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);
}
// Creates the preNode using insertion marker and annotation lists for each sequence
static void
// Creates the preNode using insertion marker and annotation lists for each sequence
createPreNodes(RoadMapArray * rdmaps, PreGraph * preGraph,
IDnum * markerCounters, InsertionMarker * insertionMarkers,
InsertionMarker * veryLastMarker, IDnum * chains,
SequencesReader *seqReadInfo, int WORDLENGTH)
{
char *sequenceFilename = seqReadInfo->m_seqFilename;
Annotation *annot = rdmaps->annotations;
IDnum latestPreNodeID;
InsertionMarker *currentMarker = insertionMarkers;
IDnum sequenceIndex;
Coordinate currentPosition, nextStop;
IDnum preNodeCounter = 1;
FILE *file = NULL;
char line[50000];
int lineLength = 50000;
Coordinate readIndex;
boolean tooShort;
Kmer initialKmer;
char c;
RoadMap *rdmap;
IDnum annotIndex, lastAnnotIndex;
IDnum markerIndex, lastMarkerIndex;
if (!seqReadInfo->m_bIsBinary) {
file = fopen(sequenceFilename, "r");
if (file == NULL)
exitErrorf(EXIT_FAILURE, true, "Could not read %s", sequenceFilename);
// Reading sequence descriptor in first line
if (sequenceCount_pg(preGraph) > 0 && !fgets(line, lineLength, file))
exitErrorf(EXIT_FAILURE, true, "%s incomplete.", sequenceFilename);
seqReadInfo->m_pFile = file;
}
// Now that we have read all of the annotations, we go on to create the preNodes and tie them up
for (sequenceIndex = 1;
sequenceIndex <= sequenceCount_pg(preGraph);
sequenceIndex++) {
if (sequenceIndex % 1000000 == 0)
velvetLog("Sequence %li / %li\n", (long) sequenceIndex,
(long) sequenceCount_pg(preGraph));
if (!seqReadInfo->m_bIsBinary) {
while (line[0] != '>')
if (!fgets(line, lineLength, file))
exitErrorf(EXIT_FAILURE, true, "%s incomplete.", sequenceFilename);
}
rdmap = getRoadMapInArray(rdmaps, sequenceIndex - 1);
annotIndex = 0;
lastAnnotIndex = getAnnotationCount(rdmap);
markerIndex = 0;
lastMarkerIndex = markerCounters[sequenceIndex];
currentPosition = 0;
// Reading first (k-1) nucleotides
tooShort = false;
clearKmer(&initialKmer);
//velvetLog("Initial kmer: ");
TightString *tString = NULL;
char *strString = NULL;
if (seqReadInfo->m_bIsBinary) {
tString = getTightStringInArray(seqReadInfo->m_sequences->tSequences, sequenceIndex - 1);
strString = readTightString(tString);
}
for (readIndex = 0; readIndex < WORDLENGTH - 1;
readIndex++) {
if (seqReadInfo->m_bIsBinary) {
if (readIndex >= tString->length) {
tooShort = true;
break;
}
c = strString[readIndex];
} else {
c = getc(file);
while (c == '\n' || c == '\r')
c = getc(file);
if (c == '>' || c == 'M' || c == EOF) {
ungetc(c, file);
tooShort = true;
break;
}
}
switch (c) {
case 'A':
case 'N':
pushNucleotide(&initialKmer, ADENINE);
break;
case 'C':
pushNucleotide(&initialKmer, CYTOSINE);
break;
case 'G':
pushNucleotide(&initialKmer, GUANINE);
break;
case 'T':
pushNucleotide(&initialKmer, THYMINE);
break;
default:
velvetLog
("Irregular sequence file: are you sure your Sequence and Roadmap file come from the same source?\n");
fflush(stdout);
abort();
}
}
if (tooShort) {
//velvetLog("Skipping short read.. %d\n", sequenceIndex);
chains[sequenceIndex] = preNodeCounter;
if (seqReadInfo->m_bIsBinary) {
free(strString);
} else {
if (!fgets(line, lineLength, file) && sequenceIndex < sequenceCount_pg(preGraph))
