// DEBUG
void checkNode(Node* node) {
PassageMarkerI marker1 = getMarker(node);
if (marker1 == NULL_IDX)
return;
PassageMarkerI marker2 = getNextInNode(marker1);
if (marker2 == NULL_IDX)
return;
if (getStartOffset(marker1) == getStartOffset(marker2))
abort();
if (getFinishOffset(marker1) == getFinishOffset(marker2))
abort();
printf(">>>> Node %li\n", (long) getNodeID(node));
printf("Marker1: %li - %li > %li (%li) \n", (long) getStartOffset(marker1), (long) getPassageMarkerLength(marker1), (long) (getNodeLength(node) - getFinishOffset(marker1)), (long) getFinishOffset(marker1));
printf("%s\n", readPassageMarker(marker1));
printf("Marker2: %li - %li > %li (%li) \n", (long) getStartOffset(marker2), (long) getPassageMarkerLength(marker2), (long) (getNodeLength(node) - getFinishOffset(marker2)), (long) getFinishOffset(marker2));
printf("%s\n", readPassageMarker(marker2));
if (getStartOffset(marker1) < getNodeLength(node) - getFinishOffset(marker2)
&& getStartOffset(marker2) < getNodeLength(node) - getFinishOffset(marker1)) {
//abort();
;
}
}
static void updateMembers(Node * bypass, Node * nextNode)
{
PassageMarkerI marker, next, tmp;
Coordinate nextLength = getNodeLength(nextNode);
// Update marker + arc info
for (marker = getMarker(bypass); marker != NULL_IDX; marker = tmp) {
tmp = getNextInNode(marker);
if (!isTerminal(marker)
&& getNode(getNextInSequence(marker)) == nextNode) {
// Marker steps right into target
next = getNextInSequence(marker);
disconnectNextPassageMarker(marker, graph);
destroyPassageMarker(next);
} else if (getUniqueness(nextNode)
&& goesToNode(marker, nextNode)) {
// Marker goes indirectly to target
while (getNode(getNextInSequence(marker)) !=
nextNode) {
next = getNextInSequence(marker);
disconnectNextPassageMarker(marker, graph);
destroyPassageMarker(next);
}
next = getNextInSequence(marker);
disconnectNextPassageMarker(marker, graph);
destroyPassageMarker(next);
} else if (!isTerminal(marker)
&& getFinishOffset(marker) == 0) {
// Marker goes somewhere else than to target
next = getNextInSequence(marker);
incrementFinishOffset(marker, nextLength);
} else {
// Marker goes nowhere
incrementFinishOffset(marker, nextLength);
}
}
}
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;
}
