/*
* calc_chksums calculates the checksums for the blocks described in the
* descriptor block.
*/
static int calc_chksums(journal_t *journal, struct buffer_head *bh,
unsigned long long *next_log_block, __u32 *crc32_sum)
{
int i, num_blks, err;
unsigned long long io_block;
struct buffer_head *obh;
num_blks = count_tags(journal, bh);
/* Calculate checksum of the descriptor block. */
*crc32_sum = crc32_be(*crc32_sum, (void *)bh->b_data, bh->b_size);
for (i = 0; i < num_blks; i++) {
io_block = (*next_log_block)++;
wrap(journal, *next_log_block);
err = jread(&obh, journal, io_block);
if (err) {
printk(KERN_ERR "JBD: IO error %d recovering block "
"%llu in log\n", err, io_block);
return 1;
} else {
*crc32_sum = crc32_be(*crc32_sum, (void *)obh->b_data,
obh->b_size);
}
brelse(obh);
}
return 0;
}
static int do_one_pass(journal_t *journal,
struct recovery_info *info, enum passtype pass)
{
unsigned int first_commit_ID, next_commit_ID;
unsigned long next_log_block;
int err, success = 0;
journal_superblock_t * sb;
journal_header_t * tmp;
struct buffer_head * bh;
unsigned int sequence;
int blocktype;
/* Precompute the maximum metadata descriptors in a descriptor block */
int MAX_BLOCKS_PER_DESC;
MAX_BLOCKS_PER_DESC = ((journal->j_blocksize-sizeof(journal_header_t))
/ sizeof(journal_block_tag_t));
/*
* First thing is to establish what we expect to find in the log
* (in terms of transaction IDs), and where (in terms of log
* block offsets): query the superblock.
*/
sb = journal->j_superblock;
next_commit_ID = be32_to_cpu(sb->s_sequence);
next_log_block = be32_to_cpu(sb->s_start);
first_commit_ID = next_commit_ID;
if (pass == PASS_SCAN)
info->start_transaction = first_commit_ID;
jbd_debug(1, "Starting recovery pass %d\n", pass);
/*
* Now we walk through the log, transaction by transaction,
* making sure that each transaction has a commit block in the
* expected place. Each complete transaction gets replayed back
* into the main filesystem.
*/
while (1) {
int flags;
char * tagp;
journal_block_tag_t * tag;
struct buffer_head * obh;
struct buffer_head * nbh;
cond_resched(); /* We're under lock_kernel() */
/* If we already know where to stop the log traversal,
* check right now that we haven't gone past the end of
* the log. */
if (pass != PASS_SCAN)
if (tid_geq(next_commit_ID, info->end_transaction))
break;
jbd_debug(2, "Scanning for sequence ID %u at %lu/%lu\n",
next_commit_ID, next_log_block, journal->j_last);
/* Skip over each chunk of the transaction looking
* either the next descriptor block or the final commit
* record. */
jbd_debug(3, "JBD: checking block %ld\n", next_log_block);
err = jread(&bh, journal, next_log_block);
if (err)
goto failed;
next_log_block++;
wrap(journal, next_log_block);
/* What kind of buffer is it?
