/**
* Frees a singly-linked list of SeqFeature structures
* and frees the list itself.
*/
void seqfeat_slist_free(GSList *segments) {
GSList *cur;
SeqFeature *feat;
cur = segments;
while(cur != NULL) {
feat = (SeqFeature *)cur->data;
g_free(feat->c.seqname);
if(feat->name != NULL) {
g_free(feat->name);
}
if(feat->c.seqname != NULL) {
g_free(feat->c.seqname);
}
seqfeat_attrib_free(feat);
if(feat->n_sub_feat != 0) {
seqfeat_array_free(feat->sub_feats, feat->n_sub_feat);
}
g_free(feat);
cur = g_slist_next(cur);
}
g_slist_free(segments);
}
/**
* Frees an entire array of allocated SeqFeatures.
*/
void seqfeat_array_free(SeqFeature *feats, const long n) {
long i;
if(n == 0) {
return;
}
for(i = 0; i < n; i++) {
if(feats[i].name != NULL) {
g_free(feats[i].name);
}
if(feats[i].c.seqname != NULL) {
g_free(feats[i].c.seqname);
}
if(feats[i].n_sub_feat != 0) {
seqfeat_array_free(feats[i].sub_feats, feats[i].n_sub_feat);
}
seqfeat_attrib_free(&feats[i]);
}
g_free(feats);
}
/**
* Reads recombination rates from a feature-style file where the
* feature score is the rate in 10-8M and the coordinates the region.
*
* The returned rate array should be freed when it is no longer
* needed.
*/
float *dist_read_recomb_rate_feats(char *filename, long seq_len) {
long i,j, cur_pos, n_regions;
SeqFeature *rec_regions;
float *rates;
rates = g_new(float, seq_len);
/* read recombination rates from file */
rec_regions = seqfeat_read_flatfile(filename, &n_regions);
/** assume that regions in file are ordered */
cur_pos = 1;
for(i = 0; i < n_regions; i++) {
/* fill in gaps between regions with undefined recombination rates */
for(j = cur_pos; j < rec_regions[i].c.start; j++) {
rates[j-1] = DIST_NA;
}
/* fill in recombination rate of region */
for(j = rec_regions[i].c.start; j < rec_regions[i].c.end; j++) {
rates[j-1] = rec_regions[i].score;
}
cur_pos = rec_regions[i].c.end+1;
}
/* set remaining region at chr end to undefined rec rates */
for(j = cur_pos; j < seq_len; j++) {
rates[j-1] = DIST_NA;
}
seqfeat_array_free(rec_regions, n_regions);
return rates;
}
