static IntChunk_ID get_second_mate_index
(
TChunkMesg chunks[],
const Tfragment frags[],
const Tedge edges[],
const IntChunk_ID sentinel,
const IntChunk_ID b_index,
const IntChunk_ID other_index,
const float cgb_unique_cutoff
)
{
int i;
const AChunkMesg * chunk = GetVA_AChunkMesg(chunks,O2CI(b_index));
IntChunk_ID mate_index = sentinel;
IntChunk_ID temp_index = sentinel;
const int b_side = O2S(b_index);
const int32 raw_degree =
(b_side == 1) ? chunk->b_degree_raw : chunk->a_degree_raw;
const IntEdge_ID edge_id = (b_side == 1) ? chunk->b_list_raw : chunk->a_list_raw;
// loop over the edges
for( i = 0; i < raw_degree; i++ )
{
const Tnes edge = get_nes_edge( edges, edge_id + i );
// if it's the right kind of edge
if( AS_CGB_INTERCHUNK_EDGE == edge )
{
// get the chunk index
IntChunk_ID temp_chunk = get_chunk_index( chunks, frags,
edges, edge_id + i );
int temp_suffix = get_chunk_suffix( chunks, frags,
edges, edge_id + i );
temp_index = CIS2O( temp_chunk, temp_suffix);
if( (temp_index != other_index )
#ifdef UUNIQUE
&&
(GetVA_AChunkMesg( chunks, temp_chunk )->coverage_stat >= cgb_unique_cutoff)
#endif
)
{
if( mate_index == sentinel )
{
// if it's the first non-other index, set the mate_index
mate_index = temp_index;
}
else if( temp_index != mate_index )
{
// it's a third mate, return sentinel
return sentinel;
}
}
}
}
// return either unique second mate or sentinel
return mate_index;
}
/*
* __async_compact --
* WT_ASYNC_OP->compact implementation for op handles.
*/
static int
__async_compact(WT_ASYNC_OP *asyncop)
{
WT_ASYNC_OP_IMPL *op;
WT_DECL_RET;
WT_SESSION_IMPL *session;
op = (WT_ASYNC_OP_IMPL *)asyncop;
ASYNCOP_API_CALL(O2C(op), session, compact);
WT_STAT_FAST_CONN_INCR(O2S(op), async_op_compact);
WT_ERR(__async_op_wrap(op, WT_AOP_COMPACT));
err: API_END_RET(session, ret);
}
/*
* __async_search --
* WT_ASYNC_OP->search implementation for op handles.
*/
static int
__async_search(WT_ASYNC_OP *asyncop)
{
WT_ASYNC_OP_IMPL *op;
WT_DECL_RET;
WT_SESSION_IMPL *session;
op = (WT_ASYNC_OP_IMPL *)asyncop;
ASYNCOP_API_CALL(O2C(op), session, search);
WT_STAT_CONN_INCR(O2S(op), async_op_search);
WT_ERR(__async_op_wrap(op, WT_AOP_SEARCH));
err: API_END_RET(session, ret);
}
static IntChunk_ID get_lone_mate_index
(
TChunkMesg chunks[],
const Tfragment frags[],
const Tedge edges[],
const IntChunk_ID sentinel,
const IntChunk_ID b_index,
const float cgb_unique_cutoff
)
{
int i;
IntChunk_ID mate_index = sentinel;
const AChunkMesg * chunk = GetVA_AChunkMesg( chunks, O2CI( b_index ) );
const int b_side = O2S( b_index );
const int32 raw_degree =
(b_side == 1) ? chunk->b_degree_raw : chunk->a_degree_raw;
const IntEdge_ID edge_id = (b_side == 1)
? chunk->b_list_raw : chunk->a_list_raw;
// loop over the edges
for( i = 0; i < raw_degree; i++ )
{
const Tnes edge = get_nes_edge( edges, edge_id + i );
// if it's the right kind of edge
if( AS_CGB_INTERCHUNK_EDGE == edge )
{
const IntChunk_ID temp_index = get_chunk_index( chunks, frags, edges, edge_id + i );
if(
(mate_index == sentinel )
#ifdef UUNIQUE
&&
(GetVA_AChunkMesg( chunks, temp_index )->coverage_stat >= cgb_unique_cutoff )
#endif
) {
// first mate found
mate_index =
CIS2O( get_chunk_index( chunks, frags, edges, edge_id + i ),
get_chunk_suffix( chunks, frags, edges, edge_id + i ) );
}
else if( O2CI( mate_index ) !=
get_chunk_index( chunks, frags, edges, edge_id + i ) ) {
// it's a second mate, return sentinel
return sentinel;
}
}
}
// return either lone mate or sentinel
return mate_index;
}
/*
* __async_set_key --
* WT_ASYNC_OP->set_key implementation for op handles.
