Add support for querying multiple regions in Bcf class

Author: kojix2

lib/hts/bcf.rb

@@ -215,13 +215,20 @@ def query(region, beg = nil, end_ = nil, copy: false, &block)
       raise "query is only available for BCF files" unless file_format == "bcf"
       raise "Index file is required to call the query method." unless index_loaded?
 
-      if beg && end_
-        tid = header.name2id(region)
-        queryi(tid, beg, end_, copy:, &block)
-      elsif beg.nil? && end_.nil?
-        querys(region, copy:, &block)
+      case region
+      when Array
+        raise ArgumentError, "beg and end must not be specified when region is an Array" unless beg.nil? && end_.nil?
+
+        query_regions(region, copy:, &block)
       else
-        raise ArgumentError, "beg and end must be specified together"
+        if beg && end_
+          tid = header.name2id(region)
+          queryi(tid, beg, end_, copy:, &block)
+        elsif beg.nil? && end_.nil?
+          querys(region, copy:, &block)
+        else
+          raise ArgumentError, "beg and end must be specified together"
+        end
       end
     end
 
@@ -243,6 +250,14 @@ def querys(region, copy: false, &block)
       end
     end
 
+    def query_regions(regions, copy: false, &block)
+      if copy
+        query_regions_copy(regions, &block)
+      else
+        query_regions_reuse(regions, &block)
+      end
+    end
+
     def queryi_reuse(tid, beg, end_, &block)
       return to_enum(__method__, tid, beg, end_) unless block_given?
 
@@ -263,6 +278,15 @@ def querys_reuse(region, &block)
       self
     end
 
+    def query_regions_reuse(regions, &block)
+      return to_enum(__method__, regions) unless block_given?
+
+      regions.each do |region|
+        querys_reuse(region, &block)
+      end
+      self
+    end
+
     def query_reuse_yield(qiter)
       bcf1 = LibHTS.bcf_init
       record = Record.new(header, bcf1)
@@ -299,6 +323,15 @@ def querys_copy(region, &block)
       self
     end
 
+    def query_regions_copy(regions, &block)
+      return to_enum(__method__, regions) unless block_given?
+
+      regions.each do |region|
+        querys_copy(region, &block)
+      end
+      self
+    end
+
     def query_copy_yield(qiter)
       loop do
         bcf1 = LibHTS.bcf_init

test/bcf_test.rb

@@ -170,6 +170,22 @@ def test_query
     assert_equal [4021, 4310, 4337], r
   end
 
+  def test_query_multi_regions
+    bcf = HTS::Bcf.open(Fixtures["test.bcf"])
+
+    r = bcf.query(["poo:4000-4100", "poo:4300-4400"]).map { |aln| aln.pos + 1 }
+    assert_equal [4021, 4310, 4337], r
+
+    r = bcf.query(["poo:4000-4100", "poo:4300-4400"], copy: true).map { |aln| aln.pos + 1 }
+    assert_equal [4021, 4310, 4337], r
+
+    r = bcf.query(["poo:4000-4500"]).map { |aln| aln.pos + 1 }
+    assert_equal [4021, 4310, 4337], r
+
+    r = bcf.query(["poo:4000-4500"], copy: true).map { |aln| aln.pos + 1 }
+    assert_equal [4021, 4310, 4337], r
+  end
+
   def test_build_index
     bcf = HTS::Bcf.open(Fixtures["test.bcf"])
     bcf.build_index("test_bcf_index_file")