static void test_penalize_0(CuTest *testCase) {
stList *observedList = stList_construct3(0, free);
stList *expectedList = stList_construct3(0, free);
stHash *observedHash = createBlockHashFromString("a score=0\n"
"s reference.chr0 0 13 + 158545518 gcagctgaaaaca\n"
"s name.chr1 0 10 + 100 ATGT---ATGCCG\n"
"s name2.chr1 0 10 + 100 ATGT---ATGCCG\n",
observedList);
stHash *expectedHash = createBlockHashFromString("a score=0\n"
"s reference.chr0 0 13 + 158545518 gcagctgaaaaca-----\n"
"s name.chr1 0 15 + 100 ATGT---ATGCCGNNNNN\n"
"s name2.chr1 0 10 + 100 ATGT---ATGCCG-----\n",
expectedList);
penalize(observedHash, "name.chr1", 5);
CuAssertTrue(testCase, hashesAreEqual(observedHash, expectedHash));
CuAssertTrue(testCase, listsAreEqual(observedList, expectedList));
// clean up
stHash_destruct(observedHash);
stHash_destruct(expectedHash);
stList_destruct(observedList);
stList_destruct(expectedList);
}
/* write a malnSet to a MAF file */
void malnSet_writeMaf(struct malnSet *malnSet, char *mafFileName) {
malnSet_assert(malnSet);
stList *sorted = buildRootSorted(malnSet);
FILE *mafFh = mustOpen(mafFileName, "w");
mafWriteStart(mafFh, NULL);
stListIterator *iter = stList_getIterator(sorted);
struct malnBlk *blk;
while ((blk = stList_getNext(iter)) != NULL) {
writeBlkToMaf(blk, mafFh);
}
stList_destructIterator(iter);
mafWriteEnd(mafFh);
carefulClose(&mafFh);
stList_destruct(sorted);
}
/* clone the root. */
static stTree *subrangeCloneRoot(stTree *srcRoot, struct malnCompCompMap *srcDestCompMap) {
// clone root, if deleted, these must only be one child (due to the way
// the trees are constructed).
stList *pendingSubtrees = stList_construct();
stTree *destRoot = subrangeCloneNode(srcRoot, srcDestCompMap, pendingSubtrees);
if (destRoot == NULL) {
if (stList_length(pendingSubtrees) > 1) {
struct mafTreeNodeCompLink *srcNcLink = getNodeCompLink(srcRoot);
errAbort("deleted tree root %s (component: %s:%d-%d/%c)) has more that one child", stTree_getLabel(srcRoot), srcNcLink->comp->seq->orgSeqName, srcNcLink->comp->start, srcNcLink->comp->end, srcNcLink->comp->strand);
} else if (stList_length(pendingSubtrees) == 1) {
destRoot = stList_pop(pendingSubtrees);
}
}
stList_destruct(pendingSubtrees);
return destRoot;
}
static void test_stSet_removeAndFreeKey(CuTest* testCase) {
stSet *set2 = stSet_construct2(free);
stList *keys = stList_construct();
int64_t keyNumber = 1000;
for (int64_t i = 0; i < keyNumber; i++) {
int64_t *key = st_malloc(sizeof(*key));
stList_append(keys, key);
stSet_insert(set2, key);
}
for (int64_t i = 0; i < keyNumber; i++) {
int64_t *key = stList_get(keys, i);
CuAssertPtrEquals(testCase, key, stSet_removeAndFreeKey(set2, key));
}
CuAssertIntEquals(testCase, 0, stSet_size(set2));
stSet_destruct(set2);
stList_destruct(keys);
}
/*
* A thread is trivial if all the segments it contains come from blocks containing only a reference segment.
* These reference only segments represent scaffold gaps. At the same time, it processes the thread string
* to remove the boolean values use to indicate if a thread is trivial or not.
*/
static bool isTrivialString(char **threadString) {
stList *strings = stString_split(*threadString); //Split splits into individual segments.
bool trivialString = 1;
for(int64_t i=0; i<stList_length(strings); i++) {
char *segmentString = stList_get(strings, i);
int64_t j = strlen(segmentString)-1; //Location of the boolean value within a segment.
assert(j > 0);
assert(segmentString[j] == '0' || segmentString[j] == '1');
if(segmentString[j] == '1') { //Found a non-trivial segment, hence the thread is non-trivial.
trivialString = 0;
}
segmentString[j] = '\0';
}
free(*threadString); //Free old thread string. Doing it this way is a bit more memory efficient, as we don't keep two copies of the string around.
*threadString = stString_join2("", strings); //Concatenation makes one sequence, now without the booleans.
stList_destruct(strings);
return trivialString;
}
void cactusDisk_destruct(CactusDisk *cactusDisk) {
Flower *flower;
MetaSequence *metaSequence;
while ((flower = stSortedSet_getFirst(cactusDisk->flowers)) != NULL) {
flower_destruct(flower, FALSE);
}
stSortedSet_destruct(cactusDisk->flowers);
stSortedSet_destruct(cactusDisk->flowerNamesMarkedForDeletion);
while ((metaSequence = stSortedSet_getFirst(cactusDisk->metaSequences)) != NULL) {
metaSequence_destruct(metaSequence);
}
stSortedSet_destruct(cactusDisk->metaSequences);
//close DB
stKVDatabase_destruct(cactusDisk->database);
//Close the sequences files.
if (cactusDisk->storeSequencesInAFile) {
free(cactusDisk->sequencesFileName);
free(cactusDisk->absSequencesFileName);
if (cactusDisk->sequencesReadFileHandle != NULL) {
fclose(cactusDisk->sequencesReadFileHandle);
}
if (cactusDisk->sequencesWriteFileHandle != NULL) {
fsync(fileno(cactusDisk->sequencesWriteFileHandle));
fclose(cactusDisk->sequencesWriteFileHandle);
}
} else {
assert(cactusDisk->sequencesFileName == NULL);
assert(cactusDisk->sequencesReadFileHandle == NULL);
assert(cactusDisk->absSequencesFileName == NULL);
}
stCache_destruct(cactusDisk->cache); //Get rid of the cache
stCache_destruct(cactusDisk->stringCache);
stList_destruct(cactusDisk->updateRequests);
free(cactusDisk);
}
stList *getComponents2(stList *adjacencyEdges, stList *stubEdges,
stList *chainEdges) {
/*
* Gets a list of connected components for a set of adjacency, stub and chain edges.
* If adjacencyEdges, stubEdges or chainEdges are NULL then they are ignored.
*/
stList *allEdges = stList_construct(); //Build a concatenated list of all the chain, stub and adjacency edges.
if (adjacencyEdges != NULL) {
stList_appendAll(allEdges, adjacencyEdges);
}
if (stubEdges != NULL) {
stList_appendAll(allEdges, stubEdges);
}
if (chainEdges != NULL) {
stList_appendAll(allEdges, chainEdges);
}
stList *components = getComponents(allEdges); //Gets the graph components.
stList_destruct(allEdges); //Cleanup the all edges.
return components;
}
static void testBulkRemoveRecords(CuTest *testCase) {
/*
* Tests doing a bulk update of a set of records.
*/
setup();
int64_t i = 100, j = 110, k = 120, l = 130;
stKVDatabase_insertRecord(database, 1, &i, sizeof(int64_t));
stKVDatabase_insertRecord(database, 2, &j, sizeof(int64_t));
stKVDatabase_insertRecord(database, 3, &k, sizeof(int64_t));
stKVDatabase_insertRecord(database, 4, &l, sizeof(int64_t));
stKVDatabase_insertRecord(database, 5, &i, 0); //Test null record addition
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, 1));
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, 2));
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, 3));
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, 4));
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, 5));
CuAssertTrue(testCase, stKVDatabase_getNumberOfRecords(database) == 5);
stList *requests = stList_construct3(0, (void(*)(void *)) stInt64Tuple_destruct);
// test empty request list
stKVDatabase_bulkRemoveRecords(database, requests);
stList_append(requests, stInt64Tuple_construct(1, (int64_t)1));
stList_append(requests, stInt64Tuple_construct(1, (int64_t)2));
stList_append(requests, stInt64Tuple_construct(1, (int64_t)3));
stList_append(requests, stInt64Tuple_construct(1, (int64_t)4));
stList_append(requests, stInt64Tuple_construct(1, (int64_t)5));
stKVDatabase_bulkRemoveRecords(database, requests);
CuAssertTrue(testCase, !stKVDatabase_containsRecord(database, 1));
CuAssertTrue(testCase, !stKVDatabase_containsRecord(database, 2));
CuAssertTrue(testCase, !stKVDatabase_containsRecord(database, 3));
CuAssertTrue(testCase, !stKVDatabase_containsRecord(database, 4));
CuAssertTrue(testCase, !stKVDatabase_containsRecord(database, 5));
CuAssertTrue(testCase, stKVDatabase_getNumberOfRecords(database) == 0);
stList_destruct(requests);
teardown();
}
static void testPinchIteratorFromFile(CuTest *testCase) {
for (int64_t test = 0; test < 100; test++) {
stList *pairwiseAlignments = getRandomPairwiseAlignments();
st_logInfo("Doing a random pinch iterator from file test %" PRIi64 " with %" PRIi64 " alignments\n", test, stList_length(pairwiseAlignments));
//Put alignments in a file
char *tempFile = "tempFileForPinchIteratorTest.cig";
FILE *fileHandle = fopen(tempFile, "w");
for (int64_t i = 0; i < stList_length(pairwiseAlignments); i++) {
cigarWrite(fileHandle, stList_get(pairwiseAlignments, i), 0);
}
fclose(fileHandle);
//Get an iterator
stPinchIterator *pinchIterator = stPinchIterator_constructFromFile(tempFile);
//Now test it
testIterator(testCase, pinchIterator, pairwiseAlignments);
//Cleanup
stPinchIterator_destruct(pinchIterator);
stFile_rmrf(tempFile);
stList_destruct(pairwiseAlignments);
}
}
void checkInputs(stSortedSet *nodes, stList *adjacencyEdges,
stList *stubEdges, stList *chainEdges) {
/*
* Checks the inputs to the algorithm are as expected.
*/
int64_t nodeNumber = stSortedSet_size(nodes);
assert(nodeNumber % 2 == 0);
if (nodeNumber > 0) {
assert(stList_length(stubEdges) > 0);
}
assert(
stList_length(stubEdges) + stList_length(chainEdges) == (nodeNumber
/ 2));
checkEdges(stubEdges, nodes, 0, 0);
checkEdges(chainEdges, nodes, 0, 0);
stList *stubsAndChainEdges = stList_copy(stubEdges, NULL);
stList_appendAll(stubsAndChainEdges, chainEdges);
checkEdges(stubsAndChainEdges, nodes, 1, 0);
stList_destruct(stubsAndChainEdges);
checkEdges(adjacencyEdges, nodes, 1, 1);
}
static void test_st_randomChoice(CuTest *testCase) {
/*
* Excercies the random int function.
*/
stList *list = stList_construct3(0, (void (*)(void *))stIntTuple_destruct);
stTry {
st_randomChoice(list);
} stCatch(except) {
CuAssertTrue(testCase, stExcept_getId(except) == RANDOM_EXCEPTION_ID);
}
stTryEnd
for(int32_t i = 0; i < 10; i++) {
stList_append(list, stIntTuple_construct(1, i));
}
for(int32_t i = 0; i < 100; i++) {
CuAssertTrue(testCase, stList_contains(list, st_randomChoice(list)));
}
stList_destruct(list);
}
stList *makeMatchingObeyCyclicConstraints(stSortedSet *nodes,
stList *chosenEdges,
stSortedSet *allAdjacencyEdges, stList *nonZeroWeightAdjacencyEdges,
stList *stubEdges, stList *chainEdges,
bool makeStubCyclesDisjoint) {
if (stSortedSet_size(nodes) == 0) { //Some of the following functions assume there are at least 2 nodes.
return stList_construct();
}
/*
* Merge in the stub free components.
