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fixing memory leaks, code simplification
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@tpesout
tpesout committed Sep 10, 2019
1 parent aceedee commit c84eec3
Showing 1 changed file with 34 additions and 35 deletions.
69 changes: 34 additions & 35 deletions marginPolish.c
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,23 @@ void usage() {
fprintf(stderr, "\n");
}

char *getTimeDescriptorFromSeconds(int64_t seconds) {
int64_t minutes = (int64_t) (seconds / 60);
int64_t hours = (int64_t) (minutes / 60);
char *timeDescriptor;

if (hours > 0) {
timeDescriptor = stString_print("%"PRId64"h %"PRId64"m", hours,
minutes - (hours * 60));
} else if (minutes > 0) {
timeDescriptor = stString_print("%"PRId64"m %"PRId64"s", minutes,
seconds - (minutes * 60));
} else {
timeDescriptor = stString_print("%"PRId64"s", seconds);
}
return timeDescriptor;
}

char *getFileBase(char *base, char *defawlt) {
struct stat fileStat;
int64_t rc = stat(base, &fileStat);
Expand Down Expand Up @@ -214,6 +231,7 @@ int main(int argc, char *argv[]) {
}

// Initialization from arguments
time_t startTime = time(NULL);
st_setLogLevelFromString(logLevelString);
free(logLevelString);
# ifdef _OPENMP
Expand Down Expand Up @@ -303,7 +321,7 @@ int main(int argc, char *argv[]) {
// multiproccess the chunks, save to results
int64_t chunkIdx;
int64_t lastReportedPercentage = 0;
time_t startTime = time(NULL);
time_t polishStartTime = time(NULL);
#pragma omp parallel for schedule(dynamic,1)
for (chunkIdx = 0; chunkIdx < bamChunker->chunkCount; chunkIdx++) {
// Time all chunks
Expand Down Expand Up @@ -334,22 +352,10 @@ int main(int argc, char *argv[]) {

if (logProgress) {
// log progress
int64_t timeTaken = (int64_t) (time(NULL) - startTime);
int64_t timeTaken = (int64_t) (time(NULL) - polishStartTime);
int64_t secondsRemaining = (int64_t) floor(1.0 * timeTaken / currentPercentage * (100 - currentPercentage));
int64_t minutesRemaining = (int64_t) floor(secondsRemaining / 60);
int64_t hoursRemaining = (int64_t) floor(minutesRemaining / 60);
char *timeDescriptor;
if (secondsRemaining == 0 && currentPercentage <= 50) {
timeDescriptor = stString_print("unknown");
} else if (hoursRemaining > 0) {
timeDescriptor = stString_print("%"PRId64"h %"PRId64"m", hoursRemaining,
minutesRemaining - (hoursRemaining * 60));
} else if (minutesRemaining > 0) {
timeDescriptor = stString_print("%"PRId64"m %"PRId64"s", minutesRemaining,
secondsRemaining - (minutesRemaining * 60));
} else {
timeDescriptor = stString_print("%"PRId64"s", secondsRemaining);
}
char *timeDescriptor = (secondsRemaining == 0 && currentPercentage <= 50 ?
stString_print("unknown") : getTimeDescriptorFromSeconds(secondsRemaining));
st_logCritical("> Polishing %2"PRId64"%% complete (%"PRId64"/%"PRId64"). Estimated time remaining: %s\n",
currentPercentage, chunkIdx, bamChunker->chunkCount, timeDescriptor);
free(timeDescriptor);
Expand Down Expand Up @@ -544,7 +550,7 @@ int main(int argc, char *argv[]) {
int64_t contigStartIdx = 0;
char *referenceSequenceName = stString_copy(bamChunker_getChunk(bamChunker, 0)->refSeqName);
lastReportedPercentage = 0;
startTime = time(NULL);
time_t mergeStartTime = time(NULL);

// for filling missing chunks with N's
int64_t spacerSize = (bamChunker->chunkBoundary == 0 ? 50 : bamChunker->chunkBoundary * 3);
Expand Down Expand Up @@ -573,24 +579,13 @@ int main(int argc, char *argv[]) {
int64_t currentPercentage = (int64_t) (100 * chunkIdx / bamChunker->chunkCount);
if (currentPercentage != lastReportedPercentage) {
lastReportedPercentage = currentPercentage;
int64_t timeTaken = (int64_t) (time(NULL) - startTime);
int64_t timeTaken = (int64_t) (time(NULL) - mergeStartTime);
int64_t secondsRemaining = (int64_t) floor(1.0 * timeTaken / currentPercentage * (100 - currentPercentage));
int64_t minutesRemaining = (int64_t) floor(secondsRemaining / 60);
int64_t hoursRemaining = (int64_t) floor(minutesRemaining / 60);
char *timeDescriptor;
if (secondsRemaining == 0 && currentPercentage <= 50) {
timeDescriptor = stString_print("unknown");
} else if (hoursRemaining > 0) {
timeDescriptor = stString_print("%"PRId64"h %"PRId64"m", hoursRemaining,
minutesRemaining - (hoursRemaining * 60));
} else if (minutesRemaining > 0) {
timeDescriptor = stString_print("%"PRId64"m %"PRId64"s", minutesRemaining,
secondsRemaining - (minutesRemaining * 60));
} else {
timeDescriptor = stString_print("%"PRId64"s", secondsRemaining);
}
char *timeDescriptor = (secondsRemaining == 0 && currentPercentage <= 50 ?
stString_print("unknown") : getTimeDescriptorFromSeconds(secondsRemaining));
st_logCritical("> Merging %2"PRId64"%% complete (%"PRId64"/%"PRId64"). Estimated time remaining: %s\n",
currentPercentage, chunkIdx, bamChunker->chunkCount, timeDescriptor);
free(timeDescriptor);
}

// Clean up
Expand All @@ -609,16 +604,16 @@ int main(int argc, char *argv[]) {
// everything has been written, cleanup merging infrastructure
fclose(polishedReferenceOutFh);
free(missingChunkSpacer);
for (chunkIdx = 0; chunkIdx < bamChunker->chunkCount; chunkIdx++) {
free(chunkResults[chunkIdx]);
}

// Cleanup
st_logCritical("> Finished polishing.\n");
bamChunker_destruct(bamChunker);
stHash_destruct(referenceSequences);
params_destruct(params);

if (trueReferenceBam != NULL) free(trueReferenceBam);
if (trueReferenceBamChunker != NULL) bamChunker_destruct(trueReferenceBamChunker);

if (regionStr != NULL) free(regionStr);
#ifdef _HDF5
if (splitWeightHDF5Files != NULL) {
Expand All @@ -633,6 +628,10 @@ int main(int argc, char *argv[]) {
free(referenceFastaFile);
free(paramsFile);

// log completion
char *timeDescriptor = getTimeDescriptorFromSeconds(time(NULL) - startTime);
st_logCritical("> Finished polishing in %s.\n", timeDescriptor);
free(timeDescriptor);

// while(1); // Use this for testing for memory leaks

Expand Down

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