int main(const int argc, char* argv[]) {
FILE *image;
enum exe_type et;
if (argc < 2) {
fprintf(stderr, "Synopsis: %s file.exe [...]\n", argv[0]);
return 0;
}
#ifdef ENABLE_DEBUG
if (!strcmp(argv[1], "--pretend") && argc >= 3) {
pretending = 1;
argv[1] = argv[2]; /* we won't be using argv[2+] anyway */
}
#endif
image = fopen(argv[1], "r");
et = detect_format(image); /* image can be NULL here */
if (et == EXE_ERROR)
perror("I/O error while reading executable");
if (image)
fclose(image);
if (et < EXE_ERROR) {
char* const handler = read_conf(et);
if (handler)
doexec(handler, argv);
}
return 127;
}
int main(int argc, char **argv) {
scram_fd **in, *out;
int n_input, i;
bam_seq_t **s;
char imode[10], *in_f = "", omode[10], *out_f = "";
int level = '\0'; // nul terminate string => auto level
int c, verbose = 0;
int s_opt = 0, S_opt = 0, embed_ref = 0;
char *ref_fn = NULL;
int start, end;
char ref_name[1024] = {0};
refs_t *refs = NULL;
/* Parse command line arguments */
while ((c = getopt(argc, argv, "u0123456789hvs:S:V:r:XI:O:R:")) != -1) {
switch (c) {
case '0': case '1': case '2': case '3': case '4':
case '5': case '6': case '7': case '8': case '9':
level = c;
break;
case 'u':
level = '0';
break;
case 'h':
usage(stdout);
return 0;
case 'v':
verbose++;
break;
case 's':
s_opt = atoi(optarg);
break;
case 'S':
S_opt = atoi(optarg);
break;
case 'V':
cram_set_option(NULL, CRAM_OPT_VERSION, optarg);
break;
case 'r':
ref_fn = optarg;
break;
case 'X':
embed_ref = 1;
break;
case 'I':
in_f = parse_format(optarg);
break;
case 'O':
out_f = parse_format(optarg);
break;
case 'R': {
char *cp = strchr(optarg, ':');
if (cp) {
*cp = 0;
switch (sscanf(cp+1, "%d-%d", &start, &end)) {
case 1:
end = start;
break;
case 2:
break;
default:
fprintf(stderr, "Malformed range format\n");
return 1;
}
} else {
start = INT_MIN;
end = INT_MAX;
}
strncpy(ref_name, optarg, 1023);
break;
}
case '?':
fprintf(stderr, "Unrecognised option: -%c\n", optopt);
usage(stderr);
return 1;
}
}
/* Open output file */
sprintf(omode, "w%s%c", out_f, level);
if (!(out = scram_open("-", omode))) {
fprintf(stderr, "Failed to open bam file %s\n", argv[optind+1]);
return 1;
}
/* Open multiple input files */
sprintf(imode, "r%s%c", in_f, level);
n_input = argc - optind;
if (!n_input) {
fprintf(stderr, "No input files specified.\n");
return 1;
}
if (!(in = malloc(n_input * sizeof(*in))))
return 1;
if (!(s = malloc(n_input * sizeof(*s))))
return 1;
for (i = 0; i < n_input; i++, optind++) {
s[i] = NULL;
if (*in_f == 0)
sprintf(imode, "r%s%c", detect_format(argv[optind]), level);
if (!(in[i] = scram_open(argv[optind], imode))) {
fprintf(stderr, "Failed to open bam file %s\n", argv[optind]);
return 1;
}
if (i && !hdr_compare(scram_get_header(in[0]),
scram_get_header(in[i]))) {
fprintf(stderr, "Incompatible reference sequence list.\n");
fprintf(stderr, "Currently the @SQ lines need to be identical"
" in all files.\n");
return 1;
}
if (!refs && scram_get_refs(in[i]))
refs = scram_get_refs(in[i]);
if (refs && scram_set_option(in[i], CRAM_OPT_SHARED_REF, refs))
return 1;
}
/* Set any format specific options */
if (refs)
scram_set_option(out, CRAM_OPT_SHARED_REF, refs);
if (scram_set_option(out, CRAM_OPT_VERBOSITY, verbose))
return 1;
if (s_opt)
if (scram_set_option(out, CRAM_OPT_SEQS_PER_SLICE, s_opt))
return 1;
if (S_opt)
if (scram_set_option(out, CRAM_OPT_SLICES_PER_CONTAINER, S_opt))
return 1;
if (embed_ref)
if (scram_set_option(out, CRAM_OPT_EMBED_REF, embed_ref))
return 1;
/* Copy header and refs from in to out, for writing purposes */
// FIXME: do proper merging of @PG lines
// FIXME: track mapping of old PG aux name to new PG aux name per seq
scram_set_header(out, sam_hdr_dup(scram_get_header(in[0])));
// Needs doing after loading the header.
