size_t fastq_fread_bytes_se(array_list_t *reads, size_t bytes, fastq_file_t *fq_file) {
size_t accumulated_size = 0;
char header1[MAX_READ_ID_LENGTH];
char sequence[MAX_READ_SEQUENCE_LENGTH];
char header2[MAX_READ_ID_LENGTH];
char qualities[MAX_READ_SEQUENCE_LENGTH];
int header_length, sequence_length, quality_length;
fastq_read_t *read;
while (accumulated_size < bytes && fgets(header1, MAX_READ_ID_LENGTH, fq_file->fd) != NULL) {
fgets(sequence, MAX_READ_SEQUENCE_LENGTH, fq_file->fd);
fgets(header2, MAX_READ_ID_LENGTH, fq_file->fd);
fgets(qualities, MAX_READ_SEQUENCE_LENGTH, fq_file->fd);
header_length = strlen(header1);
sequence_length = strlen(sequence);
quality_length = strlen(qualities);
// '\n' char is removed, but '\0' is left
chomp_at(header1, header_length - 1);
chomp_at(sequence, sequence_length - 1);
chomp_at(qualities, quality_length - 1);
read = fastq_read_new(header1, sequence, qualities);
array_list_insert(read, reads);
accumulated_size += header_length + sequence_length + quality_length;
}
return accumulated_size;
}
int fastq_fread_num_reads(fastq_read_t *buffer_fq_reads, int num_reads, fastq_file_t *fq_file) {
int count = 0;
char header1[MAX_READ_ID_LENGTH];
char sequence[MAX_READ_SEQUENCE_LENGTH];
char header2[MAX_READ_ID_LENGTH];
char qualities[MAX_READ_SEQUENCE_LENGTH];
int header_length, sequence_length, quality_length;
while (count < num_reads && fgets(header1, MAX_READ_ID_LENGTH, fq_file->fd) != NULL) {
fgets(sequence, MAX_READ_SEQUENCE_LENGTH, fq_file->fd);
fgets(header2, MAX_READ_ID_LENGTH, fq_file->fd);
fgets(qualities, MAX_READ_SEQUENCE_LENGTH, fq_file->fd);
header_length = strlen(header1);
sequence_length = strlen(sequence);
quality_length = strlen(qualities);
chomp_at(header1, header_length - 1);
chomp_at(sequence, sequence_length - 1);
chomp_at(qualities, quality_length - 1);
buffer_fq_reads[count].id = (char*)malloc(sizeof(char) * header_length);
buffer_fq_reads[count].sequence = (char*)malloc(sizeof(char) * sequence_length);
buffer_fq_reads[count].quality = (char*)malloc(sizeof(char) * quality_length);
strcpy(buffer_fq_reads[count].id, header1);
strcpy(buffer_fq_reads[count].sequence, sequence);
strcpy(buffer_fq_reads[count].quality, qualities);
count++;
}
return count;
}
size_t fastq_fread_se_ex(array_list_t *reads, size_t num_reads, fastq_file_t *fq_file) {
size_t count = 0;
char *p;
char header1[MAX_READ_ID_LENGTH];
char sequence[MAX_READ_SEQUENCE_LENGTH];
char header2[MAX_READ_ID_LENGTH];
char qualities[MAX_READ_SEQUENCE_LENGTH];
int header_length, sequence_length, quality_length;
fastq_read_t *read;
while (count < num_reads && fgets(header1, MAX_READ_ID_LENGTH, fq_file->fd) != NULL) {
char *res = fgets(sequence, MAX_READ_SEQUENCE_LENGTH, fq_file->fd);
res = fgets(header2, MAX_READ_ID_LENGTH, fq_file->fd);
res = fgets(qualities, MAX_READ_SEQUENCE_LENGTH, fq_file->fd);
header_length = strlen(header1);
sequence_length = strlen(sequence);
quality_length = strlen(qualities);
// '\n' char is removed, but '\0' is left
chomp_at(header1, header_length - 1);
if ((p = strstr(header1, " ")) != NULL) {
*p = 0;
}
chomp_at(sequence, sequence_length - 1);
chomp_at(qualities, quality_length - 1);
read = fastq_read_new(&header1[1], sequence, qualities);
array_list_insert(read, reads);
count++;
}
return count;
}
int fastq_fread_max_size(fastq_read_t *buffer_fq_reads, unsigned long max_size, fastq_file_t *fq_file) {
int count = 0;
unsigned long accumulated_size = 0;
char header1[MAX_READ_ID_LENGTH];
char sequence[MAX_READ_SEQUENCE_LENGTH];
char header2[MAX_READ_ID_LENGTH];
char qualities[MAX_READ_SEQUENCE_LENGTH];
int header_length, sequence_length, quality_length;
while (accumulated_size <= max_size && fgets(header1, MAX_READ_ID_LENGTH, fq_file->fd) != NULL) {
fgets(sequence, MAX_READ_SEQUENCE_LENGTH, fq_file->fd);
fgets(header2, MAX_READ_ID_LENGTH, fq_file->fd);
fgets(qualities, MAX_READ_SEQUENCE_LENGTH, fq_file->fd);
header_length = strlen(header1);
sequence_length = strlen(sequence);
quality_length = strlen(qualities);
chomp_at(header1, header_length - 1);
chomp_at(sequence, sequence_length - 1);
chomp_at(qualities, quality_length - 1);
buffer_fq_reads[count].id = (char*)malloc(sizeof(char) * header_length);
