int cli_chm_open(int fd, const char *dirname, chm_metadata_t *metadata, cli_ctx *ctx)
{
struct stat statbuf;
int retval;
cli_dbgmsg("in cli_chm_open\n");
if ((retval = chm_init_metadata(metadata)) != CL_SUCCESS) {
return retval;
}
if (fstat(fd, &statbuf) == 0) {
if (statbuf.st_size < CHM_ITSF_MIN_LEN) {
return CL_ESTAT;
}
metadata->m_length = statbuf.st_size;
metadata->map = fmap(fd, 0, metadata->m_length);
if (!metadata->map) {
return CL_EMAP;
}
} else {
char err[128];
cli_warnmsg("fstat() failed: %s\n", cli_strerror(errno, err, sizeof(err)));
return CL_ESTAT;
}
if (!itsf_read_header(metadata)) {
goto abort;
}
itsf_print_header(&metadata->itsf_hdr);
if (!itsp_read_header(metadata, metadata->itsf_hdr.dir_offset)) {
goto abort;
}
itsp_print_header(&metadata->itsp_hdr);
metadata->chunk_offset = metadata->itsf_hdr.dir_offset+CHM_ITSP_LEN;
/* TODO: need to check this first calculation,
currently have no files of this type */
if (metadata->itsp_hdr.index_head > 0) {
metadata->chunk_offset += metadata->itsp_hdr.index_head * metadata->itsp_hdr.block_len;
}
metadata->num_chunks = metadata->itsp_hdr.index_tail - metadata->itsp_hdr.index_head + 1;
/* Versions before 3 didn't have a data_offset */
/* TODO: need to check this calculation,
currently have no files of this type */
if (metadata->itsf_hdr.version < 3) {
metadata->itsf_hdr.data_offset = metadata->itsf_hdr.dir_offset + CHM_ITSP_LEN +
(metadata->itsp_hdr.block_len*metadata->itsp_hdr.num_blocks);
}
while (metadata->num_chunks) {
if (read_chunk(metadata) != CL_SUCCESS) {
cli_dbgmsg("read_chunk failed\n");
goto abort;
}
if (read_control_entries(metadata) == FALSE) {
goto abort;
}
metadata->num_chunks--;
metadata->chunk_offset += metadata->itsp_hdr.block_len;
}
if (!metadata->sys_content.length || !metadata->sys_control.length || !metadata->sys_reset.length) {
cli_dbgmsg("sys file missing\n");
goto abort;
}
metadata->ufd = chm_decompress_stream(fd, metadata, dirname, ctx);
if (metadata->ufd == -1) {
goto abort;
}
metadata->chunk_entries = 0;
metadata->chunk_data = NULL;
metadata->chunk_offset = metadata->itsf_hdr.dir_offset+CHM_ITSP_LEN;
metadata->num_chunks = metadata->itsp_hdr.index_tail - metadata->itsp_hdr.index_head + 1;
return CL_SUCCESS;
abort:
funmap(metadata->map);
return CL_EFORMAT;
}
int main(void)
{
char in[3000], sent[500], code[50], file[200], mime[100], moved[200], length[100], auth[200], auth_dir[500], start[100], end[100];
char *result=NULL, *hostname, *hostnamef, *lines, *ext=NULL, *extf, *auth_dirf=NULL, *authf=NULL, *rangetmp;
int buffer_chunks;
long filesize, range=0;
get_conf();
create_and_bind();
//Important stuff happens here.
while(1) {
sin_size = sizeof(struct sockaddr_in);
if ((new_fd = accept(sockfd, (struct sockaddr *)&their_addr, &sin_size)) == -1) {
perror("accept");
continue;
}
if (!fork()) {
close(sockfd);
if (read(new_fd, in, 3000) == -1) {
perror("recive");
} else {
lines = strtok(in, "\n\r");
do {
hostname = strtok(NULL, "\n\r");
if (hostname[0] == 'R' && hostname[1] == 'a' && hostname[2] == 'n' && hostname[3] == 'g' && hostname[4] == 'e') {
rangetmp = hostname;
strcpy(code, "206 Partial Content");
}
} while (hostname[0] != 'H' || hostname[1] != 'o' || hostname[2] != 's' || hostname[3] != 't');
hostnamef = strtok(hostname, " ");
hostnamef = strtok(NULL, " ");
result = strtok(lines, " ");
result = strtok(NULL, " ");
if (strcmp(code, "206 Partial Content") == 0 ) {
rangetmp = strtok(strpbrk(rangetmp, "="), "=-");
range = atoi(rangetmp);
}
strcpy(file, result);
if (opendir(file)){
if (file[strlen(file)-1] == '/'){
strcat(file, "/index.html");
openfile=fopen (file, "r");
if (openfile){
strcpy(code, "200 OK");
} else {
//Here should be some kind of directory listing
strcpy(file, "/404.html");
openfile = fopen (file, "r");
strcpy(code, "404 Not Found");
}
} else {
strcpy(code, "301 Moved Permanently");
strcpy(moved, "Location: http://");
strcat(moved, hostnamef);
strcat(moved, result);
strcat(moved, "/");
}
} else {
openfile=fopen (file, "rb");
if (openfile){
if (strlen(code) < 1) {
strcpy (code, "200 OK");
}
} else {
strcpy(file, "/404.html");
openfile = fopen (file, "r");
strcpy(code, "404 Not Found");
}
}
}
if (strcmp(code, "301 Moved Permanently") != 0){
fseek (openfile , 0 , SEEK_END);
filesize = ftell (openfile);
rewind (openfile);
if (range > 0) {
sprintf(end, "%d", filesize);
filesize = filesize - range;
sprintf(start, "%d", range);
fseek (openfile , range , SEEK_SET);
}
buffer_chunks = filesize/1048576;
if(filesize%1048576 > 0){
buffer_chunks++;
}
sprintf(length, "%d", filesize);
buffer_counter = 0;
buffer = (char*) malloc (sizeof(char)*1048576);
}
if (strcmp(code, "404 Not Found") != 0 && strcmp(code, "301 Moved Permanently") !=0){
ext = strtok(file, ".");
while(ext != NULL){
ext = strtok(NULL, ".");
if (ext != NULL){
extf = ext;
}
}
} else {
extf="html";
}
