text: #include "pysam.h"
  
  /*  bam_stat.c -- flagstat subcommand.
  
      Copyright (C) 2009, 2011, 2013-2015 Genome Research Ltd.
  
      Author: Heng Li <lh3@sanger.ac.uk>
  
  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
  in the Software without restriction, including without limitation the rights
  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  copies of the Software, and to permit persons to whom the Software is
  furnished to do so, subject to the following conditions:
  
  The above copyright notice and this permission notice shall be included in
  all copies or substantial portions of the Software.
  
  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  DEALINGS IN THE SOFTWARE.  */
  
  #include <config.h>
  
  #include <unistd.h>
  #include <stdint.h>
  #include <stdlib.h>
  #include <string.h>
  #include <stdio.h>
  #include <limits.h>
  #include <getopt.h>
  
  #include "htslib/sam.h"
  #include "samtools.h"
  
  typedef struct {
      long long n_reads[2], n_mapped[2], n_pair_all[2], n_pair_map[2], n_pair_good[2];
      long long n_sgltn[2], n_read1[2], n_read2[2];
      long long n_dup[2];
      long long n_diffchr[2], n_diffhigh[2];
      long long n_secondary[2], n_supp[2];
  } bam_flagstat_t;
  
  #define flagstat_loop(s, c) do {                                        \
          int w = ((c)->flag & BAM_FQCFAIL)? 1 : 0;                       \
          ++(s)->n_reads[w];                                              \
          if ((c)->flag & BAM_FSECONDARY ) {                              \
              ++(s)->n_secondary[w];                                      \
          } else if ((c)->flag & BAM_FSUPPLEMENTARY ) {                   \
              ++(s)->n_supp[w];                                           \
          } else if ((c)->flag & BAM_FPAIRED) {                           \
              ++(s)->n_pair_all[w];                                       \
              if (((c)->flag & BAM_FPROPER_PAIR) && !((c)->flag & BAM_FUNMAP) ) ++(s)->n_pair_good[w];    \
              if ((c)->flag & BAM_FREAD1) ++(s)->n_read1[w];              \
              if ((c)->flag & BAM_FREAD2) ++(s)->n_read2[w];              \
              if (((c)->flag & BAM_FMUNMAP) && !((c)->flag & BAM_FUNMAP)) ++(s)->n_sgltn[w];  \
              if (!((c)->flag & BAM_FUNMAP) && !((c)->flag & BAM_FMUNMAP)) { \
                  ++(s)->n_pair_map[w];                                   \
                  if ((c)->mtid != (c)->tid) {                            \
                      ++(s)->n_diffchr[w];                                \
                      if ((c)->qual >= 5) ++(s)->n_diffhigh[w];           \
                  }                                                       \
              }                                                           \
          }                                                               \
          if (!((c)->flag & BAM_FUNMAP)) ++(s)->n_mapped[w];              \
          if ((c)->flag & BAM_FDUP) ++(s)->n_dup[w];                      \
      } while (0)
  
  bam_flagstat_t *bam_flagstat_core(samFile *fp, bam_hdr_t *h)
  {
      bam_flagstat_t *s;
      bam1_t *b;
      bam1_core_t *c;
      int ret;
      s = (bam_flagstat_t*)calloc(1, sizeof(bam_flagstat_t));
      b = bam_init1();
      c = &b->core;
      while ((ret = sam_read1(fp, h, b)) >= 0)
          flagstat_loop(s, c);
      bam_destroy1(b);
      if (ret != -1)
          fprintf(pysam_stderr, "[bam_flagstat_core] Truncated file? Continue anyway.\n");
      return s;
  }
  
  static const char *percent(char *buffer, long long n, long long total)
  {
      if (total != 0) sprintf(buffer, "%.2f%%", (float)n / total * 100.0);
      else strcpy(buffer, "N/A");
      return buffer;
  }
  
