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;
}
size_t fastq_fread_bytes_pe(array_list_t *reads, size_t bytes, fastq_file_t *fq_file1, fastq_file_t *fq_file2, int mode) {
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_pe_t *read_pe;
char *res;
while (accumulated_size < bytes && fgets(header1, MAX_READ_ID_LENGTH, fq_file1->fd) != NULL) {
res = fgets(sequence1, MAX_READ_SEQUENCE_LENGTH, fq_file1->fd);
res = fgets(read_separator, MAX_READ_ID_LENGTH, fq_file1->fd);
res = 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
res = fgets(header2, MAX_READ_ID_LENGTH, fq_file2->fd);
res = fgets(sequence2, MAX_READ_SEQUENCE_LENGTH, fq_file2->fd);
res = fgets(read_separator, MAX_READ_ID_LENGTH, fq_file2->fd);
res = 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);
accumulated_size += header_length1 + sequence_length1 + quality_length1 + header_length2 + sequence_length2 + quality_length2;
}
return accumulated_size;
}
