c_cpp/faststater/chrseq.h

   1 #ifndef _G_CHRSEQ_H
   2 #define _G_CHRSEQ_H
   3
   4 #include "gtypendef.h"
   5 #include <stdint.h>     // int_fast8_t
   6 #include <stdlib.h> // malloc
   7
   8 FORCE_INLINE void NormalizeChrSeq(char *seq){
   9     while(*seq){
  10         switch (*seq) {
  11             case 'a': case 'A':
  12                     *seq = 'A';
  13                     break;
  14             case 't': case 'T':
  15                     *seq = 'T';
  16                     break;
  17             case 'c': case 'C':
  18                     *seq = 'C';
  19                     break;
  20             case 'g': case 'G':
  21                     *seq = 'G';
  22                     break;
  23             default:
  24             *seq = 'N';
  25                     break;
  26         }   // Whether a looking-up array[64] can be faster ?
  27         ++seq;
  28     }
  29 }
  30
  31 // *seq must have been Normalized to /[ATCGN]*/
  32 FORCE_INLINE char *ChrSeqRevComp(char const * seq, size_t len){
  33     char *revcomseq=malloc(len+1);
  34     const char *tmpseqin=seq+len-1; // if len is shorter than real length, trim it.
  35     char *tmpseqrc=revcomseq;
  36     while(tmpseqin>=seq){
  37         switch (*tmpseqin) {
  38             case 'A':
  39                     *tmpseqrc++ = 'T';
  40                     break;
  41             case 'T':
  42                     *tmpseqrc++ = 'A';
  43                     break;
  44             case 'C':
  45                     *tmpseqrc++ = 'G';
  46                     break;
  47             case 'G':
  48                     *tmpseqrc++ = 'C';
  49                     break;
  50             default:
  51             *tmpseqrc++ = 'N';
  52                     break;
  53         }   // Whether a looking-up array[32] can be faster ?
  54         --tmpseqin;
  55     }
  56     *tmpseqrc++ = '\0';
  57     return revcomseq;
  58 }
  59
  60 #endif  // chrseq.h
  61