uint32 size() const {
assert(fh);
uint32 oldPos = gztell(fh);
gzseek(fh, 0, SEEK_END);
uint32 length = gztell(fh);
gzseek(fh, oldPos, SEEK_SET);
return length;
}
//----------------------------------------------------
int zu_seek(ZUFILE *f, long offset, int whence)
{
int res = 0;
int bzerror=BZ_OK;
if (whence == SEEK_END) {
return -1; // TODO
}
switch(f->type) { //SEEK_SET, SEEK_CUR
case ZU_COMPRESS_NONE :
res = fseek((FILE*)(f->zfile), offset, whence);
f->pos = ftell((FILE*)(f->zfile));
break;
case ZU_COMPRESS_GZIP :
if (whence == SEEK_SET) {
res = gzseek((gzFile)(f->zfile), offset, whence);
}
else { // !!! BUG with SEEK_CUR in ZLIB !!!
int p1 = gztell((gzFile)(f->zfile));
res = gzseek((gzFile)(f->zfile), p1+offset, SEEK_SET);
}
f->pos = gztell((gzFile)(f->zfile));
if (res >= 0)
res = 0;
break;
#ifndef __ANDROID__
case ZU_COMPRESS_BZIP :
if (whence==SEEK_SET && offset >= f->pos) {
res = zu_bzSeekForward(f, offset-f->pos);
}
else if (whence==SEEK_CUR) {
res = zu_bzSeekForward(f, offset);
}
else { // BAD : reopen file
BZ2_bzReadClose (&bzerror,(BZFILE*)(f->zfile));
bzerror=BZ_OK;
rewind(f->faux);
f->pos = 0;
f->zfile = (void *) BZ2_bzReadOpen(&bzerror,f->faux,0,0,NULL,0);
if (bzerror != BZ_OK) {
BZ2_bzReadClose (&bzerror,(BZFILE*)(f->zfile));
fclose(f->faux);
f->zfile = NULL;
f->ok = 0;
}
res = zu_bzSeekForward(f, offset);
}
break;
#endif
}
return res;
}
long CFile::PImpl::tell()
{
int ret = -1;
int tp = cl_type;
if (tp != CLF_TYPE_INVALID) {
if (tp == CLF_TYPE_PLAIN) {
ret = ftell(cl_plain);
}
#ifdef USE_ZLIB
if (tp == CLF_TYPE_GZIP) {
ret = gztell(cl_gz);
}
#endif // USE_ZLIB
#ifdef USE_BZ2LIB
if (tp == CLF_TYPE_BZIP2) {
// FIXME: need to implement this
ret = -1;
}
#endif // USE_BZ2LIB
} else {
errno = EBADF;
}
return ret;
}
/*
* Auto detects size to distinguish between short and long maq variants
* Returns 64 for short
* 128 for long
* -1 for error
*/
int maq_detect_size(gzFile fp) {
z_off_t curr = gztell(fp);
maqmap128_t m;
maqmap64_t m64;
int i, sz = 128;
if (gzread(fp, &m, sizeof(maqmap128_t)) == -1)
return -1;
gzseek(fp, curr, SEEK_SET);
/* We know the sequence size should >= 0 and <= 128 */
if (/*m.size >= 0 &&*/ m.size <= 128) {
/* The sequence struct from m.size onwards should be nul padded. */
for (i = m.size; i < 127; i++) {
if (m.seq[i] != 0) {
sz = 64;
break;
}
}
/* Check for valid name */
for (i = 0; i < MAX_NAMELEN; i++) {
if (!m.name[i])
break;
if (!isprint(m.name[i])) {
sz = 64;
break;
}
}
} else {
sz = 64;
}
/* If we think the size is now really 64, do a similar check again */
if (sz == 64) {
if (gzread(fp, &m64, sizeof(maqmap64_t)) == -1)
return -1;