*/
chosenEdges = mergeSimpleCycles2(chosenEdges,
nonZeroWeightAdjacencyEdges, allAdjacencyEdges, stubEdges,
chainEdges);
st_logDebug(
"After merging in chain only cycles the matching has %" PRIi64 " edges, %" PRIi64 " cardinality and %" PRIi64 " weight\n",
stList_length(chosenEdges), matchingCardinality(chosenEdges),
matchingWeight(chosenEdges));
/*
* Split stub components.
*/
if (makeStubCyclesDisjoint) {
stList *updatedChosenEdges = splitMultipleStubCycles(chosenEdges,
nonZeroWeightAdjacencyEdges, allAdjacencyEdges, stubEdges,
chainEdges);
stList_destruct(chosenEdges);
chosenEdges = updatedChosenEdges;
st_logDebug(
"After making stub cycles disjoint the matching has %" PRIi64 " edges, %" PRIi64 " cardinality and %" PRIi64 " weight\n",
stList_length(chosenEdges), matchingCardinality(chosenEdges),
matchingWeight(chosenEdges));
} else {
st_logDebug("Not making stub cycles disjoint\n");
}
return chosenEdges;
}
char *cactusDisk_getString(CactusDisk *cactusDisk, Name name, int64_t start, int64_t length, int64_t strand,
int64_t totalSequenceLength) {
/*
* Gets a string from the database.
*
*/
assert(length >= 0);
if (length == 0) {
return stString_copy("");
}
//First try getting it from the cache
char *string = cactusDisk_getStringFromCache(cactusDisk, name, start, length, strand);
if (string == NULL) { //If not in the cache, add it to the cache and then get it from the cache.
stList *list = stList_construct3(0, (void (*)(void *)) substring_destruct);
stList_append(list, substring_construct(name, start, length));
cacheSubstringsFromDB(cactusDisk, list);
stList_destruct(list);
string = cactusDisk_getStringFromCache(cactusDisk, name, start, length, strand);
}
assert(string != NULL);
return string;
}
/*
* Recursive function which fills a givenlist with the
* connected nodes within a module and fills their lifted
* edges in the same pass
*/
static void buildFaces_fillTopNodeList2(Cap * cap, stList *list,
stHash *liftedEdgesTable) {
stList *liftedEdges = stList_construct3(2,
buildFaces_stList_destructElem);
int64_t index;
// Orientation check
cap = cap_getPositiveOrientation(cap);
// Limit of recursion
if (stList_contains(list, cap))
return;
// Actual filling
st_logInfo("Adding cap %p to face\n", cap);
stList_append(list, cap);
// Compute lifted edges
for (index = 0; index < cap_getChildNumber(cap); index++)
buildFaces_computeLiftedEdgesAtTopNode(cap_getChild(cap, index), liftedEdges);
// If emptylist...
if (stList_length(liftedEdges) == 0)
stList_destruct(liftedEdges);
// Recursion through lifted edges
else {
stHash_insert(liftedEdgesTable, cap, liftedEdges);
for (index = 0; index < stList_length(liftedEdges); index++)
buildFaces_fillTopNodeList2(
((LiftedEdge *) stList_get(liftedEdges, index))->destination,
list, liftedEdgesTable);
}
// Recursion through adjacency
if (cap_getAdjacency(cap))
buildFaces_fillTopNodeList2(cap_getAdjacency(cap),list,
liftedEdgesTable);
}
stList *getPerfectMatching(stSortedSet *nodes,
stList *adjacencyEdges,
stList *(*matchingAlgorithm)(stList *edges, int64_t nodeNumber)) {
checkEdges(adjacencyEdges, nodes, 1, 1); //Checks edges are clique
if (stSortedSet_size(nodes) == 0) { //Some of the following functions assume there are at least 2 nodes.
return stList_construct();
}
stList *nonZeroWeightAdjacencyEdges = getEdgesWithGreaterThanZeroWeight(
adjacencyEdges);
stList *chosenEdges = getSparseMatching(nodes, nonZeroWeightAdjacencyEdges, matchingAlgorithm);
stList_destruct(nonZeroWeightAdjacencyEdges);
makeMatchingPerfect(chosenEdges, adjacencyEdges, nodes);
st_logDebug(
"Chosen a perfect matching with %" PRIi64 " edges, %" PRIi64 " cardinality and %" PRIi64 " weight\n",
stList_length(chosenEdges), matchingCardinality(chosenEdges),
matchingWeight(chosenEdges));
return chosenEdges;
}
static void getComponentsP(stHash *nodesToEdges, int64_t node,
stSortedSet *component) {
stIntTuple *key = stIntTuple_construct1( node);
stList *edges = stHash_search(nodesToEdges, key);
if (edges != NULL) {
stHash_remove(nodesToEdges, key);
for (int64_t i = 0; i < stList_length(edges); i++) {
stIntTuple *edge = stList_get(edges, i);
if (stSortedSet_search(component, edge) == NULL) {
stSortedSet_insert(component, edge);
}
/*
* Recursion on stack could equal the total number of nodes.
*/
getComponentsP(nodesToEdges, stIntTuple_get(edge, 0),
component);
getComponentsP(nodesToEdges, stIntTuple_get(edge, 1),
component);
}
stList_destruct(edges);
}
stIntTuple_destruct(key);
}
static void test_stSortedSet_searchLessThan(CuTest* testCase) {
sonLibSortedSetTestSetup();
for(int32_t i=0; i<size; i++) {
stSortedSet_insert(sortedSet, stIntTuple_construct(1, input[i]));
}
//static int32_t sortedInput[] = { -10, -1, 1, 3, 5, 10, 12 };
CuAssertTrue(testCase, stSortedSet_searchLessThan(sortedSet,
stIntTuple_construct(1, -11)) == NULL);
CuAssertTrue(testCase, stSortedSet_searchLessThan(sortedSet,
stIntTuple_construct(1, -10)) == NULL);
CuAssertTrue(testCase, stSortedSet_searchLessThan(sortedSet,
stIntTuple_construct(1, -5)) == stSortedSet_search(sortedSet, stIntTuple_construct(1, -10)));
CuAssertTrue(testCase, stSortedSet_searchLessThan(sortedSet,
stIntTuple_construct(1, 13)) == stSortedSet_search(sortedSet, stIntTuple_construct(1, 12)));
CuAssertTrue(testCase, stSortedSet_searchLessThan(sortedSet,
stIntTuple_construct(1, 8)) == stSortedSet_search(sortedSet, stIntTuple_construct(1, 5)));
CuAssertTrue(testCase, stSortedSet_searchLessThan(sortedSet,
stIntTuple_construct(1, 1)) == stSortedSet_search(sortedSet, stIntTuple_construct(1, -1)));
CuAssertTrue(testCase, stSortedSet_searchLessThan(sortedSet,
stIntTuple_construct(1, 10)) == stSortedSet_search(sortedSet, stIntTuple_construct(1, 5)));
for(int32_t i=0; i<100; i++) {
stSortedSet_insert(sortedSet, stIntTuple_construct(1, st_randomInt(-1000, 1000)));
}
stList *list = stSortedSet_getList(sortedSet);
for(int32_t i=1; i<stList_length(list); i++) {
stIntTuple *p = stList_get(list, i-1);
stIntTuple *j = stList_get(list, i);
stIntTuple *k = stIntTuple_construct(1, st_randomInt(stIntTuple_getPosition(p, 0)+1, stIntTuple_getPosition(j, 0)+1));
CuAssertTrue(testCase, stSortedSet_searchLessThan(sortedSet, k) == p);
stIntTuple_destruct(k);
}
stList_destruct(list);
sonLibSortedSetTestTeardown();
}
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;
}
static void test_addBlockToHash_4(CuTest *testCase) {
// concatenation with sequnece breakpoint due to *strand* alone
// note that name3 is well within the interstitial boundary, the two blocks
// essentially looking like >>>>>>>>>>>>> <<<<< (strand diffs)
options_t *options = options_construct();
options->breakpointPenalty = 10;
options->interstitialSequence = 5;
stList *observedList = stList_construct3(0, free);
stList *expectedList = stList_construct3(0, free);
stHash *observedHash = createBlockHashFromString("a score=0\n"
"s reference.chr0 0 13 + 158545518 gcagctgaaaaca\n"
"s name.chr1 0 10 + 100 ATGT---ATGCCG\n"
"s name2.chr1 0 10 + 100 ATGT---ATGCCG\n"
"s name3.chr1 0 13 + 100 GCAGCTGAAAACA\n",
observedList
);
mafBlock_t *mb = maf_newMafBlockListFromString("a score=0 test\n"
"s reference.chr0 13 5 + 158545518 ACGTA\n"
"s name.chr1 12 5 + 100 gtcGG\n"
"s name2.chr1 10 5 + 100 ATGTg\n"
"s name3.chr1 82 5 - 100 GGGGG\n"
, 3);
stHash *expectedHash = NULL;
expectedHash = createBlockHashFromString("a score=0\n"
"s reference.chr0 0 18 + 158545518 gcagctgaaaaca------------ACGTA\n"
"s name.chr1 0 17 + 100 ATGT---ATGCCGac----------gtcGG\n"
"s name2.chr1 0 15 + 100 ATGT---ATGCCG------------ATGTg\n"
"s name3.chr1 0 28 + 100 GCAGCTGAAAACA--NNNNNNNNNNGGGGG\n",
expectedList
);
row_t *r = stHash_search(expectedHash, "name3");
r->prevRightPos = 86;
r->strand = '*';
r->prevStrand = '-';
stHash *seqHash = createSeqHashFromString("name.chr1", "ATGTATGCCGacgtc"
"GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG"
"GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG");
mtfseq_t *mtfs = newMtfseqFromString("gcagctgaaaacaACGTA"
"tttttttttttttttttttttttttttttttt"
"tttttttttttttttttttttttttttttttttttttttttttttttttt");
stHash_insert(seqHash, stString_copy("reference.chr0"), mtfs);
mtfs = newMtfseqFromString("ATGTATGCCGATGTg"
"CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"
"CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC");
stHash_insert(seqHash, stString_copy("name2.chr1"), mtfs);
mtfs = newMtfseqFromString("GCAGCTGAAAACACCCCCgggggggggggggggggggggggggggggggg"
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa"
);
stHash_insert(seqHash, stString_copy("name3.chr1"), mtfs);
addMafBlockToRowHash(observedHash, seqHash, observedList, mb, options);
CuAssertTrue(testCase, hashesAreEqual(observedHash, expectedHash));
CuAssertTrue(testCase, listsAreEqual(observedList, expectedList));
// clean up
stHash_destruct(observedHash);
stHash_destruct(expectedHash);
stHash_destruct(seqHash);
stList_destruct(observedList);
stList_destruct(expectedList);
maf_destroyMafBlockList(mb);
destroyOptions(options);
}
static void test_addBlockToHash_6(CuTest *testCase) {
// concatenation with sequence breakpoint due to sequence name
options_t *options = options_construct();
options->breakpointPenalty = 10;
options->interstitialSequence = 5;
stList *observedList = stList_construct3(0, free);
stList *expectedList = stList_construct3(0, free);
stHash *observedHash = createBlockHashFromString("a score=0\n"
"s reference.chr0 0 13 + 158545518 gcagctgaaaaca\n"
"s name.chr1 0 10 + 100 ATGT---ATGCCG\n"
"s name2.chr1 0 10 + 100 ATGT---ATGCCG\n"
"s name3.chr1 0 13 + 100 GCAGCTGAAAACA\n",
observedList
);
mafBlock_t *mb = maf_newMafBlockListFromString("a score=0 test\n"
"s reference.chr0 13 5 + 158545518 ACGTA\n"
"s name.chr1 12 5 + 100 gtcGG\n"
"s name2.chr1 10 5 + 100 ATGTg\n"
"s name3.chr2 13 5 + 100 aaaaa\n"
, 3);
stHash *expectedHash = NULL;
expectedHash = createBlockHashFromString("a score=0\n"
"s reference.chr0 0 18 + 158545518 gcagctgaaaaca------------ACGTA\n"
"s name.chr1 0 17 + 100 ATGT---ATGCCGac----------gtcGG\n"
"s name2.chr1 0 15 + 100 ATGT---ATGCCG------------ATGTg\n"
"s name3 0 28 + 28 GCAGCTGAAAACA--NNNNNNNNNNaaaaa\n",
expectedList
);
row_t *r = stHash_search(expectedHash, "name3");
r->prevRightPos = 17;
r->strand = '*';
r->prevStrand = '+';
r->multipleNames = true;
free(r->prevName);
r->prevName = stString_copy("name3.chr2");
stHash *seqHash = createSeqHashFromString("name.chr1", "ATGTATGCCGacgtc"
"GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG"
"GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG");
mtfseq_t *mtfs = newMtfseqFromString("gcagctgaaaacaACGTA"
"tttttttttttttttttttttttttttttttt"
"tttttttttttttttttttttttttttttttttttttttttttttttttt");
stHash_insert(seqHash, stString_copy("reference.chr0"), mtfs);
mtfs = newMtfseqFromString("ATGTATGCCGATGTg"
"CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"
"CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC");
stHash_insert(seqHash, stString_copy("name2.chr1"), mtfs);
mtfs = newMtfseqFromString("GCAGCTGAAAACAggggggggggggggggggggggggggggggggggggg"
"CCCCCaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa"
);
stHash_insert(seqHash, stString_copy("name3.chr1"), mtfs);
mtfs = newMtfseqFromString("TTTTTTTTTTTTTaaaaaGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG"
"CCCCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
);
stHash_insert(seqHash, stString_copy("name3.chr2"), mtfs);
addMafBlockToRowHash(observedHash, seqHash, observedList, mb, options);
CuAssertTrue(testCase, hashesAreEqual(observedHash, expectedHash));
CuAssertTrue(testCase, listsAreEqual(observedList, expectedList));
// clean up
stHash_destruct(observedHash);
stHash_destruct(expectedHash);
stHash_destruct(seqHash);
stList_destruct(observedList);
stList_destruct(expectedList);
maf_destroyMafBlockList(mb);
destroyOptions(options);
}
Name cactusDisk_addString(CactusDisk *cactusDisk, const char *string) {
/*
* Adds a string to the database.
