static void markInterestingNodes(Node * node)
{
Connection *connect;
Node *destination;
MiniConnection *localConnect;
Coordinate min_distance =
getNodeLength(node) / 2 - BACKTRACK_CUTOFF;
// Mark own node
setEmptyMiniConnection(node);
// Loop thru primary scaffold
for (connect = getConnection(node); connect != NULL;
connect = getNextConnection(connect)) {
destination = getTwinNode(getConnectionDestination(connect));
localConnect =
&localScaffold[getNodeID(destination) +
nodeCount(graph)];
if (getNodeStatus(destination)) {
readjustMiniConnection(destination, localConnect,
getConnectionDistance(connect),
min_distance,
getConnectionVariance(connect), connect,
NULL);
localConnect->backReference = NULL;
} else {
resetMiniConnection(destination, localConnect,
getConnectionDistance(connect),
getConnectionVariance(connect), connect,
NULL, true);
}
integrateDerivativeDistances(connect, min_distance, true);
}
// Loop thru twin's primary scaffold
for (connect = getConnection(getTwinNode(node)); connect != NULL;
connect = getNextConnection(connect)) {
destination = getConnectionDestination(connect);
localConnect =
&localScaffold[getNodeID(destination) +
nodeCount(graph)];
if (getNodeStatus(destination))
readjustMiniConnection(destination, localConnect,
-getConnectionDistance(connect),
min_distance,
getConnectionVariance(connect), NULL,
connect);
else
resetMiniConnection(destination, localConnect,
-getConnectionDistance(connect),
getConnectionVariance(connect), NULL,
connect, -1);
integrateDerivativeDistances(connect, min_distance, false);
}
}
static void recenterLocalScaffold(Node * node, Coordinate oldLength)
{
MiniConnection *localConnect;
Coordinate distance_shift = (getNodeLength(node) - oldLength) / 2;
Coordinate min_distance =
getNodeLength(node) / 2 - BACKTRACK_CUTOFF;
NodeList *nodeList, *next;
IDnum node2ID;
Node *node2;
for (nodeList = markedNodes; nodeList != NULL; nodeList = next) {
next = nodeList->next;
node2 = nodeList->node;
if (node2 == node) {
setSingleNodeStatus(node2, 1);
continue;
}
node2ID = getNodeID(node2);
localConnect = &localScaffold[node2ID + nodeCount(graph)];
localConnect->distance -= distance_shift;
if (localConnect->distance < min_distance
&& localConnect->backReference == NULL
&& localConnect->frontReference == NULL)
unmarkNode(node2, localConnect);
else if (getNodeStatus(node2) > 0)
setSingleNodeStatus(node2, 1);
else if (getNodeStatus(node2) < 0)
setSingleNodeStatus(node2, -1);
}
}
static void clipTipsVeryHardLocally()
{
NodeList *nodeList, *next;
Node *current, *twin;
boolean modified = true;
//velvetLog("Clipping short tips off graph HARD\n");
while (modified) {
modified = false;
for (nodeList = getMarkedNodeList(); nodeList != NULL;
nodeList = next) {
next = nodeList->next;
current = nodeList->node;
if (current == NULL || getNodeStatus(current) != 1)
continue;
if (getUniqueness(current))
continue;
//velvetLog("Checking node HARD %li %i\n", (long)getNodeID(current), simpleArcCount(current));
twin = getTwinNode(current);
if( isLocalDeadEnd(current) || isLocalTwinDeadEnd(current) ){
//velvetLog("Found tip at node %li\n", (long)getNodeID(current));
handicapNode(current);
modified = true;
}
}
}
}
void renumberLocusNodes(Locus * locus) {
IDnum index;
Node * node;
IDnum counter = 0;
Node ** newArray;
for (index = 0; index < locus->contigCount; index++) {
node = locus->contigs[index];
if (!getNodeStatus(node)) {
locus->contigs[index] = NULL;
counter++;
if (getUniqueness(node))
