Implement build_index method in Bam class and add corresponding tests

Author: kojix2

lib/hts/bam.rb

@@ -31,6 +31,25 @@ def self.open(*args, **kw)
       file
     end
 
+    def self.build_index(file_name, index_name = nil, min_shift = 0, threads = 0, verbose = true)
+      if verbose
+        if index_name
+          warn "Create index for #{file_name} to #{index_name}"
+        else
+          warn "Create index for #{file_name}"
+        end
+      end
+
+      case LibHTS.sam_index_build3(file_name, index_name, min_shift, threads)
+      when 0 # successful
+      when -1 then raise "indexing failed"
+      when -2 then raise "opening #{file_name} failed"
+      when -3 then raise "format not indexable"
+      when -4 then raise "failed to create and/or save the index"
+      else raise "unknown error"
+      end
+    end
+
     def initialize(file_name, mode = "r", index: nil, fai: nil, threads: nil,
                    build_index: false)
       if block_given?
@@ -74,22 +93,10 @@ def initialize(file_name, mode = "r", index: nil, fai: nil, threads: nil,
       @start_position = tell
     end
 
-    def build_index(index_name = nil, min_shift: 0, threads: 2)
+    def build_index(index_name = nil, min_shift: 0, threads: 2, verbose: true)
       check_closed
 
-      if index_name
-        warn "Create index for #{@file_name} to #{index_name}"
-      else
-        warn "Create index for #{@file_name}"
-      end
-      case LibHTS.sam_index_build3(@file_name, index_name, min_shift, @nthreads || threads)
-      when 0 # successful
-      when -1 then raise "indexing failed"
-      when -2 then raise "opening #{@file_name} failed"
-      when -3 then raise "format not indexable"
-      when -4 then raise "failed to create and/or save the index"
-      else raise "unknown error"
-      end
+      self.class.build_index(@file_name, index_name, min_shift, @nthreads || threads, verbose)
       self # for method chaining
     end
 

test/bam_test.rb

@@ -1,6 +1,8 @@
 # frozen_string_literal: true
 
 require_relative "test_helper"
+require "fileutils"
+require "tmpdir"
 
 class BamTest < Minitest::Test
   def teardown
@@ -334,6 +336,30 @@ def test_build_index
     File.unlink("test_bam_index_file") if File.exist?("test_bam_index_file")
   end
 
+  def test_class_build_index_with_explicit_index_name
+    Dir.mktmpdir do |dir|
+      bam_path = File.join(dir, "copy.bam")
+      index_path = File.join(dir, "copy.bam.bai")
+      FileUtils.cp(path_bam_string, bam_path)
+
+      HTS::Bam.build_index(bam_path, index_path, 0, 0, false)
+
+      assert_equal true, File.exist?(index_path)
+    end
+  end
+
+  def test_class_build_index_with_default_index_name
+    Dir.mktmpdir do |dir|
+      bam_path = File.join(dir, "copy.bam")
+      default_index_path = "#{bam_path}.bai"
+      FileUtils.cp(path_bam_string, bam_path)
+
+      HTS::Bam.build_index(bam_path, nil, 0, 0, false)
+
+      assert_equal true, File.exist?(default_index_path)
+    end
+  end
+
   # Tag writing tests
   def test_aux_update_int
     bam = HTS::Bam.new(path_bam_string)