*/
if (cactusDisk->storeSequencesInAFile) {
if (cactusDisk->sequencesWriteFileHandle == NULL) {
//We do not allow the read file handle to be open at the same time.
if (cactusDisk->sequencesReadFileHandle != NULL) {
fclose(cactusDisk->sequencesReadFileHandle);
cactusDisk->sequencesReadFileHandle = NULL;
}
cactusDisk->sequencesWriteFileHandle = fopen(cactusDisk->absSequencesFileName, "a");
assert(cactusDisk->sequencesWriteFileHandle != NULL);
}
else {
//The read file handle should not be open at the same time.
assert(cactusDisk->sequencesReadFileHandle == NULL);
}
Name name = ftell(cactusDisk->sequencesWriteFileHandle) + 1;
//Extra temporary cheesy code to avoid potential overflow in fprintf
int64_t chunkSize = 1000000000; //1 gig approx chunks, to avoid a possible overflow issue with fprintf
int64_t length = strlen(string);
if (length > chunkSize) {
fprintf(cactusDisk->sequencesWriteFileHandle, ">");
for (int64_t i = 0; i < length;) {
int64_t j = i + chunkSize <= length ? chunkSize : length - i;
char *string2 = memcpy(st_malloc(sizeof(char) * (j + 1)), string + i, sizeof(char) * j);
string2[j] = '\0';
int64_t k = fprintf(cactusDisk->sequencesWriteFileHandle, "%s", string2);
(void) k;
assert(k == j);
free(string2);
i += j;
}
} else {
//Replacing this line
int64_t k = fprintf(cactusDisk->sequencesWriteFileHandle, ">%s", string);
(void) k;
assert(k == length + 1);
}
#ifndef NDEBUG
// Extra fsync may not be necessary.
fsync(fileno(cactusDisk->sequencesWriteFileHandle));
fclose(cactusDisk->sequencesWriteFileHandle);
cactusDisk->sequencesWriteFileHandle = NULL;
cactusDisk->sequencesReadFileHandle = fopen(cactusDisk->absSequencesFileName, "r");
char *string2 = getStringFromDisk(cactusDisk->sequencesReadFileHandle, name, 0, length);
for (int64_t i = 0; i < length; i++) {
assert(string[i] == string2[i]);
}
free(string2);
#endif
return name;
} else {
int64_t stringSize = strlen(string);
int64_t intervalSize = ceil((double) stringSize / CACTUS_DISK_SEQUENCE_CHUNK_SIZE);
Name name = cactusDisk_getUniqueIDInterval(cactusDisk, intervalSize);
stList *insertRequests = stList_construct3(0, (void (*)(void *)) stKVDatabaseBulkRequest_destruct);
for (int64_t i = 0; i * CACTUS_DISK_SEQUENCE_CHUNK_SIZE < stringSize; i++) {
int64_t j =
(i + 1) * CACTUS_DISK_SEQUENCE_CHUNK_SIZE < stringSize ?
CACTUS_DISK_SEQUENCE_CHUNK_SIZE : stringSize - i * CACTUS_DISK_SEQUENCE_CHUNK_SIZE;
char *subString = stString_getSubString(string, i * CACTUS_DISK_SEQUENCE_CHUNK_SIZE, j);
stList_append(insertRequests, stKVDatabaseBulkRequest_constructInsertRequest(name + i, subString, j + 1));
free(subString);
}
stTry
{
stKVDatabase_bulkSetRecords(cactusDisk->database, insertRequests);
}
stCatch(except)
{
stThrowNewCause(except, ST_KV_DATABASE_EXCEPTION_ID,
"An unknown database error occurred when we tried to add a string to the cactus disk");
}stTryEnd
;
stList_destruct(insertRequests);
return name;
}
}
int main(int argc, char *argv[]) {
/*
* Script for adding a reference genome to a flower.
*/
/*
* Arguments/options
*/
char * logLevelString = NULL;
char * cactusDiskDatabaseString = NULL;
char * secondaryDatabaseString = NULL;
char *referenceEventString = (char *) cactusMisc_getDefaultReferenceEventHeader();
bool bottomUpPhase = 0;
///////////////////////////////////////////////////////////////////////////
// (0) Parse the inputs handed by genomeCactus.py / setup stuff.
///////////////////////////////////////////////////////////////////////////
while (1) {
static struct option long_options[] = { { "logLevel", required_argument, 0, 'a' }, { "cactusDisk", required_argument, 0, 'b' }, { "secondaryDisk", required_argument, 0, 'd' }, { "referenceEventString", required_argument, 0, 'g' }, { "help", no_argument,
0, 'h' }, { "bottomUpPhase", no_argument, 0, 'j' }, { 0, 0, 0, 0 } };
int option_index = 0;
int key = getopt_long(argc, argv, "a:b:c:d:e:g:hi:j", long_options, &option_index);
if (key == -1) {
break;
}
switch (key) {
case 'a':
logLevelString = stString_copy(optarg);
break;
case 'b':
cactusDiskDatabaseString = stString_copy(optarg);
break;
case 'd':
secondaryDatabaseString = stString_copy(optarg);
break;
case 'g':
referenceEventString = stString_copy(optarg);
break;
case 'h':
usage();
return 0;
case 'j':
bottomUpPhase = 1;
break;
default:
usage();
return 1;
}
}
///////////////////////////////////////////////////////////////////////////
// (0) Check the inputs.
///////////////////////////////////////////////////////////////////////////
assert(cactusDiskDatabaseString != NULL);
//////////////////////////////////////////////
//Set up logging
//////////////////////////////////////////////
st_setLogLevelFromString(logLevelString);
//////////////////////////////////////////////
//Load the database
//////////////////////////////////////////////
st_logInfo("referenceEventString = %s\n", referenceEventString);
st_logInfo("bottomUpPhase = %i\n", bottomUpPhase);
stKVDatabaseConf *kvDatabaseConf = stKVDatabaseConf_constructFromString(cactusDiskDatabaseString);
CactusDisk *cactusDisk = cactusDisk_construct(kvDatabaseConf, false, true);
stKVDatabaseConf_destruct(kvDatabaseConf);
st_logInfo("Set up the flower disk\n");
stKVDatabase *sequenceDatabase = NULL;
if (secondaryDatabaseString != NULL) {
kvDatabaseConf = stKVDatabaseConf_constructFromString(secondaryDatabaseString);
sequenceDatabase = stKVDatabase_construct(kvDatabaseConf, 0);
stKVDatabaseConf_destruct(kvDatabaseConf);
}
FlowerStream *flowerStream = flowerWriter_getFlowerStream(cactusDisk, stdin);
Flower *flower;
while ((flower = flowerStream_getNext(flowerStream)) != NULL) {
st_logDebug("Processing flower %" PRIi64 "\n", flower_getName(flower));
///////////////////////////////////////////////////////////////////////////
// Get the appropriate event names
///////////////////////////////////////////////////////////////////////////
st_logInfo("%s\n", eventTree_makeNewickString(flower_getEventTree(flower)));
Event *referenceEvent = eventTree_getEventByHeader(flower_getEventTree(flower), referenceEventString);
if (referenceEvent == NULL) {
st_errAbort("Reference event %s not found in tree. Check your "
"--referenceEventString option", referenceEventString);
}
Name referenceEventName = event_getName(referenceEvent);
///////////////////////////////////////////////////////////////////////////
// Now do bottom up or top down, depending
///////////////////////////////////////////////////////////////////////////
stList *flowers = stList_construct();
stList_append(flowers, flower);
preCacheNestedFlowers(cactusDisk, flowers);
if (bottomUpPhase) {
assert(sequenceDatabase != NULL);
cactusDisk_preCacheSegmentStrings(cactusDisk, flowers);
bottomUp(flowers, sequenceDatabase, referenceEventName, !flower_hasParentGroup(flower), generateJukesCantorMatrix);
// Unload the nested flowers to save memory. They haven't
// been changed, so we don't write them to the cactus
// disk.