/* Maybe I should read mime types from a file. At least for now, add here what you need.*/
if (strcmp(extf, "html") == 0){
strcpy (mime, "text/html");
} else if(strcmp(extf, "jpg") == 0){
strcpy (mime, "image/jpeg");
} else if(strcmp(extf, "gif") == 0){
strcpy (mime, "image/gif");
} else if(strcmp(extf, "css") == 0){
strcpy (mime, "text/css");
} else {
strcpy(mime, "application/octet-stream");
}
strcpy(sent, "HTTP/1.1 ");
strcat(sent, code);
strcat(sent, "\nServer: qshttpd 0.3.0\n");
if(strcmp(code, "301 Moved Permanently") == 0){
strcat(sent, moved);
strcat(sent, "\n");
}
strcat(sent, "Content-Length: ");
if(strcmp(code, "301 Moved Permanently") != 0){
strcat(sent, length);
} else {
strcat(sent, "0");
}
if(strcmp(code, "206 Partial Content") == 0) {
strcat(sent, "\nContent-Range: bytes ");
strcat(sent, start);
strcat(sent, "-");
strcat(sent, end);
strcat(sent, "/");
strcat(sent, end);
}
strcat(sent, "\nConnection: close\nContent-Type: ");
strcat(sent, mime);
strcat(sent, "; charset=");
strcat(sent, charset);
strcat(sent, "\n\n");
write(new_fd, sent, strlen(sent));
while (buffer_counter < buffer_chunks) {
read_chunk();
write(new_fd, buffer, 1048576);
}
close(new_fd);
exit(0);
}
close(new_fd);
}
return 0;
}
int cli_chm_open(const char *dirname, chm_metadata_t *metadata, cli_ctx *ctx)
{
STATBUF statbuf;
int retval;
cli_dbgmsg("in cli_chm_open\n");
if ((retval = chm_init_metadata(metadata)) != CL_SUCCESS) {
return retval;
}
metadata->map = *ctx->fmap;
if(metadata->map->len < CHM_ITSF_MIN_LEN)
return CL_ESTAT;
metadata->m_length = metadata->map->len;
if (!itsf_read_header(metadata)) {
goto abort;
}
itsf_print_header(&metadata->itsf_hdr);
if (!itsp_read_header(metadata, metadata->itsf_hdr.dir_offset)) {
goto abort;
}
itsp_print_header(&metadata->itsp_hdr);
metadata->chunk_offset = metadata->itsf_hdr.dir_offset+CHM_ITSP_LEN;
/* TODO: need to check this first calculation,
currently have no files of this type */
if (metadata->itsp_hdr.index_head > 0) {
metadata->chunk_offset += metadata->itsp_hdr.index_head * metadata->itsp_hdr.block_len;
}
metadata->num_chunks = metadata->itsp_hdr.index_tail - metadata->itsp_hdr.index_head + 1;
/* Versions before 3 didn't have a data_offset */
/* TODO: need to check this calculation,
currently have no files of this type */
if (metadata->itsf_hdr.version < 3) {
metadata->itsf_hdr.data_offset = metadata->itsf_hdr.dir_offset + CHM_ITSP_LEN +
(metadata->itsp_hdr.block_len*metadata->itsp_hdr.num_blocks);
}
while (metadata->num_chunks) {
if (read_chunk(metadata) != CL_SUCCESS) {
cli_dbgmsg("read_chunk failed\n");
goto abort;
}
if (read_control_entries(metadata) == FALSE) {
goto abort;
}
metadata->num_chunks--;
metadata->chunk_offset += metadata->itsp_hdr.block_len;
}
if (!metadata->sys_content.length || !metadata->sys_control.length || !metadata->sys_reset.length) {
cli_dbgmsg("sys file missing\n");
goto abort;
}
metadata->ufd = chm_decompress_stream(metadata, dirname, ctx);
if (metadata->ufd == -1) {
goto abort;
}
metadata->chunk_entries = 0;
metadata->chunk_data = NULL;
metadata->chunk_offset = metadata->itsf_hdr.dir_offset+CHM_ITSP_LEN;
metadata->num_chunks = metadata->itsp_hdr.index_tail - metadata->itsp_hdr.index_head + 1;
return CL_SUCCESS;
abort:
return CL_EFORMAT;
}
int open_file_tydemux(tystream_holder_t * tystream, char *filename) {
chunknumber_t probe_hz;
chunknumber_t chunk_lnr;
chunknumber_t int_chunk_nr;
vstream_t * vstream;
chunk_t * chunk;
if(infile) {
printf("Error input file allready open\n");
return(0);
}
//printf("%s:\n", filename);
infile = open_input(filename, 0);
if (infile == -1) {
totalchunks= -1; /* Total chunks */
infile = 0; /* FD of input file */
chunk_in_buf = -1;
printf("Error opening file\n");
return(0);
}
tystream->tivo_probe = 1;
probe_hz = totalchunks/10;
tystream->tivo_probe = 1;
tystream->tivo_version = V_2X;
for(chunk_lnr=1, int_chunk_nr=0 ; chunk_lnr < totalchunks; chunk_lnr = chunk_lnr + probe_hz, int_chunk_nr++ ){
vstream = new_vstream();
/* Lets fake it and do a read buffer */
vstream->start_stream = (uint8_t *)malloc(sizeof(uint8_t) * CHUNK_SIZE);
vstream->size = sizeof(uint8_t) * CHUNK_SIZE ;
vstream->current_pos = vstream->start_stream;
vstream->end_stream = vstream->start_stream + vstream->size;
read_a_chunk(infile, chunk_lnr, vstream->start_stream);
tystream->vstream = vstream;
chunk = read_chunk(tystream, (int)chunk_lnr, 1);
chunk_in_buf = chunk_lnr;
if(chunk != NULL) {
tystream->chunks = add_chunk(tystream, chunk, tystream->chunks);
}
free_vstream(vstream);
tystream->vstream=NULL;
}
if(!tivo_probe_tystream(tystream)) {
totalchunks= -1; /* Total chunks */
infile = 0; /* FD of input file */
chunk_in_buf = -1;
return(0);
}
get_start_chunk_tivo(tystream);
tystream->tivo_probe = 0;
/* We assume that the first chunk to be used is chunk 0 */
read_a_chunk(infile, (int)tystream->start_chunk, buf);
chunk_in_buf = (int)tystream->start_chunk;
return(1);
