/*
* Reads a read data block from an mFILE given a count of the number of
* flows and basecalls (from the common header and read headers).
*
* Returns the a pointer to sff_read_data on success
* NULL on failure
*/
sff_read_data *read_sff_read_data(mFILE *mf, int nflows, int nbases) {
sff_read_data *d;
int i;
if (NULL == (d = (sff_read_data *)xcalloc(1, sizeof(*d))))
return NULL;
if (NULL == (d->flowgram = (uint16_t *)xcalloc(nflows, 2)))
return free_sff_read_data(d), NULL;
if (nflows != mfread(d->flowgram, 2, nflows, mf))
return free_sff_read_data(d), NULL;
for (i = 0; i < nflows; i++)
d->flowgram[i] = be_int2(d->flowgram[i]);
if (NULL == (d->flow_index = (uint8_t *)xmalloc(nbases)))
return free_sff_read_data(d), NULL;
if (nbases != mfread(d->flow_index, 1, nbases, mf))
return free_sff_read_data(d), NULL;
if (NULL == (d->bases = (char *)xmalloc(nbases)))
return free_sff_read_data(d), NULL;
if (nbases != mfread(d->bases, 1, nbases, mf))
return free_sff_read_data(d), NULL;
if (NULL == (d->quality = (uint8_t *)xmalloc(nbases)))
return free_sff_read_data(d), NULL;
if (nbases != mfread(d->quality, 1, nbases, mf))
return free_sff_read_data(d), NULL;
/* Pad to 8 chars */
mfseek(mf, (mftell(mf) + 7)& ~7, SEEK_SET);
return d;
}
/*
* Reads a read header (including variable length components) from an mFILE.
*
* Returns the a pointer to the header on success
* NULL on failure
*/
sff_read_header *read_sff_read_header(mFILE *mf) {
sff_read_header *h;
unsigned char rhdr[16];
if (16 != mfread(rhdr, 1, 16, mf))
return NULL;
h = decode_sff_read_header(rhdr);
if (h->name_len != mfread(h->name, 1, h->name_len, mf))
return free_sff_read_header(h), NULL;
/* Pad to 8 chars */
mfseek(mf, (mftell(mf) + 7)& ~7, SEEK_SET);
return h;
}
static int audio_get_frame(void *ctx, TCFrameAudio *ptr)
{
transfer_t import_para;
TCImportData *data = ctx;
int ret = TC_OK;
if (data->fd != NULL) {
if (data->bytes && (ret = mfread(ptr->audio_buf, data->bytes, 1, data->fd)) != 1)
ret = TC_ERROR;
ptr->audio_len = data->bytes;
ptr->audio_size = data->bytes;
} else {
import_para.fd = NULL;
import_para.buffer = ptr->audio_buf;
import_para.size = data->bytes;
import_para.flag = TC_AUDIO;
import_para.attributes = ptr->attributes;
ret = tca_import(TC_IMPORT_DECODE, &import_para, data->vob);
ptr->audio_len = import_para.size;
ptr->audio_size = import_para.size;
}
return ret;
}
/*
* Reads a common header (including variable length components) from an mFILE.