*/
static void
__async_set_key(WT_ASYNC_OP *asyncop, ...)
{
WT_CURSOR *c;
va_list ap;
c = &asyncop->c;
va_start(ap, asyncop);
__wt_cursor_set_keyv(c, c->flags, ap);
if (!WT_DATA_IN_ITEM(&c->key) && !WT_CURSOR_RECNO(c))
c->saved_err = __wt_buf_set(
O2S((WT_ASYNC_OP_IMPL *)asyncop),
&c->key, c->key.data, c->key.size);
va_end(ap);
}
/*
* __async_set_value --
* WT_ASYNC_OP->set_value implementation for op handles.
*/
static void
__async_set_value(WT_ASYNC_OP *asyncop, ...)
{
WT_CURSOR *c;
va_list ap;
c = &asyncop->c;
va_start(ap, asyncop);
__wt_cursor_set_valuev(c, ap);
/* Copy the data, if it is pointing at data elsewhere. */
if (!WT_DATA_IN_ITEM(&c->value))
c->saved_err = __wt_buf_set(
O2S((WT_ASYNC_OP_IMPL *)asyncop),
&c->value, c->value.data, c->value.size);
va_end(ap);
}
static int is_hanging_chunk_end
(
TChunkMesg chunks[],
const Tfragment frags[],
const Tedge edges[],
const IntChunk_ID b_index
)
{
int i;
const AChunkMesg * chunk = GetVA_AChunkMesg( chunks, O2CI( b_index ) );
const int b_side = O2S( b_index );
const int32 raw_degree =
(b_side == 1) ? chunk->b_degree_raw : chunk->a_degree_raw;
const IntEdge_ID edge_id = (b_side == 1)
? chunk->b_list_raw : chunk->a_list_raw;
// loop over the edges
for( i = 0; i < raw_degree; i++ )
{
const Tnes edge = get_nes_edge( edges, edge_id + i );
switch(edge) {
// if it's any dovetail edge
case AS_CGB_INTERCHUNK_EDGE:
case AS_CGB_INTRACHUNK_EDGE:
case AS_CGB_TOUCHES_CONTAINED_EDGE:
case AS_CGB_BETWEEN_CONTAINED_EDGE:
//case AS_CGB_TOUCHES_CRAPPY_EDGE:
case AS_CGB_MARKED_BY_BRANCH_DVT:
case AS_CGB_REMOVED_BY_THRESHOLD_DVT:
case AS_CGB_REMOVED_BY_TRANSITIVITY_DVT:
return FALSE;
default:
break;
}
}
return TRUE;
}
uint32 count_crappies
(
const char * const crappies_report_filename,
const float cgb_unique_cutoff,
const Tfragment frags[],
const Tedge edges[],
TChunkFrag chunk_frags[],
TChunkMesg chunks[]
)
{
uint32 num_crappies = 0;
const IntChunk_ID num_chunks = GetNumVA_AChunkMesg( chunks );
const IntChunk_ID sentinel = CIS2O( num_chunks, 0 );
IntChunk_ID schunk;
int ssuffix;
FILE * fp_crappies;
fp_crappies = fopen( crappies_report_filename, "w" );
if( fp_crappies == NULL )
{
fprintf( stderr, "Failed to open file %s for writing\n",
crappies_report_filename );
return 0;
}
// loop over chunks
for( schunk = 0; schunk < num_chunks; schunk++ )
for( ssuffix = 0; ssuffix < 2; ssuffix++ )
{
const IntChunk_ID s_index = CIS2O(schunk,ssuffix);
IntChunk_ID c_index = sentinel;
IntChunk_ID d_index = sentinel;
assert( schunk == O2CI(s_index) );
// s must consist of exactly one fragment
if( (GetVA_AChunkMesg( chunks, O2CI(s_index)))->num_frags != 1 )
continue;
// s must have exactly zero b-mates
if( FALSE == is_hanging_chunk_end( chunks, frags, edges, O2O(s_index)) )
continue;
// s must have exactly one a-mate (c)
c_index =