if (ref_fn)
if (scram_set_option(out, CRAM_OPT_REFERENCE, ref_fn))
return 1;
if (scram_get_header(in[0])) {
if (scram_write_header(out))
return 1;
}
/* Do the actual file format conversion */
fprintf(stderr, "Opening and loading initial seqs\n");
for (i = 0; i < n_input; i++) {
if (scram_get_seq(in[i], &s[i]) < 0) {
if (scram_close(in[i]))
return 1;
in[i] = NULL;
free(s[i]);
continue;
}
}
fprintf(stderr, "Merging...\n");
for (;;) {
int64_t best_val = INT64_MAX;
int best_j = 0, j;
for (j = 0; j < n_input; j++) {
bam_seq_t *b = s[j];
uint64_t x;
if (!in[j])
continue;
x = (((uint64_t)bam_ref(b))<<33)
| (bam_pos(b)<<2)
| (bam_strand(b)<<1)
| !(bam_flag(b) & BAM_FREAD1);
if (best_val > x) {
best_val = x;
best_j = j;
}
}
if (best_val == INT64_MAX) { // all closed
break;
}
if (-1 == scram_put_seq(out, s[best_j]))
return 1;
if (scram_get_seq(in[best_j], &s[best_j]) < 0) {
if (scram_close(in[best_j]))
return 1;
in[best_j] = NULL;
free(s[best_j]);
}
}
for (i = 0; i < n_input; i++) {
if (!in[i])
continue;
scram_close(in[i]);
if (s[i])
free(s[i]);
}
/* Finally tidy up and close files */
if (scram_close(out))
return 1;
free(in);
free(s);
return 0;
}
void setArguments(){
/*
* Verification os file in
*/
if (fileIn == NULL){
fprintf(stderr, "There is no input file.\n");
exit(-1);
}
/*
* Verification o number of bits.
* Number default: 1.
*/
if (nbBits == -1){
nbBits = 1;
}
else{
if(nbBits>8 || nbBits <1){
fprintf(stderr, "Not possible to pattern a message with this number of bits\n");
exit(-1);
}
}
/*
* Verification of pattern
* Default pattern: Direct.
*/
if(pattern == NULL){
pattern = "DIRECT";
patternInt = 1;
}
else{
flag = validatePattern();
switch (flag){
case -1:
fprintf(stderr, "Not a valid pattern\n");
exit(-1);
case 1:
patternInt = flag; //Direct Pattern
break;
case 2:
patternInt = flag; //Inverse
break;
case 3:
fprintf(stderr, "External spiral pattern not implemented\n");
exit(-3);
case 4:
fprintf(stderr, "Internal spiral pattern not implemented\n");
exit(-4);
}
}
/**
* Setting and validation os Channels
* Default: Red,Green,Blue
*/
if (channels == NULL){
firstChannel = 2;
secondChannel = 1;
thirdChannel = 0;
}else{
setChannels();
}
/**
* Validation of Magic Number
* Default: 48454C50
*/
if(magicHexa == NULL){
magicHexa = "48454C50";
magic = hex_to_str(magicHexa); // magic = "HELP"
}else{
magic = hex_to_str(magicHexa);
}
/**
* Validation of Output
* Default: Standart (Console)
*/
if(fileOut != NULL){
isStandard = false;
}
else {
isStandard = true;
fileOut = "output.txt";
}
/**
* Validation of the format of input
* If there is no format, the program will detect.
* If the format of the image its different of the argument or it is not a format accepted,
* the program ends/error.
