MultipleInputs.addInputPath
is what you are looking for. This is how your configuration would look like. Make sure both AnyMapper1 and AnyMapper2 write the same output expected by MergeReducer
JobConf conf = new JobConf(Merge.class);
conf.setJobName("merge");
conf.setOutputKeyClass(IntWritable.class);
conf.setOutputValueClass(Text.class);
conf.setReducerClass(MergeReducer.class);
conf.setOutputFormat(TextOutputFormat.class);
MultipleInputs.addInputPath(conf, inputDir1, SequenceFileInputFormat.class, AnyMapper1.class);
MultipleInputs.addInputPath(conf, inputDir2, TextInputFormat.class, AnyMapper2.class);
FileOutputFormat.setOutputPath(conf, outputPath);