int main(int argc, char *argv[]) {
if(argc < 3)
return usage(argv);
int c;
int is_se{0};
char out_mode[4] = "wb";
opts_t opts;
while((c = getopt(argc, argv, "m:l:h?sSn")) > -1) {
switch(c) {
case 'm': opts.min_trimmed_len = (uint32_t)atoi(optarg); break;
case 'l': out_mode[2] = *optarg; break;
case 's': is_se = 1; break;
case 'S': sprintf(out_mode, "w"); break;
case 'n': opts.skip_all_ns = 1; break;
case 'h': case '?': return usage(argv, EXIT_SUCCESS);
}
}
if(argc - 2 != optind) LOG_EXIT("Required: precisely two positional arguments (in bam, out bam).\n");
dlib::BamHandle inHandle(argv[optind]);
dlib::BamHandle outHandle(argv[optind + 1], inHandle.header, out_mode);
is_se ? dlib::abstract_single_iter(inHandle.fp, inHandle.header, outHandle.fp, &trim_ns, (void *)&opts)
: dlib::abstract_pair_iter(inHandle.fp, inHandle.header, outHandle.fp, &pe_trim_ns, (void *)&opts);
return EXIT_SUCCESS;
}
int main( int argc, char **argv ) {
if ( argc <= 1 ) {
return EXIT_FAILURE;
}
// Read the word list file
std::ifstream dictFile("/var/tmp/twl06.txt");
std::vector<std::string> dictWordVector;
dictWordVector.reserve(178691);
std::string line;
if (dictFile.is_open()) {
while (! dictFile.eof() ) {
std::getline (dictFile,line);
trim(line);
std::transform(line.begin(), line.end(), line.begin(), ::tolower);
dictWordVector.push_back(line);
}
dictFile.close();
} else {
return EXIT_FAILURE;
}
BkTree *pDictionary = new BkTree();
std::vector<std::string>::const_iterator itr;
for ( itr = dictWordVector.begin(); itr != dictWordVector.end(); ++itr) {
pDictionary->insert(*itr);
}
std::ifstream inHandle(argv[1]);
std::vector<std::string> wordVector;
while (getline(inHandle, line, '\n')) {
std::istringstream iss(line);
std::copy( std::istream_iterator<std::string>(iss),
std::istream_iterator<std::string>(),
std::back_inserter<std::vector<std::string> >(wordVector));
}
inHandle.close();
std::vector<std::string>::iterator wVecIter;
int totalDistance = 0;
for ( wVecIter = wordVector.begin(); wVecIter != wordVector.end(); ++wVecIter ) {
int startDistance = 0;
while ( true ) {
int result = pDictionary->getWithinDistance( *wVecIter, startDistance );
if ( result != 0 ) {
totalDistance += startDistance;
break;
}
startDistance++;
}
}
std::cout << totalDistance << std::endl;
delete pDictionary;
return EXIT_SUCCESS;
}
exp bool CopyIn(const char* source, const char* dest) {
DirectoryEntry* entry = 0;
char* buffer = new char[bpb->bytesPerSector];
// Open file we're copying in
std::ifstream inHandle(source, std::ios::in | std::ios::binary | std::ios::ate);
if (!inHandle.is_open()) {
LastError("CopyIn", "Failed to open source file");
return false;
}
// Get size of source file
size_t inLength = (size_t)inHandle.tellg();
inHandle.seekg(std::ios::beg);
// Convert the filename into DOS8.3 format
char* dosName = new char[12];
ToDos83Name(dest, dosName);
// Check if entry exists, if so, overwrite it
entry = FindEntry(dosName, &directory);
if (entry) {
// Delete file
Delete(dest);
// Undelete entry
entry->name[0] = dosName[0];
}
// Create the directory entry
if (!entry) {
// Didn't delete file, make it
entry = MakeEntry(dosName, ATTRIB_ARCHIVE, inLength, &directory);
if (!entry) {
LastError("CopyIn", "Failed to create directory entry");
delete[] dosName;
delete[] buffer;
return false;
}
}
else {
// Deleted file, find it
entry = FindEntry(dosName, &directory);
if (!entry) {
LastError("CopyIn", "Somehow a file that was just undeleted can't be found...");
delete[] dosName;
delete[] buffer;
return false;
}
UpdateEntry(entry, 0, inLength);
}
// Write entry to disk
DirectoryWrite(&directory);
// Update FAT and then load each cluster and write it while updating the FAT
FatEntry fatEntry;
fatEntry.buffer = new char[bpb->bytesPerSector];
fatEntry.cluster = GetClusterFromEntry(entry);
fatEntry.sector = GetFATSector(fatEntry.cluster);
ReadSector(fatEntry.buffer, fatEntry.sector);
UpdateFAT(&fatEntry, FindFreeCluster());
// Write to disk
for (size_t i = 0; i < inLength; i += bpb->bytesPerSector) {
memset(buffer, 0, bpb->bytesPerSector);
if (!(i % bpb->bytesPerSector))
inHandle.read(buffer, bpb->bytesPerSector);
else
inHandle.read(buffer, i % bpb->bytesPerSector);
WriteCluster(&fatEntry, buffer);
}
delete[] dosName;
delete[] buffer;
delete[] fatEntry.buffer;
inHandle.close();
return true;
}
