void
sff_read_print(FILE *fp, sff_read_t *r, sff_header_t *gh, sff_read_header_t *rh)
{
uint32_t i;
// flowgram
for(i=0;i<gh->flow_length;i++) {
if(0 < i) {
if(-1L == fputc(',', fp)) {
ion_error(__func__, "fputc", Exit, WriteFileError);
}
}
if(fprintf(fp, "%u", r->flowgram[i]) < 0) {
ion_error(__func__, "fprintf", Exit, WriteFileError);
}
}
if(-1L == fputc('\n', fp)) {
ion_error(__func__, "fputc", Exit, WriteFileError);
}
// flow index
for(i=0;i<rh->n_bases;i++) {
if(0 < i) {
if(-1L == fputc(',', fp)) {
ion_error(__func__, "fputc", Exit, WriteFileError);
}
}
if(fprintf(fp, "%u", r->flow_index[i]) < 0) {
ion_error(__func__, "fprintf", Exit, WriteFileError);
}
}
if(-1L == fputc('\n', fp)) {
ion_error(__func__, "fputc", Exit, WriteFileError);
}
// bases
if(fprintf(fp, "%s\n", r->bases->s) < 0) {
ion_error(__func__, "fprintf", Exit, WriteFileError);
}
// quality
for(i=0;i<r->quality->l;i++) {
if(EOF == fputc(QUAL2CHAR(r->quality->s[i]), fp)) {
ion_error(__func__, "fputc", Exit, WriteFileError);
}
}
fputc('\n', fp);
}
tmap_sff_read_t *
tmap_sff_read_read(tmap_file_t *fp, tmap_sff_header_t *gh, tmap_sff_read_header_t *rh)
{
tmap_sff_read_t *r = NULL;
uint32_t i, n = 0;
r = tmap_calloc(1, sizeof(tmap_sff_read_t), "r");
r->flowgram = tmap_malloc(sizeof(uint16_t)*gh->flow_length, "r->flowgram");
r->flow_index = tmap_malloc(sizeof(uint8_t)*rh->n_bases, "r->flow_index");
r->bases = tmap_string_init(rh->n_bases+1);
r->quality = tmap_string_init(rh->n_bases+1);
if(gh->flow_length != tmap_file_fread(r->flowgram, sizeof(uint16_t), gh->flow_length, fp)
|| rh->n_bases != tmap_file_fread(r->flow_index, sizeof(uint8_t), rh->n_bases, fp)
|| rh->n_bases != tmap_file_fread(r->bases->s, sizeof(char), rh->n_bases, fp)
|| rh->n_bases != tmap_file_fread(r->quality->s, sizeof(char), rh->n_bases, fp)) {
tmap_error("tmap_file_fread", Exit, ReadFileError);
}
n += sizeof(uint16_t)*gh->flow_length + 3*sizeof(uint8_t)*rh->n_bases;
// set length and null-terminators
r->bases->l = rh->n_bases;
r->quality->l = rh->n_bases;
r->bases->s[r->bases->l]='\0';
r->quality->s[r->quality->l]='\0';
// convert qualities from int to char
for(i=0;i<r->quality->l;i++) {
r->quality->s[i] = QUAL2CHAR(r->quality->s[i]);
}
// convert flowgram to host order
for(i=0;i<gh->flow_length;i++) {
r->flowgram[i] = ntohs(r->flowgram[i]);
}
n += tmap_sff_read_padding(fp, n);
#ifdef TMAP_SFF_DEBUG
tmap_sff_read_print(stderr, r, gh, rh);
#endif
return r;
}
int32_t
tmap_sam_io_read(tmap_sam_io_t *samio, tmap_sam_t *sam)
{
if(NULL != sam->b) {
bam_destroy1(sam->b);
}
sam->b = bam_init1();
// check if we're past optional end bam virtual file offset
if (samio->bam_end_vfo > 0) {
BGZF* bgzf_fp = samio->fp->x.bam;
if (bam_tell(bgzf_fp) >= samio->bam_end_vfo) {
fprintf(stderr, "stopping at bam virtual file offset %lu\n", samio->bam_end_vfo);
return -1;
}
}
if(0 < samread(samio->fp, sam->b)) {
char *str;
int32_t i, len;
// name
str = bam1_qname(sam->b);
len = strlen(str);
tmap_sam_io_update_string(&sam->name, str, len);
sam->name->s[len] = '\0';
// seq and qual
len = sam->b->core.l_qseq;
tmap_sam_io_update_string(&sam->seq, NULL, len);
tmap_sam_io_update_string(&sam->qual, (char*)bam1_qual(sam->b), len);
for(i=0;i<len;i++) {
sam->seq->s[i] = bam_nt16_rev_table[bam1_seqi(bam1_seq(sam->b), i)];
sam->qual->s[i] = QUAL2CHAR(sam->qual->s[i]);
}
sam->seq->s[len] = sam->qual->s[len] = '\0';
// reverse compliment if necessary
if((sam->b->core.flag & BAM_FREVERSE)) {
tmap_sam_reverse_compliment(sam);
}
return 1;
}
return -1;
}
int
sff_view_main(int argc, char *argv[])
{
int i, c;
sff_file_t *sff_file_in=NULL, *sff_file_out=NULL;
sff_iter_t *sff_iter = NULL;
sff_t *sff = NULL;
char *fn_names = NULL;
char **names = NULL;
int32_t names_num = 0, names_mem = 0;
int32_t out_mode, min_row, max_row, min_col, max_col;
out_mode = 0;
min_row = max_row = min_col = max_col = -1;
while((c = getopt(argc, argv, "r:c:R:bqh")) >= 0) {
switch(c) {
case 'r':
if(ion_parse_range(optarg, &min_row, &max_row) < 0) {
