bool trueAdjacency(Cap *cap, stList *eventStrings) {
if(getTerminalAdjacencyLength(cap) > 0) {
return 0;
}
cap = getTerminalCap(cap);
assert(cap != NULL);
Cap *otherCap = cap_getAdjacency(cap);
assert(otherCap != NULL);
assert(cap_getAdjacency(otherCap) == cap);
//So is the adjacency present in one of the haplotypes? That's what we're going to answer..
End *otherEnd = end_getPositiveOrientation(cap_getEnd(otherCap));
End_InstanceIterator *endInstanceIt = end_getInstanceIterator(cap_getEnd(cap));
Cap *cap2;
while ((cap2 = end_getNext(endInstanceIt)) != NULL) {
Cap *otherCap2 = cap_getAdjacency(cap2);
assert(otherCap2 != NULL);
if (otherEnd == end_getPositiveOrientation(cap_getEnd(otherCap2))) {
//const char *eventName = event_getHeader(cap_getEvent(cap2));
assert(event_getHeader(cap_getEvent(cap2)) == event_getHeader(
cap_getEvent(otherCap2)));
if (capHasGivenEvents(cap2, eventStrings)) { //strcmp(eventName, "hapA1") == 0 || strcmp(eventName, "hapA2") == 0) {
if(getTerminalAdjacencyLength(cap2) == 0) {
end_destructInstanceIterator(endInstanceIt);
return 1;
}
}
}
}
end_destructInstanceIterator(endInstanceIt);
return 0;
}
bool endsAreAdjacent2(End *end1, End *end2, Cap **returnCap1, Cap **returnCap2, int64_t *minimumDistanceBetweenHaplotypeCaps, stList *eventStrings) {
End_InstanceIterator *instanceIterator = end_getInstanceIterator(end1);
Cap *cap1;
*returnCap1 = NULL;
*returnCap2 = NULL;
*minimumDistanceBetweenHaplotypeCaps = INT64_MAX;
bool areAdjacent = 0;
while ((cap1 = end_getNext(instanceIterator)) != NULL) {
if (capHasGivenEvents(cap1, eventStrings)) {
End_InstanceIterator *instanceIterator2 = end_getInstanceIterator(end2);
Cap *cap2;
while ((cap2 = end_getNext(instanceIterator2)) != NULL) {
int64_t i;
if (capsAreAdjacent(cap1, cap2, &i)) {
areAdjacent = 1;
if (i < *minimumDistanceBetweenHaplotypeCaps) {
*minimumDistanceBetweenHaplotypeCaps = i;
*returnCap1 = cap1;
*returnCap2 = cap2;
}
}
}
end_destructInstanceIterator(instanceIterator2);
}
}
end_destructInstanceIterator(instanceIterator);
return areAdjacent;
}
bool hasCapNotInEvent(End *end, const char *eventString) {
Cap *cap;
End_InstanceIterator *instanceIt = end_getInstanceIterator(end);
while ((cap = end_getNext(instanceIt)) != NULL) {
if (strcmp(event_getHeader(cap_getEvent(cap)), eventString) != 0) {
end_destructInstanceIterator(instanceIt);
return 1;
}
}
end_destructInstanceIterator(instanceIt);
return 0;
}
Cap *getCapForReferenceEvent(End *end, Name referenceEventName) {
/*
* Get the cap for a given event.
*/
End_InstanceIterator *it = end_getInstanceIterator(end);
Cap *cap;
while ((cap = end_getNext(it)) != NULL) {
if (event_getName(cap_getEvent(cap)) == referenceEventName) {
end_destructInstanceIterator(it);
return cap;
}
}
end_destructInstanceIterator(it);
//assert(0);
return NULL;
}
void stCaf_addAdjacencies(Flower *flower) {
//Build a list of caps.
stList *list = stList_construct();
Flower_EndIterator *endIterator = flower_getEndIterator(flower);
End *end;
while ((end = flower_getNextEnd(endIterator)) != NULL) {
End_InstanceIterator *instanceIterator = end_getInstanceIterator(end);
Cap *cap;
while ((cap = end_getNext(instanceIterator)) != NULL) {
if (!cap_getStrand(cap)) {
cap = cap_getReverse(cap);
}
stList_append(list, cap);
}
end_destructInstanceIterator(instanceIterator);
}
flower_destructEndIterator(endIterator);
assert(stList_length(list) % 2 == 0);
//Sort the list of caps.