*
* If it is a descriptor block, check that it has the
* expected sequence number. Otherwise, we're all done
* here. */
tmp = (journal_header_t *)bh->b_data;
if (tmp->h_magic != cpu_to_be32(JFS_MAGIC_NUMBER)) {
brelse(bh);
break;
}
blocktype = be32_to_cpu(tmp->h_blocktype);
sequence = be32_to_cpu(tmp->h_sequence);
jbd_debug(3, "Found magic %d, sequence %d\n",
blocktype, sequence);
if (sequence != next_commit_ID) {
brelse(bh);
break;
}
/* OK, we have a valid descriptor block which matches
* all of the sequence number checks. What are we going
* to do with it? That depends on the pass... */
switch(blocktype) {
case JFS_DESCRIPTOR_BLOCK:
/* If it is a valid descriptor block, replay it
* in pass REPLAY; otherwise, just skip over the
* blocks it describes. */
if (pass != PASS_REPLAY) {
next_log_block +=
count_tags(bh, journal->j_blocksize);
wrap(journal, next_log_block);
brelse(bh);
continue;
}
/* A descriptor block: we can now write all of
* the data blocks. Yay, useful work is finally
* getting done here! */
tagp = &bh->b_data[sizeof(journal_header_t)];
while ((tagp - bh->b_data +sizeof(journal_block_tag_t))
<= journal->j_blocksize) {
unsigned long io_block;
tag = (journal_block_tag_t *) tagp;
flags = be32_to_cpu(tag->t_flags);
io_block = next_log_block++;
wrap(journal, next_log_block);
err = jread(&obh, journal, io_block);
if (err) {
/* Recover what we can, but
* report failure at the end. */
success = err;
printk (KERN_ERR
"JBD: IO error %d recovering "
"block %ld in log\n",
err, io_block);
} else {
unsigned long blocknr;
J_ASSERT(obh != NULL);
blocknr = be32_to_cpu(tag->t_blocknr);
/* If the block has been
* revoked, then we're all done
* here. */
if (journal_test_revoke
(journal, blocknr,
next_commit_ID)) {
brelse(obh);
++info->nr_revoke_hits;
goto skip_write;
}
/* Find a buffer for the new
* data being restored */
nbh = __getblk(journal->j_fs_dev,
blocknr,
journal->j_blocksize);
if (nbh == NULL) {
printk(KERN_ERR
"JBD: Out of memory "
"during recovery.\n");
err = -ENOMEM;
brelse(bh);
brelse(obh);
goto failed;
}
lock_buffer(nbh);
memcpy(nbh->b_data, obh->b_data,
journal->j_blocksize);
if (flags & JFS_FLAG_ESCAPE) {
*((__be32 *)bh->b_data) =
cpu_to_be32(JFS_MAGIC_NUMBER);
}
BUFFER_TRACE(nbh, "marking dirty");
set_buffer_uptodate(nbh);
mark_buffer_dirty(nbh);
BUFFER_TRACE(nbh, "marking uptodate");
++info->nr_replays;
/* ll_rw_block(WRITE, 1, &nbh); */
unlock_buffer(nbh);
brelse(obh);
brelse(nbh);
}
skip_write:
tagp += sizeof(journal_block_tag_t);
if (!(flags & JFS_FLAG_SAME_UUID))
tagp += 16;
if (flags & JFS_FLAG_LAST_TAG)
break;
}
brelse(bh);
continue;
case JFS_COMMIT_BLOCK:
/* Found an expected commit block: not much to
* do other than move on to the next sequence
* number. */
brelse(bh);
next_commit_ID++;
continue;
case JFS_REVOKE_BLOCK:
/* If we aren't in the REVOKE pass, then we can
* just skip over this block. */
if (pass != PASS_REVOKE) {
brelse(bh);
continue;
}
err = scan_revoke_records(journal, bh,
next_commit_ID, info);
brelse(bh);
if (err)
goto failed;
continue;
default:
jbd_debug(3, "Unrecognised magic %d, end of scan.\n",
blocktype);
goto done;
}
}
done:
/*
* We broke out of the log scan loop: either we came to the
* known end of the log or we found an unexpected block in the
* log. If the latter happened, then we know that the "current"
* transaction marks the end of the valid log.
*/
if (pass == PASS_SCAN)
info->end_transaction = next_commit_ID;
else {
/* It's really bad news if different passes end up at
* different places (but possible due to IO errors). */
if (info->end_transaction != next_commit_ID) {
printk (KERN_ERR "JBD: recovery pass %d ended at "
"transaction %u, expected %u\n",
pass, next_commit_ID, info->end_transaction);
if (!success)
success = -EIO;
}
}
return success;
failed:
return err;
}
static int do_one_pass(journal_t *journal,
struct recovery_info *info, enum passtype pass)
{
unsigned int first_commit_ID, next_commit_ID;
unsigned long long next_log_block;
int err, success = 0;
journal_superblock_t * sb;
journal_header_t * tmp;
struct buffer_head * bh;
unsigned int sequence;
int blocktype;
int tag_bytes = journal_tag_bytes(journal);
__u32 crc32_sum = ~0; /* Transactional Checksums */
/* Precompute the maximum metadata descriptors in a descriptor block */
int MAX_BLOCKS_PER_DESC;
MAX_BLOCKS_PER_DESC = ((journal->j_blocksize-sizeof(journal_header_t))
/ tag_bytes);
/*
* First thing is to establish what we expect to find in the log
* (in terms of transaction IDs), and where (in terms of log
* block offsets): query the superblock.
