static void projectFromNode(IDnum nodeID,
ReadOccurence ** readNodes,
IDnum * readNodeCounts,
IDnum * readPairs, Category * cats,
boolean * dubious, Coordinate * lengths)
{
IDnum index;
ShortReadMarker *nodeArray, *shortMarker;
PassageMarker *marker;
Node *node;
IDnum nodeReadCount;
node = getNodeInGraph(graph, nodeID);
if (node == NULL || !getUniqueness(node))
return;
nodeArray = getNodeReads(node, graph);
nodeReadCount = getNodeReadCount(node, graph);
for (index = 0; index < nodeReadCount; index++) {
shortMarker = getShortReadMarkerAtIndex(nodeArray, index);
if (dubious[getShortReadMarkerID(shortMarker) - 1])
continue;
projectFromShortRead(node, shortMarker, readPairs, cats,
readNodes, readNodeCounts, lengths);
}
for (marker = getMarker(node); marker != NULL;
marker = getNextInNode(marker)) {
if (getPassageMarkerSequenceID(marker) > 0)
projectFromLongRead(node, marker, readPairs, cats,
readNodes, readNodeCounts,
lengths);
}
}
static Connection *createNewConnection(IDnum nodeID, IDnum node2ID,
IDnum direct_count,
IDnum paired_count,
Coordinate distance,
double variance)
{
Node *destination = getNodeInGraph(graph, node2ID);
IDnum nodeIndex = nodeID + nodeCount(graph);
Connection *connect = allocateConnection();
// Fill in
connect->destination = destination;
connect->direct_count = direct_count;
connect->paired_count = paired_count;
connect->distance = (double) distance;
connect->variance = variance;
connect->weight = 0;
connect->status = false;
// Insert in scaffold
connect->previous = NULL;
connect->next = scaffold[nodeIndex];
if (scaffold[nodeIndex] != NULL)
scaffold[nodeIndex]->previous = connect;
scaffold[nodeIndex] = connect;
if (node2ID != nodeID)
createTwinConnection(node2ID, nodeID, connect);
else
connect->twin = NULL;
return connect;
}
static void createTwinConnection(IDnum nodeID, IDnum node2ID,
Connection * connect)
{
Connection *newConnection = allocateConnection();
IDnum nodeIndex = nodeID + nodeCount(graph);
// Fill in
newConnection->distance = connect->distance;
newConnection->variance = connect->variance;
newConnection->direct_count = connect->direct_count;
newConnection->paired_count = connect->paired_count;
newConnection->destination = getNodeInGraph(graph, node2ID);
newConnection->weight = 0;
newConnection->status = false;
// Batch to twin
newConnection->twin = connect;
connect->twin = newConnection;
// Insert in scaffold
newConnection->previous = NULL;
newConnection->next = scaffold[nodeIndex];
if (scaffold[nodeIndex] != NULL)
scaffold[nodeIndex]->previous = newConnection;
scaffold[nodeIndex] = newConnection;
}
static void computePartialReadToNodeMapping(IDnum nodeID,
ReadOccurence ** readNodes,
IDnum * readNodeCounts,
boolean * readMarker,
ReadSet * reads)
{
ShortReadMarker *shortMarker;
IDnum index, readIndex;
ReadOccurence *readArray, *readOccurence;
Node *node = getNodeInGraph(graph, nodeID);
ShortReadMarker *nodeArray = getNodeReads(node, graph);
IDnum nodeReadCount = getNodeReadCount(node, graph);
PassageMarkerI marker;
for (index = 0; index < nodeReadCount; index++) {
shortMarker = getShortReadMarkerAtIndex(nodeArray, index);
readIndex = getShortReadMarkerID(shortMarker);
readArray = readNodes[readIndex];
readOccurence = &readArray[readNodeCounts[readIndex]];
readOccurence->nodeID = nodeID;
readOccurence->position =
getShortReadMarkerPosition(shortMarker);
readOccurence->offset =
getShortReadMarkerOffset(shortMarker);
readNodeCounts[readIndex]++;
}
for (marker = getMarker(node); marker != NULL_IDX;
marker = getNextInNode(marker)) {
readIndex = getPassageMarkerSequenceID(marker);
if (readIndex <= 0 || reads->categories[readIndex - 1] == REFERENCE)
continue;
if (!readMarker[readIndex]) {
readArray = readNodes[readIndex];
readOccurence =
&readArray[readNodeCounts[readIndex]];
readOccurence->nodeID = nodeID;
readOccurence->position = getStartOffset(marker);
readOccurence->offset =
getPassageMarkerStart(marker);
readNodeCounts[readIndex]++;
readMarker[readIndex] = true;
} else {
readArray = readNodes[readIndex];
readOccurence =
&readArray[readNodeCounts[readIndex] - 1];
readOccurence->position = -1;
readOccurence->offset = -1;
}
}
for (marker = getMarker(node); marker != NULL_IDX;
marker = getNextInNode(marker)) {
readIndex = getPassageMarkerSequenceID(marker);
if (readIndex > 0)
readMarker[readIndex] = false;
}
}
static IDnum *computeReadToNodeCounts()
{
IDnum readIndex, nodeIndex;
IDnum maxNodeIndex = 2 * nodeCount(graph) + 1;
IDnum maxReadIndex = sequenceCount(graph) + 1;
IDnum *readNodeCounts = callocOrExit(maxReadIndex, IDnum);
boolean *readMarker = callocOrExit(maxReadIndex, boolean);
ShortReadMarker *nodeArray, *shortMarker;
PassageMarkerI marker;
Node *node;
IDnum nodeReadCount;
//puts("Computing read to node mapping array sizes");
for (nodeIndex = 0; nodeIndex < maxNodeIndex; nodeIndex++) {
node = getNodeInGraph(graph, nodeIndex - nodeCount(graph));
if (node == NULL)
continue;
// Short reads
if (readStartsAreActivated(graph)) {
nodeArray = getNodeReads(node, graph);
nodeReadCount = getNodeReadCount(node, graph);
for (readIndex = 0; readIndex < nodeReadCount; readIndex++) {
shortMarker =
getShortReadMarkerAtIndex(nodeArray,
readIndex);
readNodeCounts[getShortReadMarkerID