buffer_fq_reads[count].sequence = (char*)malloc(sizeof(char) * sequence_length);
buffer_fq_reads[count].quality = (char*)malloc(sizeof(char) * quality_length);
strcpy(buffer_fq_reads[count].id, header1);
strcpy(buffer_fq_reads[count].sequence, sequence);
strcpy(buffer_fq_reads[count].quality, qualities);
accumulated_size += header_length + sequence_length + quality_length;
count++;
}
return count;
}
size_t fastq_fread_bytes_aligner_pe(array_list_t *reads, size_t bytes, fastq_file_t *fq_file1, fastq_file_t *fq_file2) {
size_t accumulated_size = 0;
char header1[MAX_READ_ID_LENGTH];
char header2[MAX_READ_ID_LENGTH];
char read_separator[MAX_READ_ID_LENGTH];
char sequence1[MAX_READ_SEQUENCE_LENGTH];
char sequence2[MAX_READ_SEQUENCE_LENGTH];
char qualities1[MAX_READ_SEQUENCE_LENGTH];
char qualities2[MAX_READ_SEQUENCE_LENGTH];
int header_length1, sequence_length1, quality_length1;
int header_length2, sequence_length2, quality_length2;
fastq_read_t *read1, *read2;
while (accumulated_size < bytes && fgets(header1, MAX_READ_ID_LENGTH, fq_file1->fd) != NULL) {
fgets(sequence1, MAX_READ_SEQUENCE_LENGTH, fq_file1->fd);
fgets(read_separator, MAX_READ_ID_LENGTH, fq_file1->fd);
fgets(qualities1, MAX_READ_SEQUENCE_LENGTH, fq_file1->fd);
header_length1 = strlen(header1);
sequence_length1 = strlen(sequence1);
quality_length1 = strlen(qualities1);
// '\n' char is removed, but '\0' is left
chomp_at(header1, header_length1 - 1);
chomp_at(sequence1, sequence_length1 - 1);
chomp_at(qualities1, quality_length1 - 1);
// second file
fgets(header2, MAX_READ_ID_LENGTH, fq_file2->fd);
fgets(sequence2, MAX_READ_SEQUENCE_LENGTH, fq_file2->fd);
fgets(read_separator, MAX_READ_ID_LENGTH, fq_file2->fd);
fgets(qualities2, MAX_READ_SEQUENCE_LENGTH, fq_file2->fd);
header_length2 = strlen(header2);
sequence_length2 = strlen(sequence2);
quality_length2 = strlen(qualities2);
// '\n' char is removed, but '\0' is left
chomp_at(header2, header_length2 - 1);
chomp_at(sequence2, sequence_length2 - 1);
chomp_at(qualities2, quality_length2 - 1);
read1 = fastq_read_new(header1, sequence1, qualities1);
read2 = fastq_read_new(header2, sequence2, qualities2);
array_list_insert(read1, reads);
array_list_insert(read2, reads);
accumulated_size += header_length1 + sequence_length1 + quality_length1 + header_length2 + sequence_length2 + quality_length2;
}
return accumulated_size;
}
size_t fastq_fread_pe(array_list_t *reads, size_t num_reads, fastq_file_t *fq_file1, fastq_file_t *fq_file2, int mode) {
size_t count = 0;
char header1[MAX_READ_ID_LENGTH];
char header2[MAX_READ_ID_LENGTH];
char read_separator[MAX_READ_ID_LENGTH];
char sequence1[MAX_READ_SEQUENCE_LENGTH];
char sequence2[MAX_READ_SEQUENCE_LENGTH];
char qualities1[MAX_READ_SEQUENCE_LENGTH];
char qualities2[MAX_READ_SEQUENCE_LENGTH];
int header_length1, sequence_length1, quality_length1;
int header_length2, sequence_length2, quality_length2;
fastq_read_pe_t *read_pe;
while (count < num_reads && fgets(header1, MAX_READ_ID_LENGTH, fq_file1->fd) != NULL) {
fgets(sequence1, MAX_READ_SEQUENCE_LENGTH, fq_file1->fd);
fgets(read_separator, MAX_READ_ID_LENGTH, fq_file1->fd);
fgets(qualities1, MAX_READ_SEQUENCE_LENGTH, fq_file1->fd);
header_length1 = strlen(header1);
sequence_length1 = strlen(sequence1);
quality_length1 = strlen(qualities1);
// '\n' char is removed, but '\0' is left
chomp_at(header1, header_length1 - 1);
chomp_at(sequence1, sequence_length1 - 1);
chomp_at(qualities1, quality_length1 - 1);
// second file
fgets(header2, MAX_READ_ID_LENGTH, fq_file2->fd);
fgets(sequence2, MAX_READ_SEQUENCE_LENGTH, fq_file2->fd);
fgets(read_separator, MAX_READ_ID_LENGTH, fq_file2->fd);
fgets(qualities2, MAX_READ_SEQUENCE_LENGTH, fq_file2->fd);
header_length2 = strlen(header2);
sequence_length2 = strlen(sequence2);
quality_length2 = strlen(qualities2);
// '\n' char is removed, but '\0' is left
chomp_at(header2, header_length2 - 1);
chomp_at(sequence2, sequence_length2 - 1);
chomp_at(qualities2, quality_length2 - 1);
read_pe = fastq_read_pe_new(header1, header2, sequence1, qualities1, sequence2, qualities2, mode);
array_list_insert(read_pe, reads);
count++;
}
return count;
}