}
void get_start_chunk_tivo(tystream_holder_t * tystream) {
/* interation */
int i;
/* Marker */
int gotit;
/* Chunks */
int chunk_lnr;
chunk_t * chunk;
vstream_t * vstream;
chunk_lnr=0;
gotit=0;
vstream = new_vstream();
/* Lets fake it and do a read buffer */
vstream->start_stream = (uint8_t *)malloc(sizeof(uint8_t) * CHUNK_SIZE);
vstream->size = sizeof(uint8_t) * CHUNK_SIZE ;
vstream->current_pos = vstream->start_stream;
vstream->end_stream = vstream->start_stream + vstream->size;
tystream->vstream = vstream;
while(1) {
vstream->current_pos = vstream->start_stream;
vstream->eof=0;
read_a_chunk(infile, chunk_lnr, vstream->start_stream);
chunk = read_chunk(tystream, (int64_t)chunk_lnr, 1);
chunk_in_buf = chunk_lnr;
if(chunk != NULL) {
for(i=0; i < chunk->nr_records; i++){
if(chunk->record_header[i].type == tystream->right_audio){
gotit=1;
break;
}
}
free_chunk(chunk);
}
if(!gotit) {
chunk_lnr++;
} else {
break;
}
}
free_vstream(vstream);
tystream->vstream=NULL;
tystream->start_chunk = (int64_t)chunk_lnr;
tystream->number_of_chunks = 0;
}
int main(int argc, char **argv) {
int ch;
int layout = 0;
/* handle command line options */
opt_list = 0;
opt_verbose = 0;
opt_skip = 0;
while ((ch = getopt(argc, argv, "l:tsvVh?")) > 0) {
switch (ch) {
case 'l':
if (optarg[0] < '0' ||
optarg[0] > '0' + max_layout ||
optarg[1] != '\0') usage();
layout = optarg[0] - '0';
break;
case 't':
opt_list = 1;
break;
case 'v':
opt_verbose = 1;
break;
case 's':
opt_skip = 1;
break;
case 'V':
printf("V%s\n", VERSION);
exit(0);
break;
case 'h':
case '?':
default:
usage();
break;
}
}
/* extract rest of command line parameters */
if ((argc - optind) < 1 || (argc - optind) > 2)
usage();
if (strcmp(argv[optind], "-") == 0) { /* image file from stdin ? */
img_file = 0;
} else {
img_file = open(argv[optind], O_RDONLY);
if (img_file < 0)
prt_err(1, errno, "Open image file failed");
}
if (layout == 0) {
detect_chunk_size();
} else {
chunk_size = possible_layouts[layout-1].chunk_size;
spare_size = possible_layouts[layout-1].spare_size;
}
spare_data = data + chunk_size;
// Skip first chunk
if (opt_skip)
lseek(img_file, chunk_size+spare_size, SEEK_SET);
if ((argc - optind) == 2 && !opt_list) {
if (mkdirpath(argv[optind+1]) < 0)
prt_err(1, errno, "Can't mkdir %s", argv[optind+1]);
if (chdir(argv[optind+1]) < 0)
prt_err(1, errno, "Can't chdir to %s", argv[optind+1]);
}
umask(0);
init_obj_list();
while (read_chunk()) {
process_chunk();
}
set_dirs_utime();
close(img_file);
return 0;
}
//--------------------------------------------------------------------------
int main(int argc,char *argv[]) {
int i;
fprintf(stderr,"ARM Library unpacker. Copyright 1997 by Ilfak Guilfanov. Version 1.00\n");
if ( argc < 2 ) fatal("Usage: unlib libfile");
strcpy(infile,argv[1]);
FILE *fp = qfopen(infile,"rb");
if ( fp == NULL ) fatal("Can't open library %s",infile);
chunk_header_t hd;
if ( qfread(fp, &hd, sizeof(hd)) != sizeof(hd)
|| (hd.ChunkFileId != AOF_MAGIC && hd.ChunkFileId != AOF_MAGIC_B) )
fatal("Bad library format");
if ( hd.ChunkFileId == AOF_MAGIC_B ) { // BIG ENDIAN
mf = 1;
hd.max_chunks = swap(hd.max_chunks);
hd.num_chunks = swap(hd.num_chunks);
}
chunk_entry_t *ce = qnewarray(chunk_entry_t,size_t(hd.max_chunks));
if ( ce == NULL ) nomem("chunk entries (%d)",size_t(hd.max_chunks));
qfread(fp, ce, sizeof(chunk_entry_t)*size_t(hd.max_chunks));
if ( mf ) for ( i=0; i < hd.max_chunks; i++ ) swap_chunk_entry(ce+i);
int vrsn = -1;
int diry = -1;
int data = 0;
for ( i=0; i < hd.max_chunks; i++ ) {
if ( ce[i].file_offset == 0 ) continue;
if ( strncmp(ce[i].chunkId,LIB_DIRY,sizeof(ce[i].chunkId)) == 0 ) diry = i;
if ( strncmp(ce[i].chunkId,LIB_VRSN,sizeof(ce[i].chunkId)) == 0 ) vrsn = i;
if ( strncmp(ce[i].chunkId,LIB_DATA,sizeof(ce[i].chunkId)) == 0 ) data++;
}
if ( diry == -1 ) fatal("Can't find library directory!");
if ( data == 0 ) fatal("No modules in the library!");
if ( vrsn == -1 ) fatal("Can't determine library version!");
ulong *version = (ulong *)read_chunk(fp,ce,vrsn);
if ( mf ) *version = swap(*version);
if ( *version != 1 ) fatal("Wrong library version (%ld)",*version);
qfree(version);
ulong *dir = (ulong *)read_chunk(fp,ce,diry);
ulong *end = dir + size_t(ce[diry].size/4);
while ( dir < end ) {
ulong idx = *dir++;
/* ulong elen = */ *dir++;
ulong dlen = *dir++;
if ( mf ) {
idx = swap(idx);
dlen = swap(dlen);
}
if ( idx != 0 ) {
printf("%ld. %s\n",idx,dir);
strncpy(modname,(char *)dir,sizeof(modname));
modname[sizeof(modname)-1] = '\0';
void *core = read_chunk(fp,ce,idx);
outfp = qfopen(modname,"wb");
if ( outfp == NULL ) {
warning("Can't open output file %s",modname);
} else {
qfwrite(outfp,core,size_t(ce[size_t(idx)].size));
qfclose(outfp);
}
qfree(core);
}
dir += size_t(dlen/4);
}
qfree(dir);
qfclose(fp);
return 0;
}
int main(int argc, char* argv[]) {
if (argc < 2) {
std::cerr
<< "#error missing parameter.\n"
<< std::flush
