static boolean
extractSequence(PassageMarkerI path, TightString * sequence)
{
PassageMarkerI marker;
Coordinate seqLength = 0;
Coordinate writeIndex = 0;
//velvetLog("Extracting sequence %li ... ", pathLength);
//Measure length
for (marker = getNextInSequence(path); !isTerminal(marker);
marker = getNextInSequence(marker))
seqLength += getNodeLength(getNode(marker));
if (seqLength > MAXREADLENGTH)
return false;
else
setTightStringLength(sequence, seqLength);
//Copy sequences
for (marker = getNextInSequence(path); !isTerminal(marker);
marker = getNextInSequence(marker)) {
appendNodeSequence(getNode(marker), sequence, writeIndex);
writeIndex += getNodeLength(getNode(marker));
}
return true;
}
static void cleanUpRedundancy_local()
{
PassageMarkerI current;
for (current = getNextInSequence(slowPath); !isTerminal(current);
current = getNextInSequence(current))
handicapNode(getNode(current));
destroyPaths();
}
static void destroyPaths()
{
PassageMarkerI marker;
while (slowPath != NULL_IDX) {
marker = slowPath;
slowPath = getNextInSequence(marker);
destroyPassageMarker(marker);
}
while (fastPath != NULL_IDX) {
marker = fastPath;
fastPath = getNextInSequence(marker);
destroyPassageMarker(marker);
}
}
static boolean goesToNode(PassageMarkerI marker, Node * node)
{
PassageMarkerI current;
Node * start = getNode(marker);
for (current = getNextInSequence(marker); current != NULL_IDX;
current = getNextInSequence(current)) {
if (getNode(current) == node)
return true;
else if (getNode(current) == start)
continue;
else if (getUniqueness(getNode(current)))
return false;
}
return false;
}
static boolean comesFromNode(PassageMarkerI marker, Node * node)
{
Node *source = getNode(getTwinMarker(marker));
Node *target = getTwinNode(node);
PassageMarkerI current;
for (current = getNextInSequence(getTwinMarker(marker)); current != NULL_IDX;
current = getNextInSequence(current)) {
if (getNode(current) == target)
return true;
else if (getNode(current) == source)
continue;
else if (getUniqueness(getNode(current)))
return false;
}
return false;
}
static void trimLongReadTips()
{
IDnum index;
Node *node;
PassageMarkerI marker, next;
velvetLog("Trimming read tips\n");
for (index = 1; index <= nodeCount(graph); index++) {
node = getNodeInGraph(graph, index);
if (getUniqueness(node))
continue;
for (marker = getMarker(node); marker != NULL_IDX;
marker = next) {
next = getNextInNode(marker);
if (!isInitial(marker) && !isTerminal(marker))
continue;
if (isTerminal(marker))
marker = getTwinMarker(marker);
while (!getUniqueness(getNode(marker))) {
if (next != NULL_IDX
&& (marker == next
|| marker == getTwinMarker(next)))
next = getNextInNode(next);
if (getNextInSequence(marker) != NULL_IDX) {
marker = getNextInSequence(marker);
destroyPassageMarker
(getPreviousInSequence
(marker));
} else {
destroyPassageMarker(marker);
break;
}
}
}
}
}
static boolean goesToNode(PassageMarkerI marker, Node * node)
{
PassageMarkerI current;
Node * start = getNode(marker);
Node * twinStart = getTwinNode(start);
Node * currentNode;
for (current = getNextInSequence(marker); current != NULL_IDX;
current = getNextInSequence(current)) {
currentNode = getNode(current);
if (currentNode == start || currentNode == twinStart)
return false;
else if (currentNode == node)
return true;
else if (getUniqueness(currentNode))
return false;
}
return false;
}
static boolean goesToNode(PassageMarker * marker, Node * node)
{
PassageMarker *current;
for (current = marker; current != NULL;
current = getNextInSequence(current))
if (getNode(current) == node)
return true;
return false;
}
static void destroyPaths()
{
PassageMarker *marker;
while (slowPath != NULL) {
marker = slowPath;
getNodeTime(getNode(marker));
getNodeTime(getTwinNode(getNode(marker)));
slowPath = getNextInSequence(marker);
destroyPassageMarker(marker);
}
while (fastPath != NULL) {
marker = fastPath;
getNodeTime(getNode(marker));
getNodeTime(getTwinNode(getNode(marker)));
fastPath = getNextInSequence(marker);
destroyPassageMarker(marker);
}
}
void ResourceState::removeFromNextInSequence(uint64_t ID) {
assert(NextInSequenceMask);
assert(countPopulation(ID) == 1);
if (ID > getNextInSequence())
RemovedFromNextInSequence |= ID;
NextInSequenceMask = NextInSequenceMask & (~ID);
if (!NextInSequenceMask) {
NextInSequenceMask = ResourceSizeMask;
assert(NextInSequenceMask != RemovedFromNextInSequence);
NextInSequenceMask ^= RemovedFromNextInSequence;
RemovedFromNextInSequence = 0;
}
}
static void reconnectPassageMarker(PassageMarkerI marker, Node * node,
PassageMarkerI * ptr)
{
PassageMarkerI current;
PassageMarkerI next = getNextInSequence(marker);
PassageMarkerI tmpMarker;
for (current = marker; getNode(current) != node;
current = getPreviousInSequence(current));
setPreviousInSequence(current, next);
