void PullOutMatchedReads(struct tree *t, FILE *fastq, FILE *out) {
int location = 0;
int write = 0;
char *line = NULL;
size_t length;
ssize_t read;
struct split_data *idFirst;
struct split_data *idLast;
char *tmp;
char *s;
long long int id = 0;
int i = 0;
while ((read = getline(&line, &length, fastq)) != -1) {
if (location == 0) {
idFirst = (struct split_data*)malloc(sizeof(struct split_data));
idLast = (struct split_data*)malloc(sizeof(struct split_data));
idFirst = splitData(line, " ");
idLast = splitData((idFirst->tokenize)[0], ":");
s = (char *)malloc(100*sizeof(char));
(idLast->tokenize)[idLast->elements-2] = PadWithZeros((idLast->tokenize)[idLast->elements-2]);
(idLast->tokenize)[idLast->elements-1] = PadWithZeros((idLast->tokenize)[idLast->elements-1]);
sprintf(s, "%s%s%s%s", (idLast->tokenize)[1], (idLast->tokenize)[idLast->elements-3], (idLast->tokenize)[idLast->elements-2], (idLast->tokenize)[idLast->elements-1]);
id = strtoll(s, &tmp, 0);
write = Lookup(t->root, id);
location++;
for (i = 0; i < idFirst->elements; i++) {
free((idFirst->tokenize)[i]);
}
free((idFirst->tokenize));
free(idFirst);
for (i = 0; i < idLast->elements; i++) {
free((idLast->tokenize)[i]);
}
free((idLast->tokenize));
free(idLast);
free(s);
} else if (location == 3) {
location = 0;
} else {
location++;
}
if (write) {
fprintf(out, "%s", line);
}
}
}
void DiveThroughFixrank(struct tree *t, FILE *fixrank, char *taxlevel, char *name) {
char *line = NULL;
size_t length;
ssize_t read;
char *s;
char *tmp;
long long int id;
struct split_data *nameSearch = (struct split_data*)malloc(sizeof(struct split_data));
struct split_data *idFirst = (struct split_data*)malloc(sizeof(struct split_data));
struct split_data *idLast = (struct split_data*)malloc(sizeof(struct split_data));
int i = 0;
/*Read the entire file*/
while ((read = getline(&line, &length, fixrank)) != -1) {
nameSearch = splitData(line, "\t");
for (i = 0; i < nameSearch->elements; i++) {
/*if there is a match, the next should be taxlevel*/
if (strcmp(name, (nameSearch->tokenize)[i]) == 0) {
if (strcmp(taxlevel, (nameSearch->tokenize)[i+1]) == 0) {
idLast = splitData((nameSearch->tokenize)[0], "|");
idFirst = splitData((idLast->tokenize)[0], ":");
s = (char *)malloc(100*sizeof(char));
(idFirst->tokenize)[5] = PadWithZeros((idFirst->tokenize)[5]);
(idFirst->tokenize)[6] = PadWithZeros((idFirst->tokenize)[6]);
sprintf(s, "%s%s%s%s", (idFirst->tokenize)[1], (idFirst->tokenize)[4], (idFirst->tokenize)[5], (idFirst->tokenize)[6]);
id = strtoll(s, &tmp, 0);
free(s);
AddNode(&(t->root), id);
(t->count)++;
}
free((nameSearch->tokenize)[i]);
}
}
}
//printf("%d\n", (t->count));
}
bool CTarArchive::FillHeader(const std::string& filename, posix_header& header)
{
bool Ret = false;
#if defined DEBUG && defined VERBOSE
std::cout << i8n("[DBG]File header for ") << filename << " :" << '\n';
#endif
struct stat Info;
memset(&header, 0, 512);
//Try to stat file.
if(stat(filename.c_str(), &Info) == -1)
{
std::cout << i8n("[WNG] Cannot stat file: ") << filename.c_str() << i8n(" so I skip it !") << '\n';
Ret = false;
}
else
{
std::string l_name(filename);
#if defined WIN32
// No UID or GID support for Windows - Hack it up.
strncpy(header.mode, "0100777", 8);
strncpy(header.uid, "0000000", 8);
strncpy(header.gid, "0000000", 8);
#else
int Mode = 0;
//Never reached ?
if(!(Info.st_mode & S_IFREG))
{
// Not a normal file. Let's archive it anyway, but warn the user.
std::cout << i8n("[WNG] Archiving non-ordinary file (Linked or Device file?)") << '\n';
}
// Add the normal file bit.