*/
img = cvLoadImage(fileIn, 1); // Second parameter == 1 (RGB) || == 0 (GREY)
if (img){ //Try to load the image by OpenCv
if(formatIn == NULL){
int format = detect_format(fileIn);
if (format == -1){
fprintf(stderr, "Not possible to detect format\n");
exit(-1);
}
}
else {
flag = validateFormat();
switch (flag) {
case 0: //Accepted
break;
case -1:
fprintf(stderr, "%s is not a format accepted\n", formatIn);
exit(-1);
case -2:
fprintf(stderr, "This format is not the format of the image\n");
exit(-2);
case -3:
fprintf(stderr, "Not a format valid\n");
exit(-2);
}
}
}else{
fprintf(stderr, "Could not open the file\n");
exit(-3);
}
}
int main(int argc, char **argv) {
scram_fd *in, *out;
bam_seq_t *s;
char imode[10], *in_f = "", omode[10], *out_f = "";
int level = '\0'; // nul terminate string => auto level
int c, verbose = 0;
int s_opt = 0, S_opt = 0, embed_ref = 0, ignore_md5 = 0, decode_md = 0;
char *ref_fn = NULL;
int start, end, multi_seq = -1, no_ref = 0;
int use_bz2 = 0, use_arith = 0, use_lzma = 0;
char ref_name[1024] = {0};
refs_t *refs;
int nthreads = 1;
t_pool *p = NULL;
int max_reads = -1;
enum quality_binning binning = BINNING_NONE;
/* Parse command line arguments */
while ((c = getopt(argc, argv, "u0123456789hvs:S:V:r:xXeI:O:R:!MmjJZt:BN:")) != -1) {
switch (c) {
case '0': case '1': case '2': case '3': case '4':
case '5': case '6': case '7': case '8': case '9':
level = c;
break;
case 'u':
level = '0';
break;
case 'h':
usage(stdout);
return 0;
case 'v':
verbose++;
break;
case 's':
s_opt = atoi(optarg);
break;
case 'S':
S_opt = atoi(optarg);
break;
case 'm':
decode_md = 1;
break;
case 'V':
if (cram_set_option(NULL, CRAM_OPT_VERSION, optarg))
return 1;
break;
case 'r':
ref_fn = optarg;
break;
case 'X':
fprintf(stderr, "-X is deprecated in favour of -e.\n");
case 'e':
embed_ref = 1;
break;
case 'x':
no_ref = 1;
break;
case 'I':
in_f = parse_format(optarg);
break;
case 'O':
out_f = parse_format(optarg);
break;
case 'R': {
char *cp = strchr(optarg, ':');
if (cp) {
*cp = 0;
switch (sscanf(cp+1, "%d-%d", &start, &end)) {
case 1:
end = start;
break;
case 2:
break;
default:
fprintf(stderr, "Malformed range format\n");
return 1;
}
} else {
start = INT_MIN;
end = INT_MAX;
}
strncpy(ref_name, optarg, 1023);
break;
}
case '!':
ignore_md5 = 1;
break;
case 'M':
multi_seq = 1;
break;
case 'j':
#ifdef HAVE_LIBBZ2
use_bz2 = 1;
#else
fprintf(stderr, "Warning: bzip2 support is not compiled into this"
" version.\nPlease recompile.\n");
#endif
break;
case 'J':
use_arith = 1;
break;
case 'Z':
#ifdef HAVE_LIBLZMA
use_lzma = 1;
#else
fprintf(stderr, "Warning: lzma support is not compiled into this"
" version.\nPlease recompile.\n");
#endif
break;
case 't':
nthreads = atoi(optarg);
if (nthreads < 1) {
fprintf(stderr, "Number of threads needs to be >= 1\n");
return 1;
}
break;
case 'B':