*
* Returns the a pointer to the header on success
* NULL on failure
*/
sff_common_header *read_sff_common_header(mFILE *mf) {
sff_common_header *h;
unsigned char chdr[31];
if (31 != mfread(chdr, 1, 31, mf))
return NULL;
h = decode_sff_common_header(chdr);
if (h->flow_len != mfread(h->flow, 1, h->flow_len, mf))
return free_sff_common_header(h), NULL;
if (h->key_len != mfread(h->key , 1, h->key_len, mf))
return free_sff_common_header(h), NULL;
/* Pad to 8 chars */
mfseek(mf, (mftell(mf) + 7)& ~7, SEEK_SET);
return h;
}
char *mfgets(MEMFILE *mf,char *string,unsigned int size)
{
char *ptr;
unsigned int read;
long seek;
assert(mf!=NULL);
read=mfread(mf,(unsigned char *)string,size);
if (read==0)
return NULL;
seek=0L;
/* make sure that the string is zero-terminated */
assert(read<=size);
if (read<size) {
string[read]='\0';
} else {
string[size-1]='\0';
seek=-1; /* undo reading the character that gets overwritten */
} /* if */
/* find the first '\n' */
ptr=strchr(string,'\n');
if (ptr!=NULL) {
*(ptr+1)='\0';
seek=(long)(ptr-string)+1-(long)read;
} /* if */
/* undo over-read */
assert(seek<=0); /* should seek backward only */
if (seek!=0)
mfseek(mf,seek,SEEK_CUR);
return string;
}
/* for backward compatibility with the original lib */
void midifile()
{
mfread();
}
/* for backward compatibility with the original lib */
DECLSPEC void midifile(void)
{
mfread();
}
int main(void)
{
MEMFILE *file, *file2, *file3;
char test[] = "This is a very long string that just goes on and on, but it can surely tell us a few things about how this code is working.";
char test2[] = "This is the second string, and should get cat'd right up behind the first string.";
char buffer[512];
printf("\n--------- open should fail (file doesn't exist)\n");
file = mfopen( "dummy", "r+b" );
printf("fopen(\"dummy\",\"r+b\") -> 0x%x\n", file );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- open should succeed (truncated on open)\n");
file = mfopen( "dummy", "w+b" );
printf("fopen(\"dummy\",\"w+b\") -> 0x%x\n", file );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("growth increment was %d\n", _mfsetgrowincrement( file, 64 ) );
printf("growth increment is now %d\n", _mfsetgrowincrement( file, 0 ) );
printf("\n--------- should be zero offset, and eof == false\n");
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- should write %d bytes\n", strlen(test));
printf( "fwrite( [], %d, %d, file ) -> %d\n", strlen(test), sizeof(char),
mfwrite( test, strlen(test), sizeof(char), file ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- should read the string back in\n");
printf( "rewind(file) \n" ); mrewind(file);
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
memset( buffer, 0, sizeof( buffer ));
printf( "fread( [], %d, %d, file ) -> %d\n", sizeof(buffer), sizeof(char),
mfread( buffer, sizeof(buffer), sizeof(char), file ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- should cat the second string to the first\n");
printf( "fwrite( [], %d, %d, file ) -> %d\n", sizeof(char), strlen(test2),
mfwrite( test2, strlen(test2), sizeof(char), file ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- should read zero (fp is at eof)\n");
memset( buffer, 0, sizeof( buffer ));
printf( "fread( [], %d, %d, file ) -> %d\n", sizeof(buffer), sizeof(char),
mfread( buffer, sizeof(buffer), sizeof(char), file ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- seek test\n");
printf( "filelength( fileno( file ) )-> %ld\n", mfilelength( mfileno( file ) ) );
printf( "seek(file,64,0)-> %d\n", mfseek( file, 64, SEEK_SET ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- read after seek test, should read filelen-64 bytes\n");
memset( buffer, 0, sizeof( buffer ));
printf( "fread( [], %d, %d, file ) -> %d\n", sizeof(buffer), sizeof(char),
mfread( buffer, sizeof(buffer), sizeof(char), file ) );
printf( "-> \"%s\"\n", buffer );
printf("\n--------- change size test\n");
printf( "filelength( fileno( file ) )-> %ld\n", mfilelength( mfileno( file ) ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf( "ftruncate(fileno(file),10) -> %d\n", mftruncate( mfileno( file ), 10 ) );
printf( "filelength( fileno( file ) )-> %ld\n", mfilelength( mfileno( file ) ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- negative seek test\n");
