static void assignEventsAndSequences(Event *parentEvent, stTree *tree,
stSet *outgroupNameSet,
char *argv[], int64_t *j) {
Event *myEvent = NULL; // To distinguish from the global "event" variable.
assert(tree != NULL);
totalEventNumber++;
if (stTree_getChildNumber(tree) > 0) {
myEvent = event_construct3(stTree_getLabel(tree),
stTree_getBranchLength(tree), parentEvent,
eventTree);
for (int64_t i = 0; i < stTree_getChildNumber(tree); i++) {
assignEventsAndSequences(myEvent, stTree_getChild(tree, i),
outgroupNameSet, argv, j);
}
}
if (stTree_getChildNumber(tree) == 0 || (stTree_getLabel(tree) != NULL && (stSet_search(outgroupNameSet, (char *)stTree_getLabel(tree)) != NULL))) {
// This event is a leaf and/or an outgroup, so it has
// associated sequence.
assert(stTree_getLabel(tree) != NULL);
assert(stTree_getBranchLength(tree) != INFINITY);
if (stTree_getChildNumber(tree) == 0) {
// Construct the leaf event
myEvent = event_construct3(stTree_getLabel(tree), stTree_getBranchLength(tree), parentEvent, eventTree);
}
char *fileName = argv[*j];
if (!stFile_exists(fileName)) {
st_errAbort("File does not exist: %s\n", fileName);
}
// Set the global "event" variable, which is needed for the
// function provided to fastaReadToFunction.
event = myEvent;
if (stFile_isDir(fileName)) {
st_logInfo("Processing directory: %s\n", fileName);
stList *filesInDir = stFile_getFileNamesInDirectory(fileName);
for (int64_t i = 0; i < stList_length(filesInDir); i++) {
char *absChildFileName = stFile_pathJoin(fileName, stList_get(filesInDir, i));
assert(stFile_exists(absChildFileName));
setCompleteStatus(absChildFileName); //decide if the sequences in the file should be free or attached.
FILE *fileHandle = fopen(absChildFileName, "r");
fastaReadToFunction(fileHandle, processSequence);
fclose(fileHandle);
free(absChildFileName);
}
stList_destruct(filesInDir);
} else {
st_logInfo("Processing file: %s\n", fileName);
setCompleteStatus(fileName); //decide if the sequences in the file should be free or attached.
FILE *fileHandle = fopen(fileName, "r");
fastaReadToFunction(fileHandle, processSequence);
fclose(fileHandle);
}
(*j)++;
}
}
int main(int argc, char *argv[]) {
int64_t j = 0;
char *npReadFile = NULL;
char *templateModelFile = stString_print("../models/testModelR9_template.model");
char *complementModelFile = stString_print("../models/testModelR9_complement_pop2.model");
double threshold = 0.8;
int key;
while (1) {
static struct option long_options[] = {
{"help", no_argument, 0, 'h'},
{"templateModel", required_argument, 0, 'T'},
{"complementModel", required_argument, 0, 'C'},
{"npRead", required_argument, 0, 'q'},
{"threshold", required_argument, 0, 'D'},
{0, 0, 0, 0} };
int option_index = 0;
key = getopt_long(argc, argv, "h:T:C:q:f:b:D:m:",
long_options, &option_index);
if (key == -1) {
//usage();
break;
}
switch (key) {
case 'h':
usage();
return 1;
case 'T':
templateModelFile = stString_copy(optarg);
break;
case 'C':
complementModelFile = stString_copy(optarg);
break;
case 'q':
npReadFile = stString_copy(optarg);
break;
case 'D':
j = sscanf(optarg, "%lf", &threshold);
assert (j == 1);
assert (threshold >= 0);
break;
default:
usage();
return 1;
}
}
if (!stFile_exists(npReadFile)) {
st_errAbort("Could not find npRead here: %s\n", npReadFile);
}
// read in the .npRead file
NanoporeRead *npRead = nanopore_loadNanoporeReadFromFile(npReadFile);
// build state machines (to use the look up table)
StateMachine *sMt = getStateMachine3(templateModelFile);
//StateMachine *sMc = getStateMachine3(complementModelFile);
// make 1D map of events (mean, noise) to kmers
stList *templateMap = signalUtils_templateOneDAssignmentsFromRead(npRead, sMt, ASSIGNMENT_THRESHOLD);
//stList *complementMap = signalUtils_complementOneDAssignmentsFromRead(npRead, sMc, ASSIGNMENT_THRESHOLD);
// convert template to log normal
// NB only need this if you're estimating the NOISE parameteres
//nanopore_convert_to_lognormal_params(sMt->alphabetSize, sMt->kmerLength, sMt->EMISSION_MATCH_MATRIX, templateMap);
// convert complement to log normal
//nanopore_convert_to_lognormal_params(sMc->alphabetSize, sMc->kmerLength, sMc->EMISSION_MATCH_MATRIX, complementMap);
// error log report
st_uglyf("SENTINEL - Before: shift: %f scale: %f var: %f [template]\n",
npRead->templateParams.shift, npRead->templateParams.scale, npRead->templateParams.var);
// compute template params
//nanopore_compute_noise_scale_params(sMt->EMISSION_MATCH_MATRIX, templateMap, &npRead->templateParams);
// compute complement params
//nanopore_compute_noise_scale_params(sMc->EMISSION_MATCH_MATRIX, complementMap, &npRead->complementParams);
// error log report
signalUtils_estimateNanoporeParams(sMt, npRead, &npRead->templateParams, ASSIGNMENT_THRESHOLD,
signalUtils_templateOneDAssignmentsFromRead, nanopore_dontAdjustEvents);
//signalUtils_estimateNanoporeParams(sMc, npRead, &npRead->complementParams, ASSIGNMENT_THRESHOLD,
// signalUtils_complementOneDAssignmentsFromRead, nanopore_dontAdjustEvents);
st_uglyf("SENTINEL - After: shift: %f scale: %f var: %f [template]\n",
npRead->templateParams.shift, npRead->templateParams.scale, npRead->templateParams.var);
//st_uglyf("SENTINEL - After: shift_sd: %f scale_sd: %f var_sd: %f [template]\n",
// npRead->complementParams.shift_sd, npRead->complementParams.scale_sd, npRead->complementParams.var_sd);
stList *templateKmers = lineTokensFromFile(npReadFile, 10);
//stList *complementKmers = lineTokensFromFile(npReadFile, 12);
//printEventNoisesAndParams(npRead, templateKmers, complementKmers);
printEventMeansAndParams(npRead, templateKmers, NULL);
stList_destruct(templateKmers);
//stList_destruct(complementKmers);
stList_destruct(templateMap);
//stList_destruct(complementMap);
nanopore_nanoporeReadDestruct(npRead);
stateMachine_destruct(sMt);
//stateMachine_destruct(sMc);
(void) j; // silence unused variable warning.
return 0;
}