int stSortedSet_equals(stSortedSet *sortedSet1, stSortedSet *sortedSet2) {
if(stSortedSet_size(sortedSet1) != stSortedSet_size(sortedSet2)) {
return 0;
}
if(!stSortedSet_comparatorsEqual(sortedSet1, sortedSet2)) {
return 0;
}
int (*cmpFn)(const void *, const void *) = stSortedSet_getComparator(sortedSet1)->compareFn;
stSortedSetIterator *it1 = stSortedSet_getIterator(sortedSet1);
stSortedSetIterator *it2 = stSortedSet_getIterator(sortedSet2);
void *o1 = stSortedSet_getNext(it1), *o2 = stSortedSet_getNext(it2);
while(o1 != NULL && o2 != NULL) {
if(cmpFn(o1, o2) != 0) {
stSortedSet_destructIterator(it1);
stSortedSet_destructIterator(it2);
return 0;
}
o1 = stSortedSet_getNext(it1);
o2 = stSortedSet_getNext(it2);
}
stSortedSet_destructIterator(it1);
stSortedSet_destructIterator(it2);
return 1;
}
static void checkComponents(CuTest *testCase, stList *filteredEdges) {
stHash *nodesToComponents = getComponents(filteredEdges);
//Check all components are smaller than threshold
stList *components = stHash_getValues(nodesToComponents);
for (int64_t i = 0; i < stList_length(components); i++) {
stSortedSet *component = stList_get(components, i);
CuAssertTrue(testCase, stSortedSet_size(component) <= maxComponentSize);
CuAssertTrue(testCase, stSortedSet_size(component) >= 1);
}
//Check no edges can be added from those filtered.
stSortedSet *filteredEdgesSet = stList_getSortedSet(filteredEdges, (int(*)(const void *, const void *)) stIntTuple_cmpFn);
for (int64_t i = 0; i < stList_length(edges); i++) {
stIntTuple *edge = stList_get(edges, i);
if (stSortedSet_search(filteredEdgesSet, edge) == NULL) {
stIntTuple *node1 = stIntTuple_construct1( stIntTuple_get(edge, 1));
stIntTuple *node2 = stIntTuple_construct1( stIntTuple_get(edge, 2));
stSortedSet *component1 = stHash_search(nodesToComponents, node1);
stSortedSet *component2 = stHash_search(nodesToComponents, node2);
CuAssertTrue(testCase, component1 != NULL && component2 != NULL);
CuAssertTrue(testCase, component1 != component2);
CuAssertTrue(testCase, stSortedSet_size(component1) + stSortedSet_size(component2) > maxComponentSize);
stIntTuple_destruct(node1);
stIntTuple_destruct(node2);
}
}
stSortedSet_destruct(filteredEdgesSet);
//Cleanup the components
stSortedSet *componentsSet = stList_getSortedSet(components, NULL);
stList_destruct(components);
stSortedSet_setDestructor(componentsSet, (void(*)(void *)) stSortedSet_destruct);
stSortedSet_destruct(componentsSet);
stHash_destruct(nodesToComponents);
}
stList *stSortedSet_getList(stSortedSet *sortedSet) {
stList *list = stList_construct2(stSortedSet_size(sortedSet));
stSortedSetIterator *it = stSortedSet_getIterator(sortedSet);
void *o;
int32_t i=0;
while((o = stSortedSet_getNext(it)) != NULL) {
stList_set(list, i++, o);
}
assert(i == stSortedSet_size(sortedSet));
stSortedSet_destructIterator(it);
return list;
}
static void test_stSortedSet_copyConstruct(CuTest* testCase) {
sonLibSortedSetTestSetup();
CuAssertTrue(testCase, sortedSet != NULL);
int32_t i;
for(i=0; i<size; i++) {
stSortedSet_insert(sortedSet, stIntTuple_construct(1, input[i]));
}
stSortedSet *sortedSet2 = stSortedSet_copyConstruct(sortedSet, NULL);
CuAssertTrue(testCase, stSortedSet_size(sortedSet2) == stSortedSet_size(sortedSet));
CuAssertTrue(testCase, stSortedSet_equals(sortedSet2, sortedSet));
stSortedSet_destruct(sortedSet2);
sonLibSortedSetTestTeardown();
}
static void makeMatchingPerfect(stList *chosenEdges, stList *adjacencyEdges,
stSortedSet *nodes) {
/*
* While the the number of edges is less than a perfect matching add random edges.
