int main(int argc, char *argv[]){
Read *Read = CreateRead(65536+GUARD, 65535+GUARD);
int32_t seqSize = 0, x, n;
uint64_t cutted = 0, totalReads = 0;
if(argc < 2 || ArgBin(0, argv, argc, "-h") || ArgBin(0, argv, argc, "?")){
PrintArgs(argv[0]);
return EXIT_SUCCESS;
}
int k = ArgNum(5, argv, argc, "-k", 0, 9999999);
int min_QS_window = ArgNum(25, argv, argc, "-w", 0, 9999999);
int min_QS = ArgNum(33, argv, argc, "-m", 0, 9999999);
fprintf(stderr, "Minimum QS: %d\n", min_QS);
uint32_t position = 0;
while(GetRead(stdin, Read)){
seqSize = strlen((char *) Read->bases) - 1;
for(x = seqSize ; x >= 0 ; x--){
if(x >= k){
int tmp_QS = 0;
for(n = 0 ; n < k ; ++n){
tmp_QS += ((int) Read->scores[x - 1 - n]) - min_QS;
}
if(((double) tmp_QS / k) < (double) min_QS_window){
++cutted;
position = x;
break;
}
}
}
++totalReads;
if(x > seqSize - k) continue;
// PRINT READ
fprintf(stdout, "@");
for(n = 0 ; n < strlen((char *) Read->header1) ; ++n)
fprintf(stdout, "%c", Read->header1[n]);
for(n = position ; n < seqSize ; ++n)
fprintf(stdout, "%c", Read->bases[n]);
fprintf(stdout, "\n+\n");
for(n = position ; n < seqSize ; ++n)
fprintf(stdout, "%c", Read->scores[n]);
fprintf(stdout, "\n");
}
fprintf(stderr, "Total reads : %"PRIu64"\n", totalReads);
fprintf(stderr, "Trimmed reads : %"PRIu64"\n", cutted);
FreeRead(Read);
return EXIT_SUCCESS;
}
void Act_SetI()
{
int n=ArgNum();
ITEM *i=ArgItem();
if(n==1)
Item1=i;
else
Item2=i;
}
int main(int argc, char *argv[]){
Read *Read = CreateRead(65536+GUARD, 65535+GUARD);
uint32_t seqSize = 0, totalQS = 0, N = 0, x, n;
uint64_t okReads = 0, totalReads = 0;
if(ArgBin(0, argv, argc, "-h") || ArgBin(0, argv, argc, "?")){
PrintArgs(argv[0]);
return EXIT_SUCCESS;
}
int max_n = ArgNum(0, argv, argc, "-n", 0, 9999999);
int k = ArgNum(5, argv, argc, "-k", 0, 9999999);
int min_QS_window = ArgNum(25, argv, argc, "-w", 0, 9999999);
int min_avg_qs = ArgNum(25, argv, argc, "-a", 0, 9999999);
int min_read_size = ArgNum(35, argv, argc, "-m", 0, 9999999);
// LOAD PARAMETERS
while(GetRead(stdin, Read)){
seqSize = strlen((char *) Read->bases) - 1;
totalQS = 0;
N = 0;
for(x = 0 ; x < seqSize ; ++x){
if(Read->bases[x] == 'N'){
++N;
}
totalQS += ((int) Read->scores[x]) - 33; // PHRED +33
if(x < seqSize - k){
int tmp_QS = 0;
for(n = 0 ; n < k ; ++n)
tmp_QS += ((int) Read->scores[x + n]) - 33;
if(tmp_QS / k < min_QS_window)
break;
}
}
++totalReads;
// EVALUATE TO DISCARD:
if(N > max_n) continue;
if((totalQS / seqSize) < min_avg_qs) continue;
if(x < min_read_size) continue;
// PRINT READ
for(n = 0 ; n < strlen((char *) Read->header1) ; ++n)
fprintf(stdout, "%c", Read->header1[n]);
for(n = 0 ; n < x ; ++n)
fprintf(stdout, "%c", Read->bases[n]);
fprintf(stdout, "\n+\n");
for(n = 0 ; n < x ; ++n)
fprintf(stdout, "%c", Read->scores[n]);
fprintf(stdout, "\n");
++okReads;
}
fprintf(stderr, "Total reads : %"PRIu64"\n", totalReads);
fprintf(stderr, "Filtered reads : %"PRIu64"\n", totalReads-okReads);
FreeRead(Read);
return EXIT_SUCCESS;
}