stList_sort(list, (int(*)(const void *, const void *)) addAdjacenciesPP);
//Now make the adjacencies.
for (int64_t i = 1; i < stList_length(list); i += 2) {
Cap *cap = stList_get(list, i - 1);
Cap *cap2 = stList_get(list, i);
cap_makeAdjacent(cap, cap2);
}
//Clean up.
stList_destruct(list);
}
void testEnd_instanceIterator(CuTest* testCase) {
cactusEndTestSetup();
End_InstanceIterator *iterator = end_getInstanceIterator(end);
CuAssertTrue(testCase, iterator != NULL);
CuAssertTrue(testCase, end_getNext(iterator) == cap_getReverse(rootCap));
CuAssertTrue(testCase, end_getNext(iterator) == cap_getReverse(leaf1Cap));
End_InstanceIterator *iterator2 = end_copyInstanceIterator(iterator);
CuAssertTrue(testCase, end_getNext(iterator) == leaf2Cap);
CuAssertTrue(testCase, end_getNext(iterator) == cap_getReverse(leaf3Cap));
CuAssertTrue(testCase, end_getNext(iterator) == NULL);
CuAssertTrue(testCase, end_getPrevious(iterator) == cap_getReverse(leaf3Cap));
CuAssertTrue(testCase, end_getPrevious(iterator) == leaf2Cap);
CuAssertTrue(testCase, end_getPrevious(iterator) == cap_getReverse(leaf1Cap));
CuAssertTrue(testCase, end_getPrevious(iterator) == cap_getReverse(rootCap));
CuAssertTrue(testCase, end_getPrevious(iterator) == NULL);
CuAssertTrue(testCase, end_getNext(iterator2) == leaf2Cap);
CuAssertTrue(testCase, end_getNext(iterator2) == cap_getReverse(leaf3Cap));
CuAssertTrue(testCase, end_getNext(iterator2) == NULL);
CuAssertTrue(testCase, end_getPrevious(iterator2) == cap_getReverse(leaf3Cap));
CuAssertTrue(testCase, end_getPrevious(iterator2) == leaf2Cap);
CuAssertTrue(testCase, end_getPrevious(iterator2) == cap_getReverse(leaf1Cap));
CuAssertTrue(testCase, end_getPrevious(iterator2) == cap_getReverse(rootCap));
CuAssertTrue(testCase, end_getPrevious(iterator2) == NULL);
end_destructInstanceIterator(iterator);
end_destructInstanceIterator(iterator2);
iterator = end_getInstanceIterator(end_getReverse(end));
CuAssertTrue(testCase, end_getNext(iterator) == rootCap);
CuAssertTrue(testCase, end_getNext(iterator) == leaf1Cap);
CuAssertTrue(testCase, end_getNext(iterator) == cap_getReverse(leaf2Cap));
CuAssertTrue(testCase, end_getNext(iterator) == leaf3Cap);
CuAssertTrue(testCase, end_getNext(iterator) == NULL);
CuAssertTrue(testCase, end_getPrevious(iterator) == leaf3Cap);
CuAssertTrue(testCase, end_getPrevious(iterator) == cap_getReverse(leaf2Cap));
CuAssertTrue(testCase, end_getPrevious(iterator) == leaf1Cap);
CuAssertTrue(testCase, end_getPrevious(iterator) == rootCap);
CuAssertTrue(testCase, end_getPrevious(iterator) == NULL);
end_destructInstanceIterator(iterator);
cactusEndTestTeardown();
}
bool endsAreConnected(End *end1, End *end2, stList *eventStrings) {
if (end_getName(end1) == end_getName(end2)) { //Then the ends are the same and are part of the same chromosome by definition.
