void FASTAReader::add_char_to_id(char ch)
{
(*this->seqs_ids)[current_seq].push_back(ch);
current = fgetc_unlocked(file_);
}
static int snappy_in_java_uncompress(FILE *infp, FILE *outfp)
{
snappy_in_java_header_t header;
work_buffer_t wb;
int err = 1;
int outfd;
wb.c = NULL;
wb.uc = NULL;
/* read header */
if (fread(&header, sizeof(header), 1, infp) != 1) {
print_error("Failed to read a file: %s\n", strerror(errno));
goto cleanup;
}
/* check header */
if (memcmp(header.magic, SNAPPY_IN_JAVA_MAGIC, SNAPPY_IN_JAVA_MAGIC_LEN) != 0) {
print_error("This is not a snappy-java file.\n");
goto cleanup;
}
/* Use a file descriptor 'outfd' instead of the stdio file pointer 'outfp'
* to reduce the number of write system calls.
*/
fflush(outfp);
outfd = fileno(outfp);
/* read body */
work_buffer_init(&wb, MAX_BLOCK_SIZE);
for (;;) {
int compressed_flag;
size_t length = 0;
unsigned int crc32c = 0;
/* read compressed flag */
compressed_flag = fgetc_unlocked(infp);
switch (compressed_flag) {
case EOF:
/* read all blocks */
err = 0;
goto cleanup;
case COMPRESSED_FLAG:
case UNCOMPRESSED_FLAG:
/* pass */
break;
default:
print_error("Unknown compressed flag 0x%02x\n", compressed_flag);
goto cleanup;
}
/* read data length. */
length |= (fgetc_unlocked(infp) << 8);
length |= (fgetc_unlocked(infp) << 0);
/* read crc32c. */
crc32c |= (fgetc_unlocked(infp) << 24);
crc32c |= (fgetc_unlocked(infp) << 16);
crc32c |= (fgetc_unlocked(infp) << 8);
crc32c |= (fgetc_unlocked(infp) << 0);
/* check read error */
if (feof(infp)) {
print_error("Unexpected end of file.\n");
goto cleanup;
} else if (ferror(infp)) {
print_error("Failed to read a file: %s\n", strerror(errno));
goto cleanup;
}
/* read data */
if (fread(wb.c, length, 1, infp) != 1) {
if (feof(infp)) {
print_error("Unexpected end of file\n");
} else {
print_error("Failed to read a file: %s\n", strerror(errno));
}
goto cleanup;
}
trace("read %ld bytes.\n", (long)(length));
if (compressed_flag == COMPRESSED_FLAG) {
/* check the uncompressed length */
size_t uncompressed_length;
err = snappy_uncompressed_length(wb.c, length, &uncompressed_length);
if (err != 0) {
print_error("Invalid data: GetUncompressedLength failed %d\n", err);
goto cleanup;
}
err = 1;
if (uncompressed_length > wb.uclen) {
print_error("Invalid data: too long uncompressed length\n");
goto cleanup;
}
/* uncompress and write */
if (snappy_uncompress(wb.c, length, wb.uc, &uncompressed_length)) {
print_error("Invalid data: RawUncompress failed\n");
goto cleanup;
}
if (check_and_write_block(outfd, wb.uc, uncompressed_length, 1, crc32c)) {
goto cleanup;
}
} else {
if (check_and_write_block(outfd, wb.c, length, 1, crc32c)) {
goto cleanup;
}
}
}
cleanup:
work_buffer_free(&wb);
return err;
}
FASTAReader::FASTAReader(std::string filename) :
file_(fopen(filename.c_str(), "r")), seq_sizes(VSIZE)
{
current = fgetc_unlocked(file_);
}
FASTAReader::FASTAReader(char* filename) :
file_(fopen(filename, "r")), seq_sizes(VSIZE)
{
current = fgetc_unlocked(file_);
}
static int snappy_java_uncompress(FILE *infp, FILE *outfp)
{
snappy_java_header_t header;
work_buffer_t wb;
int err = 1;
int outfd;
wb.c = NULL;
wb.uc = NULL;
/* read header */
if (fread(&header, sizeof(header), 1, infp) != 1) {
print_error("Failed to read a file: %s\n", strerror(errno));
goto cleanup;
}
/* check header */
if (memcmp(header.magic, SNAPPY_JAVA_MAGIC, SNAPPY_JAVA_MAGIC_LEN) != 0) {
print_error("This is not a snappy-java file.\n");
goto cleanup;
}
header.version = ntohl(header.version);
if (header.version != SNAPPY_JAVA_FILE_VERSION) {
print_error("Unknown snappy-java version %d\n", header.version);
goto cleanup;
}
header.compatible_version = ntohl(header.compatible_version);
if (header.compatible_version != SNAPPY_JAVA_FILE_VERSION) {
print_error("Unknown snappy-java compatible version %d\n", header.compatible_version);
goto cleanup;
}
/* Use a file descriptor 'outfd' instead of the stdio file pointer 'outfp'
* to reduce the number of write system calls.
