void update_seed_right(alig_out_t *alig_out, seed_t *seed, seed_cal_t *cal) {
if (alig_out->match > 0) {
//if (score > 0 || (alig_out.map_len1 + suffix_len) > 20) {
// update seed
seed->num_mismatches += alig_out->mismatch;
seed->num_open_gaps += alig_out->gap_open;
seed->num_extend_gaps += alig_out->gap_extend;
seed->read_end += alig_out->map_len1;
seed->genome_end += alig_out->map_len2;
// update cigar with the sw output
if (alig_out->cigar.num_ops > 0) {
cigar_concat(&alig_out->cigar, &seed->cigar);
}
}
}
void update_seed_left(alig_out_t *alig_out, seed_t *seed, seed_cal_t *cal) {
if (alig_out->match > 0) {
// update seed
seed->num_mismatches += alig_out->mismatch;
seed->num_open_gaps += alig_out->gap_open;
seed->num_extend_gaps += alig_out->gap_extend;
seed->read_start -= alig_out->map_len1;
seed->genome_start -= alig_out->map_len2;
// update cigar with the sw output
if (alig_out->cigar.num_ops > 0) {
cigar_t cigar;
cigar_init(&cigar);
cigar_concat(&seed->cigar, &alig_out->cigar);
cigar_init(&seed->cigar);
cigar_copy(&seed->cigar, &alig_out->cigar);
}
}
}
int sa_sam_writer(void *data) {
sa_wf_batch_t *wf_batch = (sa_wf_batch_t *) data;
sa_mapping_batch_t *mapping_batch = (sa_mapping_batch_t *) wf_batch->mapping_batch;
if (mapping_batch == NULL) {
printf("bam_writer1: error, NULL mapping batch\n");
return 0;
}
/*
for (int i = 0; i < NUM_COUNTERS; i++) {
counters[i] += mapping_batch->counters[i];
}
*/
#ifdef _TIMING
for (int i = 0; i < NUM_TIMING; i++) {
func_times[i] += mapping_batch->func_times[i];
}
#endif
int num_mismatches, num_cigar_ops;
size_t flag, pnext = 0, tlen = 0;
char *cigar_string, *cigar_M_string, *rnext = "*";
fastq_read_t *read;
array_list_t *read_list = mapping_batch->fq_reads;
array_list_t *mapping_list, *mate_list;
FILE *out_file = (FILE *) wf_batch->writer_input->bam_file;
sa_genome3_t *genome = wf_batch->sa_index->genome;
size_t num_reads, num_mappings, num_mate_mappings;
num_reads = mapping_batch->num_reads;
if (mapping_batch->options->pair_mode != SINGLE_END_MODE) {
// PAIR MODE
int len;
char *sequence, *quality;
char *seq, *opt_fields;
alignment_t *alig;
for (size_t i = 0; i < num_reads; i++) {
read = (fastq_read_t *) array_list_get(i, read_list);
// seq = read->sequence;
/*
if (i % 2 == 0) {
mate_list = mapping_batch->mapping_lists[i+1];
num_mate_mappings = array_list_size(mate_list);
} else {
mate_list = mapping_list;
num_mate_mappings = num_mappings;
}
*/
mapping_list = mapping_batch->mapping_lists[i];
num_mappings = array_list_size(mapping_list);
num_total_mappings += num_mappings;
#ifdef _VERBOSE
if (num_mappings > 1) {
num_dup_reads++;
num_total_dup_reads += num_mappings;
}
#endif
if (num_mappings > 0) {
num_mapped_reads++;
if (num_mappings > 1) {
num_multihit_reads++;
}
for (size_t j = 0; j < num_mappings; j++) {
alig = (alignment_t *) array_list_get(j, mapping_list);
/*
// update alignment
alig->secondary_alignment = 0;
if (num_mate_mappings != 1) {
alig->is_mate_mapped = 0;
alig->is_paired_end_mapped = 0;
alig->mate_strand = 0;
}
*/
if (alig->optional_fields) {
opt_fields = (char *) calloc(strlen(alig->optional_fields) + 100, sizeof(char));
sprintf(opt_fields, "NH:i:%i\t%s", num_mappings, alig->optional_fields);