End_InstanceIterator *instanceIterator = end_getInstanceIterator(end1);
Cap *cap1;
while ((cap1 = end_getNext(instanceIterator)) != NULL) {
if (capHasGivenEvents(cap1, eventStrings)) {
end_destructInstanceIterator(instanceIterator);
return 1;
}
}
return 0;
}
End_InstanceIterator *instanceIterator = end_getInstanceIterator(end1);
Cap *cap1;
while ((cap1 = end_getNext(instanceIterator)) != NULL) {
if (capHasGivenEvents(cap1, eventStrings)) {
End_InstanceIterator *instanceIterator2 = end_getInstanceIterator(end2);
Cap *cap2;
while ((cap2 = end_getNext(instanceIterator2)) != NULL) {
assert(cap_getName(cap2) != cap_getName(cap1)); //This could only happen if end1 == end2
if (sequence_getMetaSequence(cap_getSequence(cap1)) == sequence_getMetaSequence(cap_getSequence(cap2))) {
assert(strcmp(event_getHeader(cap_getEvent(cap1)),
event_getHeader(cap_getEvent(cap2))) == 0);
assert(cap_getPositiveOrientation(cap1)
!= cap_getPositiveOrientation(cap2));
assert(cap_getName(cap1) != cap_getName(cap2));
//they could have the same coordinate if they represent two ends of a block of length 1.
end_destructInstanceIterator(instanceIterator);
end_destructInstanceIterator(instanceIterator2);
return 1;
}
}
end_destructInstanceIterator(instanceIterator2);
}
}
end_destructInstanceIterator(instanceIterator);
return 0;
}
static stSortedSet *getEventStrings(End *end, stList *eventStrings) {
stSortedSet *eventStringsSet = stSortedSet_construct3(
(int(*)(const void *, const void *)) strcmp, NULL);
End_InstanceIterator *instanceIt = end_getInstanceIterator(end);
Cap *cap;
while ((cap = end_getNext(instanceIt)) != NULL) {
const char *header = event_getHeader(cap_getEvent(cap));
for(int64_t i=0; i<stList_length(eventStrings); i++) {
if(strcmp(stList_get(eventStrings, i), header) == 0) {
stSortedSet_insert(eventStringsSet,
(void *) header);
}
}
}
end_destructInstanceIterator(instanceIt);
return eventStringsSet;
}
int64_t flower_getTotalBaseLength(Flower *flower) {
/*
* The implementation of this function is very like that in group_getTotalBaseLength, with a few differences. Consider merging them.
*/
Flower_EndIterator *endIterator = flower_getEndIterator(flower);
End *end;
int64_t totalLength = 0;
while ((end = flower_getNextEnd(endIterator)) != NULL) {
if (!end_isBlockEnd(end)) {
End_InstanceIterator *instanceIterator = end_getInstanceIterator(end);
Cap *cap;
while ((cap = end_getNext(instanceIterator)) != NULL) {
cap = cap_getStrand(cap) ? cap : cap_getReverse(cap);
if (!cap_getSide(cap) && cap_getSequence(cap) != NULL) {
Cap *cap2 = cap_getAdjacency(cap);
assert(cap2 != NULL);
while (end_isBlockEnd(cap_getEnd(cap2))) {
Segment *segment = cap_getSegment(cap2);
assert(segment != NULL);
assert(segment_get5Cap(segment) == cap2);
cap2 = cap_getAdjacency(segment_get3Cap(segment));
assert(cap2 != NULL);
assert(cap_getStrand(cap2));
assert(cap_getSide(cap2));
}
assert(cap_getStrand(cap2));
assert(cap_getSide(cap2));
int64_t length = cap_getCoordinate(cap2) - cap_getCoordinate(cap) - 1;
assert(length >= 0);
totalLength += length;
}
}
end_destructInstanceIterator(instanceIterator);
}
}
flower_destructEndIterator(endIterator);
return totalLength;
}
static stList *getSubstringsForFlowers(stList *flowers) {
/*
* Get the set of substrings for sequence intervals in the given set of flowers.
*/
stList *substrings = stList_construct3(0, (void (*)(void *)) substring_destruct);
for (int64_t i = 0; i < stList_length(flowers); i++) {
Flower *flower = stList_get(flowers, i);
Flower_EndIterator *endIt = flower_getEndIterator(flower);
End *end;
while ((end = flower_getNextEnd(endIt)) != NULL) {
if (end_isStubEnd(end)) {
End_InstanceIterator *instanceIt = end_getInstanceIterator(end);
Cap *cap;
while ((cap = end_getNext(instanceIt)) != NULL) {
Sequence *sequence;
if ((sequence = cap_getSequence(cap)) != NULL) {
cap = cap_getStrand(cap) ? cap : cap_getReverse(cap);
if (!cap_getSide(cap)) { //We have a sequence interval of interest
Cap *adjacentCap = cap_getAdjacency(cap);
assert(adjacentCap != NULL);
int64_t length = cap_getCoordinate(adjacentCap) - cap_getCoordinate(cap) - 1;
assert(length >= 0);
if (length > 0) {
stList_append(substrings,
substring_construct(sequence_getMetaSequence(sequence)->stringName,
cap_getCoordinate(cap) + 1 - sequence_getStart(sequence), length));
}
}
}
}
end_destructInstanceIterator(instanceIt);
}
}
flower_destructEndIterator(endIt);
}
return substrings;
}
stSortedSet *makeEndAlignment(StateMachine *sM, End *end, int64_t spanningTrees, int64_t maxSequenceLength,
bool useProgressiveMerging, float gapGamma,
PairwiseAlignmentParameters *pairwiseAlignmentBandingParameters) {
//Make an alignment of the sequences in the ends
//Get the adjacency sequences to be aligned.