*/
sb = journal->j_superblock;
next_commit_ID = be32_to_cpu(sb->s_sequence);
next_log_block = be32_to_cpu(sb->s_start);
first_commit_ID = next_commit_ID;
if (pass == PASS_SCAN)
info->start_transaction = first_commit_ID;
jbd_debug(1, "Starting recovery pass %d\n", pass);
/*
* Now we walk through the log, transaction by transaction,
* making sure that each transaction has a commit block in the
* expected place. Each complete transaction gets replayed back
* into the main filesystem.
*/
while (1) {
int flags;
char * tagp;
journal_block_tag_t * tag;
struct buffer_head * obh;
struct buffer_head * nbh;
cond_resched();
/* If we already know where to stop the log traversal,
* check right now that we haven't gone past the end of
* the log. */
if (pass != PASS_SCAN)
if (tid_geq(next_commit_ID, info->end_transaction))
break;
jbd_debug(2, "Scanning for sequence ID %u at %lu/%lu\n",
next_commit_ID, next_log_block, journal->j_last);
/* Skip over each chunk of the transaction looking
* either the next descriptor block or the final commit
* record. */
jbd_debug(3, "JBD: checking block %ld\n", next_log_block);
err = jread(&bh, journal, next_log_block);
if (err)
goto failed;
next_log_block++;
wrap(journal, next_log_block);
/* What kind of buffer is it?
*
* If it is a descriptor block, check that it has the
* expected sequence number. Otherwise, we're all done
* here. */
tmp = (journal_header_t *)bh->b_data;
if (tmp->h_magic != cpu_to_be32(JFS_MAGIC_NUMBER)) {
brelse(bh);
break;
}
blocktype = be32_to_cpu(tmp->h_blocktype);
sequence = be32_to_cpu(tmp->h_sequence);
jbd_debug(3, "Found magic %d, sequence %d\n",
blocktype, sequence);
if (sequence != next_commit_ID) {
brelse(bh);
break;
}
/* OK, we have a valid descriptor block which matches
* all of the sequence number checks. What are we going
* to do with it? That depends on the pass... */
switch(blocktype) {
case JFS_DESCRIPTOR_BLOCK:
/* If it is a valid descriptor block, replay it
* in pass REPLAY; if journal_checksums enabled, then
* calculate checksums in PASS_SCAN, otherwise,
* just skip over the blocks it describes. */
if (pass != PASS_REPLAY) {
if (pass == PASS_SCAN &&
JFS_HAS_COMPAT_FEATURE(journal,
JFS_FEATURE_COMPAT_CHECKSUM) &&
!info->end_transaction) {
if (calc_chksums(journal, bh,
&next_log_block,
&crc32_sum)) {
brelse(bh);
break;
}
brelse(bh);
continue;
}
next_log_block += count_tags(journal, bh);
wrap(journal, next_log_block);
brelse(bh);
continue;
}
/* A descriptor block: we can now write all of
* the data blocks. Yay, useful work is finally
* getting done here! */
tagp = &bh->b_data[sizeof(journal_header_t)];
while ((tagp - bh->b_data + tag_bytes)
<= journal->j_blocksize) {
unsigned long long io_block;
tag = (journal_block_tag_t *) tagp;
flags = be32_to_cpu(tag->t_flags);
io_block = next_log_block++;
wrap(journal, next_log_block);
err = jread(&obh, journal, io_block);
if (err) {
/* Recover what we can, but
* report failure at the end. */
success = err;
printk (KERN_ERR
"JBD: IO error %d recovering "
"block %llu in log\n",
err, io_block);
} else {
unsigned long long blocknr;
J_ASSERT(obh != NULL);
blocknr = read_tag_block(tag_bytes,
tag);
/* If the block has been
* revoked, then we're all done
* here. */
if (journal_test_revoke
(journal, blocknr,
next_commit_ID)) {
brelse(obh);
++info->nr_revoke_hits;
goto skip_write;
}
/* Find a buffer for the new
* data being restored */
nbh = __getblk(journal->j_fs_dev,
blocknr,
journal->j_blocksize);
if (nbh == NULL) {
printk(KERN_ERR
"JBD: Out of memory "
"during recovery.\n");
err = -ENOMEM;
brelse(bh);
brelse(obh);
goto failed;
}
lock_buffer(nbh);
memcpy(nbh->b_data, obh->b_data,
journal->j_blocksize);
if (flags & JFS_FLAG_ESCAPE) {
journal_header_t *header;
header = (journal_header_t *) &nbh->b_data[0];
header->h_magic = cpu_to_be32(JFS_MAGIC_NUMBER);
}
BUFFER_TRACE(nbh, "marking dirty");
set_buffer_uptodate(nbh);
mark_buffer_dirty(nbh);
BUFFER_TRACE(nbh, "marking uptodate");
++info->nr_replays;
/* ll_rw_block(WRITE, 1, &nbh); */
unlock_buffer(nbh);
brelse(obh);
brelse(nbh);
}
skip_write:
tagp += tag_bytes;
if (!(flags & JFS_FLAG_SAME_UUID))
tagp += 16;
if (flags & JFS_FLAG_LAST_TAG)
break;
}
brelse(bh);
continue;
case JFS_COMMIT_BLOCK:
jbd_debug(3, "Commit block for #%u found\n",
next_commit_ID);
/* How to differentiate between interrupted commit
* and journal corruption ?
