void eventTree_check(EventTree *eventTree) {
Event *event;
EventTree_Iterator *eventIterator = eventTree_getIterator(eventTree);
while((event = eventTree_getNext(eventIterator)) != NULL) {
event_check(event);
}
eventTree_destructIterator(eventIterator);
}
Event *eventTree_getEventByHeader(EventTree *eventTree, const char *eventHeader) {
EventTree_Iterator *it = eventTree_getIterator(eventTree);
Event *event;
while ((event = eventTree_getNext(it)) != NULL) {
if (strcmp(event_getHeader(event), eventHeader) == 0) {
eventTree_destructIterator(it);
return event;
}
}
eventTree_destructIterator(it);
return NULL;
}
void testEventTree_iterator(CuTest* testCase) {
cactusEventTreeTestSetup();
EventTree_Iterator *iterator = eventTree_getIterator(eventTree);
CuAssertTrue(testCase, eventTree_getNext(iterator) == rootEvent);
CuAssertTrue(testCase, eventTree_getNext(iterator) == internalEvent);
EventTree_Iterator *iterator2 = eventTree_copyIterator(iterator);
CuAssertTrue(testCase, eventTree_getNext(iterator) == leafEvent1);
CuAssertTrue(testCase, eventTree_getNext(iterator) == leafEvent2);
CuAssertTrue(testCase, eventTree_getNext(iterator) == NULL);
CuAssertTrue(testCase, eventTree_getNext(iterator2) == leafEvent1);
CuAssertTrue(testCase, eventTree_getNext(iterator2) == leafEvent2);
CuAssertTrue(testCase, eventTree_getNext(iterator2) == NULL);
CuAssertTrue(testCase, eventTree_getPrevious(iterator2) == leafEvent2);
CuAssertTrue(testCase, eventTree_getPrevious(iterator2) == leafEvent1);
CuAssertTrue(testCase, eventTree_getPrevious(iterator2) == internalEvent);
CuAssertTrue(testCase, eventTree_getPrevious(iterator2) == rootEvent);
CuAssertTrue(testCase, eventTree_getPrevious(iterator2) == NULL);
eventTree_destructIterator(iterator);
eventTree_destructIterator(iterator2);
cactusEventTreeTestTeardown();
}
int main(int argc, char *argv[]) {
//////////////////////////////////////////////
//Parse the inputs
//////////////////////////////////////////////
parseBasicArguments(argc, argv, "coverageStats");
assert(referenceEventString != NULL);
assert(otherReferenceEventString != NULL);
assert(outgroupEventString != NULL);
///////////////////////////////////////////////////////////////////////////
// Calculate and print to file a crap load of numbers.
///////////////////////////////////////////////////////////////////////////
Sequence *referenceSequence = NULL;
Sequence *otherReferenceSequence = NULL;
Flower_SequenceIterator *sequenceIt = flower_getSequenceIterator(flower);
Sequence *sequence;
while ((sequence = flower_getNextSequence(sequenceIt)) != NULL) {
const char *eventHeader = event_getHeader(sequence_getEvent(sequence));
if (eventHeader != NULL && strcmp(eventHeader, referenceEventString)
== 0) {
if (referenceSequence == NULL || sequence_getLength(sequence)
>= sequence_getLength(referenceSequence)) {
referenceSequence = sequence;
}
}
if (eventHeader != NULL && strcmp(eventHeader,
otherReferenceEventString) == 0) {
if (otherReferenceSequence == NULL || sequence_getLength(sequence)
>= sequence_getLength(otherReferenceSequence)) {
otherReferenceSequence = sequence;
}
}
}
flower_destructSequenceIterator(sequenceIt);
assert(referenceSequence != NULL);
assert(otherReferenceSequence != NULL);
FILE *fileHandle = fopen(outputFile, "w");
fprintf(
fileHandle,
"<coverageStats referenceSequenceLength=\"%i\" otherReferenceSequenceLength=\"%i\">\n",
sequence_getLength(referenceSequence),
sequence_getLength(otherReferenceSequence));
EventTree_Iterator *eventIt = eventTree_getIterator(
flower_getEventTree(flower));
eventNumber = eventTree_getEventNumber(flower_getEventTree(flower));
Event * event;
totalBaseCoverages = st_calloc(sizeof(int32_t), eventNumber + 1);
totalReferenceBases = 0;
totalOtherReferenceBases = 0;
int32_t totalSamples = 0;
ignoreOtherReferenceBlocks = 0;
while ((event = eventTree_getNext(eventIt)) != NULL) {
sampleEventString = event_getHeader(event);
if (sampleEventString != NULL && strcmp(sampleEventString, "ROOT")
!= 0 && strcmp(sampleEventString, "") != 0) {
baseCoverages = st_calloc(sizeof(int32_t), eventNumber + 1);
baseCoverages[0] = strcmp(sampleEventString, referenceEventString) != 0 ? getTotalLengthOfAdjacencies(flower,
sampleEventString) : 0;
referenceBases = 0;
otherReferenceBases = 0;
getMAFs(flower, fileHandle, getMAFBlock2);
if(strcmp(sampleEventString, referenceEventString) == 0) {
for(int32_t i=2; i<eventNumber + 1; i++) {
baseCoverages[i-1] = baseCoverages[i];
}
baseCoverages[eventNumber] = 0;
}
printStatsForSample(
strcmp(sampleEventString, referenceEventString) != 0 && strcmp(sampleEventString, outgroupEventString) != 0,
fileHandle, 1);
free(baseCoverages);
totalSamples += (strcmp(sampleEventString, referenceEventString)
!= 0 && strcmp(sampleEventString, outgroupEventString) != 0) ? 1 : 0;
}
}
eventTree_destructIterator(eventIt);
//Do average base coverages..
sampleEventString = "average";
baseCoverages = totalBaseCoverages;
referenceBases = totalReferenceBases;
otherReferenceBases = totalOtherReferenceBases;
printStatsForSample(0, fileHandle, totalSamples);
//Do all..
sampleEventString = referenceEventString;
baseCoverages = st_calloc(sizeof(int32_t), eventNumber + 1);
baseCoverages[0] = totalBaseCoverages[0];
referenceBases = 0;
getMAFs(flower, fileHandle, getMAFBlock2);
for(int32_t i=2; i<eventNumber + 1; i++) {
baseCoverages[i-1] = baseCoverages[i];
}
baseCoverages[eventNumber] = 0;
otherReferenceBases = sequence_getLength(otherReferenceSequence);
sampleEventString = "all";
printStatsForSample(0, fileHandle, 1);
free(baseCoverages);
//Do blocks without other reference
ignoreOtherReferenceBlocks = 1;
sampleEventString = referenceEventString;
baseCoverages = st_calloc(sizeof(int32_t), eventNumber + 1);
baseCoverages[0] = totalBaseCoverages[0] - getTotalLengthOfAdjacencies(flower,
otherReferenceEventString);
referenceBases = 0;
otherReferenceBases = 0;
getMAFs(flower, fileHandle, getMAFBlock2);
for(int32_t i=2; i<eventNumber + 1; i++) {
baseCoverages[i-1] = baseCoverages[i];
}
baseCoverages[eventNumber] = 0;
sampleEventString = "minusOtherReference";
printStatsForSample(0, fileHandle, 1);
free(baseCoverages);
fprintf(fileHandle, "</coverageStats>\n");
st_logInfo("Finished writing out the stats.\n");
fclose(fileHandle);
return 0;
}