*/
stSortedSet *attachedNodes = getNodeSetOfEdges(chosenEdges);
stHash *nodesToAdjacencyEdges = getNodesToEdgesHash(adjacencyEdges);
stIntTuple *pNode = NULL;
stSortedSetIterator *it = stSortedSet_getIterator(nodes);
stIntTuple *node;
while((node = stSortedSet_getNext(it)) != NULL) {
if (stSortedSet_search(attachedNodes, node) == NULL) {
if (pNode == NULL) {
pNode = node;
} else {
stList_append(chosenEdges,
getEdgeForNodes(stIntTuple_get(pNode, 0), stIntTuple_get(node, 0), nodesToAdjacencyEdges));
pNode = NULL;
}
}
}
stSortedSet_destructIterator(it);
assert(pNode == NULL);
stSortedSet_destruct(attachedNodes);
assert(stList_length(chosenEdges) * 2 == stSortedSet_size(nodes));
stHash_destruct(nodesToAdjacencyEdges);
}
stList *getMatchingWithCyclicConstraints(stSortedSet *nodes,
stList *adjacencyEdges, stList *stubEdges, stList *chainEdges,
bool makeStubCyclesDisjoint,
stList *(*matchingAlgorithm)(stList *edges, int64_t nodeNumber)) {
/*
* Check the inputs.
*/
checkInputs(nodes, adjacencyEdges, stubEdges, chainEdges);
st_logDebug("Checked the inputs\n");
if (stSortedSet_size(nodes) == 0) { //Some of the following functions assume there are at least 2 nodes.
return stList_construct();
}
stList *chosenEdges = getPerfectMatching(nodes, adjacencyEdges, matchingAlgorithm);
stSortedSet *allAdjacencyEdges = stList_getSortedSet(adjacencyEdges,
(int(*)(const void *, const void *)) stIntTuple_cmpFn);
stList *nonZeroWeightAdjacencyEdges = getEdgesWithGreaterThanZeroWeight(
adjacencyEdges);
stList *updatedChosenEdges = makeMatchingObeyCyclicConstraints(nodes, chosenEdges, allAdjacencyEdges, nonZeroWeightAdjacencyEdges, stubEdges, chainEdges, makeStubCyclesDisjoint);
stList_destruct(chosenEdges);
chosenEdges = updatedChosenEdges;
stList_destruct(nonZeroWeightAdjacencyEdges);
stSortedSet_destruct(allAdjacencyEdges);
return chosenEdges;
}
static void test_stSortedSetIntersection(CuTest* testCase) {
sonLibSortedSetTestSetup();
//Check intersection of empty sets is okay..
stSortedSet *sortedSet3 = stSortedSet_getIntersection(sortedSet, sortedSet2);
CuAssertTrue(testCase, stSortedSet_size(sortedSet3) == 0);
stSortedSet_destruct(sortedSet3);
int32_t i;
for(i=0; i<size; i++) {
stSortedSet_insert(sortedSet, stIntTuple_construct(1, input[i]));
}
//Check intersection of empty and non-empty set is empty.
sortedSet3 = stSortedSet_getIntersection(sortedSet, sortedSet2);
CuAssertTrue(testCase, stSortedSet_size(sortedSet3) == 0);
stSortedSet_destruct(sortedSet3);
//Check intersection of two non-empty, overlapping sets in correct.
stSortedSet_insert(sortedSet2, stIntTuple_construct(1, 0));
stSortedSet_insert(sortedSet2, stIntTuple_construct(1, 1));
stSortedSet_insert(sortedSet2, stIntTuple_construct(1, 5));
sortedSet3 = stSortedSet_getIntersection(sortedSet, sortedSet2);
CuAssertTrue(testCase, stSortedSet_size(sortedSet3) == 2);
stIntTuple *intTuple = stIntTuple_construct(1, 1);
CuAssertTrue(testCase, stSortedSet_search(sortedSet3, intTuple) != NULL);
stIntTuple_destruct(intTuple);
intTuple = stIntTuple_construct(1, 5);
CuAssertTrue(testCase, stSortedSet_search(sortedSet3, intTuple) != NULL);
stIntTuple_destruct(intTuple);
stSortedSet_destruct(sortedSet3);
//Check we get an exception with sorted sets with different comparators.
