c_cpp/libgFileIO/2bitseq.c

   1 #include "2bitseq.h"
   2 #include <string.h> // strcpy
   3
   4 char *unit2basechr(uint64_t seq32mer){
   5     char *basechar=malloc(33);
   6     char *tmpbc;
   7     tmpbc=basechar;
   8     int i;
   9     for(i=0;i<64;i+=2) {
  10         *tmpbc++ = DBIT2BASE((seq32mer&(3LLU<<i))>>i);
  11         //*tmpbc++ = '0' + ((seq32mer&(3u<<i))>>i);
  12         //printf("=%lx,%lx,%lx,%lx=\n",seq32mer,3LLU<<i,seq32mer&(3LLU<<i),(seq32mer&(3LLU<<i))>>i);
  13     }
  14     *tmpbc++=0;
  15     return basechar;
  16 }
  17
  18 char *dib2basechr(uint64_t *diBseq, size_t len){
  19     char *basechar=malloc(len+1);
  20     char *tmpstr;
  21     size_t i;
  22     for (i=0;i<len/32;i++) {
  23         tmpstr=unit2basechr(diBseq[i]);
  24         strcpy(basechar+i*32,tmpstr);
  25         free(tmpstr);
  26     }
  27     tmpstr=unit2basechr(diBseq[i]);
  28     strncpy(basechar+i*32,tmpstr,len % 32);
  29     free(tmpstr);
  30     *(basechar+len)='\0';
  31     return basechar;
  32 }
  33
  34 /*
  35 |000000000>||111111111>||2222222>...|, lastBits=7, nullBits=3 (%10)
  36 |...0000000||00>1111111||11>2222222>|. Well, left is right here ...
  37 |11>2222222>||00>1111111||...0000000|
  38 |<2222222<11||1111111<00||0000000...|
  39 */
  40 uint64_t *dibrevcomp(uint64_t const *const inseq, size_t len){
  41     size_t needtomallocQQW = (len+31u)>>5;
  42     uint64_t *outseq = malloc(needtomallocQQW*8);
  43     char lastBits = 2*(len % 64);   // well "% 64" will also be "andl $63,%esi"
  44     char nullBits = 64-lastBits;  //(-lastBits) % 64; only use if lastBits.
  45     uint64_t tmpstr=0;
  46     uint64_t highmask = ~((1LLU<<lastBits)-1U);
  47 //printf("QQW:%zu,L:%d,N:%d,M:%lx\n",needtomallocQQW,lastBits,nullBits,highmask);
  48     for (size_t i=0;i<needtomallocQQW;i++) {    // from 0
  49         *(outseq+needtomallocQQW-1-i)=unitReverseComp((*(inseq+i)<<nullBits) | tmpstr);
  50         //*(outseq+needtomallocQQW-1-i)=(*(inseq+i)<<nullBits) | tmpstr;
  51         if (lastBits) { // this if will be optimized outsides of for, so I can have a rest here.
  52             tmpstr = (*(inseq+i) & highmask)>>lastBits;
  53         }
  54     }
  55     return outseq;
  56 }
  57