Flower_GroupIterator *groupIt = flower_getGroupIterator(flower);
Group *group;
while ((group = flower_getNextGroup(groupIt)) != NULL) {
if (!group_isLeaf(group)) {
flower_unload(group_getNestedFlower(group));
}
}
flower_destructGroupIterator(groupIt);
assert(!flower_isParentLoaded(flower));
// Write this flower to disk.
cactusDisk_addUpdateRequest(cactusDisk, flower);
} else {
topDown(flower, referenceEventName);
// We've changed the nested flowers, but not this
// flower. We write the nested flowers to disk, then
// unload them to save memory. This flower will be
// unloaded by the flower-stream code.
Flower_GroupIterator *groupIt = flower_getGroupIterator(flower);
Group *group;
while ((group = flower_getNextGroup(groupIt)) != NULL) {
if (!group_isLeaf(group)) {
cactusDisk_addUpdateRequest(cactusDisk, group_getNestedFlower(group));
flower_unload(group_getNestedFlower(group));
}
}
flower_destructGroupIterator(groupIt);
}
stList_destruct(flowers);
}
///////////////////////////////////////////////////////////////////////////
// Write the flower(s) back to disk.
///////////////////////////////////////////////////////////////////////////
cactusDisk_write(cactusDisk);
st_logInfo("Updated the flower on disk\n");
///////////////////////////////////////////////////////////////////////////
//Clean up.
///////////////////////////////////////////////////////////////////////////
if (sequenceDatabase != NULL) {
stKVDatabase_destruct(sequenceDatabase);
}
cactusDisk_destruct(cactusDisk);
return 0; //Exit without clean up is quicker, enable cleanup when doing memory leak detection.
free(cactusDiskDatabaseString);
free(referenceEventString);
free(logLevelString);
st_logInfo("Cleaned stuff up and am finished\n");
return 0;
}
static void cacheSubstringsFromDB(CactusDisk *cactusDisk, stList *substrings) {
/*
* Caches the given set of substrings in the cactusDisk cache.
*/
if (cactusDisk->storeSequencesInAFile) {
if (cactusDisk->sequencesReadFileHandle == NULL) {
if(cactusDisk->sequencesWriteFileHandle != NULL) {
fsync(fileno(cactusDisk->sequencesWriteFileHandle));
fclose(cactusDisk->sequencesWriteFileHandle);
cactusDisk->sequencesWriteFileHandle = NULL;
}
cactusDisk->sequencesReadFileHandle = fopen(cactusDisk->absSequencesFileName, "r");
assert(cactusDisk->sequencesReadFileHandle != NULL);
}
else {
assert(cactusDisk->sequencesWriteFileHandle == NULL);
}
for (int64_t i = 0; i < stList_length(substrings); i++) {
Substring *substring = stList_get(substrings, i);
char *string = getStringFromDisk(cactusDisk->sequencesReadFileHandle, substring->name, substring->start,
substring->length);
stCache_setRecord(cactusDisk->stringCache, substring->name, substring->start, substring->length, string);
#ifndef NDEBUG
int64_t bytesRead;
char *string2 = stCache_getRecord(cactusDisk->stringCache, substring->name, substring->start,
substring->length, &bytesRead);
assert(bytesRead == substring->length);
for (int64_t j = 0; j < substring->length; j++) {
assert(string2[j] == string[j]);
}
free(string2);
#endif
free(string);
}
} else {
stList *getRequests = stList_construct3(0, free);
for (int64_t i = 0; i < stList_length(substrings); i++) {
Substring *substring = stList_get(substrings, i);
int64_t intervalSize = (substring->length + substring->start - 1) / CACTUS_DISK_SEQUENCE_CHUNK_SIZE
- substring->start / CACTUS_DISK_SEQUENCE_CHUNK_SIZE + 1;
Name shiftedName = substring->name + substring->start / CACTUS_DISK_SEQUENCE_CHUNK_SIZE;
for (int64_t j = 0; j < intervalSize; j++) {
int64_t *k = st_malloc(sizeof(int64_t));
k[0] = shiftedName + j;
stList_append(getRequests, k);
}
}
if (stList_length(getRequests) == 0) {
stList_destruct(getRequests);
return;
}
stList *records = NULL;
stTry
{
records = stKVDatabase_bulkGetRecords(cactusDisk->database, getRequests);
}
stCatch(except)
{
stThrowNewCause(except, ST_KV_DATABASE_EXCEPTION_ID,
"An unknown database error occurred when getting a sequence string");
}stTryEnd
;
assert(records != NULL);
assert(stList_length(records) == stList_length(getRequests));
stList_destruct(getRequests);
stListIterator *recordsIt = stList_getIterator(records);
for (int64_t i = 0; i < stList_length(substrings); i++) {
Substring *substring = stList_get(substrings, i);
int64_t intervalSize = (substring->length + substring->start - 1) / CACTUS_DISK_SEQUENCE_CHUNK_SIZE
- substring->start / CACTUS_DISK_SEQUENCE_CHUNK_SIZE + 1;
stList *strings = stList_construct();
while (intervalSize-- > 0) {
int64_t recordSize;
stKVDatabaseBulkResult *result = stList_getNext(recordsIt);
assert(result != NULL);
char *string = stKVDatabaseBulkResult_getRecord(result, &recordSize);
assert(string != NULL);
assert(strlen(string) == recordSize - 1);
stList_append(strings, string);
assert(recordSize <= CACTUS_DISK_SEQUENCE_CHUNK_SIZE + 1);
}
assert(stList_length(strings) > 0);
char *joinedString = stString_join2("", strings);
stCache_setRecord(cactusDisk->stringCache, substring->name,
(substring->start / CACTUS_DISK_SEQUENCE_CHUNK_SIZE) * CACTUS_DISK_SEQUENCE_CHUNK_SIZE,
strlen(joinedString), joinedString);
free(joinedString);
stList_destruct(strings);
}
assert(stList_getNext(recordsIt) == NULL);
stList_destructIterator(recordsIt);
stList_destruct(records);
}
}
static void teardown() {
if(list != NULL) {
stList_destruct(list);
list = NULL;
}
}
int main(int argc, char *argv[]) {
/*
* Script for adding alignments to cactus tree.
*/
int64_t startTime;
stKVDatabaseConf *kvDatabaseConf;
CactusDisk *cactusDisk;
int key, k;
bool (*filterFn)(stPinchSegment *, stPinchSegment *) = NULL;
stSet *outgroupThreads = NULL;
/*
* Arguments/options
*/
char * logLevelString = NULL;
char * alignmentsFile = NULL;
char * constraintsFile = NULL;
char * cactusDiskDatabaseString = NULL;
char * lastzArguments = "";
int64_t minimumSequenceLengthForBlast = 1;
//Parameters for annealing/melting rounds
int64_t *annealingRounds = NULL;
int64_t annealingRoundsLength = 0;
int64_t *meltingRounds = NULL;
int64_t meltingRoundsLength = 0;
//Parameters for melting
float maximumAdjacencyComponentSizeRatio = 10;
int64_t blockTrim = 0;
int64_t alignmentTrimLength = 0;
int64_t *alignmentTrims = NULL;
int64_t chainLengthForBigFlower = 1000000;
int64_t longChain = 2;
int64_t minLengthForChromosome = 1000000;
float proportionOfUnalignedBasesForNewChromosome = 0.8;
bool breakChainsAtReverseTandems = 1;
int64_t maximumMedianSequenceLengthBetweenLinkedEnds = INT64_MAX;
bool realign = 0;
char *realignArguments = "";
bool removeRecoverableChains = false;
bool (*recoverableChainsFilter)(stCactusEdgeEnd *, Flower *) = NULL;
int64_t maxRecoverableChainsIterations = 1;
int64_t maxRecoverableChainLength = INT64_MAX;
//Parameters for removing ancient homologies
bool doPhylogeny = false;
int64_t phylogenyNumTrees = 1;
enum stCaf_RootingMethod phylogenyRootingMethod = BEST_RECON;
enum stCaf_ScoringMethod phylogenyScoringMethod = COMBINED_LIKELIHOOD;
double breakpointScalingFactor = 1.0;
bool phylogenySkipSingleCopyBlocks = 0;
int64_t phylogenyMaxBaseDistance = 1000;
int64_t phylogenyMaxBlockDistance = 100;
bool phylogenyKeepSingleDegreeBlocks = 0;
stList *phylogenyTreeBuildingMethods = stList_construct();
enum stCaf_TreeBuildingMethod defaultMethod = GUIDED_NEIGHBOR_JOINING;
stList_append(phylogenyTreeBuildingMethods, &defaultMethod);
double phylogenyCostPerDupPerBase = 0.2;
double phylogenyCostPerLossPerBase = 0.2;
const char *debugFileName = NULL;
const char *referenceEventHeader = NULL;
double phylogenyDoSplitsWithSupportHigherThanThisAllAtOnce = 1.0;
int64_t numTreeBuildingThreads = 2;
int64_t minimumBlockDegreeToCheckSupport = 10;
double minimumBlockHomologySupport = 0.7;
double nucleotideScalingFactor = 1.0;
HomologyUnitType phylogenyHomologyUnitType = BLOCK;
enum stCaf_DistanceCorrectionMethod phylogenyDistanceCorrectionMethod = JUKES_CANTOR;
bool sortAlignments = false;
///////////////////////////////////////////////////////////////////////////
// (0) Parse the inputs handed by genomeCactus.py / setup stuff.