locus->longContigCount--;
}
}
if (counter == 0)
return;
newArray = callocOrExit(locus->contigCount - counter, Node *);
counter = 0;
for (index = 0; index < locus->contigCount; index++) {
node = locus->contigs[index];
if (node == NULL)
counter++;
else
newArray[index - counter] = node;
}
free(locus->contigs);
locus->contigs = newArray;
locus->contigCount -= counter;
}
void handicapNode(Node * node)
{
if (getNodeStatus(node) > 0)
setSingleNodeStatus(node, 10);
else
setSingleNodeStatus(node, -10);
}
static void extendComponentToNode(Node * node)
{
if (getNodeStatus(node))
return;
setSingleNodeStatus(node, true);
recordNode(node);
}
static boolean isLocalDeadEnd(Node * node)
{
Arc *arc;
for (arc = getArc(node); arc != NULL; arc = getNextArc(arc))
if (getNodeStatus(getDestination(arc)) == 1)
return false;
return true;
}
static void setNodeConnectionStatus(Node * node, boolean status)
{
Connection *connect;
for (connect = getConnection(node); connect;
connect = getNextConnection(connect))
if (getNodeStatus
(getTwinNode(getConnectionDestination(connect))))
setConnectionStatus(connect, status);
}
Connection *getReverseActiveConnection(Node * node)
{
Connection *connect;
for (connect = getConnection(getTwinNode(node)); connect;
connect = getNextConnection(connect))
if (getNodeStatus(getConnectionDestination(connect)))
return connect;
return NULL;
}
static boolean hasNoActiveConnections(Node * node)
{
Connection *connect;
for (connect = getConnection(node); connect;
connect = getNextConnection(connect))
if (getNodeStatus
(getTwinNode(getConnectionDestination(connect))))
return false;
return true;
}
static IDnum getReverseDegree(Node * node)
{
Connection *connect;
IDnum counter = 0;
for (connect = getConnection(node); connect;
connect = getNextConnection(connect))
if (getNodeStatus(getConnectionDestination(connect)))
counter++;
return counter;
}
static void tourBusNode_local(Node * node)
{
Arc *arc;
Node *destination;
Time nodeTime = getNodeTime(node);
//velvetLog("Node %li %f %i %p\n", getNodeID(node),
// times[getNodeID(node) + nodeCount(graph)], simpleArcCount(node),
// node);
for (arc = getArc(node); arc != NULL; arc = getNextArc(arc)) {
destination = getDestination(arc);
// Node doesn't belong to the marked node area
if (getNodeStatus(getDestination(arc)) != 1)
continue;
tourBusArc_local(node, arc, nodeTime);
if (getNodeStatus(node) != 1)
break;
}
}
static inline boolean isNodeMemorized(Node * node, SmallNodeList * nodePile)
{
#ifdef OPENMP
/* SF TODO There must be a faster way to do this: bit mask, hash table, tree, ... ? */
SmallNodeList * list;
for (list = nodePile; list; list = list->next)
if (list->node == node)
return true;
return false;
#else
return getNodeStatus(node);
#endif
}
void redraw(const uavcan::TimerEvent&)
{
std::cout << "\x1b\x5b\x48" << "\x1b\x5b\x32\x4a"
<< " NID | Status | Uptime\n"
<< "-----+---------------+--------\n";
for (unsigned i = 1; i <= uavcan::NodeID::Max; i++)
{
const auto s = getNodeStatus(i);
if (s.known)
{
printStatusLine(i, s);
}
}
std::cout << std::flush;
}
static void propagateComponent(Node * node)
{
Connection *connect;
if (getNodeStatus(node) || !getUniqueness(node))
return;
setNodeStatus(node, true);
for (connect = getConnection(node); connect != NULL;
connect = getNextConnection(connect))
propagateComponent(getConnectionDestination(connect));
for (connect = getConnection(getTwinNode(node)); connect != NULL;
connect = getNextConnection(connect))
