Loosen type requirements for coverage

BioJulia · May 1, 2023 · a4af60a · a4af60a
1 parent 5d6c21e
commit a4af60a
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Showing 2 changed files with 12 additions and 4 deletions.
diff --git a/src/coverage.jl b/src/coverage.jl
@@ -39,6 +39,10 @@ GenomicIntervalCollection{GenomicInterval{UInt32}} with 5 intervals:
 """
 function coverage(stream, groupname_isless::Function=isless)
     cov = GenomicIntervalCollection{UInt32}()
+    return coverage!(cov, stream, groupname_isless)
+end
+
+function coverage!(cov::GenomicIntervalCollection{GenomicInterval{N}}, stream, groupname_isless::Function=isless) where N <: Integer
     lasts = Int64[]
 
     stream_next = iterate(stream)
@@ -84,7 +88,7 @@ function coverage(stream, groupname_isless::Function=isless)
                 current_coverage -= 1
             else
                 @assert pos >= coverage_first
-                push!(cov, GenomicInterval{UInt32}(coverage_groupname, coverage_first, pos, STRAND_BOTH, current_coverage))
+                push!(cov, GenomicInterval{N}(coverage_groupname, coverage_first, pos, STRAND_BOTH, current_coverage))
                 current_coverage -= 1
                 coverage_first = pos + 1
             end
@@ -96,7 +100,7 @@ function coverage(stream, groupname_isless::Function=isless)
                 current_coverage += 1
             else
                 if current_coverage > 0
-                    push!(cov, GenomicInterval{UInt32}(coverage_groupname, coverage_first, leftposition(interval) - 1, STRAND_BOTH, current_coverage))
+                    push!(cov, GenomicInterval{N}(coverage_groupname, coverage_first, leftposition(interval) - 1, STRAND_BOTH, current_coverage))
                 end
                 current_coverage += 1
                 coverage_first = leftposition(interval)
@@ -118,14 +122,14 @@ function coverage(stream, groupname_isless::Function=isless)
 end
 
 # Helper function for coverage. Process remaining interval end points after all intervals have been read.
-function coverage_process_lasts_heap!(cov::GenomicIntervalCollection{GenomicInterval{UInt32}}, current_coverage, coverage_groupname, coverage_first, lasts)
+function coverage_process_lasts_heap!(cov::GenomicIntervalCollection{GenomicInterval{N}}, current_coverage, coverage_groupname, coverage_first, lasts) where N <: Integer
     while !isempty(lasts)
         pos = DataStructures.heappop!(lasts)
         if pos == coverage_first - 1
             current_coverage -= 1
         else
             @assert pos >= coverage_first
-            push!(cov, GenomicInterval{UInt32}(coverage_groupname, coverage_first, pos, STRAND_BOTH, current_coverage))
+            push!(cov, GenomicInterval{N}(coverage_groupname, coverage_first, pos, STRAND_BOTH, current_coverage))
             current_coverage -= 1
             coverage_first = pos + 1
         end

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -443,6 +443,10 @@ end #testset Constructor Conversions
         end
 
         @test sort(simple_coverage(intervals)) == sort(collect(coverage(ic)))
+
+        # Check coverage operation with different Integer type.
+        cov = GenomicIntervalCollection{GenomicInterval{Int64}}()
+        @test sort(simple_coverage(intervals)) == collect(GenomicFeatures.coverage!(cov, ic))
     end
 
     @testset "eachoverlap" begin