// sprintf(opt_fields, "NH:i:%i\t%s\tXU:i:%i", num_mappings, alig->optional_fields, mapping_batch->status[i]);
} else {
opt_fields = (char *) calloc(100, sizeof(char));
sprintf(opt_fields, "NH:i:%i", num_mappings);
// sprintf(opt_fields, "NH:i:%i\tXU:i:%i", num_mappings, mapping_batch->status[i]);
}
/*
// update alignment
alig->secondary_alignment = 0;
if (num_mate_mappings != 1) {
alig->is_mate_mapped = 0;
alig->is_paired_end_mapped = 0;
alig->mate_strand = 0;
}
*/
flag = 0;
if (alig->is_paired_end) flag += BAM_FPAIRED;
if (alig->is_paired_end_mapped) flag += BAM_FPROPER_PAIR;
if (!alig->is_seq_mapped) flag += BAM_FUNMAP;
if ((!alig->is_mate_mapped) && (alig->is_paired_end)) flag += BAM_FMUNMAP;
if (alig->mate_strand) flag += BAM_FMREVERSE;
if (alig->pair_num == 1) flag += BAM_FREAD1;
if (alig->pair_num == 2) flag += BAM_FREAD2;
if (alig->secondary_alignment) flag += BAM_FSECONDARY;
if (alig->fails_quality_check) flag += BAM_FQCFAIL;
if (alig->pc_optical_duplicate) flag += BAM_FDUP;
if (alig->seq_strand) flag += BAM_FREVERSE;
fprintf(out_file, "%s\t%lu\t%s\t%i\t%i\t%s\t%s\t%i\t%i\t%s\t%s\t%s\n",
read->id,
flag,
genome->chrom_names[alig->chromosome],
alig->position + 1,
(num_mappings > 1 ? 0 : alig->mapq), //60, //(alig->map_quality > 3 ? 0 : alig->map_quality),
alig->cigar,
(alig->chromosome == alig->mate_chromosome ? "=" : genome->chrom_names[alig->mate_chromosome]),
alig->mate_position + 1,
alig->template_length,
alig->sequence,
alig->quality,
opt_fields
);
// free memory
free(opt_fields);
alignment_free(alig);
} // end for num_mappings
} else {
num_unmapped_reads++;
opt_fields = (char *) calloc(100, sizeof(char));
sprintf(opt_fields, "XM:i:%i XU:i:%i", num_mappings, mapping_batch->status[i]);
if (read->adapter) {
len = read->length + abs(read->adapter_length);
sequence = (char *) malloc(len + 1);
quality = (char *) malloc(len + 1);
if (read->adapter_length < 0) {
strcpy(quality, read->adapter_quality);
strcat(quality, read->quality);
} else {
strcpy(quality, read->quality);
strcat(quality, read->adapter_quality);
}
if ((read->adapter_strand == 0 && read->adapter_length < 0) ||
(read->adapter_strand == 1 && read->adapter_length > 0)) {
strcpy(sequence, read->adapter);
strcat(sequence, read->sequence);
} else {
strcpy(sequence, read->sequence);
strcat(sequence, read->adapter);
}
sequence[len] = 0;
quality[len] = 0;
} else {
sequence = read->sequence;
quality = read->quality;
}
fprintf(out_file, "%s\t4\t*\t0\t0\t*\t*\t0\t0\t%s\t%s\t%s\n",
read->id,
sequence,
quality,
opt_fields
);
free(opt_fields);
if (read->adapter) {
free(sequence);
free(quality);
}
}
array_list_free(mapping_list, (void *) NULL);
}
} else {
// SINGLE MODE
int len, mapq;
char *seq;
seed_cal_t *cal;
cigar_t *cigar;
char *sequence, *revcomp, *quality;
for (size_t i = 0; i < num_reads; i++) {
read = (fastq_read_t *) array_list_get(i, read_list);
mapping_list = mapping_batch->mapping_lists[i];
num_mappings = array_list_size(mapping_list);
num_total_mappings += num_mappings;
#ifdef _VERBOSE
if (num_mappings > 1) {
num_dup_reads++;
num_total_dup_reads += num_mappings;
}
#endif
if (num_mappings > 0) {
num_mapped_reads++;
if (num_mappings > 1) {
num_multihit_reads++;
}
for (size_t j = 0; j < num_mappings; j++) {