binning = BINNING_ILLUMINA;
break;
case 'N': // For debugging
max_reads = atoi(optarg);
break;
case '?':
fprintf(stderr, "Unrecognised option: -%c\n", optopt);
usage(stderr);
return 1;
}
}
if (argc - optind > 2) {
fprintf(stderr, "Usage: scramble [input_file [output_file]]\n");
return 1;
}
/* Open up input and output files */
sprintf(imode, "r%s%c", in_f, level);
if (argc - optind > 0) {
if (*in_f == 0)
sprintf(imode, "r%s%c", detect_format(argv[optind]), level);
if (!(in = scram_open(argv[optind], imode))) {
fprintf(stderr, "Failed to open file %s\n", argv[optind]);
return 1;
}
} else {
if (!(in = scram_open("-", imode))) {
fprintf(stderr, "Failed to open file %s\n", argv[optind]);
return 1;
}
}
if (!in->is_bam && ref_fn) {
cram_load_reference(in->c, ref_fn);
if (!in->c->refs && !embed_ref) {
fprintf(stderr, "Unable to find an appropriate reference.\n"
"Please specify a valid reference with "
"-r ref.fa option.\n");
return 1;
}
}
sprintf(omode, "w%s%c", out_f, level);
if (argc - optind > 1) {
if (*out_f == 0)
sprintf(omode, "w%s%c", detect_format(argv[optind+1]), level);
if (!(out = scram_open(argv[optind+1], omode))) {
fprintf(stderr, "Failed to open file %s\n", argv[optind+1]);
return 1;
}
} else {
if (!(out = scram_open("-", omode))) {
fprintf(stderr, "Failed to open file %s\n", argv[optind+1]);
return 1;
}
}
/* Set any format specific options */
scram_set_refs(out, refs = scram_get_refs(in));
scram_set_option(out, CRAM_OPT_VERBOSITY, verbose);
if (s_opt)
if (scram_set_option(out, CRAM_OPT_SEQS_PER_SLICE, s_opt))
return 1;
if (S_opt)
if (scram_set_option(out, CRAM_OPT_SLICES_PER_CONTAINER, S_opt))
return 1;
if (embed_ref)
if (scram_set_option(out, CRAM_OPT_EMBED_REF, embed_ref))
return 1;
if (use_bz2)
if (scram_set_option(out, CRAM_OPT_USE_BZIP2, use_bz2))
return 1;
if (use_arith)
if (scram_set_option(out, CRAM_OPT_USE_ARITH, use_arith))
return 1;
if (use_lzma)
if (scram_set_option(out, CRAM_OPT_USE_LZMA, use_lzma))
return 1;
if (binning != BINNING_NONE)
if (scram_set_option(out, CRAM_OPT_BINNING, binning))
return 1;
if (no_ref)
if (scram_set_option(out, CRAM_OPT_NO_REF, no_ref))
return 1;
if (multi_seq)
if (scram_set_option(out, CRAM_OPT_MULTI_SEQ_PER_SLICE, multi_seq))
return 1;
if (decode_md) {
if (no_ref) {
fprintf(stderr, "Cannot use -m in conjunction with -x.\n");
return 1;
}
if (scram_set_option(in, CRAM_OPT_DECODE_MD, decode_md))
return 1;
}
if (nthreads > 1) {
if (NULL == (p = t_pool_init(nthreads*2, nthreads)))
return 1;
if (scram_set_option(in, CRAM_OPT_THREAD_POOL, p))
return 1;
if (scram_set_option(out, CRAM_OPT_THREAD_POOL, p))
return 1;
}
if (ignore_md5)
if (scram_set_option(in, CRAM_OPT_IGNORE_MD5, ignore_md5))
return 1;
/* Copy header and refs from in to out, for writing purposes */
scram_set_header(out, scram_get_header(in));
// Needs doing after loading the header.
