/**
* Mount directory and check that we mounted the right directory.
*/
static int seunshare_mount(const char *src, const char *dst, struct stat *src_st)
{
int flags = 0;
int is_tmp = 0;
if (verbose)
printf(_("Mounting %s on %s\n"), src, dst);
if (strcmp("/tmp", dst) == 0) {
flags = flags | MS_NODEV | MS_NOSUID | MS_NOEXEC;
is_tmp = 1;
}
/* mount directory */
if (mount(src, dst, NULL, MS_BIND | flags, NULL) < 0) {
fprintf(stderr, _("Failed to mount %s on %s: %s\n"), src, dst, strerror(errno));
return -1;
}
/* verify whether we mounted what we expected to mount */
if (verify_directory(dst, src_st, NULL) < 0) return -1;
/* bind mount /tmp on /var/tmp too */
if (is_tmp) {
if (verbose)
printf(_("Mounting /tmp on /var/tmp\n"));
if (mount("/tmp", "/var/tmp", NULL, MS_BIND | flags, NULL) < 0) {
fprintf(stderr, _("Failed to mount /tmp on /var/tmp: %s\n"), strerror(errno));
return -1;
}
}
return 0;
}
int main(int argc, char *argv[] )
{
char archive[1024];
char *p;
if ( argc < 3 ) {
#ifndef PLAT_UNIX
printf( "Usage: %s archive_name src_dir\n", argv[0] );
printf( "Example: %s freespace c:\\freespace\\data\n", argv[0] );
printf( "Creates an archive named freespace out of the\nfreespace data tree\n" );
printf( "Press any key to exit...\n" );
getch();
return 1;
#else
print_instructions();
#endif
}
strcpy( archive, argv[1] );
p = strchr( archive, '.' );
if (p) *p = 0; // remove extension
strcpy( archive_dat, archive );
strcat( archive_dat, ".vp" );
strcpy( archive_hdr, archive );
strcat( archive_hdr, ".hdr" );
fp_out = fopen( archive_dat, "wb" );
if ( !fp_out ) {
printf( "Couldn't open '%s'!\n", archive_dat );
#ifndef PLAT_UNIX
printf( "Press any key to exit...\n" );
getch();
return 1;
#else
exit(1);
#endif
}
fp_out_hdr = fopen( archive_hdr, "wb" );
if ( !fp_out_hdr ) {
printf( "Couldn't open '%s'!\n", archive_hdr );
#ifndef PLAT_UNIX
printf( "Press any key to exit...\n" );
getch();
return 1;
#else
exit(2);
#endif
}
if ( verify_directory( argv[2] ) != 0 ) {
printf("Warning! Last directory must be named \"data\" (not case sensitive)\n");
exit(3);
}
write_header();
pack_directory( argv[2] );
// in case the directory doesn't exist
if ( no_dir )
exit(4);
write_header();
fclose(fp_out);
fclose(fp_out_hdr);
printf( "Data files written, appending index...\n" );
if (!write_index(archive_hdr, archive_dat)) {
printf("Error appending index!\n");
#ifndef PLAT_UNIX
printf("Press any key to exit...\n");
getch();
#endif
return 1;
}
printf( "%d total KB.\n", Total_size/1024 );
return 0;
}
/*! \brief The main function of the **rm_reads** tool. */
int main(int argc, char ** argv)
{
Node root('0');
std::vector <std::pair<std::string, Node::Type> > patterns;
std::string kmers, reads, out_dir;
std::string reads1, reads2;
char rez = 0;
int length = 0;
int polyG = 0;
int dust_k = 4;
int dust_cutoff = 0;
int errors = 0;
const struct option long_options[] = {
{"fragments",required_argument,NULL,'f'},
{"errors",required_argument,NULL,'e'},
{NULL,0,NULL,0}
};
while ((rez = getopt_long(argc, argv, "1:2:f:i:o:", long_options, NULL)) != -1) {
switch (rez) {
case 'f':
kmers = optarg;
break;
case 'i':
reads = optarg;
break;
case '1':