(shortMarker)]++;
}
}
// Long reads
for (marker = getMarker(node); marker != NULL_IDX;
marker = getNextInNode(marker)) {
readIndex = getPassageMarkerSequenceID(marker);
if (readIndex < 0)
continue;
if (readMarker[readIndex])
continue;
readNodeCounts[readIndex]++;
readMarker[readIndex] = true;
}
// Clean up marker array
for (marker = getMarker(node); marker != NULL_IDX;
marker = getNextInNode(marker)) {
readIndex = getPassageMarkerSequenceID(marker);
if (readIndex > 0)
readMarker[readIndex] = false;
}
}
free(readMarker);
return readNodeCounts;
}
static void measureCoOccurences(Coordinate ** coOccurences, boolean * interestingReads, ReadOccurence ** readNodes, IDnum * readNodeCounts, IDnum * readPairs, Category * cats) {
IDnum coOccurencesIndex[CATEGORIES + 1];
IDnum observationIndex;
IDnum readIndex, readPairIndex;
IDnum readNodeCount;
IDnum readOccurenceIndex, readPairOccurenceIndex;
ReadOccurence * readOccurence, *readPairOccurence;
Category libID;
for (libID = 0; libID < CATEGORIES + 1; libID++)
coOccurencesIndex[libID] = 0;
for (readIndex = 0; readIndex < sequenceCount(graph); readIndex++) {
// Eliminating dodgy, unpaired, already counted or user-specified reads
if (!interestingReads[readIndex])
continue;
// Find co-occurence
// We know that for each read the read occurences are ordered by increasing node ID
libID = cats[readIndex]/2;
readPairIndex = readPairs[readIndex];
observationIndex = coOccurencesIndex[libID];
readOccurence = readNodes[readIndex + 1];
readOccurenceIndex = 0;
readNodeCount = readNodeCounts[readIndex + 1];
readPairOccurenceIndex = readNodeCounts[readPairIndex + 1] - 1;
readPairOccurence = &(readNodes[readPairIndex + 1][readPairOccurenceIndex]);
while (readOccurenceIndex < readNodeCount && readPairOccurenceIndex >= 0) {
if (readOccurence->nodeID == -readPairOccurence->nodeID) {
if (readOccurence->position > 0 && readPairOccurence->position > 0) {
coOccurences[libID][observationIndex] =
getNodeLength(getNodeInGraph(graph, readOccurence->nodeID))
+ getWordLength(graph) - 1
- (readOccurence->position - readOccurence->offset)
- (readPairOccurence->position - readPairOccurence->offset);
coOccurencesIndex[libID]++;
break;
} else {
readOccurence++;
readOccurenceIndex++;
readPairOccurence--;
readPairOccurenceIndex--;
}
} else if (readOccurence->nodeID < -readPairOccurence->nodeID) {
readOccurence++;
readOccurenceIndex++;
} else {
readPairOccurence--;
readPairOccurenceIndex--;
}
}
}
}
void readCoherentGraph(Graph * inGraph, boolean(*isUnique) (Node * node),
double coverage, ReadSet * reads)
{
IDnum nodeIndex;
Node *node;
IDnum previousNodeCount = 0;
graph = inGraph;
listMemory = newRecycleBin(sizeof(PassageMarkerList), 100000);
expected_coverage = coverage;
sequences = reads->tSequences;
velvetLog("Read coherency...\n");
resetNodeStatus(graph);
identifyUniqueNodes(isUnique);
trimLongReadTips();
previousNodeCount = 0;
while (previousNodeCount != nodeCount(graph)) {
previousNodeCount = nodeCount(graph);
for (nodeIndex = 1; nodeIndex <= nodeCount(graph);
nodeIndex++) {
node = getNodeInGraph(graph, nodeIndex);
if (node == NULL || !getUniqueness(node))
continue;
while (uniqueNodesConnect(node))
node = bypass();
node = getTwinNode(node);
while (uniqueNodesConnect(node))
node = bypass();
}
renumberNodes(graph);
}
destroyRecycleBin(listMemory);
destroyRecycleBin(nodeListMemory);
velvetLog("Confronted to %li multiple hits and %li null over %li\n",
(long) multCounter, (long) nullCounter, (long) dbgCounter);
velvetLog("Read coherency over!\n");
}
static IDnum expectedNumberOfConnections(IDnum IDA, Connection * connect,
IDnum ** counts, Category cat)
{
Node *A = getNodeInGraph(graph, IDA);
Node *B = connect->destination;
IDnum IDB = getNodeID(B);
double left, middle, right;
Coordinate longLength, shortLength, D;
double M, N, O, P;
Coordinate mu = getInsertLength(graph, cat);
double sigma = sqrt(getInsertLength_var(graph, cat));
double result;
double densityA, densityB, minDensity;
if (mu <= 0)
return 0;
if (getNodeLength(A) == 0 || getNodeLength(B) == 0)
return 0;
if (getNodeLength(A) < getNodeLength(B)) {
longLength = getNodeLength(B);
shortLength = getNodeLength(A);
} else {
longLength = getNodeLength(A);
shortLength = getNodeLength(B);
}
densityA = counts[cat][IDA + nodeCount(graph)] / (double) getNodeLength(A);
densityB = counts[cat][IDB + nodeCount(graph)] / (double) getNodeLength(B);
minDensity = densityA > densityB ? densityB : densityA;
D = getConnectionDistance(connect) - (longLength +
shortLength) / 2;
M = (D - mu) / sigma;
N = (D + shortLength - mu) / sigma;
O = (D + longLength - mu) / sigma;
P = (D + shortLength + longLength - mu) / sigma;
left = ((norm(M) - norm(N)) - M * normInt(M, N)) * sigma;
middle = shortLength * normInt(N, O);
right = ((norm(O) - norm(P)) - P * normInt(O, P)) * (-sigma);
result = (minDensity * (left + middle + right));
if (result > 0)
return (IDnum) result;
else
return 0;
}
static void projectFromSingleRead(Node * node,
ReadOccurence * readOccurence,
Coordinate position,
Coordinate offset, Coordinate length)
{
Coordinate distance = 0;
Node *target = getNodeInGraph(graph, -readOccurence->nodeID);
double variance = 1;
if (target == getTwinNode(node) || target == node)