///////////////////////////////////////////////////////////////////////////
while (1) {
static struct option long_options[] = { { "logLevel", required_argument, 0, 'a' }, { "alignments", required_argument, 0, 'b' }, {
"cactusDisk", required_argument, 0, 'c' }, { "lastzArguments", required_argument, 0, 'd' },
{ "help", no_argument, 0, 'h' }, { "annealingRounds", required_argument, 0, 'i' }, { "trim", required_argument, 0, 'k' }, {
"trimChange", required_argument, 0, 'l', }, { "minimumTreeCoverage", required_argument, 0, 'm' }, { "blockTrim",
required_argument, 0, 'n' }, { "deannealingRounds", required_argument, 0, 'o' }, { "minimumDegree",
required_argument, 0, 'p' }, { "minimumIngroupDegree", required_argument, 0, 'q' }, {
"minimumOutgroupDegree", required_argument, 0, 'r' }, { "alignmentFilter", required_argument, 0, 't' }, {
"minimumSequenceLengthForBlast", required_argument, 0, 'v' }, { "maxAdjacencyComponentSizeRatio",
required_argument, 0, 'w' }, { "constraints", required_argument, 0, 'x' }, { "minLengthForChromosome",
required_argument, 0, 'y' }, { "proportionOfUnalignedBasesForNewChromosome", required_argument, 0, 'z' },
{ "maximumMedianSequenceLengthBetweenLinkedEnds", required_argument, 0, 'A' },
{ "realign", no_argument, 0, 'B' }, { "realignArguments", required_argument, 0, 'C' },
{ "phylogenyNumTrees", required_argument, 0, 'D' },
{ "phylogenyRootingMethod", required_argument, 0, 'E' },
{ "phylogenyScoringMethod", required_argument, 0, 'F' },
{ "phylogenyBreakpointScalingFactor", required_argument, 0, 'G' },
{ "phylogenySkipSingleCopyBlocks", no_argument, 0, 'H' },
{ "phylogenyMaxBaseDistance", required_argument, 0, 'I' },
{ "phylogenyMaxBlockDistance", required_argument, 0, 'J' },
{ "phylogenyDebugFile", required_argument, 0, 'K' },
{ "phylogenyKeepSingleDegreeBlocks", no_argument, 0, 'L' },
{ "phylogenyTreeBuildingMethod", required_argument, 0, 'M' },
{ "phylogenyCostPerDupPerBase", required_argument, 0, 'N' },
{ "phylogenyCostPerLossPerBase", required_argument, 0, 'O' },
{ "referenceEventHeader", required_argument, 0, 'P' },
{ "phylogenyDoSplitsWithSupportHigherThanThisAllAtOnce", required_argument, 0, 'Q' },
{ "numTreeBuildingThreads", required_argument, 0, 'R' },
{ "phylogeny", no_argument, 0, 'S' },
{ "minimumBlockHomologySupport", required_argument, 0, 'T' },
{ "phylogenyNucleotideScalingFactor", required_argument, 0, 'U' },
{ "minimumBlockDegreeToCheckSupport", required_argument, 0, 'V' },
{ "removeRecoverableChains", required_argument, 0, 'W' },
{ "minimumNumberOfSpecies", required_argument, 0, 'X' },
{ "phylogenyHomologyUnitType", required_argument, 0, 'Y' },
{ "phylogenyDistanceCorrectionMethod", required_argument, 0, 'Z' },
{ "maxRecoverableChainsIterations", required_argument, 0, '1' },
{ "maxRecoverableChainLength", required_argument, 0, '2' },
{ 0, 0, 0, 0 } };
int option_index = 0;
key = getopt_long(argc, argv, "a:b:c:hi:k:m:n:o:p:q:r:stv:w:x:y:z:A:BC:D:E:", long_options, &option_index);
if (key == -1) {
break;
}
switch (key) {
case 'a':
logLevelString = stString_copy(optarg);
st_setLogLevelFromString(logLevelString);
break;
case 'b':
alignmentsFile = stString_copy(optarg);
break;
case 'c':
cactusDiskDatabaseString = stString_copy(optarg);
break;
case 'd':
lastzArguments = stString_copy(optarg);
break;
case 'h':
usage();
return 0;
case 'i':
annealingRounds = getInts(optarg, &annealingRoundsLength);
break;
case 'o':
meltingRounds = getInts(optarg, &meltingRoundsLength);
break;
case 'k':
alignmentTrims = getInts(optarg, &alignmentTrimLength);
break;
case 'm':
k = sscanf(optarg, "%f", &minimumTreeCoverage);
assert(k == 1);
break;
case 'n':
k = sscanf(optarg, "%" PRIi64 "", &blockTrim);
assert(k == 1);
break;
case 'p':
k = sscanf(optarg, "%" PRIi64 "", &minimumDegree);
assert(k == 1);
break;
case 'q':
k = sscanf(optarg, "%" PRIi64 "", &minimumIngroupDegree);
assert(k == 1);
break;
case 'r':
k = sscanf(optarg, "%" PRIi64 "", &minimumOutgroupDegree);
assert(k == 1);
break;
case 't':
if (strcmp(optarg, "singleCopyOutgroup") == 0) {
sortAlignments = true;
filterFn = stCaf_filterByOutgroup;
} else if (strcmp(optarg, "relaxedSingleCopyOutgroup") == 0) {
sortAlignments = true;
filterFn = stCaf_relaxedFilterByOutgroup;
} else if (strcmp(optarg, "singleCopy") == 0) {
sortAlignments = true;
filterFn = stCaf_filterByRepeatSpecies;
} else if (strcmp(optarg, "relaxedSingleCopy") == 0) {
sortAlignments = true;
filterFn = stCaf_relaxedFilterByRepeatSpecies;
} else if (strcmp(optarg, "singleCopyChr") == 0) {
sortAlignments = true;
filterFn = stCaf_singleCopyChr;
} else if (strcmp(optarg, "singleCopyIngroup") == 0) {
sortAlignments = true;
filterFn = stCaf_singleCopyIngroup;
} else if (strcmp(optarg, "relaxedSingleCopyIngroup") == 0) {
sortAlignments = true;
filterFn = stCaf_relaxedSingleCopyIngroup;
} else if (strcmp(optarg, "none") == 0) {
sortAlignments = false;
filterFn = NULL;
} else {
st_errAbort("Could not recognize alignmentFilter option %s", optarg);
}
break;
case 'v':
k = sscanf(optarg, "%" PRIi64 "", &minimumSequenceLengthForBlast);
assert(k == 1);
break;
case 'w':
k = sscanf(optarg, "%f", &maximumAdjacencyComponentSizeRatio);
assert(k == 1);
break;
case 'x':
constraintsFile = stString_copy(optarg);
break;
case 'y':
k = sscanf(optarg, "%" PRIi64 "", &minLengthForChromosome);
assert(k == 1);
break;
case 'z':
k = sscanf(optarg, "%f", &proportionOfUnalignedBasesForNewChromosome);
assert(k == 1);
break;
case 'A':
k = sscanf(optarg, "%" PRIi64 "", &maximumMedianSequenceLengthBetweenLinkedEnds);
assert(k == 1);
break;
case 'B':
realign = 1;
break;
case 'C':
realignArguments = stString_copy(optarg);
break;
case 'D':
k = sscanf(optarg, "%" PRIi64, &phylogenyNumTrees);
assert(k == 1);
break;
case 'E':
if (!strcmp(optarg, "outgroupBranch")) {
phylogenyRootingMethod = OUTGROUP_BRANCH;
} else if (!strcmp(optarg, "longestBranch")) {
phylogenyRootingMethod = LONGEST_BRANCH;
} else if (!strcmp(optarg, "bestRecon")) {
phylogenyRootingMethod = BEST_RECON;
} else {
st_errAbort("Invalid tree rooting method: %s", optarg);
}
break;
case 'F':
if (!strcmp(optarg, "reconCost")) {
phylogenyScoringMethod = RECON_COST;
} else if (!strcmp(optarg, "nucLikelihood")) {
phylogenyScoringMethod = NUCLEOTIDE_LIKELIHOOD;
} else if (!strcmp(optarg, "reconLikelihood")) {
phylogenyScoringMethod = RECON_LIKELIHOOD;
} else if (!strcmp(optarg, "combinedLikelihood")) {
phylogenyScoringMethod = COMBINED_LIKELIHOOD;
} else {
st_errAbort("Invalid tree scoring method: %s", optarg);
}
break;
case 'G':
k = sscanf(optarg, "%lf", &breakpointScalingFactor);
assert(k == 1);
break;
case 'H':
phylogenySkipSingleCopyBlocks = true;
break;
case 'I':
k = sscanf(optarg, "%" PRIi64, &phylogenyMaxBaseDistance);
assert(k == 1);
break;
case 'J':
k = sscanf(optarg, "%" PRIi64, &phylogenyMaxBlockDistance);
assert(k == 1);
break;
case 'K':
debugFileName = stString_copy(optarg);
break;
case 'L':
phylogenyKeepSingleDegreeBlocks = true;
break;
case 'M':
// clear the default setting of the list
stList_destruct(phylogenyTreeBuildingMethods);
phylogenyTreeBuildingMethods = stList_construct();
stList *methodStrings = stString_splitByString(optarg, ",");
for (int64_t i = 0; i < stList_length(methodStrings); i++) {
char *methodString = stList_get(methodStrings, i);
enum stCaf_TreeBuildingMethod *method = st_malloc(sizeof(enum stCaf_TreeBuildingMethod));
if (strcmp(methodString, "neighborJoining") == 0) {
*method = NEIGHBOR_JOINING;
} else if (strcmp(methodString, "guidedNeighborJoining") == 0) {
*method = GUIDED_NEIGHBOR_JOINING;
} else if (strcmp(methodString, "splitDecomposition") == 0) {
*method = SPLIT_DECOMPOSITION;
} else if (strcmp(methodString, "strictSplitDecomposition") == 0) {
*method = STRICT_SPLIT_DECOMPOSITION;
} else if (strcmp(methodString, "removeBadChains") == 0) {
*method = REMOVE_BAD_CHAINS;
} else {
st_errAbort("Unknown tree building method: %s", methodString);
}
stList_append(phylogenyTreeBuildingMethods, method);
}
stList_destruct(methodStrings);
break;
case 'N':
k = sscanf(optarg, "%lf", &phylogenyCostPerDupPerBase);
assert(k == 1);
break;
case 'O':
k = sscanf(optarg, "%lf", &phylogenyCostPerLossPerBase);
assert(k == 1);
break;
case 'P':
referenceEventHeader = stString_copy(optarg);
break;
case 'Q':
k = sscanf(optarg, "%lf", &phylogenyDoSplitsWithSupportHigherThanThisAllAtOnce);
assert(k == 1);
break;
case 'R':
k = sscanf(optarg, "%" PRIi64, &numTreeBuildingThreads);
assert(k == 1);
break;
case 'S':
doPhylogeny = true;
break;
case 'T':
k = sscanf(optarg, "%lf", &minimumBlockHomologySupport);
assert(k == 1);
assert(minimumBlockHomologySupport <= 1.0);
assert(minimumBlockHomologySupport >= 0.0);
break;
case 'U':
k = sscanf(optarg, "%lf", &nucleotideScalingFactor);
assert(k == 1);
break;
case 'V':
k = sscanf(optarg, "%" PRIi64, &minimumBlockDegreeToCheckSupport);
assert(k == 1);
break;
case 'W':
if (strcmp(optarg, "1") == 0) {
removeRecoverableChains = true;
recoverableChainsFilter = NULL;
} else if (strcmp(optarg, "unequalNumberOfIngroupCopies") == 0) {
removeRecoverableChains = true;
recoverableChainsFilter = stCaf_chainHasUnequalNumberOfIngroupCopies;
} else if (strcmp(optarg, "unequalNumberOfIngroupCopiesOrNoOutgroup") == 0) {
removeRecoverableChains = true;
recoverableChainsFilter = stCaf_chainHasUnequalNumberOfIngroupCopiesOrNoOutgroup;
} else if (strcmp(optarg, "0") == 0) {
removeRecoverableChains = false;
} else {
st_errAbort("Could not parse removeRecoverableChains argument");
}
break;
case 'X':
k = sscanf(optarg, "%" PRIi64, &minimumNumberOfSpecies);
if (k != 1) {
st_errAbort("Error parsing the minimumNumberOfSpecies argument");
}
break;
case 'Y':
if (strcmp(optarg, "chain") == 0) {
phylogenyHomologyUnitType = CHAIN;
} else if (strcmp(optarg, "block") == 0) {
phylogenyHomologyUnitType = BLOCK;
} else {
st_errAbort("Could not parse the phylogenyHomologyUnitType argument");
}
break;
case 'Z':
if (strcmp(optarg, "jukesCantor") == 0) {
phylogenyDistanceCorrectionMethod = JUKES_CANTOR;
} else if (strcmp(optarg, "none") == 0 ) {
phylogenyDistanceCorrectionMethod = NONE;
} else {
st_errAbort("Could not parse the phylogenyDistanceCorrectionMethod argument");
}
break;
case '1':
k = sscanf(optarg, "%" PRIi64, &maxRecoverableChainsIterations);
if (k != 1) {
st_errAbort("Error parsing the maxRecoverableChainsIterations argument");
}
break;
case '2':
k = sscanf(optarg, "%" PRIi64, &maxRecoverableChainLength);
if (k != 1) {
st_errAbort("Error parsing the maxRecoverableChainLength argument");
}
break;
default:
usage();
return 1;
}
}
///////////////////////////////////////////////////////////////////////////
// (0) Check the inputs.
