void removeLowCovEdges (int lenCutoff, unsigned short covCutoff)
{
unsigned int bal_ed;
unsigned int arcRight_n, arcLeft_n;
ARC *arcLeft, *arcRight;
unsigned int i;
int counter = 0;
for (i = 1; i <= num_ed; i++)
{
if (edge_array[i].deleted || edge_array[i].cvg == 0 || edge_array[i].cvg > covCutoff * 10 || edge_array[i].length >= lenCutoff || EdSameAsTwin (i) || edge_array[i].length == 0)
{
continue;
}
bal_ed = getTwinEdge (i);
arcRight = arcCount (i, &arcRight_n);
arcLeft = arcCount (bal_ed, &arcLeft_n);
if (arcLeft_n < 1 || arcRight_n < 1)
{
continue;
}
destroyEdge (i);
counter++;
}
printf ("Remove low coverage(%d): %d inner edges destroyed\n", covCutoff, counter);
removeDeadArcs ();
linearConcatenate ();
compactEdgeArray ();
}
void removeWeakEdges (int lenCutoff, unsigned int multiCutoff)
{
unsigned int bal_ed;
unsigned int arcRight_n, arcLeft_n;
ARC *arcLeft, *arcRight;
unsigned int i;
int counter = 0;
for (i = 1; i <= num_ed; i++)
{
if (edge_array[i].deleted || edge_array[i].length == 0 || edge_array[i].length > lenCutoff || EdSameAsTwin (i))
{
continue;
}
bal_ed = getTwinEdge (i);
arcRight = arcCount (i, &arcRight_n);
if (arcRight_n > 1 || !arcRight || arcRight->multiplicity > multiCutoff)
{
continue;
}
arcLeft = arcCount (bal_ed, &arcLeft_n);
if (arcLeft_n > 1 || !arcLeft || arcLeft->multiplicity > multiCutoff)
{
continue;
}
destroyEdge (i);
counter++;
}
printf ("%d weak inner edges destroyed\n", counter);
removeDeadArcs ();
/*
linearConcatenate();
compactEdgeArray();
*/
}
boolean isUnreliableTip_strict (unsigned int edgeid, int cutLen)
{
unsigned int arcRight_n, arcLeft_n;
unsigned int bal_ed;
unsigned int currentEd = edgeid;
int length = 0;
unsigned int mult = 0;
ARC *arc, *activeArc = NULL, *tempArc;
if (edgeid == 0)
{
return 0;
}
bal_ed = getTwinEdge (edgeid);
if (bal_ed == edgeid)
{
return 0;
}
arcCount (bal_ed, &arcLeft_n);
if (arcLeft_n > 0)
{
return 0;
}
while (currentEd)
{
arcCount (bal_ed, &arcLeft_n);
tempArc = arcCount (currentEd, &arcRight_n);
if (arcLeft_n > 1 || arcRight_n > 1)
{
if (arcLeft_n == 0 || length == 0)
{
return 0;
}
else
{
break;
}
}
length += edge_array[currentEd].length;
if (length >= cutLen)
{
return 0;
}
if (tempArc)
{
activeArc = tempArc;
currentEd = activeArc->to_ed;
bal_ed = getTwinEdge (currentEd);
}
else
{
currentEd = 0;
}
}
if (currentEd == 0)
{
caseA++;
return 1;
}
if (!activeArc)
{
printf ("no activeArc while checking edge %d\n", edgeid);
}
if (activeArc->multiplicity == 1)
{
caseB++;
return 1;
}
for (arc = edge_array[bal_ed].arcs; arc != NULL; arc = arc->next)
if (arc->multiplicity > mult)
{
mult = arc->multiplicity;
}
if (mult > activeArc->multiplicity)
{
caseC++;
}
return mult > activeArc->multiplicity;
}
static boolean uniqueNodesConnect(Node * startingNode)
{
Node *destination = NULL;
PassageMarkerI startMarker, currentMarker;
RBConnection *newList;
RBConnection *list = NULL;
boolean multipleHits = false;
if (arcCount(startingNode) == 0)
return false;
if (getMarker(startingNode) == NULL_IDX)
return false;
dbgCounter++;
// Checking for multiple destinations
for (startMarker = getMarker(startingNode); startMarker != NULL_IDX;
startMarker = getNextInNode(startMarker)) {
if (getFinishOffset(startMarker) >
2 * getWordLength(graph))
continue;
for (currentMarker = getNextInSequence(startMarker);
currentMarker != NULL_IDX;
currentMarker = getNextInSequence(currentMarker)) {
if (!getUniqueness(getNode(currentMarker))) {
continue;
} else if (getNodeStatus(getNode(currentMarker))) {
if (getStartOffset(currentMarker) >
2 * getWordLength(graph))
break;
for (newList = list; newList != NULL;
newList = newList->next) {
if (newList->node ==
getNode(currentMarker)) {
newList->multiplicity++;
break;
}
}
if (newList == NULL)
abort();
break;
} else {
if (getStartOffset(currentMarker) >
2 * getWordLength(graph))
break;
setSingleNodeStatus(getNode(currentMarker),
true);
newList = allocateRBConnection();
newList->node = getNode(currentMarker);
newList->multiplicity = 1;
newList->marker = startMarker;
newList->next = list;
list = newList;
break;
}
}
}
while (list != NULL) {
newList = list;
list = newList->next;
setSingleNodeStatus(newList->node, false);
if (newList->multiplicity >= MULTIPLICITY_CUTOFF) {
if (destination == NULL) {
destination = newList->node;
path = newList->marker;
} else if (destination != newList->node)
multipleHits = true;
}
deallocateRBConnection(newList);
}
if (multipleHits) {
multCounter++;
setUniqueness(startingNode, false);
return false;
}
if (destination == NULL || destination == startingNode
|| destination == getTwinNode(startingNode)) {
nullCounter++;
return false;
}
// Check for reciprocity
for (startMarker = getMarker(getTwinNode(destination));
startMarker != NULL_IDX;
startMarker = getNextInNode(startMarker)) {
if (getFinishOffset(startMarker) >
2 * getWordLength(graph))
continue;
for (currentMarker = getNextInSequence(startMarker);
currentMarker != NULL_IDX;
currentMarker = getNextInSequence(currentMarker)) {
if (!getUniqueness(getNode(currentMarker))) {
continue;
} else if (getNodeStatus(getNode(currentMarker))) {
if (getStartOffset(currentMarker) >
2 * getWordLength(graph))
break;
for (newList = list; newList != NULL;
newList = newList->next) {
if (newList->node ==
getNode(currentMarker)) {
newList->multiplicity++;
break;
}
}
if (newList == NULL)
abort();
break;
} else {
if (getStartOffset(currentMarker) >
2 * getWordLength(graph))
break;
setSingleNodeStatus(getNode(currentMarker),
true);
newList = allocateRBConnection();
newList->node = getNode(currentMarker);
newList->multiplicity = 1;
newList->next = list;
list = newList;
break;
}
}
}
while (list != NULL) {
newList = list;
list = newList->next;
setSingleNodeStatus(newList->node, false);
if (newList->multiplicity >= MULTIPLICITY_CUTOFF
&& newList->node != getTwinNode(startingNode))
multipleHits = true;
deallocateRBConnection(newList);
}
if (multipleHits) {
multCounter++;
setUniqueness(destination, false);
return false;
}
// Aligning long reads to each other:
// TODO
// Merge pairwise alignments and produce consensus
// TODO
return true;
}