Cap *cap;
End_InstanceIterator *it = end_getInstanceIterator(end);
stList *sequences = stList_construct3(0, (void (*)(void *))adjacencySequence_destruct);
stList *seqFrags = stList_construct3(0, (void (*)(void *))seqFrag_destruct);
stHash *endInstanceNumbers = stHash_construct2(NULL, free);
while((cap = end_getNext(it)) != NULL) {
if(cap_getSide(cap)) {
cap = cap_getReverse(cap);
}
AdjacencySequence *adjacencySequence = adjacencySequence_construct(cap, maxSequenceLength);
stList_append(sequences, adjacencySequence);
assert(cap_getAdjacency(cap) != NULL);
End *otherEnd = end_getPositiveOrientation(cap_getEnd(cap_getAdjacency(cap)));
stList_append(seqFrags, seqFrag_construct(adjacencySequence->string, 0, end_getName(otherEnd)));
//Increase count of seqfrags with a given end.
int64_t *c = stHash_search(endInstanceNumbers, otherEnd);
if(c == NULL) {
c = st_calloc(1, sizeof(int64_t));
assert(*c == 0);
stHash_insert(endInstanceNumbers, otherEnd, c);
}
(*c)++;
}
end_destructInstanceIterator(it);
//Get the alignment.
MultipleAlignment *mA = makeAlignment(sM, seqFrags, spanningTrees, 100000000, useProgressiveMerging, gapGamma, pairwiseAlignmentBandingParameters);
//Build an array of weights to reweight pairs in the alignment.
int64_t *pairwiseAlignmentsPerSequenceNonCommonEnds = st_calloc(stList_length(seqFrags), sizeof(int64_t));
int64_t *pairwiseAlignmentsPerSequenceCommonEnds = st_calloc(stList_length(seqFrags), sizeof(int64_t));
//First build array on number of pairwise alignments to each sequence, distinguishing alignments between sequences sharing
//common ends.
for(int64_t i=0; i<stList_length(mA->chosenPairwiseAlignments); i++) {
stIntTuple *pairwiseAlignment = stList_get(mA->chosenPairwiseAlignments, i);
int64_t seq1 = stIntTuple_get(pairwiseAlignment, 1);
int64_t seq2 = stIntTuple_get(pairwiseAlignment, 2);
assert(seq1 != seq2);
SeqFrag *seqFrag1 = stList_get(seqFrags, seq1);
SeqFrag *seqFrag2 = stList_get(seqFrags, seq2);
int64_t *pairwiseAlignmentsPerSequence = seqFrag1->rightEndId == seqFrag2->rightEndId
? pairwiseAlignmentsPerSequenceCommonEnds : pairwiseAlignmentsPerSequenceNonCommonEnds;
pairwiseAlignmentsPerSequence[seq1]++;
pairwiseAlignmentsPerSequence[seq2]++;
}
//Now calculate score adjustments.