if (ref_fn) {
if (scram_set_option(out, CRAM_OPT_REFERENCE, ref_fn))
return 1;
} else {
// Attempt to fill out a cram->refs[] array from @SQ headers
scram_set_option(out, CRAM_OPT_REFERENCE, NULL);
}
if (scram_get_header(out)) {
char *arg_list = stringify_argv(argc, argv);
if (!arg_list)
return 1;
if (sam_hdr_add_PG(scram_get_header(out), "scramble",
"VN", PACKAGE_VERSION,
"CL", arg_list, NULL))
return 1;
if (scram_write_header(out))
return 1;
free(arg_list);
}
/* Support for sub-range queries, currently implemented for CRAM only */
if (*ref_name != 0) {
cram_range r;
int refid;
if (in->is_bam) {
fprintf(stderr, "Currently the -R option is only implemented for CRAM indices\n");
return 1;
}
cram_index_load(in->c, argv[optind]);
refid = sam_hdr_name2ref(in->c->header, ref_name);
if (refid == -1 && *ref_name != '*') {
fprintf(stderr, "Unknown reference name '%s'\n", ref_name);
return 1;
}
r.refid = refid;
r.start = start;
r.end = end;
if (scram_set_option(in, CRAM_OPT_RANGE, &r))
return 1;
}
/* Do the actual file format conversion */
s = NULL;
while (scram_get_seq(in, &s) >= 0) {
if (-1 == scram_put_seq(out, s)) {
fprintf(stderr, "Failed to encode sequence\n");
return 1;
}
if (max_reads >= 0)
if (--max_reads == 0)
break;
}
if (max_reads == -1) {
switch(scram_eof(in)) {
case 0:
fprintf(stderr, "Failed to decode sequence\n");
return 1;
case 2:
fprintf(stderr, "Warning: no end-of-file block identified. "
"File may be truncated.\n");
break;
case 1: default:
// expected case
break;
}
}
/* Finally tidy up and close files */
if (scram_close(in))
return 1;
if (scram_close(out))
return 1;
if (p)
t_pool_destroy(p, 0);
if (s)
free(s);
return 0;
}
int main(int argc, char **argv) {
scram_fd *in;
bam_seq_t *s;
char imode[10], *in_f = "";
int level = '\0'; // nul terminate string => auto level
int c;
char *ref_fn = NULL;
int start, end, ignore_md5 = 0;
char ref_name[1024] = {0};
bam_flagstat_t st;
int nthreads = 1;
memset(&st, 0, sizeof(st));
/* Parse command line arguments */
while ((c = getopt(argc, argv, "hI:R:r:!t:")) != -1) {
switch (c) {
case 'h':
usage(stdout);
return 0;
case 'r':
ref_fn = optarg;
break;
case 'I':
in_f = parse_format(optarg);
break;
case 'R': {
char *cp = strchr(optarg, ':');
if (cp) {
*cp = 0;
switch (sscanf(cp+1, "%d-%d", &start, &end)) {
case 1:
end = start;
break;
case 2:
break;
default:
fprintf(stderr, "Malformed range format\n");
return 1;
}
} else {
start = INT_MIN;
end = INT_MAX;
}
strncpy(ref_name, optarg, 1023);
break;
}
case '!':
ignore_md5 = 1;
break;
case 't':
nthreads = atoi(optarg);
if (nthreads < 1) {
fprintf(stderr, "Number of threads needs to be >= 1\n");
return 1;
}
break;
case '?':
fprintf(stderr, "Unrecognised option: -%c\n", optopt);
usage(stderr);
return 1;
}
}
if (argc - optind > 2) {
fprintf(stderr, "Usage: scramble [input_file [output_file]]\n");
return 1;
}
/* Open up input and output files */
sprintf(imode, "r%s%c", in_f, level);
if (argc - optind > 0) {
if (*in_f == 0)
sprintf(imode, "r%s%c", detect_format(argv[optind]), level);
if (!(in = scram_open(argv[optind], imode))) {
fprintf(stderr, "Failed to open file %s\n", argv[optind]);
return 1;
}
} else {
if (!(in = scram_open("-", imode))) {
fprintf(stderr, "Failed to open file %s\n", argv[optind]);
return 1;
}
}
if (!in->is_bam && ref_fn)
cram_load_reference(in->c, ref_fn);
if (nthreads > 1)
if (scram_set_option(in, CRAM_OPT_NTHREADS, nthreads))
return 1;
if (ignore_md5)
if (scram_set_option(in, CRAM_OPT_IGNORE_MD5, ignore_md5))
return 1;
/* Support for sub-range queries, currently implemented for CRAM only */
if (*ref_name != 0) {
cram_range r;
int refid;
if (in->is_bam) {
fprintf(stderr, "Currently the -R option is only implemented for CRAM indices\n");
return 1;
}
cram_index_load(in->c, argv[optind]);
refid = sam_hdr_name2ref(in->c->header, ref_name);