  static void usage_exit(FILE *fp, int exit_status)
  {
      fprintf(fp, "Usage: samtools flagstat [--input-fmt-option OPT=VAL] <in.bam>\n");
      exit(exit_status);
  }
  
  int bam_flagstat(int argc, char *argv[])
  {
      samFile *fp;
      bam_hdr_t *header;
      bam_flagstat_t *s;
      char b0[16], b1[16];
      hts_opt *in_opts = NULL;
      int c;
  
      enum {
          INPUT_FMT_OPTION = CHAR_MAX+1,
      };
  
      static const struct option lopts[] = {
          {"input-fmt-option",  required_argument, NULL, INPUT_FMT_OPTION},
          {NULL, 0, NULL, 0}
      };
  
      while ((c = getopt_long(argc, argv, "", lopts, NULL)) >= 0) {
          switch (c) {
          case INPUT_FMT_OPTION:
              if (hts_opt_add(&in_opts, optarg) < 0)
                  usage_exit(pysam_stderr, EXIT_FAILURE);
              break;
          default:
              usage_exit(pysam_stderr, EXIT_FAILURE);
          }
      }
  
      if (argc != optind+1) {
          if (argc == optind) usage_exit(pysam_stdout, EXIT_SUCCESS);
          else usage_exit(pysam_stderr, EXIT_FAILURE);
      }
      fp = sam_open(argv[optind], "r");
      if (fp == NULL) {
          print_error_errno("flagstat", "Cannot open input file \"%s\"", argv[optind]);
          return 1;
      }
      if (hts_opt_apply(fp, in_opts)) {
          fprintf(pysam_stderr, "Failed to apply input-fmt-options\n");
          return 1;
      }
  
      if (hts_set_opt(fp, CRAM_OPT_REQUIRED_FIELDS,
                      SAM_FLAG | SAM_MAPQ | SAM_RNEXT)) {
          fprintf(pysam_stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n");
          return 1;
      }
  
      if (hts_set_opt(fp, CRAM_OPT_DECODE_MD, 0)) {
          fprintf(pysam_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
          return 1;
      }
  
      header = sam_hdr_read(fp);
      if (header == NULL) {
          fprintf(pysam_stderr, "Failed to read header for \"%s\"\n", argv[optind]);
          return 1;
      }
      s = bam_flagstat_core(fp, header);
      fprintf(pysam_stdout, "%lld + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]);
      fprintf(pysam_stdout, "%lld + %lld secondary\n", s->n_secondary[0], s->n_secondary[1]);
      fprintf(pysam_stdout, "%lld + %lld supplementary\n", s->n_supp[0], s->n_supp[1]);
      fprintf(pysam_stdout, "%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]);
      fprintf(pysam_stdout, "%lld + %lld mapped (%s : %s)\n", s->n_mapped[0], s->n_mapped[1], percent(b0, s->n_mapped[0], s->n_reads[0]), percent(b1, s->n_mapped[1], s->n_reads[1]));
      fprintf(pysam_stdout, "%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]);
      fprintf(pysam_stdout, "%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]);
      fprintf(pysam_stdout, "%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]);
      fprintf(pysam_stdout, "%lld + %lld properly paired (%s : %s)\n", s->n_pair_good[0], s->n_pair_good[1], percent(b0, s->n_pair_good[0], s->n_pair_all[0]), percent(b1, s->n_pair_good[1], s->n_pair_all[1]));
      fprintf(pysam_stdout, "%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]);
      fprintf(pysam_stdout, "%lld + %lld singletons (%s : %s)\n", s->n_sgltn[0], s->n_sgltn[1], percent(b0, s->n_sgltn[0], s->n_pair_all[0]), percent(b1, s->n_sgltn[1], s->n_pair_all[1]));
      fprintf(pysam_stdout, "%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]);
      fprintf(pysam_stdout, "%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]);
      free(s);
      bam_hdr_destroy(header);
      sam_close(fp);
      hts_opt_free(in_opts);
      return 0;
  }
  