void bam_header_destroy(bam_header_t *header)
{
int32_t i;
extern void bam_destroy_header_hash(bam_header_t *header);
if (header == 0) return;
if (header->target_name) {
for (i = 0; i < header->n_targets; ++i)
free(header->target_name[i]);
free(header->target_name);
free(header->target_len);
}
free(header->text);
if (header->dict) sam_header_free(header->dict);
if (header->rg2lib) sam_tbl_destroy(header->rg2lib);
bam_destroy_header_hash(header);
free(header);
}
void bam_header_destroy(bam_header_t *header)
{
int32_t i;
extern void bam_destroy_header_hash(bam_header_t *header);
if (header == 0) return;
if (header->target_name) {
for (i = 0; i < header->n_targets; ++i)
free(header->target_name[i]);
free(header->target_name);
free(header->target_len);
}
free(header->text);
#ifndef BAM_NO_HASH
bam_destroy_header_hash(header);
#endif
free(header);
}
/* will return non-0 on error. parsed error prof will be written to
* alnerrprof. values are allocated here and should be freed with
* free_alnerrprof */
int
parse_alnerrprof_statsfile(alnerrprof_t *alnerrprof, const char *path, bam_header_t *bam_header)
{
char line[BUF_SIZE];
int i;
int *max_obs_pos;
const int default_read_len = 250;
int free_bam_header_hash = 0;
int rc;
FILE *in = fopen(path, "r");
/* needed for finding tid from tname */
if (bam_header->hash == 0) {
bam_init_header_hash(bam_header);
free_bam_header_hash = 1;
}
max_obs_pos = calloc(bam_header->n_targets, sizeof(int));
alnerrprof->num_targets = bam_header->n_targets;
alnerrprof->prop_len = calloc(alnerrprof->num_targets, sizeof(int));
alnerrprof->props = calloc(alnerrprof->num_targets, sizeof(double *));
for (i=0; i<alnerrprof->num_targets; i++) {
alnerrprof->prop_len[i] = default_read_len;/* default alloc here and realloc later */
alnerrprof->props[i] = calloc(alnerrprof->prop_len[i], sizeof(double));
}
i=-1; /* make sure value is not reused by accident; triggers clang warning though */
while (NULL != fgets(line, BUF_SIZE, in)) {
int pos = -1;
char tname[BUF_SIZE];
double prop = -1;
unsigned long int count = -1;
int tid = -1;
if (line[0]=='#') {
continue;
}
if (4 != sscanf(line, "%s\t%d\t%lg\t%lu\n", tname, &pos, &prop, &count)) {
LOG_ERROR("Couldn't parse line %s\n", line);
rc = 1;
goto free_and_exit;
}
assert(prop>=0.0 && prop<=1.0);
pos = pos - 1;
assert(pos<MAX_READ_LEN);
tid = bam_get_tid(bam_header, tname);
if (-1 == tid) {
LOG_ERROR("Target name '%s' found in error profile doesn't match any of the sequences in BAM header. Skipping and trying to continue...\n", tname);
continue;
}
assert(tid<alnerrprof->num_targets);
/* for later downsizing */
if (pos+1 > max_obs_pos[tid]) {
max_obs_pos[tid] = pos+1;
}
/* upsize if necessary */
while (pos >= alnerrprof->prop_len[tid]) {
LOG_DEBUG("upsizing pos+1=%d alnerrprof->prop_len[tid=%d]=%d\n\n", pos+1, tid, alnerrprof->prop_len[tid]);
alnerrprof->prop_len[tid] *= 2;
alnerrprof->props[tid] = realloc(alnerrprof->props[tid], alnerrprof->prop_len[tid] * sizeof(double));
}
alnerrprof->props[tid][pos] = prop;
}
/* downsize */
for (i=0; i<alnerrprof->num_targets; i++) {
if (max_obs_pos[i]) {
LOG_DEBUG("downsizing alnerrprof->prop_len[tid=%d] to max %d\n", i, max_obs_pos[i]);
alnerrprof->props[i] = realloc(alnerrprof->props[i], max_obs_pos[i] * sizeof(double));
} else {
free(alnerrprof->props[i]);/* no data for this tid: free */
}
alnerrprof->prop_len[i] = max_obs_pos[i];
}
#if 0
{/* fixme report */
for (i=0; i<alnerrprof->num_targets; i++) {
int j;
fprintf(stderr, "tid=%d len=%d: ", i, alnerrprof->prop_len[i]);
for (j=0; j<alnerrprof->prop_len[i]; j++) {
fprintf(stderr, " %d:%g ", j, alnerrprof->props[i][j]);
}
fprintf(stderr, "\n");
fprintf(stderr, "median for tid %d: %g for size %d\n",
i,
dbl_median(alnerrprof->props[i], alnerrprof->prop_len[i]),
alnerrprof->prop_len[i]);
}
}
#endif
rc = 0;
free_and_exit:
free(max_obs_pos);
free_bam_header_hash = 0; /* FIXME segfaults often for unknown reason */
if (free_bam_header_hash) {
bam_destroy_header_hash(bam_header);
}
fclose(in);
return rc;
}