Mode += 100000;
// Find out the file permissions.
if(Info.st_mode & TUREAD)
Mode += 400;
if(Info.st_mode & TUWRITE)
Mode += 200;
if(Info.st_mode & TUEXEC)
Mode += 100;
if(Info.st_mode & TGREAD)
Mode += 40;
if(Info.st_mode & TGWRITE)
Mode += 20;
if(Info.st_mode & TGEXEC)
Mode += 10;
if(Info.st_mode & TOREAD)
Mode += 4;
if(Info.st_mode & TOWRITE)
Mode += 2;
if(Info.st_mode & TOEXEC)
Mode += 1;
std::string Modestr(itos(Mode));
Modestr = PadWithZeros(Modestr, 8);
strncpy(header.mode, Modestr.c_str(), 8);
//UID
std::string l_uid(DecToOct(Info.st_uid));
l_uid = PadWithZeros(l_uid, 8);
strncpy(header.uid, l_uid.c_str(), 8);
//GID
std::string l_gid(DecToOct(Info.st_gid));
l_gid = PadWithZeros(l_gid, 8);
strncpy(header.gid, l_gid.c_str(), 8);
// File Size.
std::string Size = DecToOct(Info.st_size);
Size = PadWithZeros(Size, 12);
strncpy(header.size, Size.c_str(), 12);
// Time of modification
std::string l_mtime = DecToOct(time(0));
l_mtime = PadWithZeros(l_mtime, 12);
strncpy(header.mtime, l_mtime.c_str(), 12);
// Type of file.
header.typeflag = REGTYPE;
if (S_ISLNK(Info.st_mode))
header.typeflag = SYMTYPE;
else
{
if (S_ISDIR(Info.st_mode))
{
header.typeflag = DIRTYPE;
l_name += "/";
}
}
strncpy(header.name, l_name.c_str(), 100);
strncpy(header.linkname, "", 100);
// Magic
strncpy(header.magic, TMAGIC, TMAGLEN);
strncpy(header.version, TVERSION, TVERSLEN);
// Windows again, let's cheat.
#if defined WIN32
strncpy(header.uname, "root", 32);
strncpy(header.gname, "root", 32);
#else
passwd* l_pwdFileInfo = getpwuid(Info.st_uid);
group* l_grpFileInfo = getgrgid(Info.st_gid);
if(!l_pwdFileInfo || !l_grpFileInfo)
{
// No entry. Let's fake it.
strncpy(header.uname, header.uid, 32);
strncpy(header.gname, header.gid, 32);
}
else
{
strncpy(header.uname, l_pwdFileInfo->pw_name, 32);
strncpy(header.gname, l_grpFileInfo->gr_name, 32);
}
#endif
// Skip devminor and devmajor.
strncpy(header.devmajor, "", 8);
strncpy(header.devminor, "", 8);
// Fill the prefix.
strncpy(header.prefix, "", 167);
// Initialize our pointer.
char* l_startheaderPtr = reinterpret_cast<char*>(&header);
char* lheaderPtr ;
int l_checksum = 0;
// Find the checksum.
for(lheaderPtr = l_startheaderPtr; (lheaderPtr - l_startheaderPtr) < 512; ++lheaderPtr)
l_checksum += static_cast<int>(*lheaderPtr);
// Add 256 (2^8)
l_checksum += 256;
// Get it to Octal.
std::string l_checksumstr = DecToOct(l_checksum);
l_checksumstr = PadWithZeros(l_checksumstr, 8);
strncpy(header.chksum, l_checksumstr.c_str(), 8);
#if defined DEBUG && defined VERBOSE
Log::CLog::Instance()->Log(__FILE__, __LINE__, "Mode (8bytes) : ", header.mode, true);
Log::CLog::Instance()->Log(__FILE__, __LINE__, "UID (8b) : ", header.uid, true);
Log::CLog::Instance()->Log(__FILE__, __LINE__, "GID (8b) : ", header.gid, true);
Log::CLog::Instance()->Log(__FILE__, __LINE__, "Size (12b) : ", header.size, true);
Log::CLog::Instance()->Log(__FILE__, __LINE__, "Time (12b) : ", header.mtime, true);
Log::CLog::Instance()->Log(__FILE__, __LINE__, "Checksum : ", header.chksum, true);
#endif
#endif
Ret=true;
}
return Ret;
}
