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;
}
exp bool CopyOut(const char* source, const char* dest) {
// Convert the filename into DOS8.3 format
char* dosName = new char[12];
ToDos83Name(source, dosName);
// Find the file on the disk
DirectoryEntry* entry = FindEntry(dosName, &directory);
if (!entry) {
LastError("CopyOut", "File doesn't exist");
return false;
}
if (!(entry->attrib & ATTRIB_ARCHIVE)) {
LastError("CopyOut", "This is not a file");
return false;
}
// Update the entry
UpdateEntry(entry, 0, 0);
std::ofstream outHandle(dest, std::ios::out | std::ios::binary);
if (!outHandle.is_open())
return false;
// Set up a FatEntry
FatEntry fatEntry;
fatEntry.cluster = GetClusterFromEntry(entry);
fatEntry.sector = GetFATSector(fatEntry.cluster);
fatEntry.buffer = new char[bpb->bytesPerSector];
ReadSector(fatEntry.buffer, fatEntry.sector);
char* sectorData = new char[bpb->bytesPerSector];
// Read Data
while (ReadCluster(&fatEntry, sectorData))
outHandle.write(sectorData, 512);
if (!(entry->size % bpb->bytesPerSector))
outHandle.write(sectorData, 512);
else
outHandle.write(sectorData, entry->size % bpb->bytesPerSector);
delete[] fatEntry.buffer;
delete[] sectorData;
delete[] dosName;
outHandle.close();
return true;
}