stSortedSet *sortedSet4 = stSortedSet_construct();
stTry {
stSortedSet_getIntersection(sortedSet, sortedSet4);
} stCatch(except) {
CuAssertTrue(testCase, stExcept_getId(except) == SORTED_SET_EXCEPTION_ID);
}
stTryEnd
stSortedSet_destruct(sortedSet4);
sonLibSortedSetTestTeardown();
}
static void test_stSortedSetDifference(CuTest* testCase) {
sonLibSortedSetTestSetup();
//Check difference of empty sets is okay..
stSortedSet *sortedSet3 = stSortedSet_getDifference(sortedSet, sortedSet2);
CuAssertTrue(testCase, stSortedSet_size(sortedSet3) == 0);
stSortedSet_destruct(sortedSet3);
int32_t i;
for(i=0; i<size; i++) {
stSortedSet_insert(sortedSet, stIntTuple_construct(1, input[i]));
}
//Check difference of non-empty set / empty set is the non-empty.
sortedSet3 = stSortedSet_getDifference(sortedSet, sortedSet2);
CuAssertTrue(testCase, stSortedSet_equals(sortedSet, sortedSet3));
stSortedSet_destruct(sortedSet3);
//Check difference of two non-empty, overlapping sets in correct.
stSortedSet_insert(sortedSet2, stIntTuple_construct(1, 0));
stSortedSet_insert(sortedSet2, stIntTuple_construct(1, 1));
stSortedSet_insert(sortedSet2, stIntTuple_construct(1, 5));
sortedSet3 = stSortedSet_getDifference(sortedSet, sortedSet2);
CuAssertTrue(testCase, stSortedSet_size(sortedSet3) == stSortedSet_size(sortedSet) - 2);
CuAssertTrue(testCase, !stSortedSet_equals(sortedSet, sortedSet3));
stSortedSet_insert(sortedSet3, stIntTuple_construct(1, 1));
stSortedSet_insert(sortedSet3, stIntTuple_construct(1, 5));
CuAssertTrue(testCase, stSortedSet_equals(sortedSet, sortedSet3));
stSortedSet_destruct(sortedSet3);
//Check we get an exception when merging sorted sets with different comparators.
stSortedSet *sortedSet4 = stSortedSet_construct();
stTry {
stSortedSet_getDifference(sortedSet, sortedSet4);
CuAssertTrue(testCase, 0);
} stCatch(except) {
CuAssertTrue(testCase, stExcept_getId(except) == SORTED_SET_EXCEPTION_ID);
}
stTryEnd
stSortedSet_destruct(sortedSet4);
sonLibSortedSetTestTeardown();
}
static void testBreakUpComponentGreedily(CuTest *testCase) {
//return;
for (int64_t test = 0; test < 100; test++) {
st_logInfo("Starting break up giant components random test %" PRIi64 "\n", test);
setup();
stList *edgesToDelete = stCaf_breakupComponentGreedily(nodes, edges, maxComponentSize);
stSortedSet *edgesSet = stList_getSortedSet(edges, (int(*)(const void *, const void *)) stIntTuple_cmpFn);
stSortedSet *edgesToDeleteSet = stList_getSortedSet(edgesToDelete, (int(*)(const void *, const void *)) stIntTuple_cmpFn);
stSortedSet *filteredEdgesSet = stSortedSet_getDifference(edgesSet, edgesToDeleteSet);
stList *filteredEdges = stSortedSet_getList(filteredEdgesSet);
assert(stSortedSet_size(edgesToDeleteSet) + stSortedSet_size(filteredEdgesSet) == stSortedSet_size(edgesSet));
checkComponents(testCase, filteredEdges);
stSortedSet_destruct(edgesSet);
stSortedSet_destruct(edgesToDeleteSet);
stSortedSet_destruct(filteredEdgesSet);
stList_destruct(filteredEdges);
stList_destruct(edgesToDelete);
teardown();
}
}
static void test_stSortedSet(CuTest* testCase) {
sonLibSortedSetTestSetup();
int32_t i;
CuAssertIntEquals(testCase, 0, stSortedSet_size(sortedSet));
for(i=0; i<size; i++) {
stSortedSet_insert(sortedSet, stIntTuple_construct(1, input[i]));
}
CuAssertIntEquals(testCase, sortedSize, stSortedSet_size(sortedSet));