*
* {nth transaction}
* Checksum Verification Failed
* |
* ____________________
* | |
* async_commit sync_commit
* | |
* | GO TO NEXT "Journal Corruption"
* | TRANSACTION
* |
* {(n+1)th transanction}
* |
* _______|______________
* | |
* Commit block found Commit block not found
* | |
* "Journal Corruption" |
* _____________|_________
* | |
* nth trans corrupt OR nth trans
* and (n+1)th interrupted interrupted
* before commit block
* could reach the disk.
* (Cannot find the difference in above
* mentioned conditions. Hence assume
* "Interrupted Commit".)
*/
/* Found an expected commit block: if checksums
* are present verify them in PASS_SCAN; else not
* much to do other than move on to the next sequence
* number. */
if (pass == PASS_SCAN &&
JFS_HAS_COMPAT_FEATURE(journal,
JFS_FEATURE_COMPAT_CHECKSUM)) {
int chksum_err, chksum_seen;
struct commit_header *cbh =
(struct commit_header *)bh->b_data;
unsigned found_chksum =
be32_to_cpu(cbh->h_chksum[0]);
chksum_err = chksum_seen = 0;
jbd_debug(3, "Checksums %x %x\n",
crc32_sum, found_chksum);
if (info->end_transaction) {
journal->j_failed_commit =
info->end_transaction;
brelse(bh);
break;
}
if (crc32_sum == found_chksum &&
cbh->h_chksum_type == JBD2_CRC32_CHKSUM &&
cbh->h_chksum_size ==
JBD2_CRC32_CHKSUM_SIZE)
chksum_seen = 1;
else if (!(cbh->h_chksum_type == 0 &&
cbh->h_chksum_size == 0 &&
found_chksum == 0 &&
!chksum_seen))
/*
* If fs is mounted using an old kernel and then
* kernel with journal_chksum is used then we
* get a situation where the journal flag has
* checksum flag set but checksums are not
* present i.e chksum = 0, in the individual
* commit blocks.
* Hence to avoid checksum failures, in this
* situation, this extra check is added.
*/
chksum_err = 1;
if (chksum_err) {
info->end_transaction = next_commit_ID;
jbd_debug(1, "Checksum_err %x %x\n",
crc32_sum, found_chksum);
if (!JFS_HAS_INCOMPAT_FEATURE(journal,
JFS_FEATURE_INCOMPAT_ASYNC_COMMIT)){
journal->j_failed_commit =
next_commit_ID;
brelse(bh);
break;
}
}
crc32_sum = ~0;
}
brelse(bh);
next_commit_ID++;
continue;
case JFS_REVOKE_BLOCK:
/* If we aren't in the REVOKE pass, then we can
* just skip over this block. */
if (pass != PASS_REVOKE) {
brelse(bh);
continue;
}
err = scan_revoke_records(journal, bh,
next_commit_ID, info);
brelse(bh);
if (err)
goto failed;
continue;
default:
jbd_debug(3, "Unrecognised magic %d, end of scan.\n",
blocktype);
brelse(bh);
goto done;
}
}
done:
/*
* We broke out of the log scan loop: either we came to the
* known end of the log or we found an unexpected block in the
* log. If the latter happened, then we know that the "current"
* transaction marks the end of the valid log.