propagateComponent(getConnectionDestination(connect));
}
void unmarkNode(Node * node, MiniConnection * localConnect)
{
if (localConnect->frontReference != NULL
|| localConnect->backReference != NULL) {
if (getNodeStatus(node) > 0)
setSingleNodeStatus(node, 10);
else
setSingleNodeStatus(node, -10);
} else {
setSingleNodeStatus(node, false);
destroyNodeList(localConnect->nodeList);
localConnect->frontReference = NULL;
localConnect->backReference = NULL;
localConnect->nodeList = NULL;
}
}
static void fillUpComponent(Node * node)
{
Connection *connect;
if (getNodeStatus(node) || !getUniqueness(node))
return;
setSingleNodeStatus(node, true);
recordNode(node);
for (connect = getConnection(node); connect != NULL;
connect = getNextConnection(connect))
fillUpComponent(getTwinNode
(getConnectionDestination(connect)));
for (connect = getConnection(getTwinNode(node)); connect != NULL;
connect = getNextConnection(connect))
fillUpComponent(getConnectionDestination(connect));
}
static Connection *getSecondReverseActiveConnection(Node * node)
{
Connection *connect;
boolean firstFound = false;
for (connect = getConnection(getTwinNode(node)); connect;
connect = getNextConnection(connect)) {
if (getNodeStatus(getConnectionDestination(connect))) {
if (firstFound)
return connect;
else
firstFound = true;
}
}
return false;
}
static IDnum countConnectedComponents(Graph * graph)
{
IDnum index;
IDnum count = 0;
Node *node;
resetNodeStatus(graph);
for (index = 1; index <= nodeCount(graph); index++) {
node = getNodeInGraph(graph, index);
if (!getNodeStatus(node) && getUniqueness(node)) {
count++;
propagateComponent(node);
}
}
return count;
}
static Locus *extractConnectedComponents(IDnum locusCount)
{
Locus *loci = allocateLocusArray(locusCount);
Locus *locus;
IDnum index;
IDnum locusIndex = 0;
IDnum nodeIndex;
Node *node;
resetNodeStatus(graph);
for (index = 1; index <= nodeCount(graph); index++) {
node = getNodeInGraph(graph, index);
if (!getNodeStatus(node) && getUniqueness(node)) {
locus = getLocus(loci, locusIndex++);
clearLocus(locus);
// Long contigs
fillUpComponent(node);
setLongContigCount(locus, countMarkedNodes());
while (existsMarkedNode())
addContig(locus, popNodeRecord());
// Secondary contigs
extendComponent(locus);
setContigCount(locus, getLongContigCount(locus) + countMarkedNodes());
while (existsMarkedNode())
addContig(locus, popNodeRecord());
// Mark primary nodes so that their twins are not reused
for (nodeIndex = 0;
nodeIndex < getLongContigCount(locus);
nodeIndex++)
setNodeStatus(getContig(locus, nodeIndex), true);
// Unmark secondary nodes so that they are available to other loci
for (nodeIndex = getLongContigCount(locus);
nodeIndex < getContigCount(locus); nodeIndex++)
setNodeStatus(getContig(locus, nodeIndex), false);
}
}
return loci;
}
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;
}
static void ghostThreadSequenceThroughGraph(TightString * tString,
KmerOccurenceTable *
kmerOccurences, Graph * graph,
IDnum seqID, Category category,
boolean readTracking,
boolean double_strand)
{
Kmer word;
Kmer antiWord;
Coordinate readNucleotideIndex;
KmerOccurence *kmerOccurence;
int wordLength = getWordLength(graph);
Nucleotide nucleotide;
Node *node;
Node *previousNode = NULL;
clearKmer(&word);
clearKmer(&antiWord);
// Neglect any read which will not be short paired
if ((!readTracking && category % 2 == 0)
|| category / 2 >= CATEGORIES)
return;
// Neglect any string shorter than WORDLENGTH :
if (getLength(tString) < wordLength)
