void makeCactusTree_chain(Chain *chain, FILE *fileHandle,
const char *parentNodeName, const char *parentEdgeColour) {
//Write the flower nodes.
char *chainNameString = cactusMisc_nameToString(chain_getName(chain));
const char *edgeColour = graphViz_getColour();
addNodeToGraph(chainNameString, fileHandle,
chain_getAverageInstanceBaseLength(chain) / totalProblemSize,
"box", chainNameString);
//Write in the parent edge.
if (parentNodeName != NULL) {
graphViz_addEdgeToGraph(parentNodeName, chainNameString, fileHandle,
"", parentEdgeColour, 10, 1, "forward");
}
//Create the linkers to the nested flowers.
Link *link = chain_getFirst(chain);
while(link != NULL) {
Group *group = link_getGroup(link);
assert(group != NULL);
assert(!group_isLeaf(group));
if (!group_isLeaf(group)) {
makeCactusTree_flower(group_getNestedFlower(group), fileHandle,
chainNameString, edgeColour);
}
link = link_getNextLink(link);
}
free(chainNameString);
}
void flower_checkRecursive(Flower *flower) {
flower_check(flower);
Flower_GroupIterator *groupIt = flower_getGroupIterator(flower);
Group *group;
while ((group = flower_getNextGroup(groupIt)) != NULL) {
if (!group_isLeaf(group)) {
flower_checkRecursive(group_getNestedFlower(group));
}
}
flower_destructGroupIterator(groupIt);
}
void testGroup_makeNonLeaf(CuTest *testCase) {
cactusGroupTestSetup();
CuAssertTrue(testCase, group_isLeaf(group2));
end_setGroup(end4, group2);
group_makeNestedFlower(group2);
CuAssertTrue(testCase, !group_isLeaf(group2));
Flower *nestedFlower = group_getNestedFlower(group2);
CuAssertTrue(testCase, nestedFlower != NULL);
CuAssertTrue(testCase, !flower_builtBlocks(flower));
CuAssertTrue(testCase, !flower_builtTrees(flower));
CuAssertTrue(testCase, !flower_builtFaces(flower));
CuAssertTrue(testCase, flower_getName(nestedFlower) == group_getName(group2));
CuAssertTrue(testCase, flower_getParentGroup(nestedFlower) == group2);
CuAssertTrue(testCase, flower_getEndNumber(nestedFlower) == 1);
End *nestedEnd = flower_getFirstEnd(nestedFlower);
CuAssertTrue(testCase, end_getName(end4) == end_getName(nestedEnd));
CuAssertTrue(testCase, end_getGroup(nestedEnd) != NULL);
CuAssertTrue(testCase, flower_getGroupNumber(nestedFlower) == 1);
CuAssertTrue(testCase, flower_isTerminal(nestedFlower));
cactusGroupTestTeardown();
}
bool flower_isLeaf(Flower *flower) {
Group *group;
Flower_GroupIterator *iterator = flower_getGroupIterator(flower);
while ((group = flower_getNextGroup(iterator)) != NULL) {
if (!group_isLeaf(group)) {
flower_destructGroupIterator(iterator);
return 0;
}
}
flower_destructGroupIterator(iterator);
return 1;
}
static void setAdjacencyLengthsAndRecoverNewCapsAndBrokenAdjacencies(Cap *cap, stList *recoveredCaps) {
/*
* Sets the coordinates of the caps to be equal to the length of the adjacency sequence between them.
* Used to build the reference sequence bottom up.
*
* One complexity is that a reference thread between the two caps
* in each flower f may be broken into two in the children of f.
* Therefore, for each flower f first identify attached stub ends present in the children of f that are
* not present in f and copy them into f, reattaching the reference caps as needed.
*/
while (1) {
Cap *adjacentCap = cap_getAdjacency(cap);
assert(adjacentCap != NULL);
assert(cap_getCoordinate(cap) == INT64_MAX);
assert(cap_getCoordinate(adjacentCap) == INT64_MAX);
assert(cap_getStrand(cap) == cap_getStrand(adjacentCap));
assert(cap_getSide(cap) != cap_getSide(adjacentCap));
Group *group = end_getGroup(cap_getEnd(cap));
assert(group != NULL);
if (!group_isLeaf(group)) { //Adjacency is not terminal, so establish its sequence.