double *scoreAdjustmentsNonCommonEnds = st_malloc(stList_length(seqFrags) * sizeof(double));
double *scoreAdjustmentsCommonEnds = st_malloc(stList_length(seqFrags) * sizeof(double));
for(int64_t i=0; i<stList_length(seqFrags); i++) {
SeqFrag *seqFrag = stList_get(seqFrags, i);
End *otherEnd = flower_getEnd(end_getFlower(end), seqFrag->rightEndId);
assert(otherEnd != NULL);
assert(stHash_search(endInstanceNumbers, otherEnd) != NULL);
int64_t commonInstanceNumber = *(int64_t *)stHash_search(endInstanceNumbers, otherEnd);
int64_t nonCommonInstanceNumber = stList_length(seqFrags) - commonInstanceNumber;
assert(commonInstanceNumber > 0 && nonCommonInstanceNumber >= 0);
assert(pairwiseAlignmentsPerSequenceNonCommonEnds[i] <= nonCommonInstanceNumber);
assert(pairwiseAlignmentsPerSequenceNonCommonEnds[i] >= 0);
assert(pairwiseAlignmentsPerSequenceCommonEnds[i] < commonInstanceNumber);
assert(pairwiseAlignmentsPerSequenceCommonEnds[i] >= 0);
//scoreAdjustmentsNonCommonEnds[i] = ((double)nonCommonInstanceNumber + commonInstanceNumber - 1)/(pairwiseAlignmentsPerSequenceNonCommonEnds[i] + pairwiseAlignmentsPerSequenceCommonEnds[i]);
//scoreAdjustmentsCommonEnds[i] = scoreAdjustmentsNonCommonEnds[i];
if(pairwiseAlignmentsPerSequenceNonCommonEnds[i] > 0) {
scoreAdjustmentsNonCommonEnds[i] = ((double)nonCommonInstanceNumber)/pairwiseAlignmentsPerSequenceNonCommonEnds[i];
assert(scoreAdjustmentsNonCommonEnds[i] >= 1.0);
assert(scoreAdjustmentsNonCommonEnds[i] <= nonCommonInstanceNumber);
}
else {
scoreAdjustmentsNonCommonEnds[i] = INT64_MIN;
}
if(pairwiseAlignmentsPerSequenceCommonEnds[i] > 0) {
scoreAdjustmentsCommonEnds[i] = ((double)commonInstanceNumber-1)/pairwiseAlignmentsPerSequenceCommonEnds[i];
assert(scoreAdjustmentsCommonEnds[i] >= 1.0);
assert(scoreAdjustmentsCommonEnds[i] <= commonInstanceNumber-1);
}
else {
scoreAdjustmentsCommonEnds[i] = INT64_MIN;
}
}
//Convert the alignment pairs to an alignment of the caps..
stSortedSet *sortedAlignment =
stSortedSet_construct3((int (*)(const void *, const void *))alignedPair_cmpFn,
(void (*)(void *))alignedPair_destruct);
while(stList_length(mA->alignedPairs) > 0) {
stIntTuple *alignedPair = stList_pop(mA->alignedPairs);
assert(stIntTuple_length(alignedPair) == 5);
int64_t seqIndex1 = stIntTuple_get(alignedPair, 1);
int64_t seqIndex2 = stIntTuple_get(alignedPair, 3);
AdjacencySequence *i = stList_get(sequences, seqIndex1);
AdjacencySequence *j = stList_get(sequences, seqIndex2);
assert(i != j);
int64_t offset1 = stIntTuple_get(alignedPair, 2);
int64_t offset2 = stIntTuple_get(alignedPair, 4);
int64_t score = stIntTuple_get(alignedPair, 0);
if(score <= 0) { //Happens when indel probs are included
score = 1; //This is the minimum
}
assert(score > 0 && score <= PAIR_ALIGNMENT_PROB_1);
SeqFrag *seqFrag1 = stList_get(seqFrags, seqIndex1);
SeqFrag *seqFrag2 = stList_get(seqFrags, seqIndex2);
assert(seqFrag1 != seqFrag2);
double *scoreAdjustments = seqFrag1->rightEndId == seqFrag2->rightEndId ? scoreAdjustmentsCommonEnds : scoreAdjustmentsNonCommonEnds;
assert(scoreAdjustments[seqIndex1] != INT64_MIN);
assert(scoreAdjustments[seqIndex2] != INT64_MIN);
AlignedPair *alignedPair2 = alignedPair_construct(
i->subsequenceIdentifier, i->start + (i->strand ? offset1 : -offset1), i->strand,
j->subsequenceIdentifier, j->start + (j->strand ? offset2 : -offset2), j->strand,
score*scoreAdjustments[seqIndex1], score*scoreAdjustments[seqIndex2]); //Do the reweighting here.
