Fragment shader (built for Flixel) which replaces a specific color with another.

replaceColor.frag

// A vec4 represents the red, green, blue, alpha of a pixel with values from [0.0, 1.0].
const vec4 MAGENTA = vec4(1.0, 0.0, 1.0, 1.0);
const vec4 GREEN = vec4(0.0, 1.0, 0.0, 1.0);

vec4 doWhatever() {
	// This function just returns green, but you could add more complex logic here.
	return GREEN;
}

void main() {
	// Get the color of the texture at the current pixel.
	vec4 textureColor = flixel_texture2D(bitmap, openfl_TextureCoordv);

	if (textureColor == MAGENTA) {
		// If the texture at this pixel is opaque magenta, replace it.
		textureColor = doWhatever();
	}

	// Return the result.
	gl_FragColor = textureColor;
}