return;
if (position < 0) {
variance += getNodeLength(node) * getNodeLength(node) / 16;
// distance += 0;
} else {
// variance += 0;
distance += position - offset - getNodeLength(node) / 2;
}
if (readOccurence->position < 0) {
variance +=
getNodeLength(target) * getNodeLength(target) / 16;
//distance += 0;
} else {
// variance += 0;
distance +=
-readOccurence->position + readOccurence->offset +
getNodeLength(target) / 2;
}
if (position < 0 || readOccurence->position < 0) {
if (offset < readOccurence->offset && distance - getNodeLength(node)/2 - getNodeLength(target)/2 < -10)
return;
if (offset > readOccurence->offset && distance - getNodeLength(node)/2 - getNodeLength(target)/2 > 10)
return;
variance += length * length / 16;
createConnection(getNodeID(node), getNodeID(target), 1, 0,
distance, variance);
createConnection(-getNodeID(node), -getNodeID(target), 1,
0, -distance, variance);
} else if (distance > 0) {
createConnection(getNodeID(node), getNodeID(target), 1, 0,
distance, variance);
} else {
createConnection(-getNodeID(node), -getNodeID(target), 1,
0, -distance, variance);
}
}
static Connection *findConnection(IDnum nodeID, IDnum node2ID)
{
Node *node2 = getNodeInGraph(graph, node2ID);
Connection *connect;
if (node2 == NULL)
return NULL;
for (connect = scaffold[nodeID + nodeCount(graph)];
connect != NULL; connect = connect->next)
if (connect->destination == node2)
break;
return connect;
}
static void computeLocalNodeToNodeMappings()
{
IDnum index;
Node *node;
puts("Computing local connections");
activateArcLookupTable(graph);
for (index = -nodeCount(graph); index <= nodeCount(graph); index++) {
node = getNodeInGraph(graph, index);
if (node && getUniqueness(node))
computeLocalNodeToNodeMappingsFromNode(node);
}
deactivateArcLookupTable(graph);
}
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 IDnum expectedNumberOfConnections(IDnum IDA, Connection * connect,
IDnum ** counts, Category cat)
{
Node *A = getNodeInGraph(graph, IDA);
Node *B = connect->destination;
double left, middle, right;
Coordinate longLength, shortLength, D;
IDnum longCount;
double M, N, O, P;
Coordinate mu = getInsertLength(graph, cat);
double sigma = sqrt(getInsertLength_var(graph, cat));
double result;
if (mu <= 0)
return 0;
if (getNodeLength(A) < getNodeLength(B)) {
longLength = getNodeLength(B);
shortLength = getNodeLength(A);
longCount = counts[cat][getNodeID(B) + nodeCount(graph)];
} else {
longLength = getNodeLength(A);
shortLength = getNodeLength(B);
longCount = counts[cat][IDA + nodeCount(graph)];
}
D = connect->distance - (longLength + shortLength) / 2;
M = (D - mu) / sigma;
N = (D + shortLength - mu) / sigma;
O = (D + longLength - mu) / sigma;
P = (D + shortLength + longLength - mu) / sigma;
left = ((norm(M) - norm(N)) - M * normInt(M, N)) * sigma;
middle = shortLength * normInt(N, O);
right = ((norm(O) - norm(P)) - P * normInt(O, P)) * (-sigma);
result = (longCount * (left + middle + right)) / longLength;
if (result > 0)
return (IDnum) result;
else
return 0;
}
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;
}
// Detects sequences that could be simplified through concatentation
// Iterates till graph cannot be more simplified
// Useless nodes are freed from memory and remaining ones are renumbered
void concatenateGraph(Graph * graph)
{
IDnum nodeIndex;
Node *node, *twin;
velvetLog("Concatenation...\n");
for (nodeIndex = 1; nodeIndex < nodeCount(graph); nodeIndex++) {
node = getNodeInGraph(graph, nodeIndex);
if (node == NULL)
continue;
twin = getTwinNode(node);
while (simpleArcCount(node) == 1
&&
simpleArcCount(getTwinNode
(getDestination(getArc(node)))) ==
1) {
if (getDestination(getArc(node)) == twin
|| getDestination(getArc(node)) == node)
break;
concatenateStringOfNodes(node,
graph);
}
while (simpleArcCount(twin) == 1
&&
simpleArcCount(getTwinNode
(getDestination(getArc(twin)))) ==
1) {
if (getDestination(getArc(twin)) == node
|| getDestination(getArc(twin)) == twin)
break;
concatenateStringOfNodes(twin,
graph);
}
}
renumberNodes(graph);
sortGapMarkers(graph);
velvetLog("Concatenation over!\n");
}
static void projectFromReadPair(Node * node, ReadOccurence * readOccurence,
Coordinate position, Coordinate offset,
Coordinate insertLength,
double insertVariance)
{
Coordinate distance = insertLength;
Coordinate variance = insertVariance;
Node *target = getNodeInGraph(graph, readOccurence->nodeID);
if (target == getTwinNode(node) || target == node)
return;
if (getUniqueness(target) && getNodeID(target) < getNodeID(node))
return;
if (position < 0) {
variance += getNodeLength(node) * getNodeLength(node) / 16;
// distance += 0;
} else {
// variance += 0;
distance += position - offset - getNodeLength(node) / 2;
}
if (readOccurence->position < 0) {
variance +=
getNodeLength(target) * getNodeLength(target) / 16;
//distance += 0;
} else {
// variance += 0;
distance +=
readOccurence->position - readOccurence->offset -
getNodeLength(target) / 2;
}
if (distance - getNodeLength(node)/2 - getNodeLength(target)/2 < -6 * sqrt(insertVariance))
return;
else if (distance < getNodeLength(node)/2 + getNodeLength(target)/2)
distance = getNodeLength(node)/2 + getNodeLength(target)/2;
