static void checkIsValidReference(CuTest *testCase, stList *reference,
double totalScore) {
stList *chosenEdges = convertReferenceToAdjacencyEdges(reference);
//Check that everyone has a partner.
CuAssertIntEquals(testCase, nodeNumber, stList_length(chosenEdges) * 2);
stSortedSet *nodes = stSortedSet_construct3((int(*)(const void *, const void *)) stIntTuple_cmpFn,
(void(*)(void *)) stIntTuple_destruct);
for (int64_t i = 0; i < nodeNumber; i++) {
stSortedSet_insert(nodes, stIntTuple_construct1( i));
}
checkEdges(chosenEdges, nodes, 1, 0);
//Check that the score is correct
double totalScore2 = calculateZScoreOfReference(reference, nodeNumber, zMatrix);
CuAssertDblEquals(testCase, totalScore2, totalScore, 0.000001);
//Check that the stubs are properly connected.
stList *allEdges = stList_copy(chosenEdges, NULL);
stList_appendAll(allEdges, stubs);
stList_appendAll(allEdges, chains);
stList *components = getComponents(allEdges);
CuAssertIntEquals(testCase, stList_length(stubs), stList_length(reference));
CuAssertIntEquals(testCase, stList_length(stubs), stList_length(components));
//Cleanup
stList_destruct(components);
stSortedSet_destruct(nodes);
stList_destruct(allEdges);
stList_destruct(chosenEdges);
}
static stSortedSet *getSetOfMergedLists(stList *list1, stList *list2) {
/*
* Returns a sorted set of two input lists.
*/
stList *list3 = stList_copy(list1, NULL);
stList_appendAll(list3, list2);
stSortedSet *set = stList_getSortedSet(list3, NULL);
stList_destruct(list3);
return set;
}
stList *splitMultipleStubCycles(stList *chosenEdges,
stList *nonZeroWeightAdjacencyEdges, stSortedSet *allAdjacencyEdges,
stList *stubEdges, stList *chainEdges) {
/*
* Returns an updated list of adjacency edges, such that each stub edge is a member of exactly one cycle.
*/
/*
* Calculate components.
*/
stList *cycles = getComponents2(chosenEdges, stubEdges, chainEdges);
/*
* Find components with multiple stub edges.
*/
stList *singleStubEdgeCycles = stList_construct3(0,
(void(*)(void *)) stList_destruct);
for (int64_t i = 0; i < stList_length(cycles); i++) {
stList *subCycle = stList_get(cycles, i);
stList *subAdjacencyEdges;
stList *subStubEdges;
stList *subChainEdges;
splitIntoAdjacenciesStubsAndChains(subCycle,
nonZeroWeightAdjacencyEdges, stubEdges, chainEdges,
&subAdjacencyEdges, &subStubEdges, &subChainEdges);
stList *splitCycles = splitMultipleStubCycle(subCycle,
subAdjacencyEdges, allAdjacencyEdges, subStubEdges,
subChainEdges);
stList_appendAll(singleStubEdgeCycles, splitCycles);
stList_setDestructor(splitCycles, NULL); //Do this to avoid destroying the underlying lists
stList_destruct(splitCycles);
stList_destruct(subAdjacencyEdges);
stList_destruct(subStubEdges);
stList_destruct(subChainEdges);
}
stList_destruct(cycles);
/*
* Remove the stub/chain edges from the components.
*/
stSortedSet *stubAndChainEdgesSet = getSetOfMergedLists(stubEdges,
chainEdges);
stList *adjacencyOnlyComponents = filterListsToExclude(
singleStubEdgeCycles, stubAndChainEdgesSet);
stList_destruct(singleStubEdgeCycles);
stSortedSet_destruct(stubAndChainEdgesSet);
/*
* Merge the adjacency edges in the components into a single list.
*/
stList *updatedChosenEdges = stList_join(adjacencyOnlyComponents);
stList_destruct(adjacencyOnlyComponents);
return updatedChosenEdges;
}
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;
}
void test_stList_appendAll(CuTest *testCase) {
setup();
stList *list2 = stList_copy(list, NULL);
stList_appendAll(list, list2);
CuAssertTrue(testCase, stList_length(list) == stringNumber * 2);
int64_t i;
for(i=0; i<stringNumber*2; i++) {
CuAssertTrue(testCase, stList_get(list, i) == strings[i % stringNumber]);
}
stList_destruct(list2);
teardown();
}
int main(int argc, char *argv[]) {
//////////////////////////////////////////////
//Parse the inputs
//////////////////////////////////////////////
parseBasicArguments(argc, argv, "linkageStats");
///////////////////////////////////////////////////////////////////////////
// Get the intervals
///////////////////////////////////////////////////////////////////////////
stList *haplotypeEventStrings = getEventStrings(
treatHaplotype1AsContamination ? NULL : hap1EventString,
treatHaplotype2AsContamination ? NULL : hap2EventString);
stList *assemblyEventStringInList = stList_construct();
stList_append(assemblyEventStringInList, assemblyEventString);
stList *intervals = stList_construct3(0, (void (*)(void *))sequenceInterval_destruct);
for(int64_t i=0; i<stList_length(haplotypeEventStrings); i++) {
const char *hapEventString = stList_get(haplotypeEventStrings, i);
st_logInfo("Getting contig paths for haplotype: %s", hapEventString);
stList *contigPaths = getContigPaths(flower, hapEventString, assemblyEventStringInList);
stList *hapIntervals = getSplitContigPathIntervals(flower, contigPaths, hapEventString,
assemblyEventStringInList);
stList_destruct(contigPaths);
st_logInfo("Getting contig paths\n");
stList_appendAll(intervals, hapIntervals);
stList_setDestructor(hapIntervals, NULL);
stList_destruct(hapIntervals);
}
st_logDebug("Got a total of %" PRIi64 " intervals\n", stList_length(intervals));
///////////////////////////////////////////////////////////////////////////
// Write it out.
///////////////////////////////////////////////////////////////////////////
FILE *fileHandle = fopen(outputFile, "w");
for (int64_t i = 0; i < stList_length(intervals); i++) {
SequenceInterval *sequenceInterval = stList_get(intervals, i);
st_logDebug("We have a path interval %s %" PRIi64 " %" PRIi64 "\n", sequenceInterval->sequenceName,
sequenceInterval->start, sequenceInterval->end);
fprintf(fileHandle, "%s %" PRIi64 " %" PRIi64 "\n", sequenceInterval->sequenceName,
sequenceInterval->start, sequenceInterval->end);
}
st_logInfo("Finished writing out the stats.\n");
fclose(fileHandle);
return 0;
}
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 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;
}