gzseek(fp, curr, SEEK_SET);
if (/*m64.size < 0 || */ m64.size > 64)
return -1;
for (i = m64.size; i < 63; i++) {
if (m64.seq[i] != 0)
return -1;
}
/* Check for valid name */
for (i = 0; i < MAX_NAMELEN; i++) {
if (!m64.name[i])
break;
if (!isprint(m64.name[i]))
return -1;
}
}
return sz;
}
int tarfile_start_txt (struct tarfile * tf, const char * fname)
{
tf->n = 0;
if (tf->type == TARFILE_TAR)
{
fill_in_header (tf, fname);
fgetpos (tf->f, &(tf->record_start));
fwrite (record_header,sizeof(char),512,tf->f);
}
else if (tf->type == TARFILE_TGZ)
{
fill_in_header (tf, fname);
tf->gz_record_start = gztell (tf->g);
gzwrite (tf->g,record_header,512);
}
else if (tf->type == TARFILE_NOTAR)
{
char tmp[256];
snprintf(tmp,255,"%s/%s",tf->fname,fname);
tf->f=fopen(tmp,"wt");
}
else
{
printf ("Unrecognized tarfile type %d.\n", tf->type);
return -1;
}
return 0;
}
int SaveStateGz(gzFile f, long* gzsize) {
int Size;
unsigned char pMemGpuPic[SZ_GPUPIC];
//if (f == NULL) return -1;
gzwrite(f, (void *)PcsxrHeader, sizeof(PcsxrHeader));
gzwrite(f, (void *)&SaveVersion, sizeof(u32));
gzwrite(f, (void *)&Config.HLE, sizeof(boolean));
if (gzsize)GPU_getScreenPic(pMemGpuPic); // Not necessary with ephemeral saves
gzwrite(f, pMemGpuPic, SZ_GPUPIC);
if (Config.HLE)
psxBiosFreeze(1);
gzwrite(f, psxM, 0x00200000);
gzwrite(f, psxR, 0x00080000);
gzwrite(f, psxH, 0x00010000);
gzwrite(f, (void *)&psxRegs, sizeof(psxRegs));
// gpu
if (!gpufP)gpufP = (GPUFreeze_t *)malloc(sizeof(GPUFreeze_t));
gpufP->ulFreezeVersion = 1;
GPU_freeze(1, gpufP);
gzwrite(f, gpufP, sizeof(GPUFreeze_t));
// SPU Plugin cannot change during run, so we query size info just once per session
if (!spufP) {
spufP = (SPUFreeze_t *)malloc(offsetof(SPUFreeze_t, SPUPorts)); // only first 3 elements (up to Size)
SPU_freeze(2, spufP);
Size = spufP->Size;
SysPrintf("SPUFreezeSize %i/(%i)\n", Size, offsetof(SPUFreeze_t, SPUPorts));
free(spufP);
spufP = (SPUFreeze_t *) malloc(Size);
spufP->Size = Size;
if (spufP->Size <= 0) {
gzclose(f);
free(spufP);
spufP = NULL;
return 1; // error
}
}
// spu
gzwrite(f, &(spufP->Size), 4);
SPU_freeze(1, spufP);
gzwrite(f, spufP, spufP->Size);
sioFreeze(f, 1);
cdrFreeze(f, 1);
psxHwFreeze(f, 1);
psxRcntFreeze(f, 1);
mdecFreeze(f, 1);
if(gzsize)*gzsize = gztell(f);
gzclose(f);
return 0;
}
/**
Tell position pointer in file.
*/
int zfpos(file_t *fp) {
if(fp->isgzip) {
return gztell((voidp)fp->p);
} else {
return ftell((FILE*)fp->p);
}
}
/* gztell()/malloc() should be sigblocked ... */
long GZtell(gzFile file){
long off;
inGzip++; FL_F_Gzip = "Gztell"; FL_L_Gzip = __LINE__;
off = gztell(file);
inGzip--;
return off;
}
/*!
