static void trim_polyA_align(struct edit_script_list **Sptr, Exon *lblock, Exon **exons, const int bc, int *pA, uchar *s1,uchar *s2)
{
edit_script_list *head = *Sptr;
edit_script *tp;
int tmpi = 0, num, idents = 0;
uchar *a, *b;
Exon *prev;
int i, j; /* i index in the cDNA */
if (bc>head->offset2+head->len2-1) {
*pA = bc;
return;
}
if (bc==head->offset2) {
/* cDNA gap: remove the entire script; this should be properly sorted */
*Sptr = head->next_script;
Free_script(head->script);
free(head);
while ((*exons)->from2>=bc) {
prev = find_previous(lblock,*exons);
prev->next_exon = (*exons)->next_exon;
free(*exons); *exons = prev;
}
*pA = bc;
return;
}
Flip_script(&(head->script));
i = head->offset2 + head->len2 -1;
j = head->offset1 + head->len1 -1;
tp = head->script;
while (i>=bc && tp) {
num = tp->num;
switch (tp->op_type) {
case INSERT:
if (i>=bc && bc>i-num+1) {
tmpi += i-bc+1; tp->num -= i-bc+1; i = bc-1;
} else {
i -= num; tmpi += num; head->script = tp->next;
free(tp); tp = head->script;
}
break;
case DELETE:
j -= num; tmpi += num; head->script = tp->next;
free(tp); tp = head->script;
break;
case SUBSTITUTE:
if (i>=bc && bc>i-num+1) {
a = s2+i-1; b = s1+j-1;
while (a>=s2+bc-1) {
if (*a--!=*b--) tmpi++; else idents++;
}
j -= i-bc+1; tp->num -= i-bc+1; i = bc-1;
} else {
/* at most 1 nt remaining */
a = s2+i-1; b = s1+j-1;
while (a>=s2+i-num) {
if (*a--!=*b--) tmpi++; else idents++;
}
i -= num; j -= num;
head->script = tp->next;
free(tp); tp = head->script;
}
break;
default: fatalf("Unrecognized opcode %d.\n",tp->op_type);
}
/* indel walk */
}
assert(i==bc-1);
while (tp->op_type!=SUBSTITUTE && j+1>=(*exons)->from1) {
if (tp->op_type==INSERT) {
i -= tp->num; tmpi += tp->num;
} else if (j<(*exons)->from1 && i<(*exons)->from2) {
j -= tp->num;
} else {
j -= tp->num; tmpi += tp->num;
}
head->script = tp->next;
free(tp); tp = head->script;
}
if (head->script==NULL) {
*Sptr = head->next_script;
free(head);
} else {
head->len1 = j-head->offset1+1;
head->len2 = i-head->offset2+1;
head->score -= tmpi;
Flip_script(&(head->script));
}
if ((*exons)->from2>i) {
prev = find_previous(lblock,*exons);
prev->next_exon = (*exons)->next_exon;
free(*exons); *exons = prev;
} else {
double tmp_matches;
(*exons)->to2 = i;
(*exons)->to1 = j;
(*exons)->length = (*exons)->to2-(*exons)->from2+1;
tmp_matches = (*exons)->nmatches - idents;
(*exons)->alen -= tmpi+idents;
(*exons)->match = (int)(100*tmp_matches/(*exons)->alen);
}
*pA = i+1;
return;
}
void
Sim4::trim_polyA_align(struct edit_script_list **Sptr, Exon *lblock, Exon **exons, const int bc, int *pA, char *s1,char *s2)
{
edit_script_list *head = *Sptr;
edit_script *tp;
int tmpi = 0, num, idents = 0, identsN = 0;
char *a, *b;
Exon *prev;
int i, j; /* i index in the cDNA */
if (bc>head->offset2+head->len2-1) {
*pA = bc;
return;
}
if (bc==head->offset2) {
/* cDNA gap: remove the entire script; is this properly sorted? LLL */
*Sptr = head->next_script;
Free_script(head->script);
ckfree(head);
while ((*exons)->frEST>=bc) {
prev = find_previous(lblock,*exons);
if (prev == 0L) {
fprintf(stderr, "trim_polyA_align(): Corrupted exon list, cannot find the previous exon (remove entire script).\n");