concatenatePassageMarkers(current, marker);
// Removing node and all intermediaries
while (marker != current) {
tmpMarker = getPreviousInSequence(marker);
if (*ptr == marker || *ptr == getTwinMarker(marker))
*ptr = getNextInNode(*ptr);
setNextInSequence(marker, NULL_IDX);
setPreviousInSequence(NULL_IDX, marker);
destroyPassageMarker(marker);
marker = tmpMarker;
}
}
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);
}
}
}
// Replaces two consecutive nodes into a single equivalent node
// The extra memory is freed
void concatenateStringOfNodes(Node * nodeA, Graph * graph)
{
Node *twinA = getTwinNode(nodeA);
Node * nodeB = nodeA;
Node * twinB;
Node *currentNode, *nextNode;
Coordinate totalLength = 0;
PassageMarkerI marker, tmpMarker;
Arc *arc;
Category cat;
while (simpleArcCount(nodeB) == 1
&&
simpleArcCount(getTwinNode
(getDestination(getArc(nodeB)))) ==
1
&& getDestination(getArc(nodeB)) != getTwinNode(nodeB)
&& getDestination(getArc(nodeB)) != nodeA) {
totalLength += getNodeLength(nodeB);
nodeB = getDestination(getArc(nodeB));
}
twinB = getTwinNode(nodeB);
totalLength += getNodeLength(nodeB);
reallocateNodeDescriptor(nodeA, totalLength);
currentNode = nodeA;
while (currentNode != nodeB) {
currentNode = getDestination(getArc(currentNode));
// Passage marker management in node A:
for (marker = getMarker(nodeA); marker != NULL_IDX;
marker = getNextInNode(marker))
if (getNode(getNextInSequence(marker)) != currentNode)
incrementFinishOffset(marker,
getNodeLength(currentNode));
// Swapping new born passageMarkers from B to A
for (marker = getMarker(currentNode); marker != NULL_IDX; marker = tmpMarker) {
tmpMarker = getNextInNode(marker);
if (isInitial(marker)
|| getNode(getPreviousInSequence(marker)) != nodeA) {
extractPassageMarker(marker);
transposePassageMarker(marker, nodeA);
incrementFinishOffset(getTwinMarker(marker),
getNodeLength(nodeA));
} else
disconnectNextPassageMarker(getPreviousInSequence
(marker), graph);
}
// Read starts
concatenateReadStarts(nodeA, currentNode, graph);
// Gaps
appendNodeGaps(nodeA, currentNode, graph);
// Update uniqueness:
setUniqueness(nodeA, getUniqueness(nodeA) || getUniqueness(currentNode));
// Update virtual coverage
for (cat = 0; cat < CATEGORIES; cat++)
incrementVirtualCoverage(nodeA, cat,
getVirtualCoverage(currentNode, cat));
// Update original virtual coverage
for (cat = 0; cat < CATEGORIES; cat++)
incrementOriginalVirtualCoverage(nodeA, cat,
getOriginalVirtualCoverage
(currentNode, cat));
// Descriptor management (node)
directlyAppendDescriptors(nodeA, currentNode, totalLength);
}
// Correct arcs
for (arc = getArc(nodeB); arc != NULL; arc = getNextArc(arc)) {
if (getDestination(arc) != twinB)
createAnalogousArc(nodeA, getDestination(arc),
arc, graph);
else
createAnalogousArc(nodeA, twinA, arc, graph);
}
// Freeing gobbled nodes
currentNode = getTwinNode(nodeB);
while (currentNode != getTwinNode(nodeA)) {
arc = getArc(currentNode);
nextNode = getDestination(arc);
destroyNode(currentNode, graph);
currentNode = nextNode;
}
}
static Node *bypass()
{
Node *bypass = getNode(path);
Node *next = NULL;
Arc *arc;
PassageMarkerI nextMarker;
// Remove unwanted arcs
while (getArc(bypass) != NULL)
destroyArc(getArc(bypass), graph);
// Update extensive variables (length + descriptors + passage markers)
while (!isTerminal(path)) {
nextMarker = getNextInSequence(path);
next = getNode(nextMarker);
while (next == bypass) {
disconnectNextPassageMarker(path, graph);
destroyPassageMarker(nextMarker);
nextMarker = getNextInSequence(path);
next = getNode(nextMarker);
}
if (next == NULL)
return bypass;
// Overall node update
if (!getUniqueness(next)) {
adjustShortReads(bypass, getNextInSequence(path));
appendSequence(bypass, sequences,
getNextInSequence(path), graph);
} else {
concatenateReadStarts(bypass, next, graph);
#ifndef SINGLE_COV_CAT
Category cat;
for (cat = 0; cat < CATEGORIES; cat++) {
// Update virtual coverage
incrementVirtualCoverage(bypass, cat,
getVirtualCoverage(next, cat));
// Update original virtual coverage
incrementOriginalVirtualCoverage(bypass, cat,
getOriginalVirtualCoverage(next, cat));
}
#else
incrementVirtualCoverage(bypass, getVirtualCoverage(next));
#endif
appendDescriptors(bypass, next);
}
// Members
updateMembers(bypass, next);
// Termination
if (isTerminal(path) || getUniqueness(next))
break;
}
// Remove unique groupies from arrival
admitGroupies(next, bypass);
// Copy destination arcs
for (arc = getArc(next); arc != NULL; arc = getNextArc(arc)) {
if (getDestination(arc) == next)
continue;
else if (getDestination(arc) == getTwinNode(next))
createAnalogousArc(bypass, getTwinNode(bypass),
arc, graph);
else
createAnalogousArc(bypass, getDestination(arc),
arc, graph);
}
destroyNode(next, graph);
return bypass;
}
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;
}
