Merge branch 'release/v0.1.2'

Author: CiaranOMara

.github/workflows/UnitTests.yml

@@ -14,12 +14,12 @@ jobs:
         julia-version:
           - '1.0' # LTS
           - '1'
-        julia-arch: [x86]
+        julia-arch: [x64, x86]
         os: [ubuntu-latest, windows-latest, macOS-latest]
         experimental: [false]
         include:
           - julia-version: nightly
-            julia-arch: x86
+            julia-arch: x64
             os: ubuntu-latest
             experimental: true
 

Project.toml

@@ -1,7 +1,7 @@
 name = "Indexes"
 uuid = "4ffb77ac-cb80-11e8-1b35-4b78cc642f6d"
 authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <benjward@protonmail.com>", "Ciarán O’Mara <CiaranOMara@utas.edu.au>"]
-version = "0.1.1"
+version = "0.1.2"
 
 [deps]
 BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"

src/overlap.jl

@@ -76,13 +76,13 @@ function Base.iterate(iter::TabixOverlapIterator, state)
 end
 
 function icmp(record, interval)
-    c = cmp(BioCore.seqname(record), interval.seqname)
+    c = cmp(BioCore.seqname(record), BioCore.seqname(interval))
 
-    if c < 0 || (c == 0 && BioCore.rightposition(record) < interval.first)
+    if c < 0 || (c == 0 && BioCore.rightposition(record) < BioCore.leftposition(interval))
         return -1
     end
 
-    if c > 0 || (c == 0 && BioCore.leftposition(record) > interval.last)
+    if c > 0 || (c == 0 && BioCore.leftposition(record) > BioCore.rightposition(interval))
         return +1
     end
 

src/tabix.jl

@@ -77,11 +77,11 @@ Return chunks possibly overlapping with the range specified by `interval`.
 Note that records within the returned chunks are not guaranteed to actually overlap the query interval.
 """
 function overlapchunks(tabix::Tabix, interval::Interval)
-    seqid = findfirst(isequal(interval.seqname), tabix.names)
+    seqid = findfirst(isequal(BioCore.seqname(interval)), tabix.names)
     if seqid == 0
-        throw(ArgumentError("failed to find sequence name '$(interval.seqname)'"))
+        throw(ArgumentError("failed to find sequence name '$(BioCore.seqname(interval))'"))
     end
-    return overlapchunks(tabix.index, seqid, interval.first:interval.last)
+    return overlapchunks(tabix.index, seqid, BioCore.leftposition(interval):BioCore.rightposition(interval))
 end
 
 # Check if `format` follows the BED rule (half-closed-half-open and 0-based).