reads1 = optarg;
break;
case '2':
reads2 = optarg;
break;
case 'o':
out_dir = optarg;
break;
case '?':
print_help();
return -1;
}
}
if (errors < 0 || errors > 2) {
std::cerr << "possible errors count are 0, 1, 2" << std::endl;
return -1;
}
if (kmers.empty() || out_dir.empty() || (
reads.empty() &&
(reads1.empty() || reads2.empty()))) {
print_help();
return -1;
}
if (!verify_directory(out_dir)) {
std::cerr << "Output directory does not exist, failed to create" << std::endl;
return -1;
}
std::ifstream kmers_f (kmers.c_str());
if (!kmers_f.good()) {
std::cerr << "Cannot open kmers file" << std::endl;
print_help();
return -1;
}
init_type_names(length, polyG, dust_k, dust_cutoff);
build_patterns(kmers_f, patterns);
/*
for (std::vector <std::string> ::iterator it = patterns.begin(); it != patterns.end(); ++it) {
std::cout << *it << std::endl;
}
*/
if (patterns.empty()) {
std::cerr << "patterns are empty" << std::endl;
return -1;
}
std::cerr << "Building trie..." << std::endl;
build_trie(root, patterns, errors);
add_failures(root);
if (!reads.empty()) {
std::string reads_base = basename(reads);
std::ifstream reads_f (reads.c_str());
std::ofstream ok_f((out_dir + "/" + reads_base + ".ok.fastq").c_str(), std::ofstream::out);
std::ofstream bad_f((out_dir + "/" + reads_base + ".filtered.fastq").c_str(), std::ofstream::out);
if (!reads_f.good()) {
std::cerr << "Cannot open reads file" << std::endl;
print_help();
return -1;
}
if (!ok_f.good() || !bad_f.good()) {
std::cerr << "Cannot open output file" << std::endl;
print_help();
return -1;
}
Stats stats(reads);
filter_single_reads(reads_f, ok_f, bad_f, stats, &root, patterns, length, dust_k, dust_cutoff, errors);
std::cout << stats;
ok_f.close();
bad_f.close();
reads_f.close();
} else {
std::string reads1_base = basename(reads1);
std::string reads2_base = basename(reads2);
std::ifstream reads1_f(reads1.c_str());
std::ifstream reads2_f(reads2.c_str());
std::ofstream ok1_f((out_dir + "/" + reads1_base + ".ok.fastq").c_str(),
std::ofstream::out);
std::ofstream ok2_f((out_dir + "/" + reads2_base + ".ok.fastq").c_str(),
std::ofstream::out);
std::ofstream se1_f((out_dir + "/" + reads1_base + ".se.fastq").c_str(),
std::ofstream::out);
std::ofstream se2_f((out_dir + "/" + reads2_base + ".se.fastq").c_str(),
std::ofstream::out);
std::ofstream bad1_f((out_dir + "/" + reads1_base + ".filtered.fastq").c_str(),
std::ofstream::out);
std::ofstream bad2_f((out_dir + "/" + reads2_base + ".filtered.fastq").c_str(),
std::ofstream::out);
if (!reads1_f.good() || !reads2_f.good()) {
std::cerr << "reads file is bad" << std::endl;
print_help();
return -1;
}
if (!ok1_f.good() || !ok2_f.good() || !bad1_f.good() || !bad2_f.good() ||
!se1_f.good() || !se2_f.good()) {
std::cerr << "out file is bad" << std::endl;
print_help();
return -1;
}
Stats stats1(reads1);
Stats stats2(reads2);
filter_paired_reads(reads1_f, reads2_f, ok1_f, ok2_f,
bad1_f, bad2_f, se1_f, se2_f,
stats1, stats2,
&root, patterns, length, dust_k, dust_cutoff, errors);
std::cout << stats1;
std::cout << stats2;
ok1_f.close();
ok2_f.close();
bad1_f.close();
bad2_f.close();
reads1_f.close();
reads2_f.close();
}
}
