static rc_t walk_ref_iter( ReferenceIterator *ref_iter,
bool skip_empty,
bool nodebug )
{
rc_t rc = 0;
while( rc == 0 )
{
struct ReferenceObj const * refobj;
INSDC_coord_zero first_pos;
INSDC_coord_len len;
rc = ReferenceIteratorNextReference( ref_iter, &first_pos, &len, &refobj );
if ( rc == 0 && refobj != NULL )
{
const char *name;
rc = ReferenceObj_SeqId( refobj, &name );
if ( rc != 0 )
LOGERR( klogInt, rc, "ReferenceObj_SeqId() failed" );
else
{
OUTMSG(( "walking ref-iter on reference: >%s< ( from %u to %u )\n",
name, first_pos, first_pos + len - 1 ));
rc = walk_ref_iter_reference( ref_iter, refobj, skip_empty, nodebug );
}
}
}
if ( GetRCState( rc ) == rcDone ) rc = 0;
return rc;
}
static rc_t walk_ref_iter_position( ReferenceIterator *ref_iter,
struct ReferenceObj const * refobj,
bool skip_empty,
bool nodebug )
{
INSDC_coord_zero pos;
uint32_t depth;
INSDC_4na_bin base;
rc_t rc = ReferenceIteratorPosition ( ref_iter, &pos, &depth, &base );
if ( rc != 0 )
{
if ( GetRCState( rc ) != rcDone )
LOGERR( klogInt, rc, "ReferenceIteratorNextPos() failed" );
}
else
{
rc_t rc1 = 0;
const char * reference_name = NULL;
char c = _4na_to_ascii( base, false );
rc = ReferenceObj_SeqId( refobj, &reference_name );
if ( rc == 0 )
{
OUTMSG(( "%s\t%u\t%c\t%u", reference_name, pos, c, depth ));
if ( depth > 0 )
{
const PlacementRecord *rec;
rc1 = ReferenceIteratorNextPlacement ( ref_iter, &rec );
if ( rc1 == 0 )
{
uint8_t qualities[ 4096 ];
uint32_t i = 0;
OUTMSG(( "\t" ));
while ( rc1 == 0 )
{
handle_base_pos( ref_iter, rec, &( qualities[ i++ ] ), nodebug );
rc1 = ReferenceIteratorNextPlacement ( ref_iter, &rec );
}
OUTMSG(( "\t" ));
for ( i = 0; i < depth; ++i )
{
char c = ( qualities[ i ] + 33 );
OUTMSG(( "%c", c ));
}
}
}
OUTMSG(( "\n" ));
}
if ( GetRCState( rc1 ) == rcDone ) rc1 = 0;
rc = rc1;
}
return rc;
}
static rc_t build_seq_id_tree( BSTree * tree, input_files * ifs )
{
rc_t rc = 0;
uint32_t i;
for ( i = 0; i < ifs->database_count && rc == 0; ++i )
{
input_database * id = VectorGet( &ifs->dbs, i );
if ( id != NULL )
{
uint32_t rcount;
rc = ReferenceList_Count( id->reflist, &rcount );
if ( rc == 0 && rcount > 0 )
{
uint32_t r_idx;
for ( r_idx = 0; r_idx < rcount && rc == 0; ++r_idx )
{
const ReferenceObj * ref_obj;
rc = ReferenceList_Get( id->reflist, &ref_obj, r_idx );
if ( rc == 0 && ref_obj != NULL )
{
const char * seqid;
rc = ReferenceObj_SeqId( ref_obj, &seqid );
if ( rc == 0 )
{
const char * name;
rc = ReferenceObj_Name( ref_obj, &name );
if ( rc == 0 )
{
INSDC_coord_len seq_len;
rc = ReferenceObj_SeqLength( ref_obj, &seq_len );
if ( rc == 0 )
{
seq_id_node * node = find_seq_id_node( tree, seqid );
if ( node != NULL )
{
if ( node->seq_len != seq_len )
rc = RC( rcApp, rcNoTarg, rcConstructing, rcData, rcInvalid );
}
else
rc = add_seq_id_node( tree, seqid, name, seq_len );
}
}
}
}
}
}
}
}
return rc;
}
static rc_t report_ref_obj( const VDBManager *vdb_mgr, VFSManager * vfs_mgr, const char * path, uint32_t idx,
const ReferenceObj* ref_obj, bool extended )
{
const char * s;
const char * seq_id;
INSDC_coord_len len;
bool circular, external;
int64_t start, stop;