;
return 0;
}
std::ifstream ifs(argv[1], std::ios_base::in | std::ios_base::binary);
std::istreambuf_iterator<char> it(ifs);
std::istreambuf_iterator<char> last;
std::cout
<< "#if defined(COMPOST_LOADING_SOURCE_VERSION)\n"
"\n"
"COMPOST_SRC_VERSION(0)\n"
"\n"
"#elif defined(COMPOST_LOADING_SOURCE_INFO)\n"
"\n"
;
if (read_chunk(it) != "RIFF") {
std::cerr
<< "#error not RIFF file.\n"
<< std::flush
;
return EXIT_FAILURE;
}
/*auto file_size = */read_int<std::uint32_t>(it);
if (read_chunk(it) != "WAVE") {
std::cerr
<< "#error not WAVE format.\n"
<< std::flush
;
return EXIT_FAILURE;
}
while (read_chunk(it) != "fmt ") {
auto chunk_size = read_int<std::uint32_t>(it);
std::advance(it, chunk_size);
}
auto fmt_size = read_int<std::uint32_t>(it);
auto format_tag = read_int<std::uint16_t>(it);
auto channels = read_int<std::uint16_t>(it);
auto samples_per_sec = read_int<std::uint32_t>(it);
auto bytes_per_sec = read_int<std::uint32_t>(it);
auto block_size = read_int<std::uint16_t>(it);
auto bits_per_sample = read_int<std::uint16_t>(it);
std::cout
<< format_tag << ",\n"
<< channels << ",\n"
<< samples_per_sec << ",\n"
<< bytes_per_sec << ",\n"
<< block_size << ",\n"
<< bits_per_sample << ",\n"
;
std::advance(it, fmt_size - 16);
while (read_chunk(it) != "data") {
auto chunk_size = read_int<std::uint32_t>(it);
std::advance(it, chunk_size);
}
auto data_size = read_int<std::uint32_t>(it);
std::size_t size = data_size / (bits_per_sample / CHAR_BIT);
std::cout
<< size << "\n"
<< "\n"
"#elif defined(COMPOST_LOADING_SOURCE_DATA)\n"
"\n"
;
if (size > 0) {
if (bits_per_sample == 16) {
for (std::size_t i = 1; i != size; ++i) {
std::cout
<< read_int<std::int16_t>(it) << ",\n"
;
}
std::cout
<< read_int<std::int16_t>(it) << "\n"
;
} else if (bits_per_sample == 8) {
for (std::size_t i = 1; i != size; ++i) {
std::cout
<< read_int<std::uint8_t>(it) << ",\n"
;
}
std::cout
<< read_int<std::uint8_t>(it) << "\n"
;
}
}
std::cout
<< "\n"
"#endif\n"
<< std::flush
;
}
void process_chunk(void) {
yaffs_ObjectHeader oh;
yaffs_PackedTags2 *pt;
object *obj, *eq_obj;
int out_file, remain, s;
oh = *(yaffs_ObjectHeader *)chunk_data;
pt = (yaffs_PackedTags2 *)spare_data;
if (pt->t.byteCount == 0xffffffff) /* empty object */
return;
else if (pt->t.byteCount != 0xffff) { /* not a new object */
prt_err(0, 0, "Warning: Invalid header at chunk #%d, skipping...",
chunk_no);
if (++warn_count >= MAX_WARN)
prt_err(1, 0, "Giving up");
return;
}
obj = add_object(&oh, pt);
/* listing */
if (opt_verbose)
prt_node(obj->path_name, &oh);
else if (opt_list)
printf("%s\n", obj->path_name);
if (opt_list) {
if (oh.type == YAFFS_OBJECT_TYPE_FILE) {
remain = oh.fileSize; /* skip over data chunks */
while(remain > 0) {
if (!read_chunk())
prt_err(1, 0, "Broken image file");
remain -= pt->t.byteCount;
}
}
return;
}
switch(oh.type) {
case YAFFS_OBJECT_TYPE_FILE:
remain = oh.fileSize;
out_file = creat(obj->path_name, oh.yst_mode & STD_PERMS);
if (out_file < 0)
prt_err(1, errno, "Can't create file %s", obj->path_name);
while(remain > 0) {
if (!read_chunk())
prt_err(1, 0, "Broken image file");
s = (remain < pt->t.byteCount) ? remain : pt->t.byteCount;
if (xwrite(out_file, chunk_data, s) < 0)
prt_err(1, errno, "Can't write to %s", obj->path_name);
remain -= s;
}
close(out_file);
lchown(obj->path_name, oh.yst_uid, oh.yst_gid);
if ((oh.yst_mode & EXTRA_PERMS) != 0 &&
chmod(obj->path_name, oh.yst_mode) < 0)
prt_err(0, errno, "Warning: Can't chmod %s", obj->path_name);
break;
case YAFFS_OBJECT_TYPE_SYMLINK:
if (symlink(oh.alias, obj->path_name) < 0)
prt_err(1, errno, "Can't create symlink %s", obj->path_name);
lchown(obj->path_name, oh.yst_uid, oh.yst_gid);
break;
case YAFFS_OBJECT_TYPE_DIRECTORY:
if (pt->t.objectId != YAFFS_OBJECTID_ROOT &&
mkdir(obj->path_name, oh.yst_mode & STD_PERMS) < 0)
prt_err(1, errno, "Can't create directory %s", obj->path_name);
lchown(obj->path_name, oh.yst_uid, oh.yst_gid);
if ((pt->t.objectId == YAFFS_OBJECTID_ROOT ||
(oh.yst_mode & EXTRA_PERMS) != 0) &&
chmod(obj->path_name, oh.yst_mode) < 0)
prt_err(0, errno, "Warning: Can't chmod %s", obj->path_name);
break;
case YAFFS_OBJECT_TYPE_HARDLINK:
eq_obj = get_object(oh.equivalentObjectId);
if (eq_obj == NULL)
prt_err(1, 0, "Invalid equivalentObjectId %u in object %u (%s)",
oh.equivalentObjectId, pt->t.objectId, oh.name);
if (link(eq_obj->path_name, obj->path_name) < 0)
prt_err(1, errno, "Can't create hardlink %s", obj->path_name);
break;
case YAFFS_OBJECT_TYPE_SPECIAL:
if (mknod(obj->path_name, oh.yst_mode, oh.yst_rdev) < 0) {
if (errno == EPERM || errno == EINVAL)
prt_err(0, errno, "Warning: Can't create device %s", obj->path_name);
else
prt_err(1, errno, "Can't create device %s", obj->path_name);
}
lchown(obj->path_name, oh.yst_uid, oh.yst_gid);
break;
case YAFFS_OBJECT_TYPE_UNKNOWN:
break;
}
/* set file date and time */
switch(oh.type) {
case YAFFS_OBJECT_TYPE_FILE:
