void findBestDupes(duplicate_t *head, char *consensus) {
// For each duplicate list, go through its mafline list and find the best line and move it
// to the head of the list.
duplicate_t *d = head;
scoredMafLine_t *sml = NULL;
while (d != NULL) {
if (d->numSequences < 2) {
// if there's only one sequence, who cares
d = d->next;
continue;
}
// score all the maf lines
sml = d->headScoredMaf;
while (sml != NULL) {
sml->score = scoreSequence(consensus, maf_mafLine_getSequence(sml->mafLine));
sml = sml->next;
}
// sort on scores
scoredMafLine_t **mafLineArray = (scoredMafLine_t**) de_malloc(sizeof(*mafLineArray) * d->numSequences);
populateMafLineArray(d->headScoredMaf, mafLineArray);
qsort(mafLineArray, d->numSequences, sizeof(scoredMafLine_t *), cmp_by_score);
// move the top score to the head of the list
d->headScoredMaf = mafLineArray[0];
sml = d->headScoredMaf;
for (unsigned i = 1; i < d->numSequences; ++i) {
// rebuild the linked list
sml->next = mafLineArray[i];
sml = sml->next;
}
sml->next = NULL;
d = d->next;
free(mafLineArray);
}
}
void findBestDupes(duplicate_t *head, char *consensus) {
// For each duplicate, go through its mafline list and find the best line and move it
// to the head of the list.
duplicate_t *d = head;
scoredMafLine_t *m = NULL;
debug("findBestDupes()\n");
while (d != NULL) {
debug(" d is not NULL\n");
debug(" species: %s", d->headScoredMaf->mafLine->species);
m = d->headScoredMaf;
unsigned n = numberOfSequencesScoredMafLineList(m);
if (n < 2) {
d = d->next;
debug(" ... not dup.\n");
continue;
}
debug(" ... DUP.\n");
// score all the dupes
while (m != NULL) {
m->score = scoreSequence(consensus, m->mafLine->sequence);
m = m->next;
}
// sort on scores
scoredMafLine_t *mafLineArray[n];
populateMafLineArray(d->headScoredMaf, mafLineArray);
qsort(mafLineArray, n, sizeof(scoredMafLine_t *), cmp_by_score);
// move the top score to the head of the list
d->headScoredMaf = mafLineArray[0];
m = d->headScoredMaf;
for (unsigned i = 1; i < n; ++i) {
m->next = mafLineArray[i];
m = m->next;
}
m->next = NULL;
d = d->next;
}
}