return;
// Verify that all short reads are reasonnably short
if (getLength(tString) > USHRT_MAX) {
printf("Short read of length %lli, longer than limit %i\n",
(long long) getLength(tString), SHRT_MAX);
puts("You should better declare this sequence as long, because it genuinely is!");
exit(1);
}
// Allocate memory for the read pairs
if (!readStartsAreActivated(graph))
activateReadStarts(graph);
// Fill in the initial word :
for (readNucleotideIndex = 0;
readNucleotideIndex < wordLength - 1; readNucleotideIndex++) {
nucleotide = getNucleotide(readNucleotideIndex, tString);
pushNucleotide(&word, nucleotide);
if (double_strand) {
#ifdef COLOR
reversePushNucleotide(&antiWord, nucleotide);
#else
reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
}
}
// Go through sequence
while (readNucleotideIndex < getLength(tString)) {
// Shift word:
nucleotide = getNucleotide(readNucleotideIndex++, tString);
pushNucleotide(&word, nucleotide);
if (double_strand) {
#ifdef COLOR
reversePushNucleotide(&antiWord, nucleotide);
#else
reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
}
// Search in table
if ((!double_strand || compareKmers(&word, &antiWord) <= 0)
&& (kmerOccurence =
findKmerOccurenceInSortedTable(&word,
kmerOccurences))) {
node =
getNodeInGraph(graph, kmerOccurence->nodeID);
} else if ((double_strand && compareKmers(&word, &antiWord) > 0)
&& (kmerOccurence =
findKmerOccurenceInSortedTable(&antiWord,
kmerOccurences)))
{
node =
getNodeInGraph(graph, -kmerOccurence->nodeID);
} else {
node = NULL;
if (previousNode)
break;
}
previousNode = node;
// Fill in graph
if (node && !getNodeStatus(node)) {
incrementReadStartCount(node, graph);
setSingleNodeStatus(node, true);
memorizeNode(node);
}
}
unlockMemorizedNodes();
}
static void threadSequenceThroughGraph(TightString * tString,
KmerOccurenceTable * kmerOccurences,
Graph * graph,
IDnum seqID, Category category,
boolean readTracking,
boolean double_strand)
{
Kmer word;
Kmer antiWord;
Coordinate readNucleotideIndex;
Coordinate kmerIndex;
KmerOccurence *kmerOccurence;
int wordLength = getWordLength(graph);
PassageMarker *marker = NULL;
PassageMarker *previousMarker = NULL;
Node *node;
Node *previousNode = NULL;
Coordinate coord;
Coordinate previousCoord = 0;
Nucleotide nucleotide;
clearKmer(&word);
clearKmer(&antiWord);
// Neglect any string shorter than WORDLENGTH :
if (getLength(tString) < wordLength)
return;
// Fill in the initial word :
for (readNucleotideIndex = 0;
readNucleotideIndex < wordLength - 1; readNucleotideIndex++) {
nucleotide = getNucleotide(readNucleotideIndex, tString);
pushNucleotide(&word, nucleotide);
if (double_strand) {
#ifdef COLOR
reversePushNucleotide(&antiWord, nucleotide);
#else
reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
}
}
// Go through sequence
while (readNucleotideIndex < getLength(tString)) {
nucleotide = getNucleotide(readNucleotideIndex++, tString);
pushNucleotide(&word, nucleotide);
if (double_strand) {
#ifdef COLOR
reversePushNucleotide(&antiWord, nucleotide);
#else
reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
}
// Search in table
if ((!double_strand || compareKmers(&word, &antiWord) <= 0)
&& (kmerOccurence =
findKmerOccurenceInSortedTable(&word,
kmerOccurences))) {
node =
getNodeInGraph(graph, kmerOccurence->nodeID);
coord = kmerOccurence->position;
} else if ((double_strand && compareKmers(&word, &antiWord) > 0)
&& (kmerOccurence =
findKmerOccurenceInSortedTable(&antiWord,
kmerOccurences)))