Flower *nestedFlower = group_getNestedFlower(group);
Cap *nestedCap = flower_getCap(nestedFlower, cap_getName(cap));
assert(nestedCap != NULL);
Cap *nestedAdjacentCap = flower_getCap(nestedFlower, cap_getName(adjacentCap));
assert(nestedAdjacentCap != NULL);
Cap *breakerCap;
int64_t adjacencyLength = traceThreadLength(nestedCap, &breakerCap);
assert(cap_getOrientation(nestedAdjacentCap));
if (cap_getPositiveOrientation(breakerCap) != nestedAdjacentCap) { //The thread is broken at the lower level.
//Copy cap into higher level graph.
breakerCap = copyCapToParent(breakerCap, recoveredCaps);
assert(cap_getSide(breakerCap));
cap_makeAdjacent(cap, breakerCap);
setAdjacencyLength(cap, breakerCap, adjacencyLength);
adjacencyLength = traceThreadLength(nestedAdjacentCap, &breakerCap);
assert(cap_getPositiveOrientation(breakerCap) != cap);
breakerCap = copyCapToParent(breakerCap, recoveredCaps);
assert(!cap_getSide(breakerCap));
cap_makeAdjacent(breakerCap, adjacentCap);
setAdjacencyLength(adjacentCap, breakerCap, adjacencyLength);
} else { //The thread is not broken at the lower level
setAdjacencyLength(cap, adjacentCap, adjacencyLength);
}
} else {
//Set the coordinates of the caps to the adjacency size
setAdjacencyLength(cap, adjacentCap, 0);
}
if ((cap = cap_getOtherSegmentCap(adjacentCap)) == NULL) {
break;
}
}
}
bool flower_removeIfRedundant(Flower *flower) {
if (!flower_isLeaf(flower) && flower_getParentGroup(flower) != NULL && flower_getBlockNumber(flower) == 0) { //We will remove this flower..
Group *parentGroup = flower_getParentGroup(flower); //This group will be destructed
//Deal with any parent chain..
if (group_isLink(parentGroup)) {
link_split(group_getLink(parentGroup));
}
Flower *parentFlower = group_getFlower(parentGroup); //We will add the groups in the flower to the parent
/*
* For each group in the flower we take its nested flower and attach it to the parent.
*/
Group *group;
Flower_GroupIterator *groupIt = flower_getGroupIterator(flower);
while ((group = flower_getNextGroup(groupIt)) != NULL) {
if (!group_isLeaf(group)) {
//Copy the group into the parent..
Flower *nestedFlower = group_getNestedFlower(group);
assert(nestedFlower != NULL);
Group *newParentGroup = group_construct(parentFlower, nestedFlower);
flower_setParentGroup(nestedFlower, newParentGroup);
group_constructChainForLink(newParentGroup);
} else {
Group *newParentGroup = group_construct2(parentFlower);
End *end;
Group_EndIterator *endIt = group_getEndIterator(group);
while ((end = group_getNextEnd(endIt)) != NULL) {
End *parentEnd = flower_getEnd(parentFlower, end_getName(end));
assert(parentEnd != NULL);
end_setGroup(parentEnd, newParentGroup);
}
group_destructEndIterator(endIt);
group_constructChainForLink(newParentGroup);
}
}
flower_destructGroupIterator(groupIt);
//The group attached to the flower should now be empty
assert(group_getEndNumber(parentGroup) == 0);
group_destruct(parentGroup);
//Now wipe the flower out..
