Merge pull request #3 from paulsengroup/fix/query-mirroring

Bugfix: query mirroring

conanfile.txt

@@ -55,6 +55,7 @@ hdf5*:enable_cxx=False
 hdf5*:hl=False
 hdf5*:threadsafe=False
 hdf5*:parallel=False
+hictk*:with_eigen=False
 highfive*:with_boost=False
 highfive*:with_eigen=False
 highfive*:with_opencv=False

src/hictkr_file.cpp

@@ -255,13 +255,16 @@ static Rcpp::NumericMatrix fetch_as_matrix(const Selector &sel) {
  matrix.at(i1, i2) = tp.count;
 
  if (mirror_matrix) {
- // Mirror matrix below diagonal
- if (i2 - i1 < num_rows && i1 < num_cols && i2 < num_rows) {
+ const auto delta = i2 - i1;
+ if (delta >= 0 && delta < num_rows && i1 < num_cols && i2 < num_rows) {
  matrix.at(i2, i1) = tp.count;
- } else if (i2 - i1 > num_cols && i1 < num_cols && i2 < num_rows) {
+ } else if ((delta < 0 || delta > num_cols) && i1 < num_cols && i2 < num_rows) {
  const auto i3 = static_cast<std::int64_t>(tp.bin2_id - row_offset);
  const auto i4 = static_cast<std::int64_t>(tp.bin1_id - col_offset);
- matrix.at(i3, i4) = tp.count;
+
+ if (i3 >= 0 && i3 < num_rows && i4 >= 0 && i4 < num_cols) {
+ matrix.at(i3, i4) = tp.count;
+ }
  }
  }
  });

tests/testthat/test-fetch-dense.R

@@ -19,7 +19,7 @@ for (path in test_files) {
  expect_equal(sum_, 178263235)
  })
 
- test_that("HiCFile: fetch (dense) cis", {
+ test_that("HiCFile: fetch (dense) symmetric cis", {
  f <- File(path, 100000)
 
  m <- fetch(f, "chr2R:10,000,000-15,000,000", type="dense")
@@ -31,6 +31,35 @@ for (path in test_files) {
  expect_equal(sum_, 6029333)
  })
 
+ test_that("HiCFile: fetch (dense) asymmetric cis", {
+ f <- File(path, 100000)
+
+ m <- fetch(f, "chr2L:0-10,000,000", "chr2L:5,000,000-20,000,000", type="dense")
+
+ shape <- dim(m)
+ sum_ <- sum(m)
+
+ expect_equal(shape, c(100, 150))
+ expect_equal(sum_, 6287451)
+
+
+ m <- fetch(f, "chr2L:0-10,000,000", "chr2L:10,000,000-20,000,000", type="dense")
+
+ shape <- dim(m)
+ sum_ <- sum(m)
+
+ expect_equal(shape, c(100, 100))
+ expect_equal(sum_, 761223)
+
+ m <- fetch(f, "chr2L:0-10,000,000", "chr2L:0-15,000,000", type="dense")
+
+ shape <- dim(m)
+ sum_ <- sum(m)
+
+ expect_equal(shape, c(100, 150))
+ expect_equal(sum_, 12607205)
+ })
+
  test_that("HiCFile: fetch (dense) cis BED queries", {
  f <- File(path, 100000)