{
node =
getNodeInGraph(graph, -kmerOccurence->nodeID);
coord =
getNodeLength(node) - kmerOccurence->position -
1;
} else {
node = NULL;
if (previousNode) {
break;
}
}
// Fill in graph
if (node) {
kmerIndex = readNucleotideIndex - wordLength;
if (previousNode == node
&& previousCoord == coord - 1) {
if (category / 2 >= CATEGORIES) {
setPassageMarkerFinish(marker,
kmerIndex +
1);
setFinishOffset(marker,
getNodeLength(node)
- coord - 1);
} else {
incrementVirtualCoverage(node,
category /
2, 1);
incrementOriginalVirtualCoverage
(node, category / 2, 1);
}
} else {
if (category / 2 >= CATEGORIES) {
marker =
newPassageMarker(seqID,
kmerIndex,
kmerIndex + 1,
coord,
getNodeLength
(node) -
coord - 1);
transposePassageMarker(marker,
node);
connectPassageMarkers
(previousMarker, marker,
graph);
previousMarker = marker;
} else {
if (readTracking) {
if (!getNodeStatus(node)) {
addReadStart(node,
seqID,
coord,
graph,
kmerIndex);
setSingleNodeStatus
(node, true);
memorizeNode(node);
} else {
blurLastShortReadMarker
(node, graph);
}
}
incrementVirtualCoverage(node,
category /
2, 1);
incrementOriginalVirtualCoverage
(node, category / 2, 1);
}
createArc(previousNode, node, graph);
}
previousNode = node;
previousCoord = coord;
}
}
unlockMemorizedNodes();
}
bool ZDvidTarget::readOnly() const
{
return m_readOnly || getNodeStatus() == ZDvid::NODE_LOCKED;
}
static boolean pushNeighbours(Node * node, Node * oppositeNode,
Coordinate distance, boolean force_jumps)
{
Node *candidate;
Coordinate oldLength = getNodeLength(node);
MiniConnection *localConnect;
NodeList *path, *tmp;
if ((path = pathIsClear(node, oppositeNode, distance))) {
while (path) {
candidate = path->node;
tmp = path->next;
deallocateNodeList(path);
path = tmp;
///////////////////////////////////////
// Stepping forward to destination //
///////////////////////////////////////
if (getUniqueness(candidate)) {
concatenateReadStarts(node, candidate,
graph);
concatenateLongReads(node, candidate,
graph);
absorbExtension(node, candidate);
// Scaffold changes
recenterNode(node, oldLength);
recenterLocalScaffold(node, oldLength);
absorbExtensionInScaffold(node, candidate);
// Read coverage
#ifndef SINGLE_COV_CAT
Category cat;
for (cat = 0; cat < CATEGORIES; cat++) {
incrementVirtualCoverage(node, cat,
getVirtualCoverage(candidate, cat));
incrementOriginalVirtualCoverage(node, cat,
getOriginalVirtualCoverage(candidate, cat));
}
#else
incrementVirtualCoverage(node, getVirtualCoverage(candidate));
#endif
if (getNodeStatus(candidate)) {
localConnect =
&localScaffold[getNodeID
(candidate) +
nodeCount
(graph)];
if (localConnect->frontReference) {
destroyConnection
(localConnect->
frontReference,
getNodeID(node));
localConnect->
frontReference = NULL;
}
if (localConnect->backReference) {
destroyConnection
(localConnect->
backReference,
-getNodeID(node));
localConnect->
backReference = NULL;
}
unmarkNode(candidate,
localConnect);
}
if (getNodeStatus(getTwinNode(candidate))) {
localConnect =
&localScaffold[-getNodeID
(candidate) +
nodeCount
(graph)];
if (localConnect->frontReference) {
destroyConnection
(localConnect->
frontReference,
getNodeID(node));
localConnect->
frontReference = NULL;
}
if (localConnect->backReference) {
destroyConnection
(localConnect->
backReference,
-getNodeID(node));
localConnect->
backReference = NULL;
}
unmarkNode(getTwinNode(candidate),
localConnect);
}
destroyNode(candidate, graph);
return true;
} else {
adjustShortReads(node, candidate);