for (; lblock; lblock = lblock->next_exon)
fprintf(stderr, " GEN f=%8d t=%8d EST f=%8d t=%8d flag=%d\n",
lblock->frGEN, lblock->toGEN, lblock->frEST, lblock->toEST, lblock->flag);
kill(getpid(), SIGKILL);
}
prev->next_exon = (*exons)->next_exon;
//freeExon(*exons); garbage collected
*exons = prev;
}
*pA = bc;
return;
}
Flip_script(&(head->script));
i = head->offset2 + head->len2 -1;
j = head->offset1 + head->len1 -1;
tp = head->script;
while (i>=bc && tp) {
num = tp->num;
switch (tp->op_type) {
case INSERT:
if (i>=bc && bc>i-num+1) {
(*exons)->numInDel -= i - bc + 1;
(*exons)->numEdits -= i - bc + 1;
tmpi += i-bc+1;
tp->num -= i-bc+1;
i = bc-1;
} else {
(*exons)->numInDel -= num;
(*exons)->numEdits -= num;
tmpi += num;
i -= num;
head->script = tp->next;
ckfree(tp);
tp = head->script;
}
break;
case DELETE:
(*exons)->numInDel -= num;
(*exons)->numEdits -= num;
j -= num;
tmpi += num;
head->script = tp->next;
ckfree(tp);
tp = head->script;
break;
case SUBSTITUTE:
if (i>=bc && bc>i-num+1) {
a = s2+i-1; b = s1+j-1;
while (a>=s2+bc-1) {
if (*a != *b) {
(*exons)->numEdits--;
tmpi++;
} else {
if (*a == 'N') {
(*exons)->numNs--;
identsN++;
} else {
(*exons)->numMatches--;
idents++;
}
}
a--;
b--;
}
j -= i-bc+1; tp->num -= i-bc+1; i = bc-1;
} else {
/* at most 1 nt remaining */
a = s2+i-1; b = s1+j-1;
while (a>=s2+i-num) {
if (*a != *b) {
(*exons)->numEdits--;
tmpi++;
} else {
if (*a == 'N') {
(*exons)->numNs--;
identsN++;
} else {
(*exons)->numMatches--;
idents++;
}
}
a--;
b--;
}
i -= num; j -= num;
head->script = tp->next;
ckfree(tp);
tp = head->script;
}
break;
#if 0
default:
fatalf("Unrecognized opcode %d.\n",tp->op_type);
#endif
}
/* indel walk */
}
assert(i==bc-1);
while ((tp != 0L) &&
(tp->op_type != SUBSTITUTE) && (j+1 >= (*exons)->frGEN)) {
if (tp->op_type==INSERT) {
i -= tp->num;
tmpi += tp->num;
(*exons)->numInDel -= tp->num;
(*exons)->numEdits -= tp->num;
} else if (j<(*exons)->frGEN && i<(*exons)->frEST) {
j -= tp->num;
} else {
j -= tp->num;
tmpi += tp->num;
(*exons)->numInDel -= tp->num;
(*exons)->numEdits -= tp->num;
}
head->script = tp->next;
ckfree(tp);
tp = head->script;
}
if (head->script==NULL) {
*Sptr = head->next_script;
ckfree(head);
} else {
head->len1 = j-head->offset1+1;
head->len2 = i-head->offset2+1;
head->score -= tmpi;
Flip_script(&(head->script));
}
if ((*exons)->frEST>i) {
prev = find_previous(lblock,*exons);
if (prev == 0L) {
fprintf(stderr, "trim_polyA_align(): Corrupted exon list, cannot find the previous exon (frEST).\n");
for (; lblock; lblock = lblock->next_exon)
fprintf(stderr, " GEN f=%8d t=%8d EST f=%8d t=%8d flag=%d\n",
lblock->frGEN, lblock->toGEN, lblock->frEST, lblock->toEST, lblock->flag);
kill(getpid(), SIGKILL);
}
prev->next_exon = (*exons)->next_exon;
//freeExon(*exons); garbage collected
*exons = prev;
} else {
(*exons)->toEST = i;
(*exons)->toGEN = j;
(*exons)->length = (*exons)->toEST-(*exons)->frEST+1;
(*exons)->alignmentLength = ((*exons)->toGEN - (*exons)->frGEN + 1 +
(*exons)->toEST - (*exons)->frEST + 1 +
(*exons)->numInDel);
(*exons)->percentID = computePercentIdentity((*exons)->numEdits,
(*exons)->alignmentLength);
}
*pA = i+1;
return;
}