get_lone_mate_index( chunks, frags, edges, sentinel, s_index, cgb_unique_cutoff );
if( c_index == sentinel )
continue;
// c must have exactly two b-mates (s,d)
d_index =
get_second_mate_index( chunks, frags, edges,
sentinel, c_index, s_index, cgb_unique_cutoff );
if( d_index == sentinel )
continue;
// d must have exactly one a-mate (c)
if( get_lone_mate_index( chunks, frags, edges,
sentinel, d_index, cgb_unique_cutoff ) != c_index )
continue;
// if here, it's a crappy fragment.
if( num_crappies == 0 )
{
fprintf( fp_crappies,
"# si is the chunk consisting of single crappy fragment\n" );
fprintf( fp_crappies,
"# ci & di are split by prefix/suffix of s\n" );
fprintf( fp_crappies, "#\n" );
fprintf( fp_crappies, "# (s)\n" );
fprintf( fp_crappies, "# /\n" );
fprintf( fp_crappies, "# /\n" );
fprintf( fp_crappies, "# /\n" );
fprintf( fp_crappies, "# \\ / /\n" );
fprintf( fp_crappies, "# -(c)---------------(d)-\n" );
fprintf( fp_crappies, "# / \\\n" );
fprintf( fp_crappies, "#\n" );
fprintf( fp_crappies,
"# "
"(si,ss) (ci,cs) (di,ds)\n");
fprintf( fp_crappies,
"#-------------------------------------------------"
"----------------------------------------\n" );
}
num_crappies++;
fprintf( fp_crappies,
"(%10" F_IIDP ",%1d) (%10" F_IIDP ",%1d) (%10" F_IIDP ",%1d)\n",
O2CI(s_index ), //s_chunk->iaccession,
O2S( s_index ),
O2CI(c_index ), //c_chunk->iaccession,
O2S( c_index ),
O2CI(d_index ), //d_chunk->iaccession
O2S( d_index )
);
}
fclose( fp_crappies );
return num_crappies;
}
uint32 count_chimeras
(
const char * const chimeras_report_filename,
const float cgb_unique_cutoff,
const Tfragment frags[],
const Tedge edges[],
TChunkFrag chunk_frags[],
TChunkMesg chunks[]
)
{
uint32 num_chimeras = 0;
const IntChunk_ID num_chunks = GetNumVA_AChunkMesg( chunks );
const IntChunk_ID sentinel = CIS2O( num_chunks, 0 );
IntChunk_ID schunk;
FILE * fp_chimeras;
fp_chimeras = fopen( chimeras_report_filename, "w" );
if( fp_chimeras == NULL )
{
fprintf( stderr, "Failed to open file %s for writing\n",
chimeras_report_filename );
return 0;
}
// loop over chunks
for( schunk = 0; schunk < num_chunks; schunk++ )
{
const IntChunk_ID s_index = CIS2O(schunk,0);
IntChunk_ID a_index = sentinel;
IntChunk_ID b_index = sentinel;
IntChunk_ID c_index = sentinel;
IntChunk_ID d_index = sentinel;
assert( schunk == O2CI(s_index) );
// s must consist of exactly one fragment
if( (GetVA_AChunkMesg( chunks, O2CI(s_index)))->num_frags != 1 )
continue;
// s must have exactly one b-mate (b)
b_index =
get_lone_mate_index( chunks, frags, edges, sentinel, O2O(s_index), cgb_unique_cutoff );
if( b_index == sentinel )
continue;
// s must have exactly one a-mate (c)
c_index =
get_lone_mate_index( chunks, frags, edges, sentinel, s_index, cgb_unique_cutoff );
if( c_index == sentinel )
continue;
// b != c (chunk within a chunk?)
