Add the class handling barcode summary metadata

#ifndef SUMMARY_METADATA_H_

#define SUMMARY_METADATA_H_

#include <string>

#include <stdio.h>

#include <stdint.h>

#include "khash.h"

#include "utils.h"

// The class summarizes the overall mapping metadata 

namespace chromap {

enum {

  SUMMARY_METADATA_TOTAL = 0,

  SUMMARY_METADATA_DUP,

  SUMMARY_METADATA_UNMAPPED,

  SUMMARY_METADATA_LOWMAPQ,

  SUMMARY_METADATA_FIELDS

};

struct _barcodeSummaryMetadata {

  int counts[SUMMARY_METADATA_FIELDS];

  _barcodeSummaryMetadata() {

    memset(counts, 0, sizeof(counts));

  }

};

KHASH_MAP_INIT_INT64(k64_barcode_metadata, struct _barcodeSummaryMetadata)

class SummaryMetadata {

 public:

  SummaryMetadata() {

    barcode_metadata_ = kh_init(k64_barcode_metadata);

  }

  ~SummaryMetadata() {

    kh_destroy(k64_barcode_metadata, barcode_metadata_);

  }

  void Output(char *filename, int barcode_length) {

    FILE *fp = fopen(filename, "w") ;

    fprintf(fp, "barcode,total,duplicate,unmapped,lowmapq");   

    khiter_t k;

    for (k = kh_begin(barcode_metadata_); k != kh_end(barcode_metadata_); ++k)

      if (kh_exist(barcode_metadata_, k)) {

        fprintf(fp, "%s", Seed2Sequence(kh_key(barcode_metadata_, k), barcode_length).c_str());

        int i;

        for (i = 0; i < SUMMARY_METADATA_FIELDS; ++i) {

          fprintf(fp, ",%d", kh_value(barcode_metadata_, k).counts[i]);

        }

        fprintf(fp, "\n");

      }

    fclose(fp);

  }

  void UpdateCount(uint64_t barcode, int type, int change) {

    int khash_return_code;

    khiter_t barcode_metadata_iter = kh_put(k64_barcode_metadata, barcode_metadata_, barcode, &khash_return_code);

    kh_value(barcode_metadata_, barcode_metadata_iter).counts[type] += change;

  }

 private:

  khash_t(k64_barcode_metadata) *barcode_metadata_;    

  std::string Seed2Sequence(uint64_t seed, uint32_t seed_length) const {

    std::string sequence;

    sequence.reserve(seed_length);

    uint64_t mask_ = 3;

    for (uint32_t i = 0; i < seed_length; ++i) {

      sequence.push_back(

          Uint8ToChar((seed >> ((seed_length - 1 - i) * 2)) & mask_));

    }

    return sequence;

  }

};

} // namespace chromap

#endif