case YAFFS_OBJECT_TYPE_SPECIAL:
#ifdef HAS_LUTIMES
case YAFFS_OBJECT_TYPE_SYMLINK:
#endif
set_utime(obj->path_name,
oh.yst_atime, oh.yst_mtime);
break;
case YAFFS_OBJECT_TYPE_DIRECTORY:
default:
break;
}
}
int std_probe_tystream(tystream_holder_t * tystream) {
/* Iteration */
off64_t j;
/* File size */
off64_t in_file_size;
/* Chunks */
chunknumber_t local_nr_chunks;
chunknumber_t probe_hz;
chunknumber_t chunk_lnr;
chunknumber_t int_chunk_nr;
chunk_t * chunk;
LOG_USERDIAG("Probing TyStream .....\n");
chunk = NULL;
if(tystream->vstream) {
in_file_size=tystream->vstream->size;
} else {
in_file_size=tystream->in_file_size;
}
/* Calculate the probe rate */
local_nr_chunks = (chunknumber_t)(in_file_size/CHUNK_SIZE);
probe_hz = local_nr_chunks/10;
for(j=0, chunk_lnr=1,int_chunk_nr=0 ; j < in_file_size; j = (j + CHUNK_SIZE*probe_hz), chunk_lnr = chunk_lnr + probe_hz, int_chunk_nr++ ){
chunk = read_chunk(tystream, chunk_lnr, 2048);
if(chunk != NULL) {
tystream->chunks = add_chunk(tystream, chunk, tystream->chunks);
//printf("Chunk %i has %i records\n",int_chunk_nr,chunk->nr_records);
} else {
//printf("Chunk was null\n");
}
}
if(tystream->chunks == NULL) {
LOG_ERROR("Big ERROR - NO CHUNKS\n");
clear_tystream_audio_probe(tystream, 0);
return(0);
}
if(!probe_tystream_S2(tystream)) {
LOG_ERROR("Big ERROR - CAN'T DETECT S1/S2\n");
clear_tystream_audio_probe(tystream, 0);
return(0);
}
if(!probe_tystream_frame_rate(tystream)){
LOG_ERROR("Big ERROR - CAN'T DETECT FRAME RATE\n");
clear_tystream_audio_probe(tystream, 0);
return(0);
}
if(!probe_tystream_audio(tystream)) {
LOG_ERROR("Big ERROR - CAN'T DETECT AUDIO TYPE\n");
clear_tystream_audio_probe(tystream, 0);
return(0);
}
if(!probe_audio_tick_size(tystream)) {
LOG_ERROR("Big ERROR - CAN'T DETECT AUDIO SIZE\n");
clear_tystream_audio_probe(tystream, 1);
return(0);
}
clear_tystream_audio_probe(tystream, 1);
return(1);
}
static int dhav_read_packet(AVFormatContext *s, AVPacket *pkt)
{
DHAVContext *dhav = s->priv_data;
int64_t start;
int ret;
start = avio_tell(s->pb);
while ((ret = read_chunk(s)) == 0)
;
if (ret < 0)
return ret;
if (dhav->type == 0xfd && dhav->video_stream_index == -1) {
AVStream *st = avformat_new_stream(s, NULL);
DHAVStream *dst;
if (!st)
return AVERROR(ENOMEM);
st->codecpar->codec_type = AVMEDIA_TYPE_VIDEO;
switch (dhav->video_codec) {
case 0x1: st->codecpar->codec_id = AV_CODEC_ID_MPEG4; break;
case 0x3: st->codecpar->codec_id = AV_CODEC_ID_MJPEG; break;
case 0x2:
case 0x4:
case 0x8: st->codecpar->codec_id = AV_CODEC_ID_H264; break;
case 0xc: st->codecpar->codec_id = AV_CODEC_ID_HEVC; break;
default: avpriv_request_sample(s, "Unknown video codec %X\n", dhav->video_codec);
}
st->codecpar->width = dhav->width;
st->codecpar->height = dhav->height;
st->avg_frame_rate.num = dhav->frame_rate;
st->avg_frame_rate.den = 1;
st->priv_data = dst = av_mallocz(sizeof(DHAVStream));
if (!st->priv_data)
return AVERROR(ENOMEM);
dst->last_timestamp = AV_NOPTS_VALUE;
dhav->video_stream_index = st->index;
avpriv_set_pts_info(st, 64, 1, 1000);
} else if (dhav->type == 0xf0 && dhav->audio_stream_index == -1) {
AVStream *st = avformat_new_stream(s, NULL);
DHAVStream *dst;
if (!st)
return AVERROR(ENOMEM);
st->codecpar->codec_type = AVMEDIA_TYPE_AUDIO;
switch (dhav->audio_codec) {
case 0x07: st->codecpar->codec_id = AV_CODEC_ID_PCM_S8; break;
case 0x0c: st->codecpar->codec_id = AV_CODEC_ID_PCM_S16LE; break;
case 0x10: st->codecpar->codec_id = AV_CODEC_ID_PCM_S16LE; break;
case 0x0a: st->codecpar->codec_id = AV_CODEC_ID_PCM_MULAW; break;
case 0x16: st->codecpar->codec_id = AV_CODEC_ID_PCM_MULAW; break;
case 0x0e: st->codecpar->codec_id = AV_CODEC_ID_PCM_ALAW; break;
case 0x1a: st->codecpar->codec_id = AV_CODEC_ID_AAC; break;
case 0x1f: st->codecpar->codec_id = AV_CODEC_ID_MP2; break;
case 0x21: st->codecpar->codec_id = AV_CODEC_ID_MP3; break;
case 0x0d: st->codecpar->codec_id = AV_CODEC_ID_ADPCM_MS; break;
default: avpriv_request_sample(s, "Unknown audio codec %X\n", dhav->audio_codec);
}
st->codecpar->channels = dhav->audio_channels;
st->codecpar->sample_rate = dhav->sample_rate;
st->priv_data = dst = av_mallocz(sizeof(DHAVStream));
if (!st->priv_data)
return AVERROR(ENOMEM);
dst->last_timestamp = AV_NOPTS_VALUE;
dhav->audio_stream_index = st->index;
avpriv_set_pts_info(st, 64, 1, 1000);
}
ret = av_get_packet(s->pb, pkt, ret);
if (ret < 0)
return ret;
pkt->stream_index = dhav->type == 0xf0 ? dhav->audio_stream_index : dhav->video_stream_index;
if (dhav->type != 0xfc)
pkt->flags |= AV_PKT_FLAG_KEY;
if (pkt->stream_index >= 0)
pkt->pts = get_pts(s, s->streams[pkt->stream_index]->priv_data);
pkt->duration = 1;
pkt->pos = start;
if (avio_rl32(s->pb) != MKTAG('d','h','a','v'))
return AVERROR_INVALIDDATA;
avio_skip(s->pb, 4);
return ret;
}
void get_start_chunk(tystream_holder_t * tystream) {
/* interation */
chunknumber_t j;
int i;
/* Marker */
int gotit;