cactusDisk_deleteFlowerFromDisk(flower_getCactusDisk(flower), flower);
flower_destruct(flower, 0);
return 1;
}
return 0;
}
void flower_makeTerminalNormal(Flower *flower) {
if (!flower_isTerminal(flower)) {
Flower_GroupIterator *groupIterator;
Group *group;
groupIterator = flower_getGroupIterator(flower);
while ((group = flower_getNextGroup(groupIterator)) != NULL) {
if (group_isLeaf(group)) {
//assert(group_getTotalBaseLength(group) == 0);
Flower *nestedFlower = group_makeNestedFlower(group);
flower_setBuiltBlocks(nestedFlower, flower_builtBlocks(flower));
flower_setBuiltTrees(nestedFlower, flower_builtTrees(flower));
flower_setBuildFaces(nestedFlower, flower_builtFaces(flower));
}
}
flower_destructGroupIterator(groupIterator);
}
}
void flower_delete2(Flower *flower, bool isOnDisk) {
Flower_GroupIterator *groupIt = flower_getGroupIterator(flower);
Group *group;
while ((group = flower_getNextGroup(groupIt)) != NULL) {
if (!group_isLeaf(group)) {
flower_delete2(group_getNestedFlower(group), isOnDisk);
}
}
flower_destructGroupIterator(groupIt);
Group *parentGroup = flower_getParentGroup(flower);
if(parentGroup != NULL) {
parentGroup->leafGroup = 1;
}
//This needs modification so that we don't do this directly..
if(isOnDisk) {
cactusDisk_deleteFlowerFromDisk(flower_getCactusDisk(flower), flower);
}
flower_destruct(flower, 0);
}
void flower_checkNotEmpty(Flower *flower, bool recursive) {
//First check the flower is not empty, unless it is the parent group.
if (flower_hasParentGroup(flower)) {
assert(flower_getGroupNumber(flower) > 0);
assert(flower_getEndNumber(flower) > 0);
assert(flower_getAttachedStubEndNumber(flower) > 0); //We must have some ends to tie us into the parent problem + flower_getBlockEndNumber(flower) > 0);
}
//Now Checks that each group contains at least one end and call recursive.
Group *group;
Flower_GroupIterator *groupIt = flower_getGroupIterator(flower);
while ((group = flower_getNextGroup(groupIt)) != NULL) {
assert(group_getEndNumber(group) > 0);
assert(group_getAttachedStubEndNumber(group) + group_getBlockEndNumber(group) > 0);
if (recursive && !group_isLeaf(group)) {
flower_checkNotEmpty(group_getNestedFlower(group), 1);
}
}
flower_destructGroupIterator(groupIt);
}
bool flower_deleteIfEmpty(Flower *flower) {
if (flower_getEndNumber(flower) == 0 && flower_getParentGroup(flower) != NULL) { //contains nothing useful..
assert(flower_getChainNumber(flower) == 0);
assert(flower_getBlockNumber(flower) == 0);
while (flower_getGroupNumber(flower) > 0) {
Group *group = flower_getFirstGroup(flower);
if (!group_isLeaf(group)) {
bool i = flower_deleteIfEmpty(group_getNestedFlower(group));
(void) i;
assert(i);
}
}
assert(flower_getGroupNumber(flower) == 0);
//This needs modification so that we don't do this directly..
cactusDisk_deleteFlowerFromDisk(flower_getCactusDisk(flower), flower);
Group *parentGroup = flower_getParentGroup(flower);
group_destruct(parentGroup);
flower_destruct(flower, 0);
return 1;
}
return 0;
}
void topDown(Flower *flower, Name referenceEventName) {
/*
* Run on each flower, top down. Sets the coordinates of each reference cap to the correct
* sequence, and sets the bases of the reference sequence to be consensus bases.
