void map_reads(gzFile *output_files, gzFile multi_out_file,
gzFile unmapped_out_file, gzFile reads_f, Mapper *mapper,
int reads_format, int output_type) {
FastqRead fastq_read;
MapRead map_read;
long warn_count, n_fastq_rec, n_fastq_err;
long n_map_uniq, n_map_multi, n_map_none;
map_read.fwd_nucs = my_new(unsigned char, FASTQ_MAX_LINE);
map_read.rev_nucs = my_new(unsigned char, FASTQ_MAX_LINE);
n_map_uniq = n_map_multi = n_map_none = 0;
warn_count = n_fastq_err = n_fastq_rec = 0;
/* loop over all records in FASTQ file */
while(TRUE) {
long r = 0;
/* read fastq record from file */
if(reads_format == READS_FORMAT_FASTQ) {
r = fastq_parse_read(&fastq_read, reads_f);
}
else if(reads_format == READS_FORMAT_QSEQ) {
r = fastq_parse_qseq_read(&fastq_read, reads_f);
}
else {
my_err("%s:%d: unknown read format", __FILE__, __LINE__);
}
if(r == FASTQ_END) {
/* we have reached the end of the file */
break;
}
if(r == FASTQ_ERR) {
/* this fastq record contains an error */
if(warn_count < FASTQ_MAX_WARN) {
warn_count += 1;
my_warn("%s:%d: skipping invalid fastq record:\n",
__FILE__, __LINE__);
fprintf(stderr, " %s\n %s\n %s\n %s\n", fastq_read.line1,
fastq_read.line2, fastq_read.line3, fastq_read.line4);
}
n_fastq_err += 1;
}
else if(fastq_read.read_len != mapper->seed_finder_fwd->read_len) {
/* check that read length is correct */
warn_count += 1;
my_warn("%s:%d: specified read length is %u, but got %d, "
"skipping read\n", __FILE__, __LINE__,
mapper->seed_finder_fwd->read_len, fastq_read.read_len);
n_fastq_err += 1;
}
else if(r == FASTQ_OK) {
n_fastq_rec += 1;
read_from_fastq_record(&map_read, &fastq_read);
if((n_fastq_rec % 1000000) == 0) {
fprintf(stderr, ".");
}
/* try to map this read to genome */
mapper_map_one_read(mapper, &map_read);
if(map_read.map_code == MAP_CODE_NONE) {
/* read does not map to genome */
n_map_none += 1;
if(output_type == OUTPUT_TYPE_SINGLE) {
write_unmapped_read(output_files[0], &map_read);
} else {
write_unmapped_read(unmapped_out_file, &map_read);
}
}
else if(map_read.map_code == MAP_CODE_MULTI) {
/* read maps to multiple genomic locations */
n_map_multi += 1;
if(output_type == OUTPUT_TYPE_SINGLE) {
write_read(output_files, mapper->chr_tab, &map_read, FALSE);
} else {
write_read(&multi_out_file, mapper->chr_tab, &map_read, FALSE);
}
}
else if(map_read.map_code == MAP_CODE_UNIQUE) {
/* read maps to single genomic location */
n_map_uniq += 1;
if(output_type == OUTPUT_TYPE_SINGLE) {
write_read(output_files, mapper->chr_tab, &map_read, FALSE);
} else {
write_read(output_files, mapper->chr_tab, &map_read, TRUE);
}
}
else {
my_err("%s:%d: unknown mapping code", __FILE__, __LINE__);
}
} else {
my_err("%s:%d: unknown fastq status", __FILE__, __LINE__);
}
}
fprintf(stderr, "\ndone\n");
fprintf(stderr, "fastq errors: %ld\n", n_fastq_err);
fprintf(stderr, "fastq records (without errors): %ld\n", n_fastq_rec);
fprintf(stderr, "unmapped reads: %ld\n", n_map_none);
fprintf(stderr, "uniquely mapping reads: %ld\n", n_map_uniq);
fprintf(stderr, "multiply mapping reads: %ld\n", n_map_multi);
my_free(map_read.fwd_nucs);
my_free(map_read.rev_nucs);
}
int bam_writer(void *data) {
struct timeval start, end;
double time;
//if (time_on) { start_timer(start); }
batch_t *batch = (batch_t *) data;
fastq_read_t *fq_read;
array_list_t *array_list;
size_t num_items;
//bam1_t *bam1;
//alignment_t *alig;
mapping_batch_t *mapping_batch = (mapping_batch_t *) batch->mapping_batch;
batch_writer_input_t *writer_input = batch->writer_input;
bam_file_t *bam_file = writer_input->bam_file;
linked_list_t *linked_list = writer_input->list_p;
size_t num_reads_b = array_list_size(mapping_batch->fq_batch);
size_t num_mapped_reads = 0;
size_t total_mappings = 0;
unsigned char found_p1 = 0;
unsigned char found_p2 = 0;
int i = 0;
extern size_t bwt_correct;
extern size_t bwt_error;
extern pthread_mutex_t bwt_mutex, mutex_sp;
writer_input->total_batches++;
extern size_t *histogram_sw;
extern size_t num_reads_map;
extern size_t num_reads;
extern size_t tot_reads;
extern st_bwt_t st_bwt;
st_bwt.total_reads += num_reads_b;
free(mapping_batch->histogram_sw);
//
// DNA/RNA mode
//
for (size_t i = 0; i < num_reads_b; i++) {
num_items = array_list_size(mapping_batch->mapping_lists[i]);
total_mappings += num_items;
fq_read = (fastq_read_t *) array_list_get(i, mapping_batch->fq_batch);
// mapped or not mapped ?
if (num_items == 0) {
total_mappings++;
write_unmapped_read(fq_read, bam_file);
if (mapping_batch->mapping_lists[i]) {
array_list_free(mapping_batch->mapping_lists[i], NULL);
}
} else {
num_mapped_reads++;
if (array_list_size(mapping_batch->mapping_lists[i]) == 1) {
st_bwt.single_alig++;
} else {
st_bwt.multi_alig++;
}
write_mapped_read(mapping_batch->mapping_lists[i], bam_file);
}
}
if (mapping_batch) {
mapping_batch_free(mapping_batch);
}
if (batch) batch_free(batch);
basic_statistics_add(num_reads_b, num_mapped_reads, total_mappings, 0, basic_st);
}