exitErrorf(EXIT_FAILURE, true, "%s incomplete.", sequenceFilename);
}
continue;
}
char *currString = NULL;
if (seqReadInfo->m_bIsBinary) {
currString = &strString[readIndex];
seqReadInfo->m_ppCurrString = &currString;
}
latestPreNodeID = 0;
while (annotIndex < lastAnnotIndex) {
if (markerIndex == lastMarkerIndex
|| getPosition(annot) <=
getInsertionMarkerPosition(currentMarker))
nextStop = getPosition(annot);
else {
nextStop =
getInsertionMarkerPosition
(currentMarker);
}
if (currentPosition != nextStop) {
if (seqReadInfo->m_bIsBinary) {
if (readIndex >= tString->length) {
velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
exit(1);
}
}
//if (sequenceIndex == 481)
// velvetLog("Adding pre nodes from %lli to %lli\n", (long long) currentPosition, (long long) nextStop);
addPreNodeToPreGraph_pg(preGraph,
currentPosition,
nextStop,
seqReadInfo,
&initialKmer,
preNodeCounter);
if (latestPreNodeID == 0) {
chains[sequenceIndex] =
preNodeCounter;
}
latestPreNodeID = preNodeCounter++;
currentPosition = nextStop;
}
while (markerIndex < lastMarkerIndex
&& getInsertionMarkerPosition(currentMarker)
== nextStop) {
convertMarker(currentMarker,
latestPreNodeID);
currentMarker++;
markerIndex++;
}
while (annotIndex < lastAnnotIndex
&& getPosition(annot) == nextStop) {
for (readIndex = 0;
readIndex <
getAnnotationLength(annot);
readIndex++) {
if (seqReadInfo->m_bIsBinary) {
c = *currString;
currString += 1; // increment the pointer
} else {
c = getc(file);
while (!isalpha(c))
c = getc(file);
}
//if (sequenceIndex == 481)
// velvetLog("(%c)", c);
switch (c) {
case 'A':
case 'N':
pushNucleotide(&initialKmer, ADENINE);
break;
case 'C':
pushNucleotide(&initialKmer, CYTOSINE);
break;
case 'G':
pushNucleotide(&initialKmer, GUANINE);
break;
case 'T':
pushNucleotide(&initialKmer, THYMINE);
break;
default:
velvetLog
("Irregular sequence file: are you sure your Sequence and Roadmap file come from the same source?\n");
fflush(stdout);
#ifdef DEBUG
abort();
#endif
exit(1);
}
}
annot = getNextAnnotation(annot);
annotIndex++;
}
}
while (markerIndex < lastMarkerIndex) {
if (currentPosition ==
getInsertionMarkerPosition(currentMarker)) {
convertMarker(currentMarker,
latestPreNodeID);
currentMarker++;
markerIndex++;
} else {
nextStop =
getInsertionMarkerPosition
(currentMarker);
//if (sequenceIndex == 481)
// velvetLog("Adding pre nodes from %lli to %lli\n", (long long) currentPosition, (long long) nextStop);
addPreNodeToPreGraph_pg(preGraph,
currentPosition,
nextStop, seqReadInfo,
&initialKmer,
preNodeCounter);
if (latestPreNodeID == 0)
chains[sequenceIndex] =
preNodeCounter;
latestPreNodeID = preNodeCounter++;
currentPosition =
getInsertionMarkerPosition
(currentMarker);
}
}
if (seqReadInfo->m_bIsBinary) {
free(strString);
} else {
// End of sequence
if (!fgets(line, lineLength, file) && sequenceIndex < sequenceCount_pg(preGraph))
exitErrorf(EXIT_FAILURE, true, "%s incomplete.", sequenceFilename);
//velvetLog(" \n");
}
if (latestPreNodeID == 0)
chains[sequenceIndex] = preNodeCounter;
}
free(markerCounters);
if (!seqReadInfo->m_bIsBinary) {
fclose(file);
}
}
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;
}
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 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 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;
}
