BGI/SOAPsnp/sam/sam_view.h

   1 #ifndef SAM_VIEW_H
   2 #define SAM_VIEW_H
   3
   4
   5 static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
   6 static char *g_library, *g_rg;
   7 static int g_sol2sanger_tbl[128];
   8
   9 static void sol2sanger(bam1_t *b)
  10 {
  11         int l;
  12         uint8_t *qual = bam1_qual(b);
  13         if (g_sol2sanger_tbl[30] == 0) {
  14                 for (l = 0; l != 128; ++l) {
  15                         g_sol2sanger_tbl[l] = (int)(10.0 * log(1.0 + pow(10.0, (l - 64 + 33) / 10.0)) / log(10.0) + .499);
  16                         if (g_sol2sanger_tbl[l] >= 93) g_sol2sanger_tbl[l] = 93;
  17                 }
  18         }
  19         for (l = 0; l < b->core.l_qseq; ++l) {
  20                 int q = qual[l];
  21                 if (q > 127) q = 127;
  22                 qual[l] = g_sol2sanger_tbl[q];
  23         }
  24 }
  25
  26 static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
  27 {
  28         if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
  29                 return 1;
  30         if (g_rg) {
  31                 uint8_t *s = bam_aux_get(b, "RG");
  32                 if (s && strcmp(g_rg, (char*)(s + 1)) == 0) return 0;
  33         }
  34         if (g_library) {
  35                 const char *p = bam_get_library((bam_header_t*)h, b);
  36                 return (p && strcmp(p, g_library) == 0)? 0 : 1;
  37         }
  38         return 0;
  39 }
  40
  41
  42 #endif