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PhotoRec: try to handle Blocked GNU Zip Format (BGZF) data

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This commit is contained in:
Christophe Grenier 2018-04-10 16:37:01 +02:00
parent 9eb2aa12ce
commit cdde95797e
1 changed files with 49 additions and 4 deletions
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53
src/file_gz.c
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@ -36,7 +36,6 @@
#include "file_gz.h"
static void register_header_check_gz(file_stat_t *file_stat);
static int header_check_gz(const unsigned char *buffer, const unsigned int buffer_size, const unsigned int safe_header_only, const file_recovery_t *file_recovery, file_recovery_t *file_recovery_new);
static void file_rename_gz(file_recovery_t *file_recovery);
extern const file_hint_t file_hint_doc;
@ -59,7 +58,6 @@ struct gzip_header
uint8_t os;
} __attribute__ ((gcc_struct, __packed__));
static const unsigned char gz_header_magic[3]= {0x1F, 0x8B, 0x08};
/* flags:
bit 0 FTEXT
bit 1 FHCRC
@ -76,9 +74,38 @@ static const unsigned char gz_header_magic[3]= {0x1F, 0x8B, 0x08};
#define GZ_FNAME 8
#define GZ_FCOMMENT 0x10
static void register_header_check_gz(file_stat_t *file_stat)
static void file_check_bgzf(file_recovery_t *file_recovery)
{
register_header_check(0, gz_header_magic,sizeof(gz_header_magic), &header_check_gz, file_stat);
}
static int header_check_bgzf(const unsigned char *buffer, const unsigned char *buffer_uncompr, const unsigned int buffer_size, file_recovery_t *file_recovery_new)
{
const struct gzip_header *gz=(const struct gzip_header *)buffer;
reset_file_recovery(file_recovery_new);
file_recovery_new->min_filesize=22;
file_recovery_new->time=le32(gz->mtime);
file_recovery_new->file_rename=&file_rename_gz;
file_recovery_new->file_check=&file_check_bgzf;
if(memcmp(buffer_uncompr, "BAI\1", 4)==0)
{
/* https://github.com/samtools/hts-specs SAM/BAM and related high-throughput sequencing file formats */
file_recovery_new->extension="bai";
return 1;
}
if(memcmp(buffer_uncompr, "BAM\1", 4)==0)
{
/* https://github.com/samtools/hts-specs SAM/BAM and related high-throughput sequencing file formats */
file_recovery_new->extension="bam";
return 1;
}
if(memcmp(buffer_uncompr, "CSI\1", 4)==0)
{
/* https://github.com/samtools/hts-specs SAM/BAM and related high-throughput sequencing file formats */
file_recovery_new->extension="csi";
return 1;
}
file_recovery_new->extension=file_hint_gz.extension;
return 1;
}
static int header_check_gz(const unsigned char *buffer, const unsigned int buffer_size, const unsigned int safe_header_only, const file_recovery_t *file_recovery, file_recovery_t *file_recovery_new)
@ -86,6 +113,7 @@ static int header_check_gz(const unsigned char *buffer, const unsigned int buffe
unsigned int off=10;
const unsigned int flags=buffer[3];
const struct gzip_header *gz=(const struct gzip_header *)buffer;
int bgzf=0;
/* gzip file format:
* a 10-byte header, containing a magic number, a version number and a timestamp
* optional extra headers, such as the original file name,
@ -106,6 +134,8 @@ static int header_check_gz(const unsigned char *buffer, const unsigned int buffe
{
off+=2;
off+=buffer[10]|(buffer[11]<<8);
if(buffer[12]=='B' && buffer[13]=='C' && buffer[14]==2 && buffer[15]==0)
bgzf=1;
}
if((flags&GZ_FNAME)!=0)
{
@ -133,6 +163,11 @@ static int header_check_gz(const unsigned char *buffer, const unsigned int buffe
if(header_ignored_adv(file_recovery, file_recovery_new)==0)
return 0;
}
if(file_recovery->file_check==&file_check_bgzf)
{
header_ignored(file_recovery_new);
return 0;
}
#if defined(HAVE_ZLIB_H) && defined(HAVE_LIBZ)
{
static const unsigned char schematic_header[12]={ 0x0a, 0x00, 0x09,
@ -173,6 +208,10 @@ static int header_check_gz(const unsigned char *buffer, const unsigned int buffe
if(d_stream.total_out < 16)
return 0;
buffer_uncompr[d_stream.total_out]='\0';
if(bgzf!=0)
{
return header_check_bgzf(buffer, buffer_uncompr, d_stream.total_out, file_recovery_new);
}
reset_file_recovery(file_recovery_new);
file_recovery_new->min_filesize=22;
file_recovery_new->time=le32(gz->mtime);
@ -291,3 +330,9 @@ const char*td_zlib_version(void)
return "none";
#endif
}
static void register_header_check_gz(file_stat_t *file_stat)
{
static const unsigned char gz_header_magic[3]= {0x1F, 0x8B, 0x08};
register_header_check(0, gz_header_magic,sizeof(gz_header_magic), &header_check_gz, file_stat);
}