assert(stSortedSet_search(sortedAlignment, alignedPair2) == NULL);
assert(stSortedSet_search(sortedAlignment, alignedPair2->reverse) == NULL);
stSortedSet_insert(sortedAlignment, alignedPair2);
stSortedSet_insert(sortedAlignment, alignedPair2->reverse);
stIntTuple_destruct(alignedPair);
}
//Cleanup
stList_destruct(seqFrags);
stList_destruct(sequences);
free(pairwiseAlignmentsPerSequenceNonCommonEnds);
free(pairwiseAlignmentsPerSequenceCommonEnds);
free(scoreAdjustmentsNonCommonEnds);
free(scoreAdjustmentsCommonEnds);
multipleAlignment_destruct(mA);
stHash_destruct(endInstanceNumbers);
return sortedAlignment;
}
int main(int argc, char *argv[]) {
st_setLogLevelFromString(argv[1]);
st_logDebug("Set up logging\n");
stKVDatabaseConf *kvDatabaseConf = stKVDatabaseConf_constructFromString(argv[2]);
CactusDisk *cactusDisk = cactusDisk_construct(kvDatabaseConf, 0);
stKVDatabaseConf_destruct(kvDatabaseConf);
st_logDebug("Set up the flower disk\n");
Name flowerName = cactusMisc_stringToName(argv[3]);
Flower *flower = cactusDisk_getFlower(cactusDisk, flowerName);
int64_t totalBases = flower_getTotalBaseLength(flower);
int64_t totalEnds = flower_getEndNumber(flower);
int64_t totalFreeEnds = flower_getFreeStubEndNumber(flower);
int64_t totalAttachedEnds = flower_getAttachedStubEndNumber(flower);
int64_t totalCaps = flower_getCapNumber(flower);
int64_t totalBlocks = flower_getBlockNumber(flower);
int64_t totalGroups = flower_getGroupNumber(flower);
int64_t totalChains = flower_getChainNumber(flower);
int64_t totalLinkGroups = 0;
int64_t maxEndDegree = 0;
int64_t maxAdjacencyLength = 0;
int64_t totalEdges = 0;
Flower_EndIterator *endIt = flower_getEndIterator(flower);
End *end;
while((end = flower_getNextEnd(endIt)) != NULL) {
assert(end_getOrientation(end));
if(end_getInstanceNumber(end) > maxEndDegree) {
maxEndDegree = end_getInstanceNumber(end);
}
stSortedSet *ends = stSortedSet_construct();
End_InstanceIterator *capIt = end_getInstanceIterator(end);
Cap *cap;
while((cap = end_getNext(capIt)) != NULL) {
if(cap_getSequence(cap) != NULL) {
Cap *adjacentCap = cap_getAdjacency(cap);
assert(adjacentCap != NULL);
End *adjacentEnd = end_getPositiveOrientation(cap_getEnd(adjacentCap));
stSortedSet_insert(ends, adjacentEnd);
int64_t adjacencyLength = cap_getCoordinate(cap) - cap_getCoordinate(adjacentCap);
if(adjacencyLength < 0) {
adjacencyLength *= -1;
}
assert(adjacencyLength >= 1);
if(adjacencyLength >= maxAdjacencyLength) {
maxAdjacencyLength = adjacencyLength;
}
}
}
end_destructInstanceIterator(capIt);
totalEdges += stSortedSet_size(ends);
if(stSortedSet_search(ends, end) != NULL) { //This ensures we count self edges twice, so that the division works.
totalEdges += 1;
}
stSortedSet_destruct(ends);
}
assert(totalEdges % 2 == 0);
flower_destructEndIterator(endIt);
Flower_GroupIterator *groupIt = flower_getGroupIterator(flower);
Group *group;
while((group = flower_getNextGroup(groupIt)) != NULL) {
if(group_getLink(group) != NULL) {
totalLinkGroups++;
}
}
flower_destructGroupIterator(groupIt);
printf("flower name: %" PRIi64 " total bases: %" PRIi64 " total-ends: %" PRIi64 " total-caps: %" PRIi64 " max-end-degree: %" PRIi64 " max-adjacency-length: %" PRIi64 " total-blocks: %" PRIi64 " total-groups: %" PRIi64 " total-edges: %" PRIi64 " total-free-ends: %" PRIi64 " total-attached-ends: %" PRIi64 " total-chains: %" PRIi64 " total-link groups: %" PRIi64 "\n",
flower_getName(flower), totalBases, totalEnds, totalCaps, maxEndDegree, maxAdjacencyLength, totalBlocks, totalGroups, totalEdges/2, totalFreeEnds, totalAttachedEnds, totalChains, totalLinkGroups);
return 0;
}