/* Chunks */
int chunk_lnr;
chunk_t * chunk;
#if !defined(TIVO)
vstream_t * vstream;
uint8_t * buffer;
#endif
if(tystream->right_audio == 0x3c0) {
LOG_USERDIAG("Seeking TyStream start of MPEG Layer II audio \n");
} else {
LOG_USERDIAG("Seeking TyStream start of AC3 (Dolby Digital) audio \n");
}
gotit=0;
if(tystream->std_alone) {
for(j=0, chunk_lnr=0; j < tystream->in_file_size; j = (j + CHUNK_SIZE) + tystream->byte_offset, chunk_lnr++){
chunk = read_chunk(tystream, chunk_lnr, 1);
if(chunk != NULL) {
for(i=0; i < chunk->nr_records; i++){
if(chunk->record_header[i].type == tystream->right_audio){
gotit=1;
break;
}
}
free_chunk(chunk);
}
if(gotit){
break;
}
}
}
#if !defined(TIVO)
else {
chunk_lnr=0;
buffer = (uint8_t *)malloc(sizeof(uint8_t) * CHUNK_SIZE);
while(1) {
vstream = new_vstream();
memset(buffer,0,sizeof(uint8_t) * CHUNK_SIZE);
thread_pipe_peek(tystream->input_pipe, CHUNK_SIZE, buffer);
vstream->size = CHUNK_SIZE;
vstream->start_stream = vstream->current_pos = buffer;
vstream->end_stream = vstream->start_stream + CHUNK_SIZE;
tystream->vstream = vstream;
chunk = read_chunk(tystream, chunk_lnr, 1);
if(chunk != NULL) {
for(i=0; i < chunk->nr_records; i++){
if(chunk->record_header[i].type == tystream->right_audio){
gotit=1;
break;
}
}
free_chunk(chunk);
}
vstream->start_stream = vstream->end_stream = vstream->current_pos = NULL;
vstream->size = vstream->eof = 0;
tystream->vstream=NULL;
free(vstream);
if(!gotit) {
chunk_lnr++;
thread_pipe_read(tystream->input_pipe, CHUNK_SIZE, buffer);
} else {
break;
}
}
free(buffer);
}
#endif
tystream->start_chunk = chunk_lnr;
if(tystream->right_audio == 0x3c0) {
LOG_USERDIAG("Found start of MPEG Layer II audio \n");
} else {
LOG_USERDIAG("Found start of AC3 (Dolby Digital) audio \n");
}
LOG_USERDIAG1("Skipping to chunk " I64FORMAT " - reseting chunk numbering \n\n", tystream->start_chunk);
tystream->number_of_chunks = 0;
}
int main(int argc, char **argv) {
int ch;
char *ep;
int opt_detect;
int opt_bad;
int opt_chunk;
int opt_spare;
/* handle command line options */
opt_detect = 0;
opt_bad = 0;
opt_chunk = 0;
opt_spare = 0;
opt_list = 0;
opt_verbose = 0;
while ((ch = getopt(argc, argv, "dbc:s:tvVh?")) > 0) {
switch (ch) {
case 'd':
opt_detect = 1;
break;
case 'b':
opt_bad = 1;
break;
case 'c':
opt_chunk = strtol(optarg, &ep, 0);
if (*ep != '\0' ||
opt_chunk < 0 ||
opt_chunk > (MAX_CHUNK_SIZE / 1024) )
usage();
break;
case 's':
opt_spare = strtol(optarg, &ep, 0);
if (*ep != '\0' ||
opt_spare < 0 ||
opt_spare > MAX_SPARE_SIZE)
usage();
break;
case 't':
opt_list = 1;
break;
case 'v':
opt_verbose = 1;
break;
case 'V':
printf("V%s\n", VERSION);
exit(0);
break;
case 'h':
case '?':
default:
usage();
break;
}
}
/* extract rest of command line parameters */
if ((argc - optind) < 1 || (argc - optind) > 2)
usage();
if (strcmp(argv[optind], "-") == 0) { /* image file from stdin ? */
img_file = 0;
} else {
img_file = open(argv[optind], O_RDONLY);
if (img_file < 0)
prt_err(1, errno, "Open image file failed");
}
if (opt_detect) {
detect_flash_layout(1, 0);
return 0;
}
if (opt_chunk == 0 || opt_spare == 0) {
detect_flash_layout(0, 1);
if (opt_verbose)
prt_err(0, 0,
"Header check OK, chunk size = %dK, spare size = %d, %sbad block info.",
chunk_size/1024, spare_size, spare_off ? "" : "no ");
} else {
chunk_size = opt_chunk * 1024;
spare_size = opt_spare;
spare_off = opt_bad ? 2 : 0;
}
spare_data = data + chunk_size;
if ((argc - optind) == 2 && !opt_list) {
if (mkdirpath(argv[optind+1], 0755) < 0)
prt_err(1, errno, "Can't mkdir %s", argv[optind+1]);
if (chdir(argv[optind+1]) < 0)
prt_err(1, errno, "Can't chdir to %s", argv[optind+1]);
}
umask(0);
init_obj_list();
saved_chunk.objectId = 0;
while (read_chunk()) {
process_chunk();
}
set_dirs_utime();
close(img_file);
if (warn_chown)
#ifdef __CYGWIN__
prt_err(0, 0, "Warning: Can't restore owner/group attribute (limitation of Cygwin/Windows)");
#else
prt_err(0, 0, "Warning: Can't restore owner/group attribute, run unyaffs as root");
#endif
return 0;
}
static int
read_body_chunked(http_resp *a_resp,
http_req *a_req,
http_trans_conn *a_conn)
{
int l_rv = 0;
int l_done = 0;
do
{
/* read a chunk */
l_rv = read_chunk(a_resp, a_conn);
if (l_rv == HTTP_TRANS_ERR)
return HTTP_TRANS_ERR;
if ((a_conn->sync == HTTP_TRANS_ASYNC) && (l_rv == HTTP_TRANS_NOT_DONE))
return HTTP_TRANS_NOT_DONE;
/* see if it's the first time */
if (a_conn->sync == HTTP_TRANS_SYNC && a_conn->chunk_len > 0)
{
if (a_resp->body == NULL)
{
a_resp->body = malloc(a_conn->chunk_len);
memcpy(a_resp->body, a_conn->io_buf, a_conn->chunk_len);
a_resp->body_len = a_conn->chunk_len;
}
/* append it to the body */
else
{
a_resp->body = realloc(a_resp->body,
(a_resp->body_len + a_conn->chunk_len));
memcpy(&a_resp->body[a_resp->body_len], a_conn->io_buf, a_conn->chunk_len);
a_resp->body_len += a_conn->chunk_len;
}
}
/* make sure there's at least 2 bytes in the buffer.
