BGI/SOAPdenovo2/standardPregraph/inc/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
  14         if ( g_sol2sanger_tbl[30] == 0 )
  15         {
  16                 for ( l = 0; l != 128; ++l )
  17                 {
  18                         g_sol2sanger_tbl[l] = ( int ) ( 10.0 * log ( 1.0 + pow ( 10.0, ( l - 64 + 33 ) / 10.0 ) ) / log ( 10.0 ) + .499 );
  19
  20                         if ( g_sol2sanger_tbl[l] >= 93 ) { g_sol2sanger_tbl[l] = 93; }
  21                 }
  22         }
  23
  24         for ( l = 0; l < b->core.l_qseq; ++l )
  25         {
  26                 int q = qual[l];
  27
  28                 if ( q > 127 ) { q = 127; }
  29
  30                 qual[l] = g_sol2sanger_tbl[q];
  31         }
  32 }
  33
  34 static inline int __g_skip_aln ( const bam_header_t * h, const bam1_t * b )
  35 {
  36         if ( b->core.qual < g_min_mapQ || ( ( b->core.flag & g_flag_on ) != g_flag_on ) || ( b->core.flag & g_flag_off ) )
  37                 { return 1; }
  38
  39         if ( g_rg )
  40         {
  41                 uint8_t * s = bam_aux_get ( b, "RG" );
  42
  43                 if ( s && strcmp ( g_rg, ( char * ) ( s + 1 ) ) == 0 ) { return 0; }
  44         }
  45
  46         if ( g_library )
  47         {
  48                 const char * p = bam_get_library ( ( bam_header_t * ) h, b );
  49                 return ( p && strcmp ( p, g_library ) == 0 ) ? 0 : 1;
  50         }
  51
  52         return 0;
  53 }
  54
  55
  56 #endif