///////////////////////////////////////////////////////////////////////////
assert(cactusDiskDatabaseString != NULL);
assert(minimumTreeCoverage >= 0.0);
assert(minimumTreeCoverage <= 1.0);
assert(blockTrim >= 0);
assert(annealingRoundsLength >= 0);
for (int64_t i = 0; i < annealingRoundsLength; i++) {
assert(annealingRounds[i] >= 0);
}
assert(meltingRoundsLength >= 0);
for (int64_t i = 1; i < meltingRoundsLength; i++) {
assert(meltingRounds[i - 1] < meltingRounds[i]);
assert(meltingRounds[i - 1] >= 1);
}
assert(alignmentTrimLength >= 0);
for (int64_t i = 0; i < alignmentTrimLength; i++) {
assert(alignmentTrims[i] >= 0);
}
assert(minimumOutgroupDegree >= 0);
assert(minimumIngroupDegree >= 0);
//////////////////////////////////////////////
//Set up logging
//////////////////////////////////////////////
st_setLogLevelFromString(logLevelString);
//////////////////////////////////////////////
//Log (some of) the inputs
//////////////////////////////////////////////
st_logInfo("Flower disk name : %s\n", cactusDiskDatabaseString);
//////////////////////////////////////////////
//Load the database
//////////////////////////////////////////////
kvDatabaseConf = stKVDatabaseConf_constructFromString(cactusDiskDatabaseString);
cactusDisk = cactusDisk_construct(kvDatabaseConf, 0);
st_logInfo("Set up the flower disk\n");
///////////////////////////////////////////////////////////////////////////
// Sort the constraints
///////////////////////////////////////////////////////////////////////////
stPinchIterator *pinchIteratorForConstraints = NULL;
if (constraintsFile != NULL) {
pinchIteratorForConstraints = stPinchIterator_constructFromFile(constraintsFile);
st_logInfo("Created an iterator for the alignment constaints from file: %s\n", constraintsFile);
}
///////////////////////////////////////////////////////////////////////////
// Do the alignment
///////////////////////////////////////////////////////////////////////////
startTime = time(NULL);
stList *flowers = flowerWriter_parseFlowersFromStdin(cactusDisk);
if (alignmentsFile == NULL) {
cactusDisk_preCacheStrings(cactusDisk, flowers);
}
char *tempFile1 = NULL;
for (int64_t i = 0; i < stList_length(flowers); i++) {
flower = stList_get(flowers, i);
if (!flower_builtBlocks(flower)) { // Do nothing if the flower already has defined blocks
st_logDebug("Processing flower: %lli\n", flower_getName(flower));
stCaf_setFlowerForAlignmentFiltering(flower);
//Set up the graph and add the initial alignments
stPinchThreadSet *threadSet = stCaf_setup(flower);
//Build the set of outgroup threads
outgroupThreads = stCaf_getOutgroupThreads(flower, threadSet);
//Setup the alignments
stPinchIterator *pinchIterator;
stList *alignmentsList = NULL;
if (alignmentsFile != NULL) {
assert(i == 0);
assert(stList_length(flowers) == 1);
if (sortAlignments) {
tempFile1 = getTempFile();
stCaf_sortCigarsFileByScoreInDescendingOrder(alignmentsFile, tempFile1);
pinchIterator = stPinchIterator_constructFromFile(tempFile1);
} else {
pinchIterator = stPinchIterator_constructFromFile(alignmentsFile);
}
} else {
if (tempFile1 == NULL) {
tempFile1 = getTempFile();
}
alignmentsList = stCaf_selfAlignFlower(flower, minimumSequenceLengthForBlast, lastzArguments, realign, realignArguments, tempFile1);
if (sortAlignments) {
stCaf_sortCigarsByScoreInDescendingOrder(alignmentsList);
}
st_logDebug("Ran lastz and have %" PRIi64 " alignments\n", stList_length(alignmentsList));
pinchIterator = stPinchIterator_constructFromList(alignmentsList);
}
for (int64_t annealingRound = 0; annealingRound < annealingRoundsLength; annealingRound++) {
int64_t minimumChainLength = annealingRounds[annealingRound];
int64_t alignmentTrim = annealingRound < alignmentTrimLength ? alignmentTrims[annealingRound] : 0;
st_logDebug("Starting annealing round with a minimum chain length of %" PRIi64 " and an alignment trim of %" PRIi64 "\n", minimumChainLength, alignmentTrim);
stPinchIterator_setTrim(pinchIterator, alignmentTrim);
//Add back in the constraints
if (pinchIteratorForConstraints != NULL) {
stCaf_anneal(threadSet, pinchIteratorForConstraints, filterFn);
}
//Do the annealing
if (annealingRound == 0) {
stCaf_anneal(threadSet, pinchIterator, filterFn);
} else {
stCaf_annealBetweenAdjacencyComponents(threadSet, pinchIterator, filterFn);
}
// Dump the block degree and length distribution to a file
if (debugFileName != NULL) {
dumpBlockInfo(threadSet, stString_print("%s-blockStats-preMelting", debugFileName));
}
printf("Sequence graph statistics after annealing:\n");
printThreadSetStatistics(threadSet, flower, stdout);
// Check for poorly-supported blocks--those that have
// been transitively aligned together but with very
// few homologies supporting the transitive
// alignment. These "megablocks" can snarl up the
// graph so that a lot of extra gets thrown away in
// the first melting step.
stPinchThreadSetBlockIt blockIt = stPinchThreadSet_getBlockIt(threadSet);
stPinchBlock *block;
while ((block = stPinchThreadSetBlockIt_getNext(&blockIt)) != NULL) {
if (stPinchBlock_getDegree(block) > minimumBlockDegreeToCheckSupport) {
uint64_t supportingHomologies = stPinchBlock_getNumSupportingHomologies(block);
uint64_t possibleSupportingHomologies = numPossibleSupportingHomologies(block, flower);
double support = ((double) supportingHomologies) / possibleSupportingHomologies;
if (support < minimumBlockHomologySupport) {
fprintf(stdout, "Destroyed a megablock with degree %" PRIi64
" and %" PRIi64 " supporting homologies out of a maximum "
"of %" PRIi64 " (%lf%%).\n", stPinchBlock_getDegree(block),
supportingHomologies, possibleSupportingHomologies, support);
stPinchBlock_destruct(block);
}
}
}
//Do the melting rounds
for (int64_t meltingRound = 0; meltingRound < meltingRoundsLength; meltingRound++) {
int64_t minimumChainLengthForMeltingRound = meltingRounds[meltingRound];
st_logDebug("Starting melting round with a minimum chain length of %" PRIi64 " \n", minimumChainLengthForMeltingRound);
if (minimumChainLengthForMeltingRound >= minimumChainLength) {
break;
}
stCaf_melt(flower, threadSet, NULL, 0, minimumChainLengthForMeltingRound, 0, INT64_MAX);
} st_logDebug("Last melting round of cycle with a minimum chain length of %" PRIi64 " \n", minimumChainLength);
stCaf_melt(flower, threadSet, NULL, 0, minimumChainLength, breakChainsAtReverseTandems, maximumMedianSequenceLengthBetweenLinkedEnds);
//This does the filtering of blocks that do not have the required species/tree-coverage/degree.
stCaf_melt(flower, threadSet, blockFilterFn, blockTrim, 0, 0, INT64_MAX);
}
if (removeRecoverableChains) {
stCaf_meltRecoverableChains(flower, threadSet, breakChainsAtReverseTandems, maximumMedianSequenceLengthBetweenLinkedEnds, recoverableChainsFilter, maxRecoverableChainsIterations, maxRecoverableChainLength);
}
if (debugFileName != NULL) {
dumpBlockInfo(threadSet, stString_print("%s-blockStats-postMelting", debugFileName));
}
printf("Sequence graph statistics after melting:\n");
printThreadSetStatistics(threadSet, flower, stdout);
// Build a tree for each block, then use each tree to
// partition the homologies between the ingroups sequences
// into those that occur before the speciation with the
// outgroup and those which occur late.
if (stSet_size(outgroupThreads) > 0 && doPhylogeny) {
st_logDebug("Starting to build trees and partition ingroup homologies\n");
stHash *threadStrings = stCaf_getThreadStrings(flower, threadSet);
st_logDebug("Got sets of thread strings and set of threads that are outgroups\n");
stCaf_PhylogenyParameters params;
params.distanceCorrectionMethod = phylogenyDistanceCorrectionMethod;
params.treeBuildingMethods = phylogenyTreeBuildingMethods;
params.rootingMethod = phylogenyRootingMethod;
params.scoringMethod = phylogenyScoringMethod;
params.breakpointScalingFactor = breakpointScalingFactor;
params.nucleotideScalingFactor = nucleotideScalingFactor;
params.skipSingleCopyBlocks = phylogenySkipSingleCopyBlocks;
params.keepSingleDegreeBlocks = phylogenyKeepSingleDegreeBlocks;
params.costPerDupPerBase = phylogenyCostPerDupPerBase;
params.costPerLossPerBase = phylogenyCostPerLossPerBase;
params.maxBaseDistance = phylogenyMaxBaseDistance;
params.maxBlockDistance = phylogenyMaxBlockDistance;
params.numTrees = phylogenyNumTrees;
params.ignoreUnalignedBases = 1;
params.onlyIncludeCompleteFeatureBlocks = 0;
params.doSplitsWithSupportHigherThanThisAllAtOnce = phylogenyDoSplitsWithSupportHigherThanThisAllAtOnce;
params.numTreeBuildingThreads = numTreeBuildingThreads;
assert(params.numTreeBuildingThreads >= 1);
stCaf_buildTreesToRemoveAncientHomologies(
threadSet, phylogenyHomologyUnitType, threadStrings, outgroupThreads, flower, ¶ms,
debugFileName == NULL ? NULL : stString_print("%s-phylogeny", debugFileName), referenceEventHeader);
stHash_destruct(threadStrings);
st_logDebug("Finished building trees\n");
if (removeRecoverableChains) {
// We melt recoverable chains after splitting, as
// well as before, to alleviate coverage loss
// caused by bad splits.
stCaf_meltRecoverableChains(flower, threadSet, breakChainsAtReverseTandems, maximumMedianSequenceLengthBetweenLinkedEnds, recoverableChainsFilter, maxRecoverableChainsIterations, maxRecoverableChainLength);
}
// Enforce the block constraints on minimum degree,
// etc. after splitting.
stCaf_melt(flower, threadSet, blockFilterFn, 0, 0, 0, INT64_MAX);
}
//Sort out case when we allow blocks of degree 1
if (minimumDegree < 2) {
st_logDebug("Creating degree 1 blocks\n");
stCaf_makeDegreeOneBlocks(threadSet);
stCaf_melt(flower, threadSet, blockFilterFn, blockTrim, 0, 0, INT64_MAX);
} else if (maximumAdjacencyComponentSizeRatio < INT64_MAX) { //Deal with giant components
st_logDebug("Breaking up components greedily\n");
stCaf_breakupComponentsGreedily(threadSet, maximumAdjacencyComponentSizeRatio);
}
//Finish up
stCaf_finish(flower, threadSet, chainLengthForBigFlower, longChain, minLengthForChromosome,
proportionOfUnalignedBasesForNewChromosome); //Flower is then destroyed at this point.
st_logInfo("Ran the cactus core script\n");
//Cleanup
stPinchThreadSet_destruct(threadSet);
stPinchIterator_destruct(pinchIterator);
stSet_destruct(outgroupThreads);
if (alignmentsList != NULL) {
stList_destruct(alignmentsList);
}
st_logInfo("Cleaned up from main loop\n");
} else {
st_logInfo("We've already built blocks / alignments for this flower\n");
}
}
stList_destruct(flowers);
if (tempFile1 != NULL) {
st_system("rm %s", tempFile1);
}
if (constraintsFile != NULL) {
stPinchIterator_destruct(pinchIteratorForConstraints);
}
///////////////////////////////////////////////////////////////////////////
// Write the flower to disk.