*/
if (pass == PASS_SCAN) {
if (!info->end_transaction)
info->end_transaction = next_commit_ID;
} else {
/* It's really bad news if different passes end up at
* different places (but possible due to IO errors). */
if (info->end_transaction != next_commit_ID) {
printk (KERN_ERR "JBD: recovery pass %d ended at "
"transaction %u, expected %u\n",
pass, next_commit_ID, info->end_transaction);
if (!success)
success = -EIO;
}
}
return success;
failed:
return err;
}
static errcode_t walk_journal(ocfs2_filesys *fs, int slot,
struct journal_info *ji, char *buf, int recover)
{
errcode_t err, ret = 0;
uint32_t next_seq;
uint64_t next_block, nr;
journal_superblock_t *jsb = ji->ji_jsb;
journal_header_t jh;
next_seq = jsb->s_sequence;
next_block = jsb->s_start;
/* s_start == 0 when we have nothing to do */
if (next_block == 0)
return 0;
/* ret is set when bad tags are seen in the first scan and when there
* are io errors in the recovery scan. Only stop walking the journal
* when bad tags are seen in the first scan. */
while(recover || !ret) {
verbosef("next_seq %"PRIu32" final_seq %"PRIu32" next_block "
"%"PRIu64"\n", next_seq, ji->ji_final_seq,
next_block);
if (recover && seq_geq(next_seq, ji->ji_final_seq))
break;
/* only mark the blocks used on the first pass */
err = read_journal_block(fs, ji, next_block, buf, !recover);
if (err) {
ret = err;
break;
}
next_block = jwrap(jsb, next_block + 1);
memcpy(&jh, buf, sizeof(jh));
jh.h_magic = be32_to_cpu(jh.h_magic);
jh.h_blocktype = be32_to_cpu(jh.h_blocktype);
jh.h_sequence = be32_to_cpu(jh.h_sequence);
verbosef("jh magic %x\n", jh.h_magic);
if (jh.h_magic != JBD2_MAGIC_NUMBER)
break;
verbosef("jh block %x\n", jh.h_blocktype);
verbosef("jh seq %"PRIu32"\n", jh.h_sequence);
if (jh.h_sequence != next_seq)
break;
switch(jh.h_blocktype) {
case JBD2_DESCRIPTOR_BLOCK:
verbosef("found a desc type %x\n", jh.h_blocktype);
/* replay the blocks described in the desc block */
if (recover) {
err = replay_blocks(fs, ji, buf, next_seq,
&next_block);
if (err)
ret = err;
continue;
}
/* just record the blocks as used and carry on */
err = count_tags(fs, jsb, buf, &nr);
if (err)
ret = err;
else
next_block = jwrap(jsb, next_block + nr);
break;
case JBD2_COMMIT_BLOCK:
verbosef("found a commit type %x\n", jh.h_blocktype);
next_seq++;
break;
case JBD2_REVOKE_BLOCK:
verbosef("found a revoke type %x\n", jh.h_blocktype);
add_revoke_records(ji, buf, jsb->s_blocksize,
next_seq);
break;
default:
verbosef("unknown type %x\n", jh.h_blocktype);
break;
}
}
verbosef("done scanning with seq %"PRIu32"\n", next_seq);
if (!recover) {
ji->ji_set_final_seq = 1;
ji->ji_final_seq = next_seq;
} else if (ji->ji_final_seq != next_seq) {
printf("Replaying slot %d's journal stopped at seq %"PRIu32" "
"but an initial scan indicated that it should have "
"stopped at seq %"PRIu32"\n", ji->ji_slot, next_seq,
ji->ji_final_seq);
if (ret == 0)
err = OCFS2_ET_IO;
}
return ret;
}
errcode_t journal_find_head(journal_t *journal)
{
unsigned int next_commit_ID;
blk64_t next_log_block, head_block;
int err;
journal_superblock_t *sb;
journal_header_t *tmp;
struct buffer_head *bh;
unsigned int sequence;
int blocktype;
/*
* First thing is to establish what we expect to find in the log
* (in terms of transaction IDs), and where (in terms of log
* block offsets): query the superblock.
*/
sb = journal->j_superblock;
next_commit_ID = ext2fs_be32_to_cpu(sb->s_sequence);
next_log_block = ext2fs_be32_to_cpu(sb->s_start);
head_block = next_log_block;
if (next_log_block == 0)
return 0;
bh = getblk(journal->j_dev, 0, journal->j_blocksize);
if (bh == NULL)
return ENOMEM;
/*
* Now we walk through the log, transaction by transaction,
* making sure that each transaction has a commit block in the
* expected place. Each complete transaction gets replayed back
* into the main filesystem.