adjustLongReads(node, getNodeLength(candidate));
absorbExtension(node, candidate);
}
}
}
if (force_jumps && oppositeNode
&& abs_ID(getNodeID(oppositeNode)) < abs_ID(getNodeID(node))) {
distance -= getNodeLength(node) / 2;
distance -= getNodeLength(oppositeNode) / 2;
if (distance > 10) {
adjustShortReadsByLength(node, distance);
adjustLongReads(node, distance);
appendGap(node, distance, graph);
} else {
adjustShortReadsByLength(node, 10);
adjustLongReads(node, 10);
appendGap(node, 10, graph);
}
concatenateReadStarts(node, oppositeNode, graph);
concatenateLongReads(node, oppositeNode, graph);
absorbExtension(node, oppositeNode);
// Scaffold changes
recenterNode(node, oldLength);
recenterLocalScaffold(node, oldLength);
absorbExtensionInScaffold(node, oppositeNode);
// Read coverage
#ifndef SINGLE_COV_CAT
Category cat;
for (cat = 0; cat < CATEGORIES; cat++)
incrementVirtualCoverage(node, cat,
getVirtualCoverage(oppositeNode, cat));
#else
incrementVirtualCoverage(node, getVirtualCoverage(oppositeNode));
#endif
if (getNodeStatus(oppositeNode)) {
localConnect =
&localScaffold[getNodeID(oppositeNode) +
nodeCount(graph)];
if (localConnect->frontReference) {
destroyConnection(localConnect->
frontReference,
getNodeID(node));
localConnect->frontReference = NULL;
}
if (localConnect->backReference) {
destroyConnection(localConnect->
backReference,
-getNodeID(node));
localConnect->backReference = NULL;
}
unmarkNode(oppositeNode, localConnect);
}
if (getNodeStatus(getTwinNode(oppositeNode))) {
localConnect =
&localScaffold[-getNodeID(oppositeNode) +
nodeCount(graph)];
if (localConnect->frontReference) {
destroyConnection(localConnect->
frontReference,
getNodeID(node));
localConnect->frontReference = NULL;
}
if (localConnect->backReference) {
destroyConnection(localConnect->
backReference,
-getNodeID(node));
localConnect->backReference = NULL;
}
unmarkNode(getTwinNode(oppositeNode),
localConnect);
}
destroyNode(oppositeNode, graph);
}
return false;
}
static NodeList *pathIsClear(Node * node, Node * oppositeNode,
Coordinate distance)
{
Arc *arc;
Node *candidate, *dest, *current;
Coordinate extension_distance = 0;
boolean maxRepeat = 1;
Node *repeatEntrance = NULL;
IDnum counter = 0;
NodeList *path = NULL;
NodeList *tail = path;
setSingleNodeStatus(node, 2);
current = node;
while (true) {
//////////////////////////////////
// Selecting destination //
//////////////////////////////////
candidate = NULL;
// First round for priority nodes
for (arc = getArc(current); arc != NULL;
arc = getNextArc(arc)) {
dest = getDestination(arc);
if (dest == node || dest == getTwinNode(node))
continue;
if (getNodeStatus(dest) <= 0)
continue;
if (candidate == NULL
|| getNodeStatus(candidate) >
getNodeStatus(dest)
|| (getNodeStatus(candidate) ==
getNodeStatus(dest)
&& extension_distance >
localScaffold[getNodeID(dest) +
nodeCount(graph)].
distance - getNodeLength(dest) / 2)) {
extension_distance =
localScaffold[getNodeID(dest) +
nodeCount(graph)].
distance - getNodeLength(dest) / 2;
candidate = dest;
}
}
// In case of failure
if (candidate == NULL) {
for (arc = getArc(current); arc != NULL;
arc = getNextArc(arc)) {
dest = getDestination(arc);
if (getNodeStatus(dest) == 0)
continue;
if (dest == node
|| dest == getTwinNode(node))
continue;
if (candidate == NULL
|| getNodeStatus(candidate) <
getNodeStatus(dest)
|| (getNodeStatus(candidate) ==
getNodeStatus(dest)
&& extension_distance <
localScaffold[getNodeID(dest) +
nodeCount(graph)].