*/
Flower_EndIterator *endIt = flower_getEndIterator(flower);
End *end;
while ((end = flower_getNextEnd(endIt)) != NULL) {
Cap *cap = getCapForReferenceEvent(end, referenceEventName); //The cap in the reference
if (cap != NULL) {
cap = cap_getStrand(cap) ? cap : cap_getReverse(cap);
if (!cap_getSide(cap)) {
assert(cap_getCoordinate(cap) != INT64_MAX);
Sequence *sequence = cap_getSequence(cap);
assert(sequence != NULL);
Group *group = end_getGroup(end);
if (!group_isLeaf(group)) {
Flower *nestedFlower = group_getNestedFlower(group);
Cap *nestedCap = flower_getCap(nestedFlower, cap_getName(cap));
assert(nestedCap != NULL);
nestedCap = cap_getStrand(nestedCap) ? nestedCap : cap_getReverse(nestedCap);
assert(cap_getStrand(nestedCap));
assert(!cap_getSide(nestedCap));
int64_t endCoordinate = setCoordinates(nestedFlower, sequence_getMetaSequence(sequence),
nestedCap, cap_getCoordinate(cap));
(void) endCoordinate;
assert(endCoordinate == cap_getCoordinate(cap_getAdjacency(cap)));
assert(endCoordinate
== cap_getCoordinate(
flower_getCap(nestedFlower, cap_getName(cap_getAdjacency(cap)))));
}
}
}
}
flower_destructEndIterator(endIt);
}
void testGroup_isLeaf(CuTest *testCase) {
cactusGroupTestSetup();
CuAssertTrue(testCase, !group_isLeaf(group));
CuAssertTrue(testCase, group_isLeaf(group2));
cactusGroupTestTeardown();
}
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;
}
void makeCactusTree_flower(Flower *flower, FILE *fileHandle, const char *parentNodeName,
const char *parentEdgeColour) {
if(flower_isTerminal(flower)) {
makeCactusTree_terminalNode(flower, fileHandle, parentNodeName, parentEdgeColour);
}
else {
//Write the flower nodes.
char *flowerNameString = cactusMisc_nameToString(flower_getName(flower));
const char *edgeColour = graphViz_getColour();
addNodeToGraph(flowerNameString, fileHandle, flower_getTotalBaseLength(flower)
/ totalProblemSize, "ellipse", flowerNameString);
//Write in the parent edge.
if (parentNodeName != NULL) {
graphViz_addEdgeToGraph(parentNodeName, flowerNameString, fileHandle, "",
parentEdgeColour, 10, 1, "forward");
}
//Create the chains.
Flower_ChainIterator *chainIterator = flower_getChainIterator(flower);
Chain *chain;
while ((chain = flower_getNextChain(chainIterator)) != NULL) {
makeCactusTree_chain(chain, fileHandle, flowerNameString, edgeColour);
}
flower_destructChainIterator(chainIterator);
//Create the diamond node
char *diamondNodeNameString = st_malloc(sizeof(char) * (strlen(
flowerNameString) + 2));
sprintf(diamondNodeNameString, "z%s", flowerNameString);
const char *diamondEdgeColour = graphViz_getColour();
//Create all the groups linked to the diamond.
Flower_GroupIterator *groupIterator = flower_getGroupIterator(flower);
Group *group;
double size = 0.0; //get the size of the group organising node..
int64_t nonTrivialGroupCount = 0;
while ((group = flower_getNextGroup(groupIterator)) != NULL) {
assert(!group_isLeaf(group));
if (group_isTangle(group)) {
size += group_getTotalBaseLength(group);
nonTrivialGroupCount++;
}
}
flower_destructGroupIterator(groupIterator);
if(nonTrivialGroupCount == 0) {
assert(flower_getParentGroup(flower) == 0);
}
else {
//assert(nonTrivialGroupCount > 0);
addNodeToGraph(diamondNodeNameString, fileHandle, size
/ totalProblemSize, "diamond", "");
graphViz_addEdgeToGraph(flowerNameString, diamondNodeNameString,
fileHandle, "", edgeColour, 10, 1, "forward");
groupIterator = flower_getGroupIterator(flower);
while ((group = flower_getNextGroup(groupIterator)) != NULL) {
if (group_isTangle(group)) {
assert(!group_isLeaf(group));
makeCactusTree_flower(group_getNestedFlower(group), fileHandle,
diamondNodeNameString, diamondEdgeColour);
}
}
flower_destructGroupIterator(groupIterator);
}
free(flowerNameString);
free(diamondNodeNameString);
}
}
void testFlower_removeIfRedundant(CuTest *testCase) {
/*
* Do a simple test to see if function can remove a redundant flower.
*/
cactusFlowerTestSetup();
endsSetup();
//First construct a redundant flower from the root.