ion_error(__func__, "-r : format not recognized", Exit, OutOfRange);
}
break;
case 'c':
if(ion_parse_range(optarg, &min_col, &max_col) < 0) {
ion_error(__func__, "-c : format not recognized", Exit, OutOfRange);
}
break;
case 'R':
free(fn_names);
fn_names = strdup(optarg); break;
case 'q':
out_mode |= 1;
break;
case 'b':
out_mode |= 2;
break;
case 'h':
default:
return usage();
}
}
if(argc != 1+optind) {
return usage();
}
else {
sff_header_t *header = NULL;
if(3 == out_mode) {
ion_error(__func__, "options -b and -q cannot be used together", Exit, CommandLineArgument);
}
// open the input SFF
if(-1 != min_row || -1 != max_row || -1 != min_col || -1 != max_col) {
sff_file_in = sff_fopen(argv[optind], "rbi", NULL, NULL);
}
else {
sff_file_in = sff_fopen(argv[optind], "rb", NULL, NULL);
}
header = sff_header_clone(sff_file_in->header); /* copy header, but update n_reads if using index or names */
// read in the names
if(NULL != fn_names) {
FILE *fp = NULL;
char name[1024]="\0"; // lets hope we don't exceed this length
names_num = names_mem = 0;
names = NULL;
if(!(fp = fopen(fn_names, "rb"))) {
fprintf(stderr, "** Could not open %s for reading. **\n", fn_names);
ion_error(__func__, fn_names, Exit, OpenFileError);
}
while(EOF != fscanf(fp, "%s", name)) {
while(names_num == names_mem) {
if(0 == names_mem) names_mem = 4;
else names_mem *= 2;
names = ion_realloc(names, sizeof(char*) * names_mem, __func__, "names");
}
names[names_num] = strdup(name);
if(NULL == names[names_num]) {
ion_error(__func__, name, Exit, MallocMemory);
}
names_num++;
}
names = ion_realloc(names, sizeof(char*) * names_num, __func__, "names");
fclose(fp);
header->n_reads = names_num;
}
else {
// if using index, then iterate once through the index to count the entries
// so we can set the count correctly in the header
if (-1 != min_row || -1 != max_row || -1 != min_col || -1 != max_col) {
int entries = 0;
sff_iter = sff_iter_query(sff_file_in, min_row, max_row, min_col, max_col);
while (NULL != (sff = sff_iter_read(sff_file_in, sff_iter)))
entries++;
header->n_reads = entries;
/* reset sff_iter */
sff_iter_destroy(sff_iter);
sff_iter = sff_iter_query(sff_file_in, min_row, max_row, min_col, max_col);
}
}
// print the header
switch(out_mode) {
case 0:
sff_header_print(stdout, header);
break;
case 1:
// do nothing: FASTQ
break;
case 2:
sff_file_out = sff_fdopen(fileno(stdout), "wb", header, NULL);
break;
}
while(1) {
int32_t to_print = 1;
if(-1 != min_row || -1 != max_row || -1 != min_col || -1 != max_col) {
if(NULL == (sff = sff_iter_read(sff_file_in, sff_iter))) {
break;
}
}
else {
if(NULL == (sff = sff_read(sff_file_in))) {
break;
}
}
if(0 < names_mem) {
to_print = 0;
for(i=0;i<names_num;i++) {
if(0 == strcmp(names[i], sff_name(sff))) {
to_print = 1;
break;
}
}
// shift down
if(1 == to_print) { // i < names_num
free(names[i]);
names[i] = NULL;
for(;i<names_num-1;i++) {
names[i] = names[i+1];
names[i+1] = NULL;
}
names_num--;
}
}
if(1 == to_print) {
switch(out_mode) {
case 0:
sff_print(stdout, sff);
break;
case 1:
if(fprintf(stdout, "@%s\n%s\n+\n",
sff->rheader->name->s,
sff->read->bases->s + sff->gheader->key_length) < 0) {
ion_error(__func__, "stdout", Exit, WriteFileError);
}
for(i=sff->gheader->key_length;i<sff->read->quality->l;i++) {
if(fputc(QUAL2CHAR(sff->read->quality->s[i]), stdout) < 0) {
ion_error(__func__, "stdout", Exit, WriteFileError);
}
}
if(fputc('\n', stdout) < 0) {
ion_error(__func__, "stdout", Exit, WriteFileError);
}
break;
case 2:
sff_write(sff_file_out, sff);
break;
}
}
sff_destroy(sff);
}
sff_fclose(sff_file_in);
if(2 == out_mode) {
sff_fclose(sff_file_out);
}
if(-1 != min_row || -1 != max_row || -1 != min_col || -1 != max_col) {
sff_iter_destroy(sff_iter);
}
if(0 != names_num) {
fprintf(stderr, "** Did not find all the reads with (-R). **\n");
ion_error(__func__, fn_names, Exit, OutOfRange);
}
sff_header_destroy(header);
}
if(NULL != names && 0 < names_num) {
free(names);
}
free(fn_names);
return 0;
}