///////////////////////////////////////////////////////////////////////////
st_logDebug("Writing the flowers to disk\n");
cactusDisk_write(cactusDisk);
st_logInfo("Updated the flower on disk and %" PRIi64 " seconds have elapsed\n", time(NULL) - startTime);
///////////////////////////////////////////////////////////////////////////
// Clean up.
///////////////////////////////////////////////////////////////////////////
cactusDisk_destruct(cactusDisk);
}
int main(int argc, char *argv[]) {
// Parse arguments
if (argc != 3) {
usage(argv);
return 1;
}
// You would load a custom HMM here if you wanted using
// hmm_getStateMachine (see the realign code)
StateMachine *stateMachine = stateMachine5_construct(fiveState);
PairwiseAlignmentParameters *parameters = pairwiseAlignmentBandingParameters_construct();
stHash *targetSequences = readFastaFile(argv[1]);
stHash *querySequences = readFastaFile(argv[2]);
// For each query sequence, align it against all target sequences.
stHashIterator *queryIt = stHash_getIterator(querySequences);
char *queryHeader;
while ((queryHeader = stHash_getNext(queryIt)) != NULL) {
char *querySeq = stHash_search(querySequences, queryHeader);
stHashIterator *targetIt = stHash_getIterator(targetSequences);
char *targetHeader;
while ((targetHeader = stHash_getNext(targetIt)) != NULL) {
char *targetSeq = stHash_search(targetSequences, targetHeader);
// Here we should try both the target sequence and its
// reverse-complemented version
// Aligns the sequences.
// If you have alignment constraints (anchors) you should
// replace this with getAlignedPairsUsingAnchors.
stList *alignedPairs = getAlignedPairs(stateMachine, targetSeq,
querySeq, parameters,
true, true);
// Takes into account the probability of aligning to a
// gap, by transforming the posterior probability into the
// AMAP objective function (see Schwartz & Pachter, 2007).
alignedPairs = reweightAlignedPairs2(alignedPairs, strlen(targetSeq),
strlen(querySeq),
parameters->gapGamma);
// I think this calculates the optimal ordered set of
// alignments from the unordered set of aligned pairs, not
// completely sure.
alignedPairs = filterPairwiseAlignmentToMakePairsOrdered(alignedPairs,
targetSeq,
querySeq,
// This parameter says that the minimum posterior probability we will accept has to be at least 0.9.
0.9);
// After this the "aligned pairs" data structure changes,
// which is a little sketchy. It's just so that the
// alignment can be printed properly.
stList_mapReplace(alignedPairs, convertToAnchorPair, NULL);
stList_sort(alignedPairs, (int (*)(const void *, const void *)) stIntTuple_cmpFn);
struct PairwiseAlignment *alignment = convertAlignedPairsToPairwiseAlignment(targetHeader, queryHeader,
0, strlen(targetSeq), strlen(querySeq), alignedPairs);
// Output the cigar string
cigarWrite(stdout, alignment, 0);
stList_destruct(alignedPairs);
destructPairwiseAlignment(alignment);
}
stHash_destructIterator(targetIt);
}
stHash_destructIterator(queryIt);
// Clean up
stHash_destruct(targetSequences);
stHash_destruct(querySequences);
pairwiseAlignmentBandingParameters_destruct(parameters);
stateMachine_destruct(stateMachine);
}
static void partialRecordRetrieval(CuTest *testCase) {
setup();
//Make some number of large records
stList *records = stList_construct3(0, free);
stList *recordSizes = stList_construct3(0, (void(*)(void *)) stIntTuple_destruct);
for (int32_t i = 0; i < 300; i++) {
int32_t size = st_randomInt(0, 80);
size = size * size * size; //Use cubic size distribution
char *randomRecord = st_malloc(size * sizeof(char));
for (int32_t j = 0; j < size; j++) {
randomRecord[j] = (char) st_randomInt(0, 100);
}
stList_append(records, randomRecord);
stList_append(recordSizes, stIntTuple_construct(1, size));
CuAssertTrue(testCase, !stKVDatabase_containsRecord(database, i));
stKVDatabase_insertRecord(database, i, randomRecord, size * sizeof(char));
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, i));
//st_uglyf("I am creating the record %i %i\n", i, size);
}
while (st_random() > 0.001) {
int32_t recordKey = st_randomInt(0, stList_length(records));
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, recordKey));
char *record = stList_get(records, recordKey);
int32_t size = stIntTuple_getPosition(stList_get(recordSizes, recordKey), 0);
//Get partial record
int32_t start = size > 0 ? st_randomInt(0, size) : 0;
int32_t partialSize = size - start > 0 ? st_randomInt(start, size) - start : 0;
assert(start >= 0);
assert(partialSize >= 0);
assert(partialSize + start <= size);
//st_uglyf("I am getting record %i %i %i %i\n", recordKey, start, partialSize, size);
char *partialRecord = stKVDatabase_getPartialRecord(database, recordKey, start * sizeof(char),
partialSize * sizeof(char), size * sizeof(char));
//Check they are equivalent..
for (int32_t i = 0; i < partialSize; i++) {
if (record[start + i] != partialRecord[i]) {
st_uglyf("There was a difference %i %i for record %i %i\n", record[start + i], partialRecord[i], i,
partialSize);
}
//CuAssertTrue(testCase, record[start + i] == partialRecord[i]);
}
//Check we can not get out of bounds.. (start less than zero)
stTry {
stKVDatabase_getPartialRecord(database, recordKey, -1, 1, size * sizeof(char));
}stCatch(except)
{
CuAssertTrue(testCase, stExcept_getId(except) == ST_KV_DATABASE_EXCEPTION_ID);
}stTryEnd;
//Check we can not get out of bounds.. (start greater than index start)
stTry {
stKVDatabase_getPartialRecord(database, recordKey, size, 1, size * sizeof(char));
}stCatch(except)
{
CuAssertTrue(testCase, stExcept_getId(except) == ST_KV_DATABASE_EXCEPTION_ID);
}stTryEnd;
//Check we can not get out of bounds.. (total size if greater than record length)
stTry {
stKVDatabase_getPartialRecord(database, recordKey, 0, size + 1, size * sizeof(char));
}stCatch(except)
{
CuAssertTrue(testCase, stExcept_getId(except) == ST_KV_DATABASE_EXCEPTION_ID);
}stTryEnd;
//Check we can not get non existent record
stTry {
stKVDatabase_getPartialRecord(database, 1000000, 0, size, size * sizeof(char));
}stCatch(except)
{
CuAssertTrue(testCase, stExcept_getId(except) == ST_KV_DATABASE_EXCEPTION_ID);
}stTryEnd;
}
stList_destruct(records);
stList_destruct(recordSizes);
teardown();
}
static void testBulkGetRecords(CuTest* testCase) {
/*
* Tests the new bulk get functions
*/
setup();
int64_t i = 100, j = 110, k = 120, l = 130;
int64_t bigRecSize = 184500800;
int64_t* m = (int64_t*)st_malloc(bigRecSize);
int64_t ki = 4, kj = 5, kk = 3, kl = 1, km = 2;
stKVDatabase_insertRecord(database, 1, &i, sizeof(int64_t));
stList *requests = stList_construct3(0, (void(*)(void *)) stKVDatabaseBulkRequest_destruct);
stList_append(requests, stKVDatabaseBulkRequest_constructInsertRequest(ki, &i, sizeof(int64_t)));
stList_append(requests, stKVDatabaseBulkRequest_constructInsertRequest(kj, &j, sizeof(int64_t)));
stList_append(requests, stKVDatabaseBulkRequest_constructSetRequest(kk, &k, sizeof(int64_t)));
stList_append(requests, stKVDatabaseBulkRequest_constructUpdateRequest(kl, &l, sizeof(int64_t)));
stKVDatabase_bulkSetRecords(database, requests);
stList_destruct(requests);
stKVDatabase_setRecord(database, km, m, bigRecSize);
stList* keys = stList_construct2(5);
stList_set(keys, 0, &ki);
stList_set(keys, 1, &kj);
stList_set(keys, 2, &kk);
stList_set(keys, 3, &kl);
stList_set(keys, 4, &km);
stList* results = stKVDatabase_bulkGetRecords(database, keys);
CuAssertTrue(testCase, stList_length(results) == 5);
void* record;
int64_t size;
stKVDatabaseBulkResult* res0 = (stKVDatabaseBulkResult*)stList_get(results, 0);
record = stKVDatabaseBulkResult_getRecord(res0, &size);
CuAssertTrue(testCase, record != NULL);
CuAssertTrue(testCase, *(int64_t*)record == i && size == sizeof(int64_t));
stKVDatabaseBulkResult* res1 = (stKVDatabaseBulkResult*)stList_get(results, 1);
record = stKVDatabaseBulkResult_getRecord(res1, &size);
CuAssertTrue(testCase, record != NULL);
CuAssertTrue(testCase, *(int64_t*)record == j && size == sizeof(int64_t));
stKVDatabaseBulkResult* res2 = (stKVDatabaseBulkResult*)stList_get(results, 2);
record = stKVDatabaseBulkResult_getRecord(res2, &size);
CuAssertTrue(testCase, record != NULL);
CuAssertTrue(testCase, *(int64_t*)record == k && size == sizeof(int64_t));
stKVDatabaseBulkResult* res3 = (stKVDatabaseBulkResult*)stList_get(results, 3);
record = stKVDatabaseBulkResult_getRecord(res3, &size);
CuAssertTrue(testCase, record != NULL);
CuAssertTrue(testCase, *(int64_t*)record == l && size == sizeof(int64_t));
stKVDatabaseBulkResult* res4 = (stKVDatabaseBulkResult*)stList_get(results, 4);
record = stKVDatabaseBulkResult_getRecord(res4, &size);
CuAssertTrue(testCase, record != NULL);
CuAssertTrue(testCase, size == bigRecSize);
stList_destruct(results);
results = stKVDatabase_bulkGetRecordsRange(database, 1, 6);
CuAssertTrue(testCase, stList_length(results) == 6);
res0 = (stKVDatabaseBulkResult*)stList_get(results, 0);
record = stKVDatabaseBulkResult_getRecord(res0, &size);
CuAssertTrue(testCase, record != NULL);
CuAssertTrue(testCase, *(int64_t*)record == l && size == sizeof(int64_t));
res1 = (stKVDatabaseBulkResult*)stList_get(results, 1);
record = stKVDatabaseBulkResult_getRecord(res1, &size);
CuAssertTrue(testCase, record != NULL);
CuAssertTrue(testCase, size == bigRecSize);
res2 = (stKVDatabaseBulkResult*)stList_get(results, 2);
record = stKVDatabaseBulkResult_getRecord(res2, &size);
CuAssertTrue(testCase, record != NULL);
CuAssertTrue(testCase, *(int64_t*)record == k && size == sizeof(int64_t));
res3 = (stKVDatabaseBulkResult*)stList_get(results, 3);
record = stKVDatabaseBulkResult_getRecord(res3, &size);
CuAssertTrue(testCase, record != NULL);
CuAssertTrue(testCase, *(int64_t*)record == i && size == sizeof(int64_t));
res4 = (stKVDatabaseBulkResult*)stList_get(results, 4);
record = stKVDatabaseBulkResult_getRecord(res4, &size);
CuAssertTrue(testCase, record != NULL);
CuAssertTrue(testCase, *(int64_t*)record == j && size == sizeof(int64_t));
stKVDatabaseBulkResult* res5 = (stKVDatabaseBulkResult*)stList_get(results, 5);
record = stKVDatabaseBulkResult_getRecord(res5, &size);
CuAssertTrue(testCase, record == NULL);
stList_destruct(results);
free(m);
teardown();
}
int main(int argc, char *argv[]) {
/*
* Open the database.