createConnection(getNodeID(node), getNodeID(target), 0, 1,
distance, variance);
}
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 expandLongNodes(boolean force_jumps)
{
IDnum nodeID;
Node *node;
boolean modified = false;
for (nodeID = 1; nodeID <= nodeCount(graph); nodeID++) {
node = getNodeInGraph(graph, nodeID);
if (node != NULL && getUniqueness(node)) {
modified = expandLongNode(node, force_jumps)
|| modified;
modified =
expandLongNode(getTwinNode(node), force_jumps)
|| modified;
}
}
return modified;
}
static void identifyUniqueNodes(boolean(*isUniqueFunction) (Node *))
{
IDnum index;
Node *node;
IDnum counter = 0;
velvetLog("Identifying unique nodes\n");
for (index = 1; index <= nodeCount(graph); index++) {
node = getNodeInGraph(graph, index);
if (node == NULL)
continue;
setUniqueness(node, isUniqueFunction(node));
if (getUniqueness(node))
counter++;
}
velvetLog("Done, %li unique nodes counted\n", (long) counter);
}
static KmerOccurenceTable *referenceGraphKmers(char *preGraphFilename,
short int accelerationBits, Graph * graph, boolean double_strand)
{
FILE *file = fopen(preGraphFilename, "r");
const int maxline = MAXLINE;
char line[MAXLINE];
char c;
int wordLength;
Coordinate lineLength, kmerCount;
Kmer word;
Kmer antiWord;
KmerOccurenceTable *kmerTable = NULL;
KmerOccurence *kmerOccurences, *kmerOccurencePtr;
Coordinate kmerOccurenceIndex;
IDnum index;
IDnum nodeID = 0;
IDnum *accelPtr = NULL;
KmerKey lastHeader = 0;
KmerKey header;
Nucleotide nucleotide;
if (file == NULL)
exitErrorf(EXIT_FAILURE, true, "Could not open %s", preGraphFilename);
// Count kmers
printf("Scanning pre-graph file %s for k-mers\n",
preGraphFilename);
// First line
if (!fgets(line, maxline, file))
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
sscanf(line, "%*i\t%*i\t%i\n", &wordLength);
// Initialize kmer occurence table:
kmerTable = mallocOrExit(1, KmerOccurenceTable);
if (accelerationBits > 2 * wordLength)
accelerationBits = 2 * wordLength;
if (accelerationBits > 32)
accelerationBits = 32;
if (accelerationBits > 0) {
kmerTable->accelerationBits = accelerationBits;
kmerTable->accelerationTable =
callocOrExit((((size_t) 1) << accelerationBits) + 1,
IDnum);
accelPtr = kmerTable->accelerationTable;
kmerTable->accelerationShift =
(short int) 2 *wordLength - accelerationBits;
} else {
kmerTable->accelerationBits = 0;
kmerTable->accelerationTable = NULL;
kmerTable->accelerationShift = 0;
}
// Read nodes
if (!fgets(line, maxline, file))
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
kmerCount = 0;
while (line[0] == 'N') {
lineLength = 0;
while ((c = getc(file)) != EOF && c != '\n')
lineLength++;
kmerCount += lineLength - wordLength + 1;
if (fgets(line, maxline, file) == NULL)
break;
}
fclose(file);
// Create table
printf("%li kmers found\n", (long) kmerCount);
kmerOccurences = callocOrExit(kmerCount, KmerOccurence);
kmerOccurencePtr = kmerOccurences;
kmerOccurenceIndex = 0;
kmerTable->kmerTable = kmerOccurences;
kmerTable->kmerTableSize = kmerCount;
// Fill table
file = fopen(preGraphFilename, "r");
if (file == NULL)
exitErrorf(EXIT_FAILURE, true, "Could not open %s", preGraphFilename);
if (!fgets(line, maxline, file))
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
// Read nodes
if (!fgets(line, maxline, file))
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
while (line[0] == 'N') {
nodeID++;
// Fill in the initial word :
clearKmer(&word);
clearKmer(&antiWord);
for (index = 0; index < wordLength - 1; index++) {
c = getc(file);
if (c == 'A')
nucleotide = ADENINE;
else if (c == 'C')
nucleotide = CYTOSINE;
else if (c == 'G')
nucleotide = GUANINE;
else if (c == 'T')
nucleotide = THYMINE;
else if (c == '\n')
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
else
nucleotide = ADENINE;
pushNucleotide(&word, nucleotide);
if (double_strand) {
#ifdef COLOR
reversePushNucleotide(&antiWord, nucleotide);
#else
reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
}
}
// Scan through node
index = 0;
while((c = getc(file)) != '\n' && c != EOF) {
if (c == 'A')
nucleotide = ADENINE;
else if (c == 'C')
nucleotide = CYTOSINE;
else if (c == 'G')
nucleotide = GUANINE;
else if (c == 'T')
nucleotide = THYMINE;
else
nucleotide = ADENINE;
pushNucleotide(&word, nucleotide);
if (double_strand) {
#ifdef COLOR
reversePushNucleotide(&antiWord, nucleotide);
#else
reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
}
if (!double_strand || compareKmers(&word, &antiWord) <= 0) {
copyKmers(&kmerOccurencePtr->kmer, &word);
kmerOccurencePtr->nodeID = nodeID;
kmerOccurencePtr->position =
index;
} else {
copyKmers(&kmerOccurencePtr->kmer, &antiWord);
kmerOccurencePtr->nodeID = -nodeID;
kmerOccurencePtr->position =
getNodeLength(getNodeInGraph(graph, nodeID)) - 1 - index;
}
kmerOccurencePtr++;
kmerOccurenceIndex++;
index++;
}
if (fgets(line, maxline, file) == NULL)
break;
}
fclose(file);
// Sort table
qsort(kmerOccurences, kmerCount, sizeof(KmerOccurence),
compareKmerOccurences);
// Fill up acceleration table
if (kmerTable->accelerationTable != NULL) {
*accelPtr = (IDnum) 0;
for (kmerOccurenceIndex = 0;
kmerOccurenceIndex < kmerCount;
kmerOccurenceIndex++) {
header =
keyInAccelerationTable(&kmerOccurences
[kmerOccurenceIndex].
