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 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();
}