if (refid == -1 && *ref_name != '*') {
fprintf(stderr, "Unknown reference name '%s'\n", ref_name);
return 1;
}
r.refid = refid;
r.start = start;
r.end = end;
if (scram_set_option(in, CRAM_OPT_RANGE, &r))
return 1;
}
/* Do the actual file format conversion */
s = NULL;
while (scram_get_seq(in, &s) >= 0) {
int w = s->flag & BAM_FQCFAIL ? 1 : 0;
++st.n_reads[w];
if (s->flag & BAM_FPAIRED) {
++st.n_pair_all[w];
if (s->flag & BAM_FPROPER_PAIR)
++st.n_pair_good[w];
if (s->flag & BAM_FREAD1)
++st.n_read1[w];
if (s->flag & BAM_FREAD2)
++st.n_read2[w];
if ((s->flag & BAM_FMUNMAP) && !(s->flag & BAM_FUNMAP))
++st.n_sgltn[w];
if (!(s->flag & BAM_FUNMAP) && !(s->flag & BAM_FMUNMAP)) {
++st.n_pair_map[w];
if (s->mate_ref != s->ref) {
++st.n_diffchr[w];
if (s->map_qual >= 5)
++st.n_diffhigh[w];
}
}
}
if (!(s->flag & BAM_FUNMAP))
++st.n_mapped[w];
if (s->flag & BAM_FDUP)
++st.n_dup[w];
}
if (s)
free(s);
if (!scram_eof(in))
return 1;
if (scram_close(in))
return 1;
printf("%lld + %lld in total (QC-passed reads + QC-failed reads)\n", st.n_reads[0], st.n_reads[1]);
printf("%lld + %lld duplicates\n", st.n_dup[0], st.n_dup[1]);
printf("%lld + %lld mapped (%.2f%%:%.2f%%)\n", st.n_mapped[0], st.n_mapped[1], (float)st.n_mapped[0] / st.n_reads[0] * 100.0, (float)st.n_mapped[1] / st.n_reads[1] * 100.0);
printf("%lld + %lld paired in sequencing\n", st.n_pair_all[0], st.n_pair_all[1]);
printf("%lld + %lld read1\n", st.n_read1[0], st.n_read1[1]);
printf("%lld + %lld read2\n", st.n_read2[0], st.n_read2[1]);
printf("%lld + %lld properly paired (%.2f%%:%.2f%%)\n", st.n_pair_good[0], st.n_pair_good[1], (float)st.n_pair_good[0] / st.n_pair_all[0] * 100.0, (float)st.n_pair_good[1] / st.n_pair_all[1] * 100.0);
printf("%lld + %lld with itself and mate mapped\n", st.n_pair_map[0], st.n_pair_map[1]);
printf("%lld + %lld singletons (%.2f%%:%.2f%%)\n", st.n_sgltn[0], st.n_sgltn[1], (float)st.n_sgltn[0] / st.n_pair_all[0] * 100.0, (float)st.n_sgltn[1] / st.n_pair_all[1] * 100.0);
printf("%lld + %lld with mate mapped to a different chr\n", st.n_diffchr[0], st.n_diffchr[1]);
printf("%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", st.n_diffhigh[0], st.n_diffhigh[1]);
return 0;
}
static int
read_spec(struct mtree_reader *r, char *s)
{
struct mtree_entry *entry;
char name[MAXPATHLEN];
char *slash, *file, *word, *next;
int ret;
int skip = 0;
/* Try to detect the format if it isn't known yet. */
if (r->path_last == -1 && detect_format(r, s) == -1)
return (-1);
if (r->path_last != 1) {
/*
* Path is surely in the first field, either because we know
* the format or there is just one single field.
*/
read_word(s, &file, &next);
assert(file != NULL);
if (IS_DOTDOT(file)) {
/* Only change the parent, keywords are ignored. */
if (r->parent == NULL) {
mtree_reader_set_error(r, EINVAL,
"`..' not allowed, no parent directory");
return (-1);
}
r->parent = r->parent->parent;
return (0);
}
}
entry = mtree_entry_create_empty();
if (entry == NULL) {
mtree_reader_set_error(r, errno, NULL);
return (-1);
}
if (r->path_last != 1) {
if (next != NULL) {
/* Read keyword that follow the path. */
ret = read_keywords(r, next, &entry->data, 1);
if (ret == -1) {
mtree_entry_free(entry);
return (-1);
}
}
} else {
/* Path is at the end, read the keywords first. */
for (file = NULL; file == NULL;) {
read_word(s, &word, &next);
assert(word != NULL);
if (next != NULL) {
ret = read_keyword(r, word, &entry->data, 1);
if (ret == -1) {
mtree_entry_free(entry);
return (-1);
}
s = next;
} else
file = word;
}
assert(file != NULL);
if (IS_DOTDOT(file)) {
mtree_reader_set_error(r, EINVAL, "`..' not allowed in "
"this format");
mtree_entry_free(entry);
return (-1);
}
}
/* Copy /set values to the entry. */
mtree_entry_data_copy_keywords(&entry->data, &r->defaults,
r->defaults.keywords, 0);
/*
* See if we should skip this file.