printf( "fseek(file,-5,2)->%d\n", mfseek( file, -5, SEEK_END ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- read after seek test, should read 5 bytes\n");
memset( buffer, 0, sizeof( buffer ));
printf( "fread( [], %d, %d, file ) -> %d\n", sizeof(buffer), sizeof(char),
mfread( buffer, sizeof(buffer), sizeof(char), file ) );
printf( "-> \"%s\"\n", buffer );
printf("\n--------- open and write a second file\n");
file2 = mfopen( "dummy2", "w+b" );
printf("fopen(\"dummy2\",\"w+b\") -> 0x%x\n", file2 );
printf( "fwrite( [], %d, %d, file2 ) -> %d\n", strlen("TEST"), sizeof(char),
mfwrite( "TEST", strlen("TEST"), sizeof(char), file2 ) );
printf( "filelength( fileno( file2 ) )-> %ld\n", mfilelength( mfileno( file2 ) ) );
printf( "ftell(file2) -> %ld feof(file2)-> %d\n", mftell( file2 ), mfeof( file2 ) );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- open and write a third file\n");
file3 = mfopen( "dummy3", "w+b" );
printf("fopen(\"dummy3\",\"w+b\") -> 0x%x\n", file3 );
printf( "fwrite( [], %d, %d, file3 ) -> %d\n", strlen("BLAHBLAH"), sizeof(char),
mfwrite( "BLAHBLAH", strlen("BLAHBLAH"), sizeof(char), file3 ) );
printf( "filelength( fileno( file3 ) )-> %ld\n", mfilelength( mfileno( file3 ) ) );
printf( "ftell(file3) -> %ld feof(file3)-> %d\n", mftell( file3 ), mfeof( file3 ) );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- close second\n");
printf( "fclose(file2) -> %d\n", mfclose( file2 ) );
printf( "filelength( fileno( file2 ) )-> %ld\n", mfilelength( mfileno( file2 ) ) );
printf( "ftell(file2) -> %ld feof(file2)-> %d\n", mftell( file2 ), mfeof( file2 ) );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- check first\n");
printf( "filelength( fileno( file ) )-> %ld\n", mfilelength( mfileno( file ) ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- truncate to zero test\n");
printf( "ftruncate(fileno(file),0) -> %d\n", mftruncate( mfileno( file ), 0 ) );
printf( "filelength( fileno( file ) )-> %ld\n", mfilelength( mfileno( file ) ) );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- close first\n");
printf( "fclose(file) -> %d\n", mfclose( file ) );
printf( "filelength( fileno( file ) )-> %ld\n", mfilelength( mfileno( file ) ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- close third\n");
printf( "fclose(file3) -> %d\n", mfclose( file3 ) );
printf( "filelength( fileno( file3 ) )-> %ld\n", mfilelength( mfileno( file3 ) ) );
printf( "ftell(file3) -> %ld feof(file3)-> %d\n", mftell( file3 ), mfeof( file3 ) );
printf("#of open memstreams: %d\n", count_open_streams() );
return 0;
}
/*
* As per partial_decode_ztr in srf.c, but without uncompress_ztr.
*/
ztr_t *partial_decode_ztr2(srf_t *srf, mFILE *mf, ztr_t *z) {
ztr_t *ztr;
ztr_chunk_t *chunk;
long pos = 0;
if (z) {
/* Use existing ZTR object => already loaded header */
ztr = z;
} else {
/* Allocate or use existing ztr */
if (NULL == (ztr = new_ztr()))
return NULL;
/* Read the header */
if (-1 == ztr_read_header(mf, &ztr->header)) {
if (!z)
delete_ztr(ztr);
mrewind(mf);
return NULL;
}
/* Check magic number and version */
if (memcmp(ztr->header.magic, ZTR_MAGIC, 8) != 0) {
if (!z)
delete_ztr(ztr);
mrewind(mf);
return NULL;
}
if (ztr->header.version_major != ZTR_VERSION_MAJOR) {
if (!z)
delete_ztr(ztr);
mrewind(mf);
return NULL;
}
}
/* Load chunks */
pos = mftell(mf);
while ((chunk = ztr_read_chunk_hdr(mf))) {
chunk->data = (char *)xmalloc(chunk->dlength);
if (chunk->dlength != mfread(chunk->data, 1, chunk->dlength, mf))
break;
ztr->nchunks++;
ztr->chunk = (ztr_chunk_t *)xrealloc(ztr->chunk, ztr->nchunks *
sizeof(ztr_chunk_t));
memcpy(&ztr->chunk[ztr->nchunks-1], chunk, sizeof(*chunk));
xfree(chunk);
pos = mftell(mf);
}
/*
* At this stage we're 'pos' into the mFILE mf with any remainder being
* a partial block.
*/
if (0 == ztr->nchunks) {
if (!z)
delete_ztr(ztr);
mrewind(mf);
return NULL;
}
/* Ensure we exit at the start of a ztr CHUNK */
mfseek(mf, pos, SEEK_SET);
/* If this is the header part, ensure we uncompress and init. data */
if (!z) {
/* Force caching of huffman code_sets */
ztr_find_hcode(ztr, CODE_USER);
/* And uncompress the rest */
uncompress_ztr(ztr);
}
return ztr;
}