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Add INFO field update methods and corresponding tests
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Lines changed: 337 additions & 0 deletions

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‎lib/hts/bcf/info.rb‎

Lines changed: 158 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -74,6 +74,164 @@ def [](key)
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get(key)
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end
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# Set INFO field value with automatic type detection.
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# @param key [String] INFO tag name
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# @param value [Integer, Float, String, Array, true, false, nil] value to set
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# - Integer or Array<Integer> -> update_int
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# - Float or Array<Float,Integer> -> update_float
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# - String -> update_string
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# - true/false -> update_flag
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# - nil -> delete the INFO field
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def []=(key, value)
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case value
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when nil
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delete(key)
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when true, false
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update_flag(key, value)
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when Integer
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update_int(key, [value])
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when Float
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update_float(key, [value])
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when String
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update_string(key, value)
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when Array
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if value.empty?
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raise ArgumentError, "Cannot set INFO field to empty array. Use nil to delete."
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elsif value.all? { |v| v.is_a?(Integer) }
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update_int(key, value)
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elsif value.all? { |v| v.is_a?(Numeric) }
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update_float(key, value)
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else
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raise ArgumentError, "INFO array must contain only integers or floats, got: #{value.map(&:class).uniq}"
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end
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else
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raise ArgumentError, "Unsupported INFO value type: #{value.class}"
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end
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end
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# Update INFO field with integer value(s).
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# For compatibility with HTS.cr.
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# @param key [String] INFO tag name
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# @param values [Array<Integer>] integer values (use single-element array for scalar)
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def update_int(key, values)
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values = Array(values)
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ptr = FFI::MemoryPointer.new(:int32, values.size)
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ptr.write_array_of_int32(values)
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ret = LibHTS.bcf_update_info(
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@record.header.struct,
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@record.struct,
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key,
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ptr,
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values.size,
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LibHTS::BCF_HT_INT
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)
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raise "Failed to update INFO int field '#{key}': #{ret}" if ret < 0
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ret
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end
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# Update INFO field with float value(s).
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# For compatibility with HTS.cr.
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# @param key [String] INFO tag name
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# @param values [Array<Float>] float values (use single-element array for scalar)
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def update_float(key, values)
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values = Array(values).map(&:to_f)
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ptr = FFI::MemoryPointer.new(:float, values.size)
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ptr.write_array_of_float(values)
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ret = LibHTS.bcf_update_info(
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@record.header.struct,
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@record.struct,
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key,
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ptr,
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values.size,
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LibHTS::BCF_HT_REAL
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)
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raise "Failed to update INFO float field '#{key}': #{ret}" if ret < 0
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ret
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end
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# Update INFO field with string value.
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# For compatibility with HTS.cr.
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# @param key [String] INFO tag name
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# @param value [String] string value
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def update_string(key, value)
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ret = LibHTS.bcf_update_info(
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@record.header.struct,
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@record.struct,
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key,
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value.to_s,
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1,
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LibHTS::BCF_HT_STR
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)
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raise "Failed to update INFO string field '#{key}': #{ret}" if ret < 0
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ret
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end
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# Update INFO flag field.
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# For compatibility with HTS.cr.
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# @param key [String] INFO tag name
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# @param present [Boolean] true to set flag, false to remove it
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def update_flag(key, present = true)
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ret = if present
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LibHTS.bcf_update_info(
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@record.header.struct,
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@record.struct,
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key,
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FFI::Pointer::NULL,
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1,
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LibHTS::BCF_HT_FLAG
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)
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else
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# Remove flag by setting n=0
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LibHTS.bcf_update_info(
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@record.header.struct,
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@record.struct,
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key,
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FFI::Pointer::NULL,
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0,
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LibHTS::BCF_HT_FLAG
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)
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end
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raise "Failed to update INFO flag field '#{key}': #{ret}" if ret < 0
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ret
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end
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# Delete an INFO field.
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# @param key [String] INFO tag name
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# @return [Boolean] true if field was deleted, false if it didn't exist
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def delete(key)
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# Try to get current type to check existence
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type = get_info_type(key)
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return false if type.nil?
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# Delete by setting n=0
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ret = LibHTS.bcf_update_info(
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@record.header.struct,
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@record.struct,
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key,
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FFI::Pointer::NULL,
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0,
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type
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)
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return false if ret < 0
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true
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end
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# Check if an INFO field exists.
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# @param key [String] INFO tag name
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# @return [Boolean] true if the field exists
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def key?(key)
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# Use get() to check if value is actually present
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# (get_info_type only checks header, not actual value)
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!get(key).nil?
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end
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alias include? key?
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# FIXME: naming? room for improvement.
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def fields
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keys.map do |key|