*/
if (SKIP_TYPE(r->options, entry->data.type)) {
/*
* With directories in version 1.0 format, we'll have to worry
* about potentially setting the directory as the current
* parent, other types can be skipped immediately.
*/
if (entry->data.type != MTREE_ENTRY_DIR || r->path_last == 1)
goto skip;
else
skip = 1;
}
/* Save the file path and name. */
if (strnunvis(name, sizeof(name), file) == -1) {
mtree_reader_set_error(r, ENAMETOOLONG, "File name too long: `%s'",
file);
mtree_entry_free(entry);
return (-1);
}
if ((slash = strchr(name, '/')) != NULL) {
/*
* If the name contains a slash, it is a relative path.
* These do not change the working directory.
*/
if (skip)
goto skip;
ret = mtree_cleanup_path(name, &entry->path, &entry->name);
if (ret == -1) {
mtree_reader_set_error(r, errno, NULL);
mtree_entry_free(entry);
return (-1);
}
} else {
entry->name = strdup(name);
if (entry->name == NULL) {
mtree_reader_set_error(r, errno, NULL);
mtree_entry_free(entry);
return (-1);
}
entry->parent = r->parent;
entry->path = create_v1_path(entry);
if (entry->path == NULL) {
mtree_reader_set_error(r, errno, NULL);
mtree_entry_free(entry);
return (-1);
}
}
/*
* We may want to skip this entry if a filter told us to skip
* children of a directory, which is a parent of this entry.
*
* There is also no need to worry about changing the parent if
* this happens.
*/
if (!skip && r->skip_trie != NULL) {
char *tok;
char *endptr;
for (tok = strtok_r(name, "/", &endptr); tok != NULL;
tok = strtok_r(NULL, "/", &endptr)) {
if (mtree_trie_find(r->skip_trie, tok) != NULL) {
mtree_entry_free(entry);
return (0);
}
}
}
/*
* Mark the current entry as the current directory. This only applies
* to classic (1.0) entries and must be done after keywords are read.
*/
if (slash == NULL && entry->data.type == MTREE_ENTRY_DIR)
r->parent = entry;
if (skip)
goto skip;
if (r->filter != NULL) {
int result;
/* Apply filter. */
result = r->filter(entry, r->filter_data);
if (result & MTREE_ENTRY_SKIP_CHILDREN) {
if (entry->data.type == MTREE_ENTRY_DIR) {
struct mtree_entry *found, *start;
if (r->skip_trie == NULL) {
r->skip_trie = mtree_trie_create(NULL);
if (r->skip_trie == NULL) {
mtree_reader_set_error(r, errno,
NULL);
return (-1);
}
}
if (mtree_trie_insert(r->skip_trie, entry->path,
TRIE_ITEM) == -1) {
mtree_reader_set_error(r, errno,
NULL);
return (-1);
}
strcpy(name, entry->path);
strcat(name, "/");
/*
* Remove children that are already in the
* list.
*/
start = r->entries;
for (;;) {
found = mtree_entry_find_prefix(start,
name);
if (found == NULL)
break;
start = found->next;
r->entries = mtree_entry_unlink(
r->entries, found);
mtree_entry_free(found);
}
}
}
if (result & MTREE_ENTRY_SKIP)
goto skip;
}
r->entries = mtree_entry_prepend(r->entries, entry);
return (0);
skip:
/*
* Skipping directory which is the current parent would make its files
* end up in a wrong directory.
*
* Keep such entries in a list of `loose' entries instead, these will
* be deleted when all the work is done.
*/
if (entry == r->parent)
r->loose = mtree_entry_prepend(r->loose, entry);
else
mtree_entry_free(entry);
return (0);
}