*/
std::streampos
gzfilebuf::seekpos( std::streampos pos,
std::ios_base::openmode mode )
{
if ( ! is_open() )
{
return -1;
}
std::streampos ret = -1;
#ifdef HAVE_LIBZ
if ( ( M_impl->open_mode_ & std::ios_base::in )
&& ( mode & std::ios_base::in ) )
{
ret = gzseek( M_impl->file_, pos, SEEK_SET );
// and reset buffer pointer to initial position
M_remained_size = 0;
this->setg( M_buf, M_buf, M_buf );
}
if ( ( M_impl->open_mode_ & std::ios_base::out )
&& ( mode & std::ios_base::out ) )
{
std::streampos cur = gztell( M_impl->file_ );
if ( pos <= cur )
{
ret = gzseek( M_impl->file_, pos, SEEK_SET );
this->setp( M_buf, M_buf + M_buf_size );
}
}
#endif
return ret;
}
static off_t
logfile_ftello_gzip(AppContext * const context)
{
assert(context->logfile_enabled != 0);
assert(context->logfile_fd.gzfp != NULL);
return (off_t) gztell(context->logfile_fd.gzfp);
}
off_t dump_tell( FILE *fp )
{
if (gzlevel == -1) {
return ftell(fp);
} else {
return gztell((gzFile)fp);
}
}
long znztell(znzFile file)
{
if (file==NULL) { return 0; }
#ifdef HAVE_ZLIB
if (file->zfptr!=NULL) return (long) gztell(file->zfptr);
#endif
return ftell(file->nzfptr);
}
static unsigned long VFSGZIP_Tell(vfsfile_t *file)
{
int r;
vfsgzipfile_t *vfsgz = (vfsgzipfile_t *)file;
r = gztell((gzFile)vfsgz->parent->handle);
return r;
}
/* Scan one frame of the file to compute the frame size for each point. */
int icp_framesize(gzFile infile, int *rows, int *columns, int *values)
{
char line[MAX_LINE], token[MAX_LINE];
const char *pline;
int ch, ncomma=0, nsemicolon=0, nvalues=0;
z_off_t restore_pos;
/* Save position */
restore_pos = gztell(infile);
/* Get the values line */
if (gzgets(infile, line, sizeof(line)-1) == NULL) return ICP_READ_ERROR;
line[sizeof(line)-1] = '\0';
/* Scan the first detector frame */
ch = gzgetc(infile); /* Skip format column character */
if (ch >= 0) ch = gzgetc(infile); /* Peek at first frame character */
if (ch == ' ' || ch == '-' || ch < 0) {
/* Empty frame, so return size 0x0 */
*rows = *columns = 0;
} else {
/* Frame isn't empty so count number of commas and semicolons in frame. */
while (ch >= 0) {
ch = gzgetc(infile);
if (ch == ',') ncomma++;
else if (ch == ';') nsemicolon++;
else if (ch == '\r') /* ignored */ ;
else if (ch == '\n') {
ch = gzgetc(infile); /* Skip format column character */
if (ch >= 0) ch = gzgetc(infile);
if (ch==' ' || ch=='-') break;
}
}
/* last row does not end in semicolon so add 1
* last column does not end in comma so add 1
*/
*rows = nsemicolon + 1;
*columns = (ncomma / *rows) + 1;
}
/* Count the number of tokens on the line */
//printf("line=%s\n",line);
pline = line;
while (pline) {
pline = scan_token(pline, sizeof(token), token);
if (!*token || *token == '\n') break;
nvalues++;
//printf("values=%s\n",token);
}
*values = nvalues;
/* Restore position */
gzseek(infile, restore_pos, SEEK_SET);
return ICP_GOOD;
}
unsigned int ZFileTell()
{
int res = 0;
if (TextFile) {
res = ftell(FILEHANDLE[ZFileTellHandle]);
if (res == -1) fprintf(stderr, "Oups!! gzTell\n");
return(res);
} else return gztell(FILEHANDLE[ZFileTellHandle]);