CuAssertIntEquals(testCase, sortedInput[0], stIntTuple_getPosition(stSortedSet_getFirst(sortedSet), 0));
CuAssertIntEquals(testCase, sortedInput[sortedSize-1], stIntTuple_getPosition(stSortedSet_getLast(sortedSet), 0));
for(i=0; i<sortedSize; i++) {
CuAssertIntEquals(testCase, sortedSize-i, stSortedSet_size(sortedSet));
stIntTuple *tuple = stIntTuple_construct(1, sortedInput[i]);
CuAssertTrue(testCase, stIntTuple_getPosition(stSortedSet_search(sortedSet, tuple), 0) == sortedInput[i]);
stSortedSet_remove(sortedSet, tuple);
CuAssertTrue(testCase, stSortedSet_search(sortedSet, tuple) == NULL);
stIntTuple_destruct(tuple);
}
sonLibSortedSetTestTeardown();
}
/* Check that all tuple records in a set are present and have the expect
* value. The expected value in the set is multiplied by valueMult to get
* the actual expected value */
static void readWriteAndRemoveRecordsLotsCheck(CuTest *testCase, stSortedSet *set, int valueMult) {
CuAssertIntEquals(testCase, stSortedSet_size(set), stKVDatabase_getNumberOfRecords(database));
stSortedSetIterator *it = stSortedSet_getIterator(set);
stIntTuple *tuple;
while ((tuple = stSortedSet_getNext(it)) != NULL) {
int32_t *value = (int32_t *) stKVDatabase_getRecord(database, stIntTuple_getPosition(tuple, 0));
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, stIntTuple_getPosition(tuple, 0)));
CuAssertIntEquals(testCase, valueMult*stIntTuple_getPosition(tuple, 0), *value);
free(value);
}
stSortedSet_destructIterator(it);
}
static enum CapCode getHaplotypeSwitchCode(Cap *cap, stList *eventStrings) {
Cap *adjacentCap = cap_getAdjacency(getTerminalCap(cap));
assert(adjacentCap != NULL);
End *end = cap_getEnd(cap);
End *adjacentEnd = cap_getEnd(adjacentCap);
stSortedSet *eventStringsForEnd1 = getEventStrings(end, eventStrings);
stSortedSet *eventStringsForEnd2 = getEventStrings(adjacentEnd, eventStrings);
assert(stSortedSet_size(eventStringsForEnd1) > 0);
assert(stSortedSet_size(eventStringsForEnd2) > 0);
stSortedSet *intersectionOfEventStrings = stSortedSet_getIntersection(
eventStringsForEnd1, eventStringsForEnd2);
enum CapCode code1 = (stSortedSet_size(intersectionOfEventStrings)
!= stSortedSet_size(eventStringsForEnd1) || stSortedSet_size(
intersectionOfEventStrings)
!= stSortedSet_size(eventStringsForEnd2)) ? HAP_SWITCH
: HAP_NOTHING;
stSortedSet_destruct(eventStringsForEnd1);
stSortedSet_destruct(eventStringsForEnd2);
stSortedSet_destruct(intersectionOfEventStrings);
return code1;
}
void test_stList_getSortedSet(CuTest *testCase) {
setup();
stSortedSet *sortedSet = stList_getSortedSet(list, (int (*)(const void *, const void *))strcmp);
CuAssertTrue(testCase, stSortedSet_size(sortedSet) == stringNumber);
stSortedSetIterator *iterator = stSortedSet_getIterator(sortedSet);
CuAssertStrEquals(testCase, "five", stSortedSet_getNext(iterator));
CuAssertStrEquals(testCase, "four", stSortedSet_getNext(iterator));
CuAssertStrEquals(testCase, "one", stSortedSet_getNext(iterator));
CuAssertStrEquals(testCase, "three", stSortedSet_getNext(iterator));
CuAssertStrEquals(testCase, "two", stSortedSet_getNext(iterator));
stSortedSet_destructIterator(iterator);
stSortedSet_destruct(sortedSet);
teardown();
}
static void getMAFBlock2(Block *block, FILE *fileHandle) {
if (block_getLength(block) >= minimumBlockLength) {
//Calculate bases in the reference and other reference sequence