cal = (seed_cal_t *) array_list_get(j, mapping_list);
if (read->adapter) {
// sequences and cigar
len = read->length + abs(read->adapter_length);
sequence = (char *) malloc(len + 1);
revcomp = (char *) malloc(len + 1);
quality = (char *) malloc(len + 1);
cigar = cigar_new_empty();
if (read->adapter_length < 0) {
strcpy(quality, read->adapter_quality);
strcat(quality, read->quality);
} else {
strcpy(quality, read->quality);
strcat(quality, read->adapter_quality);
}
if ( (cal->strand == 1 &&
((read->adapter_strand == 0 && read->adapter_length > 0) ||
(read->adapter_strand == 1 && read->adapter_length < 0)))
||
(cal->strand == 0 &&
((read->adapter_strand == 0 && read->adapter_length < 0) ||
(read->adapter_strand == 1 && read->adapter_length > 0))) ) {
strcpy(sequence, read->adapter);
strcat(sequence, read->sequence);
strcpy(revcomp, read->adapter_revcomp);
strcat(revcomp, read->revcomp);
cigar_append_op(abs(read->adapter_length), 'S', cigar);
cigar_concat(&cal->cigar, cigar);
} else {
strcpy(sequence, read->sequence);
strcat(sequence, read->adapter);
strcpy(revcomp, read->revcomp);
strcat(revcomp, read->adapter_revcomp);
cigar_concat(&cal->cigar, cigar);
cigar_append_op(read->adapter_length, 'S', cigar);
}
sequence[len] = 0;
revcomp[len] = 0;
quality[len] = 0;
} else {
// sequences and cigar
sequence = read->sequence;
revcomp = read->revcomp;
quality = read->quality;
cigar = &cal->cigar;
}
if (cal->strand) {
flag = 16;
seq = revcomp;
} else {
flag = 0;
seq = sequence;
}
/*
if (i == 0) {
flag += BAM_FSECONDARY;
}
*/
cigar_string = cigar_to_string(cigar);
cigar_M_string = cigar_to_M_string(&num_mismatches, &num_cigar_ops, cigar);
if (num_mappings > 1) {
cal->mapq = 0;
}
fprintf(out_file, "%s\t%i\t%s\t%i\t%i\t%s\t%s\t%lu\t%i\t%s\t%s\tNH:i:%i\tNM:i:%i\n",
read->id,
flag,
genome->chrom_names[cal->chromosome_id],
cal->start + 1,
(num_mappings == 1 ? cal->mapq : 0),
cigar_M_string,
rnext,
pnext,
tlen,
seq,
quality,
num_mappings,
num_mismatches
);
// free memory
free(cigar_M_string);
free(cigar_string);
seed_cal_free(cal);
if (read->adapter) {
free(sequence);
free(revcomp);
free(quality);
cigar_free(cigar);
}
}
} else {
num_unmapped_reads++;
if (read->adapter) {
// sequences and cigar
len = read->length + abs(read->adapter_length);
sequence = (char *) malloc(len + 1);
quality = (char *) malloc(len + 1);
if (read->adapter_length < 0) {
strcpy(quality, read->adapter_quality);
strcat(quality, read->quality);
} else {
strcpy(quality, read->quality);
strcat(quality, read->adapter_quality);
}
if ((read->adapter_strand == 0 && read->adapter_length < 0) ||
(read->adapter_strand == 1 && read->adapter_length > 0)) {
strcpy(sequence, read->adapter);
strcat(sequence, read->sequence);
} else {
strcpy(sequence, read->sequence);
strcat(sequence, read->adapter);
}
sequence[len] = 0;
quality[len] = 0;
} else {
// sequences
sequence = read->sequence;
quality = read->quality;
}
fprintf(out_file, "%s\t4\t*\t0\t0\t*\t*\t0\t0\t%s\t%s\n",
read->id,
sequence,
quality
);
if (read->adapter) {
free(sequence);
free(quality);
}
}
array_list_free(mapping_list, (void *) NULL);
} // end for num_reads
}
// free memory
sa_mapping_batch_free(mapping_batch);
if (wf_batch) sa_wf_batch_free(wf_batch);
return 0;
}