if( O2CI( c_index ) == O2CI( b_index ) )
continue;
// b must have exactly two a-mates (s,a)
a_index =
get_second_mate_index( chunks, frags, edges,
sentinel, b_index, O2O(s_index), cgb_unique_cutoff );
if( a_index == sentinel )
continue;
// c must have exactly two b-mates (s,d)
d_index =
get_second_mate_index( chunks, frags, edges,
sentinel, c_index, s_index, cgb_unique_cutoff );
if( d_index == sentinel )
continue;
// a !=d (quadrilateral, not a Z)
if( O2CI( a_index ) == O2CI( d_index ) )
continue;
// a != c (quadrilateral, not a Z)
if( O2CI( a_index ) == O2CI( c_index ) )
continue;
// b != d (quadrilateral, not a Z)
if( O2CI( b_index ) == O2CI( d_index ) )
continue;
// a must have exactly one b-mate (b)
if( get_lone_mate_index( chunks, frags, edges,
sentinel, a_index, cgb_unique_cutoff ) != b_index )
continue;
// d must have exactly one a-mate (c)
if( get_lone_mate_index( chunks, frags, edges,
sentinel, d_index, cgb_unique_cutoff ) != c_index )
continue;
// if here, it's a chimeric fragment
if( num_chimeras == 0 )
{
fprintf( fp_chimeras,
"# s = index of chunk consisting of single chimeric fragment\n" );
fprintf( fp_chimeras,
"# a & b are split by suffix of s, c & d are split by prefix of s\n" );
fprintf( fp_chimeras,
"# a2b is 1 if suffix of a has edge with b, and so on.\n" );
fprintf( fp_chimeras, "#\n" );
fprintf( fp_chimeras, "# \\ /\n" );
fprintf( fp_chimeras, "# -(a)---------------(b)-\n" );
fprintf( fp_chimeras, "# / / \\\n" );
fprintf( fp_chimeras, "# /\n" );
fprintf( fp_chimeras, "# /\n" );
fprintf( fp_chimeras, "# /\n" );
fprintf( fp_chimeras, "# (s)\n" );
fprintf( fp_chimeras, "# /\n" );
fprintf( fp_chimeras, "# /\n" );
fprintf( fp_chimeras, "# /\n" );
fprintf( fp_chimeras, "# \\ / /\n" );
fprintf( fp_chimeras, "# -(c)---------------(d)-\n" );
fprintf( fp_chimeras, "# / \\\n" );
fprintf( fp_chimeras, "#\n" );
fprintf( fp_chimeras,
"# "
"si : (ai,as) (bi,bs) (ci,cs) (di,ds)\n");
fprintf( fp_chimeras,
"#-------------------------------------------------"
"----------------------------------------\n" );
}
num_chimeras++;
fprintf( fp_chimeras,
"%10" F_IIDP " : (%10" F_IIDP ",%1d) (%10" F_IIDP ",%1d) (%10" F_IIDP ",%1d) (%10" F_IIDP ",%1d)\n",
O2CI(s_index ), //s_chunk->iaccession,
O2CI(a_index ), //a_chunk->iaccession,
O2S( a_index ),
O2CI(b_index ), //b_chunk->iaccession,
O2S( b_index ),
O2CI(c_index ), //c_chunk->iaccession,
O2S( c_index ),
O2CI(d_index ), //d_chunk->iaccession
O2S( d_index )
);
}
fclose( fp_chimeras );
return num_chimeras;
}
/*
* __async_op_wrap --
* Common wrapper for all async operations.
*/
static int
__async_op_wrap(WT_ASYNC_OP_IMPL *op, WT_ASYNC_OPTYPE type)
{
op->optype = type;
return (__wt_async_op_enqueue(O2S(op), op));
}