*/
fflush(outfp);
outfd = fileno(outfp);
/* read body */
work_buffer_init(&wb, DEFAULT_BLOCK_SIZE);
for (;;) {
/* read the compressed length in a block */
size_t compressed_length = 0;
size_t uncompressed_length = wb.uclen;
int idx;
for (idx = 3; idx >= 0; idx--) {
int chr = fgetc_unlocked(infp);
if (chr == -1) {
if (idx == 3) {
/* read all blocks */
err = 0;
goto cleanup;
}
print_error("Unexpected end of file.\n");
goto cleanup;
}
compressed_length |= (chr << (idx * 8));
}
trace("read 4 bytes (compressed_length = %ld)\n", (long)compressed_length);
if (compressed_length == 0) {
print_error("Invalid compressed length %ld\n", (long)compressed_length);
goto cleanup;
}
if (compressed_length > wb.clen) {
work_buffer_resize(&wb, compressed_length, 0);
}
/* read the compressed data */
if (fread(wb.c, compressed_length, 1, infp) != 1) {
if (feof(infp)) {
print_error("Unexpected end of file\n");
} else {
print_error("Failed to read a file: %s\n", strerror(errno));
}
goto cleanup;
}
trace("read %ld bytes.\n", (long)(compressed_length));
/* check the uncompressed length */
err = snappy_uncompressed_length(wb.c, compressed_length, &uncompressed_length);
if (err != 0) {
print_error("Invalid data: GetUncompressedLength failed %d\n", err);
goto cleanup;
}
err = 1;
if (uncompressed_length > wb.uclen) {
work_buffer_resize(&wb, 0, uncompressed_length);
}
/* uncompress and write */
if (snappy_uncompress(wb.c, compressed_length, wb.uc, &uncompressed_length)) {
print_error("Invalid data: RawUncompress failed\n");
goto cleanup;
}
if (write_full(outfd, wb.uc, uncompressed_length) != uncompressed_length) {
print_error("Failed to write a file: %s\n", strerror(errno));
goto cleanup;
}
trace("write %ld bytes\n", (long)uncompressed_length);
}
cleanup:
work_buffer_free(&wb);
return err;
}
int __fgetc_unlocked(FILE *f) {
return fgetc_unlocked(f);
}
static int
do_test (void)
{
const char blah[] = "BLAH";
char buf[strlen (blah) + 1];
FILE *fp, *f;
const char *cp;
char *wp;
if ((fp = fdopen (fd, "w+")) == NULL)
exit (1);
flockfile (fp);
f = fp;
cp = blah;
/* These tests deliberately use fwrite_unlocked with the size
argument specified as 0, which results in "division by zero"
warnings from the expansion of that macro (in code that is not
evaluated for a size of 0). This applies to the tests of
fread_unlocked below as well. */
DIAG_PUSH_NEEDS_COMMENT;
DIAG_IGNORE_NEEDS_COMMENT (4.9, "-Wdiv-by-zero");
if (ftello (fp) != 0
|| fwrite_unlocked (blah, blah - blah, strlen (blah), f++) != 0
|| f != fp + 1
|| fwrite_unlocked ("", 5.0, 0, --f) != 0
|| f != fp
|| fwrite_unlocked (cp++, 16, 0.25, fp) != 0
|| cp != blah + 1
|| fwrite_unlocked (--cp, 0.25, 16, fp) != 0
|| cp != blah
|| fwrite_unlocked (blah, 0, -0.0, fp) != 0
|| ftello (fp) != 0)
{
puts ("One of fwrite_unlocked tests failed");
exit (1);
}
DIAG_POP_NEEDS_COMMENT;
if (fwrite_unlocked (blah, 1, strlen (blah) - 2, fp) != strlen (blah) - 2)
{
puts ("Could not write string into file");
exit (1);
}
if (putc_unlocked ('A' + 0x1000000, fp) != 'A')
{
puts ("putc_unlocked failed");
exit (1);
}
f = fp;
cp = blah + strlen (blah) - 1;
if (putc_unlocked (*cp++, f++) != 'H'
|| f != fp + 1
|| cp != strchr (blah, '\0'))
{
puts ("fputc_unlocked failed");
exit (1);
}
if (ftello (fp) != (off_t) strlen (blah))
{
printf ("Failed to write %zd bytes to temporary file", strlen (blah));
exit (1);
}
rewind (fp);
f = fp;
wp = buf;
memset (buf, ' ', sizeof (buf));
/* See explanation above. */
DIAG_PUSH_NEEDS_COMMENT;
DIAG_IGNORE_NEEDS_COMMENT (4.9, "-Wdiv-by-zero");
if (ftello (fp) != 0
|| fread_unlocked (buf, buf - buf, strlen (blah), f++) != 0
|| f != fp + 1
|| fread_unlocked (buf, 5.0, 0, --f) != 0
|| f != fp
|| fread_unlocked (wp++, 16, 0.25, fp) != 0
|| wp != buf + 1
|| fread_unlocked (--wp, 0.25, 16, fp) != 0
|| wp != buf
|| fread_unlocked (buf, 0, -0.0, fp) != 0
|| ftello (fp) != 0
|| memcmp (buf, " ", sizeof (buf)) != 0)
{
puts ("One of fread_unlocked tests failed");
exit (1);
}
DIAG_POP_NEEDS_COMMENT;
if (fread_unlocked (buf, 1, strlen (blah) - 2, fp) != strlen (blah) - 2)
{
puts ("Could not read string from file");
exit (1);
}
if (getc_unlocked (fp) != 'A')
{
puts ("getc_unlocked failed");
exit (1);
}
f = fp;
if (fgetc_unlocked (f++) != 'H'
|| f != fp + 1
|| fgetc_unlocked (--f) != EOF
|| f != fp)
{
puts ("fgetc_unlocked failed");
exit (1);
}
if (ftello (fp) != (off_t) strlen (blah))
{
printf ("Failed to read %zd bytes from temporary file", strlen (blah));
exit (1);
}
funlockfile (fp);
fclose (fp);
return 0;
}
