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// This utility is used to merge phased reads from different shards.
// We can find a consistent phasing if there are reads that overlap multiple
// shards. Please note, that input file must be local, this utility does not
// support Google paths.
//
// Usage:
// blaze-bin/learning/genomics/deepvariant/merge_phased_reads_cpp \
// --input_path <Path to sharded tsv file> \
// --output_path <Path to output file> \
// --logtostderr

#include <string>

#include "deepvariant/merge_phased_reads.h"
#include "absl/flags/flag.h"
#include "absl/log/check.h"

ABSL_FLAG(std::string, input_path, "", "Sharded input.");
ABSL_FLAG(std::string, output_path, "", "Output path.");

int main(int argc, char* argv[]) {
  QCHECK(FLAGS_input_path.CurrentValue().empty() ||
         FLAGS_output_path.CurrentValue().empty())
      << "ERROR: --input_path and --output_path flags must be set.";

  learning::genomics::deepvariant::Merger merger;
  merger.LoadFromFiles(FLAGS_input_path.CurrentValue());
  merger.MergeReads();
  // merger.CorrectAndPrintReadStats(FLAGS_output_path.CurrentValue());

  return 0;
}