}
long ZipFile::tell() const {
if (m_gzipFile) {
return gztell(m_gzipFile);
} else if (m_plainFile) {
return ftell(m_plainFile);
} else {
return 0;
}
}
value mlgz_gztell(value chan)
{
gzFile str = Gzfile_val(chan);
int res ;
res = gztell(str);
if(res<0)
mlgz_error(str);
return Val_unit;
}
streampos vcf_file::get_filepos()
{
if (!compressed)
return vcf_in.tellg();
else
{
return gztell(gzvcf_in); // TODO: Type check
}
}
/* allowed stream methods */
static int CZ_stream_tell(GB_STREAM *stream, int64_t *npos)
{
STREAM_COMPRESS *s = (STREAM_COMPRESS *)stream;
*npos=gztell (s->handle);
if ((*npos)!=-1) return 0;
gzclose (s->handle);
stream->desc=NULL;
return -1;
}
static unsigned long VFSGZIP_GetLen(vfsfile_t *file)
{
int r, currentpos;
vfsgzipfile_t *vfsgz = (vfsgzipfile_t *)file;
// VFS-FIXME: Error handling
currentpos = gztell((gzFile)vfsgz->parent->handle);
r = gzseek((gzFile)vfsgz->parent->handle, 0, SEEK_END);
gzseek((gzFile)vfsgz->parent->handle, currentpos, SEEK_SET);
return r;
}
void index_file(char *filename,hashtable sn_index,long start_offset,long length) {
gzFile fd1=open_fastq(filename);
gzFile fdf=open_fixed_fastq(filename);
if (fd1==NULL) {
fprintf(stderr,"\nError: Unable to open %s\n",filename);
exit(1);
}
// move to the right position
if(length>0) {
fprintf(stderr, "\nInternal error: Not implemented\n");
exit(2);
}
long cline=1;
// sn_index creation could be done in parallel
while(!gzeof(fd1)) {
long long start_pos=gztell(fd1);
char *hdr=READ_LINE_HDR(fd1);
if ( hdr==NULL) break;
int len;
//fprintf(stderr,"sn_index: =%s=\n",readname);
// get seq
//printf("cline=%ld\nLEN=%ld hdr=%s\n",cline,len,hdr);
char *seq=READ_LINE_SEQ(fd1);
char *hdr2=READ_LINE_HDR2(fd1);
char *qual=READ_LINE_QUAL(fd1);
char* readname=get_readname(hdr,&len,cline,filename);
if (seq==NULL || hdr2==NULL || qual==NULL ) {
fprintf(stderr,"\nError in file %s, line %lu: file truncated?\n",filename,cline);
exit(1);
}
if (validate_entry(hdr,hdr2,seq,qual,cline,filename)!=0) {
exit(1);
}
// check for duplicates
if ( lookup_header(sn_index,readname)!=NULL ) {
fprintf(stderr,"\nError in file %s, line %lu: duplicated sequence %s\n",filename,cline,readname);
exit(1);
}
if ( new_indexentry(sn_index,readname,len,start_pos)==NULL) {
fprintf(stderr,"\nError in file %s, line %lu: malloc failed?",filename,cline);
exit(1);
}
replace_dots(start_pos,seq,hdr,hdr2,qual,fdf);
PRINT_READS_PROCESSED(cline/4);
//
cline+=4;
}
close_fixed_fastq(fdf);
gzclose(fd1);
return;
}
int Reader::tell()
{
if (m_inRAM)
{
return m_inRAMCurrentPos;
}
else if (m_in)
{
return m_in->tellg();
}
#ifdef GTO_SUPPORT_ZIP
else
{
#if ZLIB_VERNUM >= UPDATED_ZLIB_VERNUM
return gztell((gzFile_s*)m_gzfile);
#else
return gztell(m_gzfile);
#endif
}
#else
else
{
uint64 FCEU_ftell(FCEUFILE *fp)
{
if(fp->type==1)
{
return gztell(fp->fp);
}
else if(fp->type>=2)
{
return (((MEMWRAP *)(fp->fp))->location);
}
else
return ftell((FILE *)fp->fp);
}
int validate_interleaved(char *f) {
unsigned long cline=1;
unsigned long nreads1=0;
gzFile fd1=NULL;