distance -
getNodeLength(dest) / 2)) {
extension_distance =
localScaffold[getNodeID(dest) +
nodeCount
(graph)].
distance -
getNodeLength(dest) / 2;
candidate = dest;
}
}
}
if (candidate == NULL) {
while (path) {
tail = path->next;
deallocateNodeList(path);
path = tail;
}
return false;
}
// Loop detection
if (candidate == repeatEntrance
&& abs_bool(getNodeStatus(candidate)) ==
maxRepeat + 1) {
while (path) {
tail = path->next;
deallocateNodeList(path);
path = tail;
}
return false;
} else if (abs_bool(getNodeStatus(candidate)) > maxRepeat) {
maxRepeat = abs_bool(getNodeStatus(candidate));
repeatEntrance = candidate;
} else if (abs_bool(getNodeStatus(candidate)) == 1) {
maxRepeat = 1;
repeatEntrance = NULL;
}
if (getNodeStatus(candidate) > 0)
setSingleNodeStatus(candidate,
getNodeStatus(candidate) + 1);
else
setSingleNodeStatus(candidate,
getNodeStatus(candidate) - 1);
if (abs_bool(getNodeStatus(candidate)) > 100
|| counter > nodeCount(graph)) {
while (path) {
tail = path->next;
deallocateNodeList(path);
path = tail;
}
return false;
}
// Missassembly detection
if (getUniqueness(candidate) && oppositeNode
&& candidate != oppositeNode
&& extension_distance > distance) {
while (path) {
tail = path->next;
deallocateNodeList(path);
path = tail;
}
return false;
}
if (path == NULL) {
path = allocateNodeList();
path->next = NULL;
path->node = candidate;
tail = path;
} else {
tail->next = allocateNodeList();
tail = tail->next;
tail->node = candidate;
tail->next = NULL;
}
if (getUniqueness(candidate))
return path;
current = candidate;
}
}
static void integrateDerivativeDistances(Connection * connect,
Coordinate min_distance,
boolean direction)
{
Node *reference = getConnectionDestination(connect);
Node *destination;
IDnum destinationID;
Coordinate distance, baseDistance;
double variance, baseVariance;
Connection *connect2;
MiniConnection *localConnect;
// debug
IDnum counter = 0;
if (!getUniqueness(reference))
return;
//velvetLog("Opposite node %li length %li at %li ± %f\n", getNodeID(reference), getNodeLength(reference), getConnectionDistance(connect), getConnectionVariance(connect));
baseDistance = getConnectionDistance(connect);
baseVariance = getConnectionVariance(connect);
for (connect2 = getConnection(reference);
connect2 != NULL; connect2 = getNextConnection(connect2)) {
// Avoid null derivative
if (connect2 == getTwinConnection(connect))
continue;
destination = getConnectionDestination(connect2);
// Beware of directionality
if (!direction)
destination = getTwinNode(destination);
// Derivate values
destinationID = getNodeID(destination);
// Beware of directionality (bis)
if (direction)
distance = baseDistance - getConnectionDistance(connect2);
else
distance = getConnectionDistance(connect2) - baseDistance;
variance = getConnectionVariance(connect2) + baseVariance;
localConnect =
&localScaffold[destinationID + nodeCount(graph)];
// Avoid over-projection
if (distance < min_distance) {
//velvetLog("Node %li not at distance %li± %f (min %li)\n", destinationID, distance, variance, min_distance);
continue;
}
counter++;
if (getNodeStatus(destination)) {
readjustMiniConnection(destination, localConnect,
distance, min_distance,
variance, NULL, NULL);
} else
resetMiniConnection(destination, localConnect,
distance, variance, NULL, NULL,
true);
//velvetLog("Node %li now at distance %li\n", destinationID, localConnect->distance);
}
//velvetLog("%li secondary distances added\n", counter);
}
static void absorbExtensionInScaffold(Node * node, Node * source)
{
IDnum nodeID = getNodeID(node);
IDnum sourceID = getNodeID(source);
IDnum sourceIndex = sourceID + nodeCount(graph);
Node *twinSource = getTwinNode(source);
IDnum twinSourceIndex = getNodeID(twinSource) + nodeCount(graph);
Connection *connect, *original;
