alignel* filter_aligns_by_num_gaps
(alignel* alignList,
s32 maxSeparateGapsCount)
{
alignel* a, *next;
alignel* head, *prev;
unspos height, width, i, j, run;
u32 opIx;
s32 numGaps;
// process each alignment, collecting a list of those that are long enough
head = prev = NULL;
for (a=alignList ; a!=NULL ; a=next)
{
next = a->next;
// if the alignment is too gappy, skip it
numGaps = 0;
height = a->end1 - a->beg1 + 1;
width = a->end2 - a->beg2 + 1;
opIx = 0;
for (i=j=0 ; (i<height)||(j<width) ; )
{
// handle the next run
run = edit_script_run_of_subs (a->script, &opIx);
i += run; j += run;
// handle the next indel
if ((i < height) || (j < width))
{
edit_script_indel_len (a->script, &opIx, &i, &j);
if (++numGaps > maxSeparateGapsCount)
break;
}
}
if (numGaps > maxSeparateGapsCount)
{ // (unwanted alignment, discard it)
free_if_valid ("filter_aligns_by_continuity a->script", a->script);
free_if_valid ("filter_aligns_by_continuity a", a);
continue;
}
// this alignment is ok, add it to the end of the new list we're
// building
if (head == NULL) head = prev = a;
else { prev->next = a; prev = a; }
a->next = NULL;
}
return head;
}
alignel* filter_aligns_by_continuity
(alignel* alignList,
float minContinuity,
float maxContinuity)
{
alignel* a, *next;
alignel* head, *prev;
unspos numer, denom;
float minCont, maxCont;
// process each alignment, collecting a list of those that are long enough
head = prev = NULL;
for (a=alignList ; a!=NULL ; a=next)
{
next = a->next;
// if the alignment is too gappy, skip it
alignment_continuity (a, &numer, &denom);
minCont = denom * minContinuity;
maxCont = denom * maxContinuity;
if ((numer < minCont) || (numer > maxCont))
{ // (unwanted alignment, discard it)
free_if_valid ("filter_aligns_by_continuity a->script", a->script);
free_if_valid ("filter_aligns_by_continuity a", a);
continue;
}
// this alignment is ok, add it to the end of the new list we're
// building
if (head == NULL) head = prev = a;
else { prev->next = a; prev = a; }
a->next = NULL;
}
return head;
}
alignel* filter_aligns_by_num_gap_columns
(alignel* alignList,
s32 maxGapColumnsCount)
{
alignel* a, *next;
alignel* head, *prev;
unspos numer, denom;
// process each alignment, collecting a list of those that are long enough
head = prev = NULL;
for (a=alignList ; a!=NULL ; a=next)
{
next = a->next;
// if the alignment is too gappy, skip it
alignment_continuity (a, &numer, &denom);
if ((denom == 0) || (denom-numer > (u32) maxGapColumnsCount))
{ // (unwanted alignment, discard it)
free_if_valid ("filter_aligns_by_continuity a->script", a->script);
free_if_valid ("filter_aligns_by_continuity a", a);
continue;
}
// this alignment is ok, add it to the end of the new list we're
// building
if (head == NULL) head = prev = a;
else { prev->next = a; prev = a; }
a->next = NULL;
}
return head;
}
void free_diag_hash
(void)
{
free_if_valid ("free_diag_hash (diagEnd)", diagEnd); diagEnd = NULL;
free_if_valid ("free_diag_hash (diagStart)", diagStart); diagStart = NULL;
free_if_valid ("free_diag_hash (diagActual)", diagActual); diagActual = NULL;
free_if_valid ("free_diag_hash (diagActive)", diagActive); diagActive = NULL;
#ifndef noSeedHitQueue
free_if_valid ("free_diag_hash (seedHitQueue)", seedHitQueue); seedHitQueue = NULL;
free_if_valid ("free_diag_hash (lastSeedHit)", lastSeedHit); lastSeedHit = NULL;
#endif // not noSeedHitQueue
}
void free_segment_table
(segtable* st)
{
free_if_valid ("free_segment_table", st);
}