Block_InstanceIterator *instanceIt = block_getInstanceIterator(block);
bool includesReference = 0;
bool includesOtherReference = 0;
Segment *segment;
while ((segment = block_getNext(instanceIt)) != NULL) {
const char *segmentEvent = event_getHeader(
segment_getEvent(segment));
if (strcmp(segmentEvent, referenceEventString) == 0) {
includesReference = 1;
} else if (strcmp(segmentEvent, otherReferenceEventString) == 0) {
includesOtherReference = 1;
}
}
block_destructInstanceIterator(instanceIt);
if (ignoreOtherReferenceBlocks && includesOtherReference) {
return;
}
stSortedSet *otherSampleEvents = stSortedSet_construct3(
(int(*)(const void *, const void *)) strcmp, NULL);
instanceIt = block_getInstanceIterator(block);
int32_t sampleNumber = 0;
while ((segment = block_getNext(instanceIt)) != NULL) {
const char *segmentEvent = event_getHeader(
segment_getEvent(segment));
if (strcmp(segmentEvent, sampleEventString) == 0) {
sampleNumber++;
} else if (strcmp(segmentEvent, referenceEventString) != 0) {
stSortedSet_insert(otherSampleEvents, (void *) segmentEvent);
}
}
block_destructInstanceIterator(instanceIt);
baseCoverages[stSortedSet_size(otherSampleEvents)] += block_getLength(
block) * sampleNumber;
stSortedSet_destruct(otherSampleEvents);
referenceBases += includesReference ? block_getLength(block)
* sampleNumber : 0;
otherReferenceBases += includesOtherReference ? block_getLength(block)
* sampleNumber : 0;
}
}
static stSortedSet *getOddNodes(stList *cycle) {
/*
* Returns alternating nodes in a simple cycle.
*/
//Set to return
stSortedSet *nodes = stSortedSet_construct3(
(int(*)(const void *, const void *)) stIntTuple_cmpFn,
(void(*)(void *)) stIntTuple_destruct);
stHash *nodesToEdges = getNodesToEdgesHash(cycle);
int64_t node = stIntTuple_get(stList_get(cycle, 0), 0);
int64_t pNode = -1;
int64_t counter = 0;
bool b = 1;
assert(stList_length(cycle) % 2 == 0);
while (counter++ < stList_length(cycle)) {
if (b) { //Make alternating
addNodeToSet(nodes, node);
b = 0;
} else {
b = 1;
}
stList *edges = getItemForNode(node, nodesToEdges);
assert(stList_length(edges) == 2);
stIntTuple *edge = stList_get(edges, 0);
int64_t node2 = getOtherPosition(edge, node);
if (node2 != pNode) {
pNode = node;
node = node2;
continue;
}
edge = stList_get(edges, 1);
node2 = getOtherPosition(edge, node);
assert(node2 != pNode);
pNode = node;
node = node2;
}
stHash_destruct(nodesToEdges);
assert(stList_length(cycle) / 2 == stSortedSet_size(nodes));
return nodes;
}
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);
}
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;
}
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;
}
int64_t flower_getSequenceNumber(Flower *flower) {
return stSortedSet_size(flower->sequences);
}
int64_t flower_getFaceNumber(Flower *flower) {
return stSortedSet_size(flower->faces);
}
int64_t flower_getChainNumber(Flower *flower) {
return stSortedSet_size(flower->chains);
}
int64_t flower_getGroupNumber(Flower *flower) {
return stSortedSet_size(flower->groups);
}
int64_t flower_getBlockNumber(Flower *flower) {
return stSortedSet_size(flower->blocks);
}
int64_t flower_getSegmentNumber(Flower *flower) {
return stSortedSet_size(flower->segments);
}
static void readWriteAndRemoveRecordsLotsIteration(CuTest *testCase, int numRecords, bool reopenDatabase) {
//Make a big old list of records..
