R:
c(person(given = "Charlotte",
family = "Soneson",
Expand Down
4 changes: 4 additions & 0 deletions NEWS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
# mutscan 0.3.3

* Bugfix in mergeReadPairPartial for situation where specified minMergedLength/maxMergedLength is larger than the total length of the two merged sequences

# mutscan 0.3.1

* Adapt summarizeExperiment to include errorStatistics in metadata(se)
Expand Down
6 changes: 6 additions & 0 deletions src/digestFastqs.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -829,6 +829,9 @@ bool mergeReadPairPartial(std::string &varSeqForward, std::vector<int> &varIntQu
if (maxMergedLength == 0) {
maxMergedLength = lenF + lenR;
}
if (maxMergedLength > lenF + lenR) {
maxMergedLength = lenF + lenR;
}
// if maxMergedLength is specified, adjust allowed minOverlap
if (minOverlap < (lenF + lenR - maxMergedLength)) {
minOverlap = (lenF + lenR - maxMergedLength);
Expand All @@ -851,6 +854,9 @@ bool mergeReadPairPartial(std::string &varSeqForward, std::vector<int> &varIntQu
minMergedLength = lenR;
}
}
if (minMergedLength > lenF + lenR) {
return true; // no valid overlap possible
}
// if minMergedLength is specified, adjust allowed maxOverlap
if (maxOverlap > (lenF + lenR - minMergedLength)) {
maxOverlap = (lenF + lenR - minMergedLength);
Expand Down
17 changes: 16 additions & 1 deletion tests/testthat/test_digestFastqs_helpers.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -397,7 +397,22 @@ test_that("mergeReadPairsPartial works", {
expect_identical(res0d$mergedQual, qF2)
expect_identical(res0d$mergedLengths, 7L)
expect_true(res0d$return)


## minMergedLength > lenF + lenR -> no valid overlap
res0e <- mutscan:::test_mergeReadPairPartial(sF2, qF2, sR2, qR2, lF2, lR2, 1, 7, 15, 9, 1, FALSE)
expect_type(res0e, "list")
expect_identical(res0e$mergedSeq, sF2)
expect_identical(res0e$mergedQual, qF2)
expect_identical(res0e$mergedLengths, 7L)
expect_true(res0e$return)
## maxMergedLength > lenF + lenR -> maxMergedLength = lenF + lenR
res0f <- mutscan:::test_mergeReadPairPartial(sF0, qF0, sR0, qR0, lF0, lR0, 1, 0, 5, 19, 1, FALSE)
expect_type(res0f, "list")
expect_identical(res0f$mergedSeq, sF0)
expect_identical(res0f$mergedQual, rep(c(10L, 40L), c(2, 5)))
expect_identical(res0f$mergedLengths, 7L)
expect_false(res0f$return)

## padded reads
for (i in 1:10) {
sF <- paste(rep(c("C","A"), c(i, 6)), collapse = "")
Expand Down
Loading