kmer, kmerTable);
while (lastHeader < header) {
lastHeader++;
accelPtr++;
*accelPtr = kmerOccurenceIndex;
}
}
while (lastHeader < (KmerKey) 1 << accelerationBits) {
lastHeader++;
accelPtr++;
*accelPtr = kmerCount;
}
}
return kmerTable;
}
static void projectFromReadPair(Node * node, ReadOccurence * readOccurence,
Coordinate position, Coordinate offset,
Coordinate insertLength,
double insertVariance, boolean weight)
{
Coordinate distance = insertLength;
Coordinate variance = insertVariance;
Node *target = getNodeInGraph(graph, readOccurence->nodeID);
Connection *connect;
double score;
// Filter for useless reads:
if (readOccurence->position == -1 && readOccurence->offset == -1)
return;
if (target == getTwinNode(node) || target == node)
return;
if (getUniqueness(target) && getNodeID(target) < getNodeID(node))
return;
if (weight) {
if (position > 0 && readOccurence->position > 0
&& (connect =
getConnectionBetweenNodes(node, target))) {
distance = getConnectionDistance(connect);
distance -=
position - offset - getNodeLength(node) / 2;
distance -=
readOccurence->position -
readOccurence->offset -
getNodeLength(target) / 2;
score =
K *
exp((insertLength - distance) * (distance -
insertLength)
/ (2 * insertVariance));
incrementConnectionWeight(connect, score);
}
return;
}
if (position < 0) {
variance += getNodeLength(node) * getNodeLength(node) / 16;
// distance += 0;
} else {
// variance += 0;
distance += position - offset - getNodeLength(node) / 2;
}
if (readOccurence->position < 0) {
variance +=
getNodeLength(target) * getNodeLength(target) / 16;
//distance += 0;
} else {
// variance += 0;
distance +=
readOccurence->position - readOccurence->offset -
getNodeLength(target) / 2;
}
if (distance - getNodeLength(node) / 2 -
getNodeLength(target) / 2 < -6 * sqrt(insertVariance))
return;
createConnection(getNodeID(node), getNodeID(target), 0, 1,
distance, variance);
}
static void projectFromSingleRead(Node * node,
ReadOccurence * readOccurence,
Coordinate position,
Coordinate offset, Coordinate length,
boolean weight)
{
Coordinate distance = 0;
Connection *connect;
Node *target = getNodeInGraph(graph, -readOccurence->nodeID);
double variance = 1;
// Filter out troublemakers
if (readOccurence->position == -1 && readOccurence->offset == -1)
return;
if (offset < 0 || readOccurence->offset < 0)
return;
if (target == getTwinNode(node) || target == node)
return;
if (weight) {
if ((connect = getConnectionBetweenNodes(node, target))) {
incrementConnectionWeight(connect, 1);
} else if ((connect = getConnectionBetweenNodes(getTwinNode(node), getTwinNode(target)))) {
incrementConnectionWeight(connect, 1);
}
return;
}
if (position < 0) {
variance += getNodeLength(node) * getNodeLength(node) / 16;
distance += getNodeLength(node) / 2;
} else {
// variance += 0;
distance += position - offset - getNodeLength(node) / 2;
}
if (readOccurence->position < 0) {
variance +=
getNodeLength(target) * getNodeLength(target) / 16;
distance += getNodeLength(target) / 2;
} else {
// variance += 0;
distance +=
-readOccurence->position + readOccurence->offset +
getNodeLength(target) / 2;
}
if (offset < readOccurence->offset) {
if (getNodeLength(node) % 2)
distance--;
createConnection(getNodeID(node), getNodeID(target), 1, 0,
distance, variance);
} else {
if (getNodeLength(target) % 2)
distance++;
createConnection(-getNodeID(node), -getNodeID(target), 1,
0, -distance, variance);
}
}
static void projectFromSingleRead(Node * node,
ReadOccurence * readOccurence,
Coordinate position,
Coordinate offset, Coordinate length)
{
Coordinate distance = 0;
Node *target = getNodeInGraph(graph, -readOccurence->nodeID);
double variance = 1;
if (target == getTwinNode(node) || target == node)
return;
if (getUniqueness(target) && getNodeID(target) < getNodeID(node))
return;
if (position < 0) {
variance += getNodeLength(node) * getNodeLength(node) / 16;
// distance += 0;
} else {
// variance += 0;
distance += position - getNodeLength(node) / 2;
}
if (readOccurence->position < 0) {
variance +=
getNodeLength(target) * getNodeLength(target) / 16;
//distance += 0;
} else {
// variance += 0;
distance +=
-readOccurence->position + getNodeLength(target) / 2;
}
if (readOccurence->offset < 0 || offset < 0) {
variance += length * length / 16;
//distance += 0;
} else {
// variance += 0;
distance += readOccurence->offset - offset;
}
// Relative ordering
if (offset > 0 && readOccurence->offset > 0) {
if (offset < readOccurence->offset) {
if (distance - getNodeLength(node)/2 - getNodeLength(target)/2 < -10)
;
else if (distance < getNodeLength(node)/2 + getNodeLength(target)/2)
createConnection(getNodeID(node), getNodeID(target), 1, 0,
getNodeLength(node)/2 + getNodeLength(target)/2, variance);
else
createConnection(getNodeID(node), getNodeID(target), 1, 0,
distance, variance);
} else if (offset > readOccurence->offset) {
if (-distance - getNodeLength(node)/2 - getNodeLength(target)/2 < -10)