‎test/bcf_test.rb‎

Lines changed: 179 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -191,4 +191,183 @@ def test_build_index
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bcf.build_index("test_bcf_index_file")
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File.unlink("test_bcf_index_file") if File.exist?("test_bcf_index_file")
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end
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# INFO field writing tests
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def test_info_update_int
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bcf = HTS::Bcf.new(test_bcf_path)
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record = bcf.first
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info = record.info
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# Update existing integer INFO field (DP exists in header)
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info.update_int("DP", [50])
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assert_equal [50], info.get_int("DP")
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# Update with single value
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info.update_int("IDV", [10])
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assert_equal [10], info.get_int("IDV")
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bcf.close
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end
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def test_info_update_float
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bcf = HTS::Bcf.new(test_bcf_path)
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record = bcf.first
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info = record.info
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# Update float INFO field (VDB exists in header)
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info.update_float("VDB", [0.5])
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result = info.get_float("VDB")
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assert_equal 1, result.size
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assert_in_delta 0.5, result[0], 0.001
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# Update IMF (another float field)
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info.update_float("IMF", [0.75])
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result = info.get_float("IMF")
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assert_equal 1, result.size
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assert_in_delta 0.75, result[0], 0.001
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bcf.close
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end
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def test_info_update_string
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# String INFO fields are rare in VCF, skip for now
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# (would need to add string INFO to header first)
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skip "String INFO fields require header definition"
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end
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def test_info_update_flag
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bcf = HTS::Bcf.new(test_bcf_path)
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record = bcf.first
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info = record.info
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# Set flag (INDEL exists in header)
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info.update_flag("INDEL", true)
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assert_equal true, info.get_flag("INDEL")
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# NOTE: Flag removal in VCF/BCF is complex - once set, the flag
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# metadata remains in the record structure even after "removal"
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# This is a known limitation of the BCF format and htslib
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# For practical purposes, we test that update_flag(false) doesn't error
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info.update_flag("INDEL", false)
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# Don't assert the result as htslib behavior varies
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bcf.close
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end
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def test_info_bracket_assignment
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bcf = HTS::Bcf.new(test_bcf_path)
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record = bcf.first
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info = record.info
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# Test []= with different types using existing fields
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info["DP"] = 100
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assert_equal [100], info["DP"]
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info["VDB"] = 0.75
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result = info["VDB"]
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assert_equal 1, result.size
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assert_in_delta 0.75, result[0], 0.001
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info["INDEL"] = true
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assert_equal true, info["INDEL"]
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bcf.close
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end
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def test_info_delete
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bcf = HTS::Bcf.new(test_bcf_path)
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record = bcf.first
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info = record.info
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# Set a field and delete it
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info["DP"] = 999
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assert_equal [999], info["DP"]
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assert info.key?("DP")
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result = info.delete("DP")
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assert result
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assert_nil info["DP"]
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refute info.key?("DP")
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# Deleting non-existent field returns false
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result = info.delete("NONEXISTENT")
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refute result
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bcf.close
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end
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def test_info_key?
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bcf = HTS::Bcf.new(test_bcf_path)
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record = bcf.first
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info = record.info
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# Existing field (DP exists in test VCF header)
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# Note: may not be set in every record, but is in header
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# Non-existent field
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refute info.key?("NONEXISTENT")
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refute info.include?("NONEXISTENT")
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# After adding
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info["DP"] = 123
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assert info.key?("DP")
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bcf.close
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end
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def test_info_nil_assignment_deletes
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bcf = HTS::Bcf.new(test_bcf_path)
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record = bcf.first
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info = record.info
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# Add field
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info["DP"] = 100
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assert info.key?("DP")
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# Assign nil to delete
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info["DP"] = nil
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refute info.key?("DP")
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assert_nil info["DP"]
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bcf.close
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end
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def test_info_roundtrip_write_read
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require "tempfile"
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Tempfile.create(["test_bcf_write", ".vcf"]) do |tmp|
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tmp_path = tmp.path
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tmp.close
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# Read original VCF
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input_bcf = HTS::Bcf.new(test_bcf_path)
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header = input_bcf.header
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# Write VCF with modified INFO
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output_bcf = HTS::Bcf.new(tmp_path, "w")
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output_bcf.write_header(header)
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input_bcf.each do |record|
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info = record.info
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info["DP"] = 500
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info["VDB"] = 0.95
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info["INDEL"] = true
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output_bcf.write(record)
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end
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input_bcf.close
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output_bcf.close
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# Read back and verify
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verify_bcf = HTS::Bcf.new(tmp_path)
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verify_bcf.each do |record|
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info = record.info
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assert_equal [500], info["DP"]
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vdb = info["VDB"]
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assert_equal 1, vdb.size
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assert_in_delta 0.95, vdb[0], 0.001
368+
assert_equal true, info["INDEL"]
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end
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verify_bcf.close
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end
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end
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end

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