*/
while (1) {
dbg_printf("Scanning for sequence ID %u at %lu/%lu\n",
next_commit_ID, (unsigned long)next_log_block,
journal->j_last);
/* Skip over each chunk of the transaction looking
* either the next descriptor block or the final commit
* record. */
err = journal_bmap(journal, next_log_block, &bh->b_blocknr);
if (err)
goto err;
mark_buffer_uptodate(bh, 0);
ll_rw_block(READ, 1, &bh);
err = bh->b_err;
if (err)
goto err;
next_log_block++;
wrap(journal, next_log_block);
/* What kind of buffer is it?
*
* If it is a descriptor block, check that it has the
* expected sequence number. Otherwise, we're all done
* here. */
tmp = (journal_header_t *)bh->b_data;
if (tmp->h_magic != ext2fs_cpu_to_be32(JFS_MAGIC_NUMBER)) {
dbg_printf("JBD2: wrong magic 0x%x\n", tmp->h_magic);
goto err;
}
blocktype = ext2fs_be32_to_cpu(tmp->h_blocktype);
sequence = ext2fs_be32_to_cpu(tmp->h_sequence);
dbg_printf("Found magic %d, sequence %d\n",
blocktype, sequence);
if (sequence != next_commit_ID) {
dbg_printf("JBD2: Wrong sequence %d (wanted %d)\n",
sequence, next_commit_ID);
goto err;
}
/* OK, we have a valid descriptor block which matches
* all of the sequence number checks. What are we going
* to do with it? That depends on the pass... */
switch (blocktype) {
case JFS_DESCRIPTOR_BLOCK:
next_log_block += count_tags(journal, bh->b_data);
wrap(journal, next_log_block);
continue;
case JFS_COMMIT_BLOCK:
head_block = next_log_block;
next_commit_ID++;
continue;
case JFS_REVOKE_BLOCK:
continue;
default:
dbg_printf("Unrecognised magic %d, end of scan.\n",
blocktype);
err = -EINVAL;
goto err;
}
}
err:
if (err == 0) {
dbg_printf("head seq=%d blk=%llu\n", next_commit_ID,
head_block);
journal->j_transaction_sequence = next_commit_ID;
journal->j_head = head_block;
}
brelse(bh);
return err;
}
int main(int argc, char **argv)
{
if (argc < 4)
errx(1,
"usage\t:%s <bam> <split out> <discord out> (optional #threads)",
argv[0]);
char *bam_file_name = argv[1];
char *split_file_name = argv[2];
char *disc_file_name = argv[3];
int threads = 2;
if (argc == 5) {
threads = atoi(argv[4]);
}
samFile *disc = sam_open(disc_file_name, "wb");
samFile *split = sam_open(split_file_name, "wb");
samFile *in = sam_open(bam_file_name, "rb");
if(in == NULL)
errx(1, "Unable to open BAM/SAM file.");
// TODO: handle cram.
