int readOEAs(int countOEA, char *fileName_OEA)
{
FILE *fp;
int OEA_id;
char *strOEA_F, *strOEA_R;
strOEA_F=(char *) malloc(max_OEA_Length * sizeof(char));
strOEA_R=(char *) malloc(max_OEA_Length * sizeof(char));
fp=fopen(fileName_OEA, "r");
countOEA_Added=0;
OEA_id=0;
// fprintf(stdout, "I AM HERE 3");
while (countOEA>0)
{
fscanf(fp,">%i R\n", &OEA_id);
fscanf(fp,"%s\n", strOEA_R);// The sequence itself is from forward strand
fscanf(fp,">%i F\n", &OEA_id);
fscanf(fp,"%s\n", strOEA_F);//The sequence it self is from reverse trand
if (strlen(strOEA_F) <= maxLen_Btw_Pairs && strlen(strOEA_R) <= maxLen_Btw_Pairs)
{
OEAArray[countOEA_Added].OEA_F=(char *) malloc((strlen(strOEA_F)+1)*sizeof(char));
OEAArray[countOEA_Added].OEA_R=(char *) malloc((strlen(strOEA_R)+1)*sizeof(char));
OEAArray[countOEA_Added].OEA_F_len = strlen(strOEA_F);
OEAArray[countOEA_Added].OEA_R_len = strlen(strOEA_R);
strcpy(OEAArray[countOEA_Added].OEA_R, reverseComp(strOEA_R));
strcpy(OEAArray[countOEA_Added].OEA_F, strOEA_F);
OEAArray[countOEA_Added].id=OEA_id;
countOEA_Added++;
}
countOEA--;
}
//printf("%s %s\n", OEAArray[181].OEA_F, OEAArray[181].OEA_R);
}
int clean(const char *devFile, const char *logFile, const char *strR1, const char *strR2, const char *strSE, int tmpforcePairs, int tmpPolyATTrim) {
int forcePairs = tmpforcePairs;
FILE *f = fopen(devFile, "r");
//FILE *f = stderr;
FILE *R1 = NULL;
FILE *R2 = NULL;
FILE *SE = NULL;
FILE *log = NULL;
struct reads r;
struct stats s;
int sum = 0, R1_len = 0, R2_len = 0, SE_len = 0;
statsConstruct(&s);
PolyATTrim = tmpPolyATTrim;
while (grabTab(f, &r, &s)) {
if ((r.r2).r_header != NULL && (r.r1).r_header != NULL) {
s.pe_kept++;
if (R1 == NULL) {
R1 = fopen(strR1, "a");
}
if (R2 == NULL) {
R2 = fopen(strR2, "a");
}
if ((r.r1).r_header[0] == '@') {
if ((r.r1).r_header[strlen((r.r1).r_header)-1] == '1') {
fprintf(R1, "%s\n%s\n+\n%s\n", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
(r.r2).r_header[strlen((r.r2).r_header)-1] = '2';
fprintf(R2, "%s\n%s\n+\n%s", (r.r2).r_header, (r.r2).r_seq, (r.r2).r_qual);
} else {
fprintf(R1, "%s/1\n%s\n+\n%s\n", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
fprintf(R2, "%s/2\n%s\n+\n%s", (r.r2).r_header, (r.r2).r_seq, (r.r2).r_qual);
}
} else {
fprintf(R1, "@%s/1\n%s\n+\n%s\n", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
fprintf(R2, "@%s/2\n%s\n+\n%s", (r.r2).r_header, (r.r2).r_seq, (r.r2).r_qual);
}
} else if (forcePairs && (r.r1).r_header != NULL) {
s.numForcedPairs++;
int loc = (strlen((r.r1).r_seq))/2;
char cSeq = (r.r1).r_seq[loc];
char cQual = (r.r1).r_qual[loc];
if (R1 == NULL) {
R1 = fopen(strR1, "a");
}
if (R2 == NULL) {
R2 = fopen(strR2, "a");
}
if ((r.r1).r_header[0] == '@') {
(r.r1).r_seq[loc] = '\0';
(r.r1).r_qual[loc] = '\0';
fprintf(R1, "%s/1\n%s\n+\n%s\n", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
(r.r1).r_seq[loc] = cSeq;
(r.r1).r_qual[loc] = cQual;
fprintf(R2, "%s/2\n%s\n+\n%s", (r.r1).r_header, reverseComp(&((r.r1).r_seq)[loc]), reverse(&((r.r1).r_qual)[loc]));
} else {
(r.r1).r_seq[loc] = '\0';
(r.r1).r_qual[loc] = '\0';
fprintf(R1, "@%s/1\n%s\n+\n%s\n", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
(r.r1).r_seq[loc] = cSeq;
(r.r1).r_qual[loc] = cQual;
fprintf(R2, "@%s/2\n%s\n+\n%s", (r.r1).r_header, reverseComp(&((r.r1).r_seq)[loc]), reverse(&((r.r1).r_qual)[loc]));
}
} else if ((r.r1).r_header != NULL) {
if (SE == NULL) {
SE = fopen(strSE, "a");
}
s.se_kept++;
if ((r.r1).r_header[0] == '@') {
fprintf(SE, "%s\n%s\n+\n%s", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
} else {
fprintf(SE, "@%s\n%s\n+\n%s", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
}
if ((r.r1).r_qual[strlen((r.r1).r_qual)-1] != '\n') {
fprintf(SE, "\n");
}
}
}
if (log == NULL) {
log = fopen(logFile, "a");
}
for (sum = 0; sum < 700; sum++) {
R1_len += (s.R1_length[sum] * sum);
R2_len += (s.R2_length[sum] * sum);
SE_len += (s.SE_length[sum] * sum);
}
fprintf(log, "A\tT\tG\tC\tN\tPolyA_Removed_Reads\tPolyT_Removed_Reads\tShort_discarded\tPE_Kept\tSE_Kept\tForced_Pairs\tR1_Ave_Len\tR2_Ave_Len\tSE_Ave_Len\tAverageQual\n");
fprintf(log, "%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t\
%.2f\t%.2f\t%.2f\t%.2f\n",
s.A, s.T, s.G, s.C, s.N, s.polyATrimmed, s.polyTTrimmed, s.r1_discarded + s.r2_discarded + s.se_discarded, s.pe_kept, s.se_kept, s.numForcedPairs,
(float)R1_len/(float)(s.pe_kept), (float)R2_len/(float)(s.pe_kept), (float)SE_len/(float)(s.se_kept), (float)((float)(s.qualTotal)/(float)(s.A + s.T + s.C + s.G + s.N)));
if (f != NULL) {
fclose(f);
}
if (R1 != NULL) {
fclose(R1);
fclose(R2);
}
if (SE != NULL) {
fclose(SE);
}
if (log != NULL) {
fclose(log);
}
return 1;
}