This happens when a read was 3 bytes as in 0\r\n
and there is still 2 bytes ( \r\n ) in the read queue. */
if ((a_conn->chunk_len == 0) && (a_conn->io_buf_alloc < 2))
{
a_conn->io_buf_io_left = ( 2 - a_conn->io_buf_alloc );
a_conn->io_buf_io_done = 0;
do
{
l_rv = http_trans_read_into_buf(a_conn);
}
while (l_rv == HTTP_TRANS_NOT_DONE);
ghttpDebug("l_rv: %d chunk_len: %d \n", l_rv, a_conn->chunk_len);
/* check for an error */
if (l_rv == HTTP_TRANS_ERR)
return HTTP_TRANS_ERR;
}
if (a_conn->chunk_len == 0)
l_done = 1;
else
{
/* clip the buffer */
http_trans_buf_clip(a_conn, &a_conn->io_buf[a_conn->chunk_len + 2]);
}
a_conn->chunk_len = 0;
}while (l_done == 0);
return HTTP_TRANS_DONE;
}
void render_region_map(image *img, const int32_t rpx, const int32_t rpy, region *reg,
region *nregions[4], const textures *tex, const options *opts)
{
open_region_file(reg);
if (reg == NULL || reg->file == NULL) return;
for (uint8_t i = 0; i < 4; i++) open_region_file(nregions[i]);
chunk_data *chunk, *prev_chunk, *new_chunk, *nchunks[4];
chunk_flags flags = {
1,
1,
opts->dark,
opts->isometric && !opts->dark && opts->shadows,
opts->biomes
};
chunk_flags nflags = {
1,
opts->isometric,
opts->isometric && opts->dark,
opts->isometric && !opts->dark && opts->shadows,
0
};
// use rotated chunk coordinates, since we need to draw them from bottom to top for isometric
for (int8_t rcz = MAX_REGION_CHUNK; rcz >= 0; rcz--)
{
for (int8_t rcx = MAX_REGION_CHUNK; rcx >= 0; rcx--)
{
// get the actual chunk from its rotated coordinates
// use the "new" chunk saved by the previous iteration if possible
chunk = rcx < MAX_REGION_CHUNK && prev_chunk != NULL ? new_chunk :
read_chunk(reg, rcx, rcz, opts->rotate, &flags, opts->ylimits);
if (chunk == NULL)
{
if (rcx < MAX_REGION_CHUNK) free_chunk(prev_chunk);
prev_chunk = NULL;
continue;
}
// get neighbouring chunks, either from this region or a neighbouring one
nchunks[TOP] = rcz > 0 ?
read_chunk(reg, rcx, rcz - 1, opts->rotate, &flags, opts->ylimits) :
read_chunk(nregions[TOP], rcx, MAX_REGION_CHUNK, opts->rotate, &nflags,
opts->ylimits);
nchunks[RIGHT] = rcx < MAX_REGION_CHUNK ? prev_chunk :
read_chunk(nregions[RIGHT], 0, rcz, opts->rotate, &nflags, opts->ylimits);
nchunks[BOTTOM] = rcz < MAX_REGION_CHUNK ?
read_chunk(reg, rcx, rcz + 1, opts->rotate, &flags, opts->ylimits) :
read_chunk(nregions[BOTTOM], rcx, 0, opts->rotate, &nflags, opts->ylimits);
nchunks[LEFT] = rcx > 0 ?
read_chunk(reg, rcx - 1, rcz, opts->rotate, &flags, opts->ylimits) :
read_chunk(nregions[LEFT], MAX_REGION_CHUNK, rcz, opts->rotate, &nflags,
opts->ylimits);
for (uint8_t i = 0; i < 4; i++)
{
if (nchunks[i] == NULL)
{
chunk->nbids[i] = NULL;
chunk->nbdata[i] = NULL;
chunk->nblight[i] = NULL;
chunk->nslight[i] = NULL;
}
else {
chunk->nbids[i] = nchunks[i]->bids;
chunk->nbdata[i] = nchunks[i]->bdata;
chunk->nblight[i] = nchunks[i]->blight;
chunk->nslight[i] = nchunks[i]->slight;
}
}
// render chunk image onto region image
uint32_t cpx, cpy;
if (opts->isometric)
{
// translate orthographic to isometric coordinates
cpx = rpx + (rcx + MAX_REGION_CHUNK - rcz) * ISO_CHUNK_X_MARGIN;
cpy = rpy + (rcx + rcz) * ISO_CHUNK_Y_MARGIN;
}
else
{
cpx = rpx + rcx * CHUNK_BLOCK_LENGTH;
cpy = rpy + rcz * CHUNK_BLOCK_LENGTH;
}
// loop through rotated chunk's blocks
for (int16_t rbz = MAX_CHUNK_BLOCK; rbz >= 0; rbz--)
for (int16_t rbx = MAX_CHUNK_BLOCK; rbx >= 0; rbx--)
if (opts->isometric)
{
// translate orthographic to isometric coordinates
uint32_t px = cpx + (rbx + MAX_CHUNK_BLOCK - rbz) * ISO_BLOCK_WIDTH / 2;
uint32_t py = cpy + (rbx + rbz) * ISO_BLOCK_TOP_HEIGHT;
render_iso_column(img, px, py, tex, chunk, rbx, rbz, opts);
}
else
render_ortho_column(img, cpx + rbx, cpy + rbz, tex, chunk, rbx, rbz, opts);
// free chunks, or save them for the next iteration if we're not at the end of a row
free_chunk(nchunks[TOP]);
free_chunk(nchunks[RIGHT]);
free_chunk(nchunks[BOTTOM]);
if (rcx == 0)
{
free_chunk(chunk);
free_chunk(nchunks[LEFT]);
}
else
{
prev_chunk = chunk;
new_chunk = nchunks[LEFT];
}
}
}
close_region_file(reg);
for (uint8_t i = 0; i < 4; i++) close_region_file(nregions[i]);
}
int do_EM (params *pars, out_data *output) {
SIG_COND = true;
catch_SIG();
int iter = ( strcmp("e", pars->init_values) == 0 ? 0 : 1 );
double lkl_epsilon = 0;
double est_epsilon = 0;
sem_init(&pars->_launch_thread_semaph, 0, pars->n_threads);
sem_init(&pars->_running_thread_semaph, 0, 0); // To avoid warnings from Valgrind
sem_init(&pars->_running_thread_semaph, 0, -pars->n_chunks);
pthread_mutex_init(&pars->_F_lock, NULL);
while( (est_epsilon > pars->min_epsilon || lkl_epsilon > pars->min_epsilon || iter <= pars->min_iters) && iter <= pars->max_iters && SIG_COND ) {
// Print of initial Lkl
if( iter == 1 && pars->verbose >= 1 ) {
output->global_lkl = full_HWE_like(pars, output->site_freq, output->indF, 0, pars->n_ind);
printf("==> Initial LogLkl: %.15f\n", output->global_lkl);
fflush(stdout);
}
// Next Iteration...