Node *destination;
IDnum destinationID;
Coordinate distance_shift =
(getNodeLength(node) - getNodeLength(source)) / 2;
Coordinate min_distance =
getNodeLength(node) / 2 - BACKTRACK_CUTOFF;
MiniConnection *localConnect;
Coordinate distance;
double variance;
IDnum direct_count;
IDnum paired_count;
while ((connect = getConnection(source))) {
destination = getTwinNode(getConnectionDestination(connect));
if (destination == getTwinNode(node)) {
localConnect = &localScaffold[twinSourceIndex];
localConnect->frontReference = NULL;
unmarkNode(twinSource, localConnect);
destroyConnection(connect, sourceID);
continue;
}
if (destination == node) {
localConnect = &localScaffold[sourceIndex];
localConnect->backReference = NULL;
unmarkNode(source, localConnect);
destroyConnection(connect, sourceID);
continue;
}
destinationID = getNodeID(destination);
localConnect =
&localScaffold[destinationID + nodeCount(graph)];
incrementConnectionDistance(connect, distance_shift);
distance = getConnectionDistance(connect);
variance = getConnectionVariance(connect);
direct_count = getConnectionDirectCount(connect);
paired_count = getConnectionPairedCount(connect);
if (getNodeStatus(destination)) {
readjustMiniConnection(destination, localConnect,
distance, min_distance,
variance, NULL, NULL);
if ((original = localConnect->frontReference))
readjustConnection(original, distance,
variance, direct_count,
paired_count);
else
localConnect->frontReference =
createNewConnection(nodeID,
-destinationID,
direct_count,
paired_count,
distance,
variance);
} else
resetMiniConnection(destination, localConnect,
distance, variance,
createNewConnection(nodeID,
-destinationID,
direct_count,
paired_count,
distance,
variance),
NULL, true);
integrateDerivativeDistances(connect, min_distance, true);
destroyConnection(connect, sourceID);
}
// Loop thru twin's primary scaffold
while ((connect = getConnection(getTwinNode(source)))) {
destination = getConnectionDestination(connect);
if (destination == node) {
localConnect = &localScaffold[sourceIndex];
localConnect->frontReference = NULL;
unmarkNode(source, localConnect);
destroyConnection(connect, -sourceID);
continue;
}
if (destination == getTwinNode(node)) {
localConnect = &localScaffold[twinSourceIndex];
localConnect->backReference = NULL;
unmarkNode(twinSource, localConnect);
destroyConnection(connect, -sourceID);
continue;
}
destinationID = getNodeID(destination);
localConnect =
&localScaffold[destinationID + nodeCount(graph)];
incrementConnectionDistance(connect, -distance_shift);
distance = getConnectionDistance(connect);
variance = getConnectionVariance(connect);
direct_count = getConnectionDirectCount(connect);
paired_count = getConnectionPairedCount(connect);
if (distance > min_distance && getNodeStatus(destination) < 0) {
readjustMiniConnection(destination, localConnect,
-distance, min_distance,
variance, NULL, NULL);
if ((original = localConnect->backReference))
readjustConnection(original, distance,
variance, direct_count,
paired_count);
} else if (getNodeStatus(destination) < 0) {
if ((original = localConnect->backReference)) {
destroyConnection(original, -nodeID);
localConnect->backReference = NULL;
}
unmarkNode(destination, localConnect);
} else if (getNodeStatus(destination) > 0) {
if ((original = localConnect->frontReference)) {
destroyConnection(original, nodeID);
localConnect->frontReference = NULL;
}
unmarkNode(destination, localConnect);
} else if (distance > min_distance) {
resetMiniConnection(destination, localConnect,
-distance, variance, NULL,
createNewConnection(-nodeID,
destinationID,
direct_count,
paired_count,
distance,
variance),
-1);
integrateDerivativeDistances(connect, min_distance, true);
}
destroyConnection(connect, -sourceID);
}
}