main()
{
char s1[100];
char *s;
strcpy(s1, "Give Him Six!");
s = revstring(s1);
strcpy(s1, "Jim");
printf("%s\n", revstring(s1));
printf("%s\n", s);
}
void tracebackLocal(DYNAM *p_dynam)
{
/**
finding traceback for local alignment
*/
int i,j,a=0,b=0;
i=p_dynam->si; /*get starting postions*/
j=p_dynam->sj; /*get starting postions*/
do{
tracer(p_dynam,&i,&j,&b,&a);
}while( fabs(maximumdouble(3,p_dynam->h[i][j],p_dynam->Ix[i][j],p_dynam->Iy[i][j])) >1e-12);
p_dynam->ac1[a++]=0;
p_dynam->ac2[b++]=0;
revstring(p_dynam->ac1);
revstring(p_dynam->ac2);
}
void tracebackGlobal(DYNAM *p_dynam)
{
/**
finding traceback for global alignment
*/
int i,j,a=0,b=0;
i=p_dynam->si; /*get starting postions*/
j=p_dynam->sj; /*get starting postions*/
do{
tracer(p_dynam,&i,&j,&b,&a);
}while(!(i==0 && j==0));
p_dynam->ac1[a++]=0;
p_dynam->ac2[b++]=0;
revstring(p_dynam->ac1);
revstring(p_dynam->ac2);
}
void tracebackOverlap(DYNAM *p_dynam)
{
/**
finding traceback for global alignment
*/
int i,j,a=0,b=0;
i=p_dynam->si;
j=p_dynam->sj;
/*dp the backtrack*/
do{
tracer(p_dynam,&i,&j,&b,&a);
}while(!(i==0 || j==0)); /*break if one of the values are true*/
p_dynam->ac1[a++]=0;
p_dynam->ac2[b++]=0;
revstring(p_dynam->ac1);
revstring(p_dynam->ac2);
}
void reverse_comp(char *reference_sequence,size_t reference_length)
{
int index;
if(reference_sequence == NULL)
return;
revstring(reference_sequence);
for(index = 0;index < reference_length;index++,reference_sequence++)
{
switch(*reference_sequence)
{
case 'A':
*reference_sequence = 'U';
break;
case 'a':
*reference_sequence = 'u';
break;
case 'G':
*reference_sequence = 'C';
break;
case 'g':
*reference_sequence = 'c';
break;
case 'C':
*reference_sequence = 'G';
break;
case 'c':
*reference_sequence = 'g';
break;
case 'U':case 'T':
*reference_sequence = 'A';
break;
case 'u':case 't':
*reference_sequence = 'a';
break;
case 0:
return;
break;
default:
break;
}
}
}
int main(int argc, char **argv)
{
ref_vector X, Xi;
exome ex;
check_syntax(argc, 4, "preprocess ref_file output_dir nucleotides");
timevars();
init_replace_table(argv[3]);
encode_reference(&X, &ex, true, argv[1]);
save_ref_vector(&X, argv[2], "X");
save_exome_file(&ex, true, argv[2]);
tic("Calc. Backward Burrows-Wheeler Transform -> Sadakane direct SAIS");
direct_bwt(X.vector, X.n, argv[2], "backward", false);
toc();
tic("Calc. Backward Suffix Array -> CSALIB DNA");
csa_new_from_bwt_gnu_bwt_wrapper(argv[2], "backward");
toc();
read_ref_vector(&Xi, argv[2], "X");
revstring(Xi.vector, Xi.n);
save_ref_vector(&Xi, argv[2], "Xi");
tic("Calc. Forward Burrows-Wheeler Transform -> Sadakane direct SAIS");
direct_bwt(Xi.vector, Xi.n, argv[2], "forward", false);
toc();
tic("Calc. Forward Suffix Array -> CSALIB DNA");
csa_new_from_bwt_gnu_bwt_wrapper(argv[2], "forward");
toc();
return 0;
}