;
else if (-distance < getNodeLength(node)/2 + getNodeLength(target)/2)
createConnection(-getNodeID(node), -getNodeID(target), 1,
0, getNodeLength(node)/2 + getNodeLength(target)/2 , variance);
else
createConnection(-getNodeID(node), -getNodeID(target), 1,
0, -distance, variance);
}
} else if (offset > 0 && position > 0) {
if (distance - offset > -getNodeLength(node)/2 && distance - offset + length > getNodeLength(node)/2)
createConnection(getNodeID(node), getNodeID(target), 1, 0,
getNodeLength(node)/2 + getNodeLength(target)/2, variance);
else if (distance - offset < -getNodeLength(node)/2 && distance - offset + length < getNodeLength(node)/2)
createConnection(-getNodeID(node), -getNodeID(target), 1, 0,
getNodeLength(node)/2 + getNodeLength(target)/2, variance);
else {
createConnection(getNodeID(node), getNodeID(target), 1, 0,
getNodeLength(node)/2 + getNodeLength(target)/2, variance);
createConnection(-getNodeID(node), -getNodeID(target), 1, 0,
getNodeLength(node)/2 + getNodeLength(target)/2, variance);
}
} else if (readOccurence->offset > 0 && readOccurence->position > 0) {
if (-distance - readOccurence->offset > -getNodeLength(target)/2 && -distance - readOccurence->offset + length > getNodeLength(target)/2)
createConnection(-getNodeID(node), -getNodeID(target), 1, 0,
getNodeLength(node)/2 + getNodeLength(target)/2, variance);
if (-distance - readOccurence->offset < -getNodeLength(target)/2 && -distance - readOccurence->offset + length < getNodeLength(target)/2)
createConnection(getNodeID(node), getNodeID(target), 1, 0,
getNodeLength(node)/2 + getNodeLength(target)/2, variance);
else {
createConnection(getNodeID(node), getNodeID(target), 1, 0,
getNodeLength(node)/2 + getNodeLength(target)/2, variance);
createConnection(-getNodeID(node), -getNodeID(target), 1, 0,
getNodeLength(node)/2 + getNodeLength(target)/2, variance);
}
} else {
createConnection(getNodeID(node), getNodeID(target), 1, 0,
getNodeLength(node)/2 + getNodeLength(target)/2, variance);
createConnection(-getNodeID(node), -getNodeID(target), 1, 0,
getNodeLength(node)/2 + getNodeLength(target)/2, variance);
}
}
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();
}
static void threadSequenceThroughGraph(TightString * tString,
KmerOccurenceTable * kmerTable,
Graph * graph,
IDnum seqID, Category category,
boolean readTracking,
boolean double_strand,
ReferenceMapping * referenceMappings,
Coordinate referenceMappingCount,
IDnum refCount,
Annotation * annotations,
IDnum annotationCount,
boolean second_in_pair)
{
Kmer word;
Kmer antiWord;
Coordinate readNucleotideIndex;
Coordinate kmerIndex;
KmerOccurence *kmerOccurence;
int wordLength = getWordLength(graph);
PassageMarkerI marker = NULL_IDX;
PassageMarkerI previousMarker = NULL_IDX;
Node *node = NULL;
Node *previousNode = NULL;
Coordinate coord = 0;
Coordinate previousCoord = 0;
Nucleotide nucleotide;
boolean reversed;
IDnum refID;
Coordinate refCoord = 0;
ReferenceMapping * refMap;
Annotation * annotation = annotations;
Coordinate index = 0;
Coordinate uniqueIndex = 0;
Coordinate annotIndex = 0;
IDnum annotCount = 0;
SmallNodeList * nodePile = NULL;
// Neglect any string shorter than WORDLENGTH :
if (getLength(tString) < wordLength)
return;
clearKmer(&word);
clearKmer(&antiWord);
// Fill in the initial word :
for (readNucleotideIndex = 0;
readNucleotideIndex < wordLength - 1; readNucleotideIndex++) {
nucleotide = getNucleotide(readNucleotideIndex, tString);
pushNucleotide(&word, nucleotide);
if (double_strand || second_in_pair) {
#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 || second_in_pair) {
#ifdef COLOR
reversePushNucleotide(&antiWord, nucleotide);
#else
reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
}
// Update annotation if necessary
if (annotCount < annotationCount && annotIndex == getAnnotationLength(annotation)) {
annotation = getNextAnnotation(annotation);
annotCount++;
annotIndex = 0;
}
// Search for reference mapping
if (category == REFERENCE) {
if (referenceMappings)
refMap = findReferenceMapping(seqID, index, referenceMappings, referenceMappingCount);
else
refMap = NULL;
if (refMap) {
node = getNodeInGraph(graph, refMap->nodeID);
if (refMap->nodeID > 0) {
coord = refMap->nodeStart + (index - refMap->referenceStart);
} else {
coord = getNodeLength(node) - refMap->nodeStart - refMap->length + (index - refMap->referenceStart);
}
} else {
node = NULL;
if (previousNode)
break;
}
}
// Search for reference-based mapping
else if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation) && getAnnotSequenceID(annotation) <= refCount && getAnnotSequenceID(annotation) >= -refCount) {
refID = getAnnotSequenceID(annotation);
if (refID > 0)
refCoord = getStart(annotation) + annotIndex;
else
refCoord = getStart(annotation) - annotIndex;
refMap = findReferenceMapping(refID, refCoord, referenceMappings, referenceMappingCount);
// If success
if (refMap) {
if (refID > 0) {