if (threads > 1) {
bgzf_mt(in->fp.bgzf, threads, 256);
}
hts_idx_t *idx = sam_index_load(in, bam_file_name);
if(idx == NULL)
errx(1,"Unable to open BAM/SAM index.");
bam_hdr_t *hdr = sam_hdr_read(in);
int r = sam_hdr_write(disc, hdr);
r = sam_hdr_write(split, hdr);
bam1_t *aln = bam_init1();
int ret;
while(ret = sam_read1(in, hdr, aln) >= 0) {
if (((aln->core.flag) & 1294) == 0)
r = sam_write1(disc, hdr, aln);
uint8_t *sa = bam_aux_get(aln, "SA");
if (sa != 0) {
char *sa_tag = strdup(bam_aux2Z(sa));
if ( count_tags(sa_tag) == 1) {
char *chrm, strand, *cigar;
uint32_t pos;
split_sa_tag(sa_tag,
&chrm,
&pos,
&strand,
&cigar);
struct line sa, al;
calcOffsets(cigar,
pos,
strand,
&sa);
sa.chrm = chrm;
sa.strand = strand;
calcAlnOffsets(bam_get_cigar(aln),
aln->core.n_cigar,
aln->core.pos,
bam_is_rev(aln) ? '-' : '+',
&al);
al.chrm = hdr->target_name[aln->core.tid];
al.strand = bam_is_rev(aln) ? '-' : '+';
struct line *left = &al, *right = &sa;
if (left->SQO > right->SQO) {
left = &sa;
right = &al;
}
int overlap = MAX(1 + MIN(left->EQO, right->EQO) -
MAX(left->SQO, right->SQO), 0);
int alen1 = 1 + left->EQO - left->SQO;
int alen2 = 1 + right->EQO - right->SQO;
int mno = MIN(alen1-overlap, alen2-overlap);
if (mno < MIN_NON_OVERLAP)
continue;
if ( (strcmp(left->chrm, right->chrm) == 0) &&
(left->strand == right->strand) ) {
int leftDiag, rightDiag, insSize;
if (left->strand == '-') {
leftDiag = left->rapos - left->sclip;
rightDiag = (right->rapos + right->raLen) -
(right->sclip + right->qaLen);
insSize = rightDiag - leftDiag;
} else {
leftDiag = (left->rapos + left->raLen) -
(left->sclip + left->qaLen);
rightDiag = right->rapos - right->sclip;
insSize = leftDiag - rightDiag;
}
int desert = right->SQO - left->EQO - 1;
if ((abs(insSize) < MIN_INDEL_SIZE) ||
((desert > 0) && (
(desert - (int)MAX(0, insSize)) >
MAX_UNMAPPED_BASES)))
continue;
}
char *qname = bam_get_qname(aln);
if ((aln->core.flag & 64) == 64)
qname[0] = 'A';
else
qname[0] = 'B';
r = sam_write1(split, hdr, aln);
}
free(sa_tag);
}
}
bam_destroy1(aln);
hts_idx_destroy(idx);
bam_hdr_destroy(hdr);
sam_close(in);
sam_close(disc);
sam_close(split);
if(ret < -1) {
errx(1, "lumpy_filter: error reading bam: %s\n", bam_file_name);
}
}
static int do_one_pass(journal_t *journal,
struct recovery_info *info, enum passtype pass)
{
unsigned int first_commit_ID, next_commit_ID;
unsigned long next_log_block;
int err, success = 0;
journal_superblock_t * sb;
journal_header_t * tmp;
struct buffer_head * bh;
unsigned int sequence;
int blocktype;
int tag_bytes = journal_tag_bytes(journal);
__u32 crc32_sum = ~0;
sb = journal->j_superblock;
next_commit_ID = be32_to_cpu(sb->s_sequence);
next_log_block = be32_to_cpu(sb->s_start);
first_commit_ID = next_commit_ID;
if (pass == PASS_SCAN)
info->start_transaction = first_commit_ID;
jbd_debug(1, "Starting recovery pass %d\n", pass);
while (1) {
int flags;
char * tagp;
journal_block_tag_t * tag;
struct buffer_head * obh;
struct buffer_head * nbh;
cond_resched();
if (pass != PASS_SCAN)
if (tid_geq(next_commit_ID, info->end_transaction))
break;
jbd_debug(2, "Scanning for sequence ID %u at %lu/%lu\n",
next_commit_ID, next_log_block, journal->j_last);
jbd_debug(3, "JBD2: checking block %ld\n", next_log_block);
err = jread(&bh, journal, next_log_block);
if (err)
goto failed;
next_log_block++;
wrap(journal, next_log_block);
tmp = (journal_header_t *)bh->b_data;
if (tmp->h_magic != cpu_to_be32(JBD2_MAGIC_NUMBER)) {
brelse(bh);
break;
}