* Construct a flower.
* Construct an event tree representing the species tree.
* For each sequence contruct two ends each containing an cap.
* Make a file for the sequence.
* Link the two caps.
* Finish!
*/
int64_t key, j;
Group *group;
Flower_EndIterator *endIterator;
End *end;
bool makeEventHeadersAlphaNumeric = 0;
/*
* Arguments/options
*/
char * logLevelString = NULL;
char * speciesTree = NULL;
char * outgroupEvents = NULL;
///////////////////////////////////////////////////////////////////////////
// (0) Parse the inputs handed by genomeCactus.py / setup stuff.
///////////////////////////////////////////////////////////////////////////
while (1) {
static struct option long_options[] = { { "logLevel", required_argument, 0, 'a' }, { "cactusDisk", required_argument, 0, 'b' }, {
"speciesTree", required_argument, 0, 'f' }, { "outgroupEvents", required_argument, 0, 'g' },
{ "help", no_argument, 0, 'h' }, { "makeEventHeadersAlphaNumeric", no_argument, 0, 'i' }, { 0, 0, 0, 0 } };
int option_index = 0;
key = getopt_long(argc, argv, "a:b:f:hg:i", long_options, &option_index);
if (key == -1) {
break;
}
switch (key) {
case 'a':
logLevelString = optarg;
break;
case 'b':
cactusDiskDatabaseString = optarg;
break;
case 'f':
speciesTree = optarg;
break;
case 'g':
outgroupEvents = optarg;
break;
case 'h':
usage();
return 0;
case 'i':
makeEventHeadersAlphaNumeric = 1;
break;
default:
usage();
return 1;
}
}
///////////////////////////////////////////////////////////////////////////
// (0) Check the inputs.
///////////////////////////////////////////////////////////////////////////
//assert(logLevelString == NULL || strcmp(logLevelString, "CRITICAL") == 0 || strcmp(logLevelString, "INFO") == 0 || strcmp(logLevelString, "DEBUG") == 0);
assert(cactusDiskDatabaseString != NULL);
assert(speciesTree != NULL);
//////////////////////////////////////////////
//Set up logging
//////////////////////////////////////////////
st_setLogLevelFromString(logLevelString);
//////////////////////////////////////////////
//Log (some of) the inputs
//////////////////////////////////////////////
st_logInfo("Flower disk name : %s\n", cactusDiskDatabaseString);
for (j = optind; j < argc; j++) {
st_logInfo("Sequence file/directory %s\n", argv[j]);
}
//////////////////////////////////////////////
//Load the database
//////////////////////////////////////////////
stKVDatabaseConf *kvDatabaseConf = kvDatabaseConf = stKVDatabaseConf_constructFromString(cactusDiskDatabaseString);
if (stKVDatabaseConf_getType(kvDatabaseConf) == stKVDatabaseTypeTokyoCabinet || stKVDatabaseConf_getType(kvDatabaseConf)
== stKVDatabaseTypeKyotoTycoon) {
assert(stKVDatabaseConf_getDir(kvDatabaseConf) != NULL);
cactusDisk = cactusDisk_construct2(kvDatabaseConf, "cactusSequences");
} else {
cactusDisk = cactusDisk_construct(kvDatabaseConf, 1);
}
st_logInfo("Set up the flower disk\n");
//////////////////////////////////////////////
//Construct the flower
//////////////////////////////////////////////
if (cactusDisk_getFlower(cactusDisk, 0) != NULL) {
cactusDisk_destruct(cactusDisk);
st_logInfo("The first flower already exists\n");
return 0;
}
flower = flower_construct2(0, cactusDisk);
assert(flower_getName(flower) == 0);
st_logInfo("Constructed the flower\n");
//////////////////////////////////////////////
//Construct the event tree
//////////////////////////////////////////////
st_logInfo("Going to build the event tree with newick string: %s\n", speciesTree);
stTree *tree = stTree_parseNewickString(speciesTree);
st_logInfo("Parsed the tree\n");
if (makeEventHeadersAlphaNumeric) {
makeEventHeadersAlphaNumericFn(tree);
}
stTree_setBranchLength(tree, INT64_MAX);
checkBranchLengthsAreDefined(tree);
eventTree = eventTree_construct2(flower); //creates the event tree and the root even
totalEventNumber = 1;
st_logInfo("Constructed the basic event tree\n");
// Construct a set of outgroup names so that ancestral outgroups
// get recognized.
stSet *outgroupNameSet = stSet_construct3(stHash_stringKey,
stHash_stringEqualKey,
free);
if(outgroupEvents != NULL) {
stList *outgroupNames = stString_split(outgroupEvents);
for(int64_t i = 0; i < stList_length(outgroupNames); i++) {
char *outgroupName = stList_get(outgroupNames, i);
stSet_insert(outgroupNameSet, stString_copy(outgroupName));
}
stList_destruct(outgroupNames);
}
//now traverse the tree
j = optind;
assignEventsAndSequences(eventTree_getRootEvent(eventTree), tree,
outgroupNameSet, argv, &j);
char *eventTreeString = eventTree_makeNewickString(eventTree);
st_logInfo(
"Constructed the initial flower with %" PRIi64 " sequences and %" PRIi64 " events with string: %s\n",
totalSequenceNumber, totalEventNumber, eventTreeString);
assert(event_getSubTreeBranchLength(eventTree_getRootEvent(eventTree)) >= 0.0);
free(eventTreeString);
//assert(0);
//////////////////////////////////////////////
//Label any outgroup events.
//////////////////////////////////////////////
if (outgroupEvents != NULL) {
stList *outgroupEventsList = stString_split(outgroupEvents);
for (int64_t i = 0; i < stList_length(outgroupEventsList); i++) {
char *outgroupEvent = makeEventHeadersAlphaNumeric ? makeAlphaNumeric(stList_get(outgroupEventsList, i)) : stString_copy(stList_get(outgroupEventsList, i));
Event *event = eventTree_getEventByHeader(eventTree, outgroupEvent);
if (event == NULL) {
st_errAbort("Got an outgroup string that does not match an event, outgroup string %s", outgroupEvent);
}
assert(!event_isOutgroup(event));
event_setOutgroupStatus(event, 1);
assert(event_isOutgroup(event));
free(outgroupEvent);
}
stList_destruct(outgroupEventsList);
}
//////////////////////////////////////////////
//Construct the terminal group.
//////////////////////////////////////////////
if (flower_getEndNumber(flower) > 0) {
group = group_construct2(flower);
endIterator = flower_getEndIterator(flower);
while ((end = flower_getNextEnd(endIterator)) != NULL) {
end_setGroup(end, group);
}
flower_destructEndIterator(endIterator);
assert(group_isLeaf(group));
// Create a one link chain if there is only one pair of attached ends..
group_constructChainForLink(group);
assert(!flower_builtBlocks(flower));
} else {
flower_setBuiltBlocks(flower, 1);
}
///////////////////////////////////////////////////////////////////////////
// Write the flower to disk.
///////////////////////////////////////////////////////////////////////////
//flower_check(flower);
cactusDisk_write(cactusDisk);
st_logInfo("Updated the flower on disk\n");
///////////////////////////////////////////////////////////////////////////
// Cleanup.
///////////////////////////////////////////////////////////////////////////
cactusDisk_destruct(cactusDisk);
return 0; //Exit without clean up is quicker, enable cleanup when doing memory leak detection.
stSet_destruct(outgroupNameSet);
stTree_destruct(tree);
stKVDatabaseConf_destruct(kvDatabaseConf);
return 0;
}
static stList *splitMultipleStubCycle(stList *cycle,
stList *nonZeroWeightAdjacencyEdges, stSortedSet *allAdjacencyEdges,
stList *stubEdges, stList *chainEdges) {
/*
* Takes a simple cycle containing k stub edges and splits into k cycles, each containing 1 stub edge.
*/
/*
* Get sub-components containing only adjacency and chain edges.
*/
stSortedSet *stubAndChainEdgesSet = getSetOfMergedLists(stubEdges,
chainEdges);
stList *adjacencyEdgeMatching =
stList_filterToExclude(cycle, stubAndChainEdgesSet); //Filter out the the non-adjacency edges
//Make it only the chain edges present in the original component
stList *stubFreePaths = getComponents2(adjacencyEdgeMatching, NULL,
chainEdges);
stList_destruct(adjacencyEdgeMatching);
assert(stList_length(stubFreePaths) >= 1);
stList *splitCycles = stList_construct3(0,
(void(*)(void *)) stList_destruct); //The list to return.
if (stList_length(stubFreePaths) > 1) {
/*
* Build the list of adjacency edges acceptable in the merge
*/
stSortedSet *oddNodes = getOddNodes(cycle);
stList *oddToEvenNonZeroWeightAdjacencyEdges =
getOddToEvenAdjacencyEdges(oddNodes,
nonZeroWeightAdjacencyEdges);
stSortedSet *oddToEvenAllAdjacencyEdges = getOddToEvenAdjacencyEdges2(oddNodes, allAdjacencyEdges);
/*
* Merge together the best two components.
*/
stList *l = filterListsToExclude(stubFreePaths, stubAndChainEdgesSet);
doBestMergeOfTwoSimpleCycles(l, oddToEvenNonZeroWeightAdjacencyEdges,
oddToEvenAllAdjacencyEdges); //This is inplace.
stList *l2 = stList_join(l);
stList_destruct(l);
l = getComponents2(l2, stubEdges, chainEdges);
assert(stList_length(l) == 2);
stList_destruct(l2);
/*
* Cleanup
*/
stSortedSet_destruct(oddNodes);
stList_destruct(oddToEvenNonZeroWeightAdjacencyEdges);
stSortedSet_destruct(oddToEvenAllAdjacencyEdges);
/*
* Call procedure recursively.
*/
for (int64_t i = 0; i < stList_length(l); i++) {
/*
* Split into adjacency edges, stub edges and chain edges.
*/
stList *subCycle = stList_get(l, i);
stList *subAdjacencyEdges;
stList *subStubEdges;
stList *subChainEdges;
splitIntoAdjacenciesStubsAndChains(subCycle,
nonZeroWeightAdjacencyEdges, stubEdges, chainEdges,
&subAdjacencyEdges, &subStubEdges, &subChainEdges);
/*
* Call recursively.
*/
l2 = splitMultipleStubCycle(subCycle, subAdjacencyEdges,
allAdjacencyEdges, subStubEdges, subChainEdges);
stList_appendAll(splitCycles, l2);
/*
* Clean up
*/
stList_setDestructor(l2, NULL);
stList_destruct(l2);
stList_destruct(subAdjacencyEdges);
stList_destruct(subStubEdges);
stList_destruct(subChainEdges);
}
stList_destruct(l);
} else {
stList_append(splitCycles, stList_copy(cycle, NULL));
}
stSortedSet_destruct(stubAndChainEdgesSet);
stList_destruct(stubFreePaths);
return splitCycles;
}