stSortedSet *set = stSortedSet_construct3((int(*)(const void *, const void *)) stIntTuple_cmpFn,
(void(*)(void *)) stIntTuple_destruct);
while (stSortedSet_size(set) < numRecords) {
int32_t key = st_randomInt(0, 100 * numRecords);
stIntTuple *tuple = stIntTuple_construct(1, key);
if (stSortedSet_search(set, tuple) == NULL) {
CuAssertTrue(testCase, !stKVDatabase_containsRecord(database, key));
stSortedSet_insert(set, tuple);
stKVDatabase_insertRecord(database, key, &key, sizeof(int32_t));
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, key));
} else {
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, key));
stIntTuple_destruct(tuple); // already in db
}
}
readWriteAndRemoveRecordsLotsCheck(testCase, set, 1);
//Update all records to negate values
stSortedSetIterator *it = stSortedSet_getIterator(set);
stIntTuple *tuple;
while ((tuple = stSortedSet_getNext(it)) != NULL) {
int32_t *value = (int32_t *) stKVDatabase_getRecord(database, stIntTuple_getPosition(tuple, 0));
*value *= -1;
stKVDatabase_updateRecord(database, stIntTuple_getPosition(tuple, 0), value, sizeof(int32_t));
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, stIntTuple_getPosition(tuple, 0)));
free(value);
}
stSortedSet_destructIterator(it);
readWriteAndRemoveRecordsLotsCheck(testCase, set, -1);
//Try optionally committing the transaction and reloading the database..
if (reopenDatabase) {
//stKVDatabase_commitTransaction(database);
stKVDatabase_destruct(database);
database = stKVDatabase_construct(conf, false);
//stKVDatabase_startTransaction(database);
}
//Now remove each one..
it = stSortedSet_getIterator(set);
while ((tuple = stSortedSet_getNext(it)) != NULL) {
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, stIntTuple_getPosition(tuple, 0)));
stKVDatabase_removeRecord(database, stIntTuple_getPosition(tuple, 0));
CuAssertTrue(testCase, !stKVDatabase_containsRecord(database, stIntTuple_getPosition(tuple, 0)));
//Test we get exception if we remove twice.
stTry {
stKVDatabase_removeRecord(database, stIntTuple_getPosition(tuple, 0));
CuAssertTrue(testCase, 0);
}
stCatch(except)
{
CuAssertTrue(testCase, stExcept_getId(except) == ST_KV_DATABASE_EXCEPTION_ID);
}stTryEnd;
}
stSortedSet_destructIterator(it);
CuAssertIntEquals(testCase, 0, stKVDatabase_getNumberOfRecords(database));
stSortedSet_destruct(set);
}
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;
}
int64_t block_getInstanceNumber(Block *block) {
return stSortedSet_size(block->blockContents->segments);
}
int64_t flower_getCapNumber(Flower *flower) {
return stSortedSet_size(flower->caps);
}
void writeEndAlignmentToDisk(End *end, stSortedSet *endAlignment, FILE *fileHandle) {
fprintf(fileHandle, "%s %" PRIi64 "\n", cactusMisc_nameToStringStatic(end_getName(end)), stSortedSet_size(endAlignment));
stSortedSetIterator *it = stSortedSet_getIterator(endAlignment);
AlignedPair *aP;
while((aP = stSortedSet_getNext(it)) != NULL) {
fprintf(fileHandle, "%" PRIi64 " %" PRIi64 " %i %" PRIi64 " ", aP->subsequenceIdentifier, aP->position, aP->strand, aP->score);
aP = aP->reverse;
fprintf(fileHandle, "%" PRIi64 " %" PRIi64 " %i %" PRIi64 "\n", aP->subsequenceIdentifier, aP->position, aP->strand, aP->score);
}
stSortedSet_destructIterator(it);
}
int64_t flower_getEndNumber(Flower *flower) {
return stSortedSet_size(flower->ends);
}