blocktype = be32_to_cpu(tmp->h_blocktype);
sequence = be32_to_cpu(tmp->h_sequence);
jbd_debug(3, "Found magic %d, sequence %d\n",
blocktype, sequence);
if (sequence != next_commit_ID) {
brelse(bh);
break;
}
switch(blocktype) {
case JBD2_DESCRIPTOR_BLOCK:
if (pass != PASS_REPLAY) {
if (pass == PASS_SCAN &&
JBD2_HAS_COMPAT_FEATURE(journal,
JBD2_FEATURE_COMPAT_CHECKSUM) &&
!info->end_transaction) {
if (calc_chksums(journal, bh,
&next_log_block,
&crc32_sum)) {
put_bh(bh);
break;
}
put_bh(bh);
continue;
}
next_log_block += count_tags(journal, bh);
wrap(journal, next_log_block);
put_bh(bh);
continue;
}
tagp = &bh->b_data[sizeof(journal_header_t)];
while ((tagp - bh->b_data + tag_bytes)
<= journal->j_blocksize) {
unsigned long io_block;
tag = (journal_block_tag_t *) tagp;
flags = be32_to_cpu(tag->t_flags);
io_block = next_log_block++;
wrap(journal, next_log_block);
err = jread(&obh, journal, io_block);
if (err) {
success = err;
printk(KERN_ERR
"JBD2: IO error %d recovering "
"block %ld in log\n",
err, io_block);
} else {
unsigned long long blocknr;
J_ASSERT(obh != NULL);
blocknr = read_tag_block(tag_bytes,
tag);
if (jbd2_journal_test_revoke
(journal, blocknr,
next_commit_ID)) {
brelse(obh);
++info->nr_revoke_hits;
goto skip_write;
}
nbh = __getblk(journal->j_fs_dev,
blocknr,
journal->j_blocksize);
if (nbh == NULL) {
printk(KERN_ERR
"JBD2: Out of memory "
"during recovery.\n");
err = -ENOMEM;
brelse(bh);
brelse(obh);
goto failed;
}
lock_buffer(nbh);
memcpy(nbh->b_data, obh->b_data,
journal->j_blocksize);
if (flags & JBD2_FLAG_ESCAPE) {
*((__be32 *)nbh->b_data) =
cpu_to_be32(JBD2_MAGIC_NUMBER);
}
BUFFER_TRACE(nbh, "marking dirty");
set_buffer_uptodate(nbh);
mark_buffer_dirty(nbh);
BUFFER_TRACE(nbh, "marking uptodate");
++info->nr_replays;
unlock_buffer(nbh);
brelse(obh);
brelse(nbh);
}
skip_write:
tagp += tag_bytes;
if (!(flags & JBD2_FLAG_SAME_UUID))
tagp += 16;
if (flags & JBD2_FLAG_LAST_TAG)
break;
}
brelse(bh);
continue;
case JBD2_COMMIT_BLOCK:
if (pass == PASS_SCAN &&
JBD2_HAS_COMPAT_FEATURE(journal,
JBD2_FEATURE_COMPAT_CHECKSUM)) {
int chksum_err, chksum_seen;
struct commit_header *cbh =
(struct commit_header *)bh->b_data;
unsigned found_chksum =
be32_to_cpu(cbh->h_chksum[0]);
chksum_err = chksum_seen = 0;
if (info->end_transaction) {
journal->j_failed_commit =
info->end_transaction;
brelse(bh);
break;
}
if (crc32_sum == found_chksum &&
cbh->h_chksum_type == JBD2_CRC32_CHKSUM &&
cbh->h_chksum_size ==
JBD2_CRC32_CHKSUM_SIZE)
chksum_seen = 1;
else if (!(cbh->h_chksum_type == 0 &&
cbh->h_chksum_size == 0 &&
found_chksum == 0 &&
!chksum_seen))
chksum_err = 1;
if (chksum_err) {
info->end_transaction = next_commit_ID;
if (!JBD2_HAS_INCOMPAT_FEATURE(journal,
JBD2_FEATURE_INCOMPAT_ASYNC_COMMIT)){
journal->j_failed_commit =
next_commit_ID;
brelse(bh);
break;
}
}
crc32_sum = ~0;
}
brelse(bh);
next_commit_ID++;
continue;
case JBD2_REVOKE_BLOCK:
if (pass != PASS_REVOKE) {
brelse(bh);
continue;
}
err = scan_revoke_records(journal, bh,
next_commit_ID, info);
brelse(bh);
if (err)
goto failed;
continue;
default:
jbd_debug(3, "Unrecognised magic %d, end of scan.\n",
blocktype);
brelse(bh);
goto done;
}
}
done:
if (pass == PASS_SCAN) {
if (!info->end_transaction)
info->end_transaction = next_commit_ID;
} else {
if (info->end_transaction != next_commit_ID) {
printk(KERN_ERR "JBD2: recovery pass %d ended at "
"transaction %u, expected %u\n",
pass, next_commit_ID, info->end_transaction);
if (!success)
success = -EIO;
}
}
return success;
failed:
return err;
}