node = getNodeInGraph(graph, refMap->nodeID);
if (refMap->nodeID > 0) {
coord = refMap->nodeStart + (refCoord - refMap->referenceStart);
} else {
coord = getNodeLength(node) - refMap->nodeStart - refMap->length + (refCoord - refMap->referenceStart);
}
} else {
node = getNodeInGraph(graph, -refMap->nodeID);
if (refMap->nodeID > 0) {
coord = getNodeLength(node) - refMap->nodeStart - (refCoord - refMap->referenceStart) - 1;
} else {
coord = refMap->nodeStart + refMap->length - (refCoord - refMap->referenceStart) - 1;
}
}
} else {
node = NULL;
if (previousNode)
break;
}
}
// Search in table
else {
reversed = false;
if (double_strand) {
if (compareKmers(&word, &antiWord) <= 0) {
kmerOccurence =
findKmerInKmerOccurenceTable(&word,
kmerTable);
} else {
kmerOccurence =
findKmerInKmerOccurenceTable(&antiWord,
kmerTable);
reversed = true;
}
} else {
if (!second_in_pair) {
kmerOccurence =
findKmerInKmerOccurenceTable(&word,
kmerTable);
} else {
kmerOccurence =
findKmerInKmerOccurenceTable(&antiWord,
kmerTable);
reversed = true;
}
}
if (kmerOccurence) {
if (!reversed) {
node = getNodeInGraph(graph, getKmerOccurenceNodeID(kmerOccurence));
coord = getKmerOccurencePosition(kmerOccurence);
} else {
node = getNodeInGraph(graph, -getKmerOccurenceNodeID(kmerOccurence));
coord = getNodeLength(node) - getKmerOccurencePosition(kmerOccurence) - 1;
}
} else {
node = NULL;
if (previousNode)
break;
}
}
// Increment positions
if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation))
annotIndex++;
else
uniqueIndex++;
// Fill in graph
if (node)
{
#ifdef OPENMP
lockNode(node);
#endif
kmerIndex = readNucleotideIndex - wordLength;
if (previousNode == node
&& previousCoord == coord - 1) {
if (category / 2 >= CATEGORIES) {
setPassageMarkerFinish(marker,
kmerIndex +
1);
setFinishOffset(marker,
getNodeLength(node)
- coord - 1);
} else {
#ifndef SINGLE_COV_CAT
incrementVirtualCoverage(node, category / 2, 1);
incrementOriginalVirtualCoverage(node, category / 2, 1);
#else
incrementVirtualCoverage(node, 1);
#endif
}
#ifdef OPENMP
unLockNode(node);
#endif
} 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 (!isNodeMemorized(node, nodePile)) {
addReadStart(node,
seqID,
coord,
graph,
kmerIndex);
memorizeNode(node, &nodePile);
} else {
blurLastShortReadMarker
(node, graph);
}
}
#ifndef SINGLE_COV_CAT
incrementVirtualCoverage(node, category / 2, 1);
incrementOriginalVirtualCoverage(node, category / 2, 1);
#else
incrementVirtualCoverage(node, 1);
#endif
}
#ifdef OPENMP
lockTwoNodes(node, previousNode);
#endif
createArc(previousNode, node, graph);
#ifdef OPENMP
unLockTwoNodes(node, previousNode);
#endif
}
previousNode = node;
previousCoord = coord;
}
index++;
}
if (readTracking && category / 2 < CATEGORIES)
unMemorizeNodes(&nodePile);
}
static void ghostThreadSequenceThroughGraph(TightString * tString,
KmerOccurenceTable *
kmerTable, Graph * graph,
IDnum seqID, Category category,
boolean readTracking,
boolean double_strand,
ReferenceMapping * referenceMappings,
Coordinate referenceMappingCount,
IDnum refCount,
Annotation * annotations,
IDnum annotationCount,
boolean second_in_pair)
{
Kmer word;
Kmer antiWord;
Coordinate readNucleotideIndex;
KmerOccurence *kmerOccurence;
int wordLength = getWordLength(graph);
Nucleotide nucleotide;
IDnum refID;
Coordinate refCoord;
ReferenceMapping * refMap = NULL;
Coordinate uniqueIndex = 0;
Coordinate annotIndex = 0;
IDnum annotCount = 0;
boolean reversed;
SmallNodeList * nodePile = NULL;
Annotation * annotation = annotations;
Node *node;
Node *previousNode = NULL;
// 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) {
velvetLog("Short read of length %lli, longer than limit %i\n",
(long long) getLength(tString), SHRT_MAX);
velvetLog("You should better declare this sequence as long, because it genuinely is!\n");
exit(1);
}
clearKmer(&word);
clearKmer(&antiWord);
// Fill in the initial word :
for (readNucleotideIndex = 0;
readNucleotideIndex < wordLength - 1; readNucleotideIndex++) {
nucleotide = getNucleotide(readNucleotideIndex, tString);
pushNucleotide(&word, nucleotide);
if (double_strand || second_in_pair) {
#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 || second_in_pair) {
#ifdef COLOR
reversePushNucleotide(&antiWord, nucleotide);
#else
reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
}
// Update annotation if necessary
if (annotCount < annotationCount && annotIndex == getAnnotationLength(annotation)) {
annotation = getNextAnnotation(annotation);
annotCount++;
annotIndex = 0;
}
// Search for reference mapping
if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation) && getAnnotSequenceID(annotation) <= refCount && getAnnotSequenceID(annotation) >= -refCount) {
refID = getAnnotSequenceID(annotation);
if (refID > 0)
refCoord = getStart(annotation) + annotIndex;
else
refCoord = getStart(annotation) - annotIndex;
refMap = findReferenceMapping(refID, refCoord, referenceMappings, referenceMappingCount);
