static void partialRecordRetrieval(CuTest *testCase) {
setup();
//Make some number of large records
stList *records = stList_construct3(0, free);
stList *recordSizes = stList_construct3(0, (void(*)(void *)) stIntTuple_destruct);
for (int32_t i = 0; i < 300; i++) {
int32_t size = st_randomInt(0, 80);
size = size * size * size; //Use cubic size distribution
char *randomRecord = st_malloc(size * sizeof(char));
for (int32_t j = 0; j < size; j++) {
randomRecord[j] = (char) st_randomInt(0, 100);
}
stList_append(records, randomRecord);
stList_append(recordSizes, stIntTuple_construct(1, size));
CuAssertTrue(testCase, !stKVDatabase_containsRecord(database, i));
stKVDatabase_insertRecord(database, i, randomRecord, size * sizeof(char));
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, i));
//st_uglyf("I am creating the record %i %i\n", i, size);
}
while (st_random() > 0.001) {
int32_t recordKey = st_randomInt(0, stList_length(records));
CuAssertTrue(testCase, stKVDatabase_containsRecord(database, recordKey));
char *record = stList_get(records, recordKey);
int32_t size = stIntTuple_getPosition(stList_get(recordSizes, recordKey), 0);
//Get partial record
int32_t start = size > 0 ? st_randomInt(0, size) : 0;
int32_t partialSize = size - start > 0 ? st_randomInt(start, size) - start : 0;
assert(start >= 0);
assert(partialSize >= 0);
assert(partialSize + start <= size);
//st_uglyf("I am getting record %i %i %i %i\n", recordKey, start, partialSize, size);
char *partialRecord = stKVDatabase_getPartialRecord(database, recordKey, start * sizeof(char),
partialSize * sizeof(char), size * sizeof(char));
//Check they are equivalent..
for (int32_t i = 0; i < partialSize; i++) {
if (record[start + i] != partialRecord[i]) {
st_uglyf("There was a difference %i %i for record %i %i\n", record[start + i], partialRecord[i], i,
partialSize);
}
//CuAssertTrue(testCase, record[start + i] == partialRecord[i]);
}
//Check we can not get out of bounds.. (start less than zero)
stTry {
stKVDatabase_getPartialRecord(database, recordKey, -1, 1, size * sizeof(char));
}stCatch(except)
{
CuAssertTrue(testCase, stExcept_getId(except) == ST_KV_DATABASE_EXCEPTION_ID);
}stTryEnd;
//Check we can not get out of bounds.. (start greater than index start)
stTry {
stKVDatabase_getPartialRecord(database, recordKey, size, 1, size * sizeof(char));
}stCatch(except)
{
CuAssertTrue(testCase, stExcept_getId(except) == ST_KV_DATABASE_EXCEPTION_ID);
}stTryEnd;
//Check we can not get out of bounds.. (total size if greater than record length)
stTry {
stKVDatabase_getPartialRecord(database, recordKey, 0, size + 1, size * sizeof(char));
}stCatch(except)
{
CuAssertTrue(testCase, stExcept_getId(except) == ST_KV_DATABASE_EXCEPTION_ID);
}stTryEnd;
//Check we can not get non existent record
stTry {
stKVDatabase_getPartialRecord(database, 1000000, 0, size, size * sizeof(char));
}stCatch(except)
{
CuAssertTrue(testCase, stExcept_getId(except) == ST_KV_DATABASE_EXCEPTION_ID);
}stTryEnd;
}
stList_destruct(records);
stList_destruct(recordSizes);
teardown();
}
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;
}