time_t iter_start = time(NULL);
if( iter > 0 && pars->verbose >= 1 )
printf("\nIteration %d:\n", iter);
////////////////////////////////
// Loop through all chunks... //
////////////////////////////////
for(uint64_t c = 0; c < pars->n_chunks; c++) {
// Wait for room to launch more threads
while( sem_wait(&pars->_launch_thread_semaph) );
if( pars->verbose >= 5 ) printf("\tChunk %lu of %lu\n", c+1, pars->n_chunks);
// Declare structure
pth_params *pth_struct = new pth_params;
// Reserve memory for chunk data
pth_struct->chunk_data = new double* [pars->max_chunk_size];
#ifdef _USE_BGZF
for(uint64_t s = 0; s < pars->max_chunk_size; s++)
pth_struct->chunk_data[s] = new double[pars->n_ind * 3];
#endif
// Fill in PThread structure
pth_struct->pars = pars;
pth_struct->chunk_size = read_chunk(pth_struct->chunk_data, pth_struct->pars, c);
pth_struct->chunk_abs_start_pos = c * pars->max_chunk_size;
pth_struct->iter = iter;
pth_struct->output = output;
// Initialize and set thread detached attribute
pthread_t thread_id;
pthread_attr_t pt_attr;
pthread_attr_init(&pt_attr);
pthread_attr_setdetachstate(&pt_attr, PTHREAD_CREATE_DETACHED);
// Launch thread
int rc = pthread_create(&thread_id, &pt_attr, run_chunk, (void*) pth_struct);
if(rc) error(__FUNCTION__,"pthread_create() failed!");
if( pars->verbose >= 6 ) {
int n_free_threads = 0;
sem_getvalue(&pars->_launch_thread_semaph, &n_free_threads);
printf("Thread launched! Available slots: %d\n", n_free_threads);
}
fflush(stdout);
}
////////////////////////////////////
// Wait for all threads to finish //
////////////////////////////////////
int n_free_threads = 0;
do {
while( sem_wait(&pars->_running_thread_semaph) );
sem_getvalue(&pars->_launch_thread_semaph, &n_free_threads);
if( pars->verbose >= 6 ) printf("Waiting for all threads to finish: %d\n", pars->n_threads - n_free_threads);
}while(n_free_threads < (int) pars->n_threads);
est_epsilon = 0;
/////////////////////////////////////
// Indiv post-iteration processing //
/////////////////////////////////////
if( pars->verbose >= 2 ) printf("\tInd F:\t");
for(uint16_t i = 0; i < pars->n_ind; i++) {
// Get new indF and check for interval...
double new_indF = check_interv(output->indF_num[i] / output->indF_den[i], false);
// If LRT, do not estimate indF (it is fixed)
if(pars->calc_LRT)
new_indF = output->indF[i];
// Calculate iter epsilon
est_epsilon += pow(new_indF - output->indF[i], 2);
// Store new indF
new_indF = ( new_indF == 1 ? 0.9999 : new_indF );
output->indF[i] = new_indF;
// Reset variables...
output->indF_num[i] = 0;
output->indF_den[i] = 0;
// Debug
if( pars->verbose >= 2 ) printf("\t%.9f", output->indF[i]);
}
if( pars->verbose >= 2 ) printf("\n");
////////////////////////////////////
// Site post-iteration processing //
////////////////////////////////////
if( pars->verbose >= 4 ) printf("\tFreq:\t");
for(uint64_t s = 0; s < pars->n_sites; s++) {
if(output->site_freq[s] == 0) continue;
if(!pars->freq_fixed){
double new_site_freq = check_interv(output->site_freq_num[s] / output->site_freq_den[s], true);
est_epsilon += pow(new_site_freq - output->site_freq[s], 2);
output->site_freq[s] = (new_site_freq > 0.99 ? 0.99 : new_site_freq);
}
// Reset variables...
output->site_freq_num[s] = 0;
output->site_freq_den[s] = 0;
output->site_prob_var[s] = output->site_tmpprob_var[s];
output->site_tmpprob_var[s] = 0;
// Debug
if( pars->verbose >= 4 ) printf("\t%.9f", output->site_freq[s]);
}
if( pars->verbose >= 4 ) printf("\n");
///////////////////
// Calculate Lkl //
///////////////////
double new_global_lkl = 0;
for(uint16_t i = 0; i < pars->n_ind; i++) {
output->ind_lkl[i] = full_HWE_like(pars, output->site_freq, output->indF, i, 1);
new_global_lkl += output->ind_lkl[i];
}
// Parameter epsilon
est_epsilon = sqrt(est_epsilon)/(pars->n_ind + pars->n_sites);
// Lkl epsilon calculation - On first iteration, since there is no global_lkl, calculate Lkl epsilon based on current lkl
lkl_epsilon = (new_global_lkl - output->global_lkl)/fabs(output->global_lkl);
output->global_lkl = new_global_lkl;
// Print iteration info
if( iter > 0 && pars->verbose >= 1 ) {
time_t iter_end = time(NULL);
printf("\tLogLkl: %.15f\t epsilon: %.15f %.15f\ttime: %.0f (s)\n", output->global_lkl, lkl_epsilon, est_epsilon, difftime(iter_end, iter_start) );
}
iter++;
fflush(stdout);
///////////////////////////////
// Dump iteration parameters //
///////////////////////////////
char* pars_file = (char*) malloc( (strlen(pars->out_file)+5+1)*sizeof(char) );
memset(pars_file, '\0', (strlen(pars->out_file)+5+1)*sizeof(char));
strcat(pars_file, pars->out_file); strcat(pars_file, ".pars");
// Write the last iteration to disk
FILE* last_est_pars = fopen(pars_file, "w");
if(last_est_pars == NULL)
error(__FUNCTION__, "Cannot open PARS file!");
fwrite(&output->global_lkl, sizeof(double), 1, last_est_pars);
fwrite(output->ind_lkl, sizeof(double), pars->n_ind, last_est_pars);
fwrite(output->indF, sizeof(double), pars->n_ind, last_est_pars);
fwrite(output->site_freq, sizeof(double), pars->n_sites, last_est_pars);
fclose(last_est_pars);
free(pars_file);
///////////////
// For debug //
///////////////
if( pars->quick ) break;
}
if( iter > pars->max_iters )
printf("WARN: Maximum number of iterations reached! Check if analysis converged... \n");
return 0;
}