// If success
if (refMap) {
if (refID > 0)
node = getNodeInGraph(graph, refMap->nodeID);
else
node = getNodeInGraph(graph, -refMap->nodeID);
} else {
node = NULL;
if (previousNode)
break;
}
}
// if not.. look in table
else {
reversed = false;
if (double_strand) {
if (compareKmers(&word, &antiWord) <= 0) {
kmerOccurence =
findKmerInKmerOccurenceTable(&word,
kmerTable);
} else {
kmerOccurence =
findKmerInKmerOccurenceTable(&antiWord,
kmerTable);
reversed = true;
}
} else {
if (!second_in_pair) {
kmerOccurence =
findKmerInKmerOccurenceTable(&word,
kmerTable);
} else {
kmerOccurence =
findKmerInKmerOccurenceTable(&antiWord,
kmerTable);
reversed = true;
}
}
if (kmerOccurence) {
if (!reversed)
node = getNodeInGraph(graph, getKmerOccurenceNodeID(kmerOccurence));
else
node = getNodeInGraph(graph, -getKmerOccurenceNodeID(kmerOccurence));
} else {
node = NULL;
if (previousNode)
break;
}
}
if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation))
annotIndex++;
else
uniqueIndex++;
previousNode = node;
// Fill in graph
if (node && !isNodeMemorized(node, nodePile))
{
#ifdef OPENMP
lockNode(node);
#endif
incrementReadStartCount(node, graph);
#ifdef OPENMP
unLockNode(node);
#endif
memorizeNode(node, &nodePile);
}
}
unMemorizeNodes(&nodePile);
}
static KmerOccurenceTable *referenceGraphKmers(char *preGraphFilename,
short int accelerationBits, Graph * graph, boolean double_strand, NodeMask * nodeMasks, Coordinate nodeMaskCount)
{
FILE *file = fopen(preGraphFilename, "r");
const int maxline = MAXLINE;
char line[MAXLINE];
char c;
int wordLength;
Coordinate lineLength, kmerCount;
Kmer word;
Kmer antiWord;
KmerOccurenceTable *kmerTable;
IDnum index;
IDnum nodeID = 0;
Nucleotide nucleotide;
NodeMask * nodeMask = nodeMasks;
Coordinate nodeMaskIndex = 0;
if (file == NULL)
exitErrorf(EXIT_FAILURE, true, "Could not open %s", preGraphFilename);
// Count kmers
velvetLog("Scanning pre-graph file %s for k-mers\n",
preGraphFilename);
// First line
if (!fgets(line, maxline, file))
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
sscanf(line, "%*i\t%*i\t%i\n", &wordLength);
kmerTable = newKmerOccurenceTable(accelerationBits, wordLength);
// Read nodes
if (!fgets(line, maxline, file))
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
kmerCount = 0;
while (line[0] == 'N') {
lineLength = 0;
while ((c = getc(file)) != EOF && c != '\n')
lineLength++;
kmerCount += lineLength - wordLength + 1;
if (fgets(line, maxline, file) == NULL)
break;
}
velvetLog("%li kmers found\n", (long) kmerCount);
for(nodeMaskIndex = 0; nodeMaskIndex < nodeMaskCount; nodeMaskIndex++) {
kmerCount -= nodeMasks[nodeMaskIndex].finish -
nodeMasks[nodeMaskIndex].start;
}
nodeMaskIndex = 0;
fclose(file);
// Create table
allocateKmerOccurences(kmerCount, kmerTable);
// Fill table
file = fopen(preGraphFilename, "r");
if (file == NULL)
exitErrorf(EXIT_FAILURE, true, "Could not open %s", preGraphFilename);
if (!fgets(line, maxline, file))
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
// Read nodes
if (!fgets(line, maxline, file))
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
while (line[0] == 'N') {
nodeID++;
// Fill in the initial word :
clearKmer(&word);
clearKmer(&antiWord);
for (index = 0; index < wordLength - 1; index++) {
c = getc(file);
if (c == 'A')
nucleotide = ADENINE;
else if (c == 'C')
nucleotide = CYTOSINE;
else if (c == 'G')
nucleotide = GUANINE;
else if (c == 'T')
nucleotide = THYMINE;
else if (c == '\n')
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
else
nucleotide = ADENINE;
pushNucleotide(&word, nucleotide);
if (double_strand) {
#ifdef COLOR
reversePushNucleotide(&antiWord, nucleotide);
#else
reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
}
}
// Scan through node
index = 0;
while((c = getc(file)) != '\n' && c != EOF) {
if (c == 'A')
nucleotide = ADENINE;
else if (c == 'C')
nucleotide = CYTOSINE;
else if (c == 'G')
nucleotide = GUANINE;
else if (c == 'T')
nucleotide = THYMINE;
else
nucleotide = ADENINE;
pushNucleotide(&word, nucleotide);
if (double_strand) {
#ifdef COLOR
reversePushNucleotide(&antiWord, nucleotide);
#else
reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
}
// Update mask if necessary
if (nodeMask) {
if (nodeMask->nodeID < nodeID || (nodeMask->nodeID == nodeID && index >= nodeMask->finish)) {
if (++nodeMaskIndex == nodeMaskCount)
nodeMask = NULL;
else
nodeMask++;
}
}
// Check if not masked!
if (nodeMask) {
if (nodeMask->nodeID == nodeID && index >= nodeMask->start && index < nodeMask->finish) {
index++;
continue;
}
}
if (!double_strand || compareKmers(&word, &antiWord) <= 0)
recordKmerOccurence(&word, nodeID, index, kmerTable);
else
recordKmerOccurence(&antiWord, -nodeID, getNodeLength(getNodeInGraph(graph, nodeID)) - 1 - index, kmerTable);
index++;
}
if (fgets(line, maxline, file) == NULL)
break;
}
fclose(file);
// Sort table
sortKmerOccurenceTable(kmerTable);
return kmerTable;
}