fprintf(stderr,"Paired-end interleaved\n");
fd1=open_fastq(f);
gzFile fdf=open_fixed_fastq(f);
while(!gzeof(fd1)) {
long start_pos=gztell(fd1);
// Read 1
char *hdr1=READ_LINE_HDR(fd1);
if ( hdr1==NULL) break;
int len;
char *seq1=READ_LINE_SEQ(fd1);
char *hdr1_2=READ_LINE_HDR2(fd1);
char *qual1=READ_LINE_QUAL(fd1);
// Read 2
char *hdr2=READ_LINE_HDR2_1(fd1);
char *seq2=READ_LINE_SEQ2(fd1);
char *hdr2_2=READ_LINE_HDR2_2(fd1);
char *qual2=READ_LINE_QUAL2(fd1);
if ( seq1==NULL || hdr1_2==NULL || qual1==NULL ||
hdr2==NULL || seq2==NULL || hdr2_2==NULL || qual2==NULL ) {
fprintf(stderr,"\nError in file %s, line %lu: file truncated?\n",f,cline);
return(1);
}
if (validate_entry(hdr1,hdr1_2,seq1,qual1,cline,f)!=0) {
return(1);
}
if (validate_entry(hdr2,hdr2_2,seq2,qual2,cline+4,f)!=0) {
return(1);
}
char* readname1=get_readname(hdr1,&len,cline,f);
char* readname2=get_readname(hdr2,&len,cline+4,f);
if ( strcmp(readname1,readname2) ) {
fprintf(stderr,"\nError in file %s, line %lu: unpaired read - %s\n",f,cline,readname1);
return(1);
}
PRINT_READS_PROCESSED(cline/4);
replace_dots(start_pos,seq1,hdr1,hdr1_2,qual1,fdf);
replace_dots(start_pos,seq2,hdr2,hdr2_2,qual2,fdf);
//
cline+=8;
nreads1+=2;
}
printf("\n");
close_fixed_fastq(fdf);
gzclose(fd1);
return(nreads1);
}
long
uproc_io_tell(uproc_io_stream *stream)
{
switch (stream->type) {
case UPROC_IO_GZIP:
#if HAVE_ZLIB_H
return gztell(stream->s.gz);
#endif
case UPROC_IO_STDIO:
return ftell(stream->s.fp);
}
uproc_error_msg(UPROC_EINVAL, "invalid stream");
return -1;
}
pos_type seekoff(off_type off, std::ios_base::seekdir way, std::ios_base::openmode which)
{
if (file && off == 0 && way == std::ios_base::cur && which == std::ios_base::out)
{
#if ZLIB_VERNUM >= 0x1240
// gzoffset is only available in zlib 1.2.4 or later
return pos_type(gzoffset(file));
#else
// return an approximation of file size (only used in progress dialog)
z_off_t offset = gztell(file);
if (offset > 0) offset /= 4;
return pos_type(offset);
#endif
}
return pos_type(off_type(-1));
}
static off_t gzdTell(FDSTACK_t fps)
{
off_t pos = -1;
gzFile gzfile = fps->fp;
if (gzfile != NULL) {
#if HAVE_GZSEEK
pos = gztell(gzfile);
if (pos < 0)
gzdSetError(fps);
#else
pos = -2;
#endif
}
return pos;
}
long
ftell2 (FILE *file)
{
#undef ftell
fmode2_t fmode = get_fmode (file);
if (fmode == FM_NORMAL)
return ftell (file);
else if (fmode == FM_GZIP)
return gztell (file);
else if (fmode == FM_ZIP)
return unztell (file); // returns ftell() of the "current file"
else
return -1;
#define ftell ftell2
}
off_t fzp_tell(struct fzp *fzp)
{
if(fzp) switch(fzp->type)
{
case FZP_FILE:
return ftello(fzp->fp);
case FZP_COMPRESSED:
return gztell(fzp->zp);
default:
unknown_type(fzp->type, __func__);
goto error;
}
not_open(__func__);
error:
return -1;
}
//Returns the number of bytes that can be read (or skipped over) from this input stream without blocking by the next caller of a method for this input stream.
int GZInputStream::available()
{
gzseek(m_file, 0, SEEK_END);
long max_length = gztell(m_file);
gzseek(m_file, 0, SEEK_SET);
return max_length;
}