Flower *flower2 = flower_construct(cactusDisk);
Group *group = group_construct(flower, flower2);
end_setGroup(end, group);
end_setGroup(end2, group);
//Now hang another couple of flowers of that.
Flower *flower3 = flower_construct(cactusDisk);
group_construct(flower2, flower3);
//Now hang another flower of that.
Group *group3b = group_construct2(flower2);
//Finally hang one more flower on the end..
Flower *flower4 = flower_construct(cactusDisk);
group_construct(flower3, flower4);
//Copy the ends into the flowers.
end_copyConstruct(end, flower2);
end_copyConstruct(end2, flower2);
end_copyConstruct(end, flower3);
end_setGroup(flower_getEnd(flower2, end_getName(end2)), group3b);
end_copyConstruct(end, flower4);
//st_uglyf("I got %" PRIi64 " %" PRIi64 " %" PRIi64 " %" PRIi64 "\n", flower_getName(flower), flower_getName(flower2), flower_getName(flower3), flower_getName(flower4));
//Write the mess to disk.
cactusDisk_write(cactusDisk);
//Now test the removal function (check we get a negative on this leaf).
CuAssertTrue(testCase, !flower_removeIfRedundant(flower4));
//Check we can't remove the root..
CuAssertTrue(testCase, !flower_removeIfRedundant(flower));
//We will remove flower2
//Before
CuAssertTrue(testCase, flower_getGroupNumber(flower) == 1);
CuAssertTrue(testCase, group_getFlower(flower_getParentGroup(flower2)) == flower);
CuAssertTrue(testCase, flower_removeIfRedundant(flower2));
//After, check the flower/group connections
CuAssertTrue(testCase, flower_getGroupNumber(flower) == 2);
CuAssertTrue(testCase, !flower_isLeaf(flower));
CuAssertTrue(testCase, group_getFlower(flower_getParentGroup(flower3)) == flower);
group3b = end_getGroup(end2);
CuAssertTrue(testCase, group_getFlower(group3b) == flower);
CuAssertTrue(testCase, group_isLeaf(group3b));
CuAssertTrue(testCase, flower_getGroup(flower, flower_getName(flower3)) == flower_getParentGroup(flower3));
//Check the ends..
CuAssertTrue(testCase, flower_getEndNumber(flower) == 2);
CuAssertTrue(testCase, flower_getEndNumber(flower3) == 1);
CuAssertTrue(testCase, group_getEndNumber(group3b) == 1);
CuAssertTrue(testCase, end_getGroup(end) == flower_getParentGroup(flower3));
CuAssertTrue(testCase, end_getGroup(end2) == group3b);
CuAssertTrue(testCase, flower_getEnd(flower3, end_getName(end)) != NULL);
//Check the child of 3 is still okay..
CuAssertTrue(testCase, group_getFlower(flower_getParentGroup(flower4)) == flower3);
//Now do removal of flower3
CuAssertTrue(testCase, !flower_removeIfRedundant(flower));
CuAssertTrue(testCase, !flower_removeIfRedundant(flower4));
CuAssertTrue(testCase, flower_removeIfRedundant(flower3));
//Check groups again
CuAssertTrue(testCase, flower_getGroupNumber(flower) == 2);
CuAssertTrue(testCase, !flower_isLeaf(flower));
CuAssertTrue(testCase, group_getFlower(flower_getParentGroup(flower4)) == flower);
CuAssertTrue(testCase, group_getFlower(group3b) == flower);
CuAssertTrue(testCase, flower_getGroup(flower, flower_getName(flower4)) == flower_getParentGroup(flower4));
//Check the ends again..
CuAssertTrue(testCase, flower_getEndNumber(flower) == 2);
CuAssertTrue(testCase, flower_getEndNumber(flower4) == 1);
CuAssertTrue(testCase, group_getEndNumber(group3b) == 1);
CuAssertTrue(testCase, end_getGroup(end) == flower_getParentGroup(flower4));
CuAssertTrue(testCase, end_getGroup(end2) == group3b);
CuAssertTrue(testCase, flower_getEnd(flower4, end_getName(end)) != NULL);
cactusFlowerTestTeardown();
}
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;
}