rc_t rc = ReferenceObj_Name( ref_obj, &s );
if ( rc == 0 )
rc = KOutMsg( "\nREF[%u].Name = '%s'\n", idx, s );
if ( rc == 0 )
rc = ReferenceObj_SeqId( ref_obj, &seq_id );
if ( rc == 0 )
rc = KOutMsg( "REF[%u].SeqId = '%s'\n", idx, seq_id );
if ( rc == 0 )
rc = ReferenceObj_SeqLength( ref_obj, &len );
if ( rc == 0 )
rc = KOutMsg( "REF[%u].Length = %,u\n", idx, len );
if ( rc == 0 )
rc = ReferenceObj_Circular( ref_obj, &circular );
if ( rc == 0 )
rc = KOutMsg( "REF[%u].Circular = %s\n", idx, circular ? "yes" : "no" );
if ( rc == 0 )
rc = ReferenceObj_IdRange( ref_obj, &start, &stop );
if ( rc == 0 )
rc = KOutMsg( "REF[%u].IdRange = [%,lu]...[%,lu]\n", idx, start, stop );
if ( rc == 0 )
rc = ReferenceObj_External( ref_obj, &external, NULL );
if ( rc == 0 )
rc = KOutMsg( "REF[%u].Extern = %s\n", idx, external ? "yes" : "no" );
if ( rc == 0 && external )
{
rc = report_ref_loc( vdb_mgr, vfs_mgr, seq_id );
}
if ( rc == 0 && extended )
rc = report_ref_table2( ref_obj, start, stop );
return rc;
}
static rc_t ref_walker_walk_ref_range( struct ref_walker * self, ref_walker_data * rwd )
{
ReferenceIterator * ref_iter;
rc_t rc = AlignMgrMakeReferenceIterator ( self->amgr, &ref_iter, &self->cb_block, self->min_mapq ); /* align/iterator.h */
if ( rc == 0 )
{
/* construct the reference iterator */
uint32_t idx, count;
uint32_t reflist_options = ref_walker_make_reflist_options( self ); /* above */
Vector cur_id_vector;
VectorInit ( &cur_id_vector, 0, 12 );
rc = VNameListCount ( self->sources, &count );
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const char * src_name = NULL;
rc = VNameListGet ( self->sources, idx, &src_name );
if ( rc == 0 && src_name != NULL )
{
const VDatabase *db;
rc = VDBManagerOpenDBRead ( self->vmgr, &db, self->vschema, "%s", src_name );
if ( rc == 0 )
{
const ReferenceList * ref_list;
rc = ReferenceList_MakeDatabase( &ref_list, db, reflist_options, 0, NULL, 0 );
if ( rc == 0 )
{
const ReferenceObj * ref_obj;
rc = ReferenceList_Find( ref_list, &ref_obj, rwd->ref_name, string_size( rwd->ref_name ) );
if ( rc == 0 )
{
INSDC_coord_len len;
rc = ReferenceObj_SeqLength( ref_obj, &len );
if ( rc == 0 )
{
if ( rwd->ref_start == 0 )
rwd->ref_start = 1;
if ( ( rwd->ref_end == 0 )||( rwd->ref_end > len + 1 ) )
rwd->ref_end = ( len - rwd->ref_start ) + 1;
if ( self->primary_alignments )
rc = ref_walker_add_iterator( self, rwd->ref_name, rwd->ref_start, rwd->ref_end, src_name,
&cur_id_vector, db, ref_obj, ref_iter, TBL_PRIM, primary_align_ids );
if ( rc == 0 && self->secondary_alignments )
rc = ref_walker_add_iterator( self, rwd->ref_name, rwd->ref_start, rwd->ref_end, src_name,
&cur_id_vector, db, ref_obj, ref_iter, TBL_SEC, secondary_align_ids );
if ( rc == 0 && self->evidence_alignments )
rc = ref_walker_add_iterator( self, rwd->ref_name, rwd->ref_start, rwd->ref_end, src_name,
&cur_id_vector, db, ref_obj, ref_iter, TBL_EV, evidence_align_ids );
}
ReferenceObj_Release( ref_obj );
}
ReferenceList_Release( ref_list );
}
VDatabaseRelease( db );
}
}
}
if ( rc == 0 )
{
/* walk the reference iterator */
struct ReferenceObj const * ref_obj;
rc = ReferenceIteratorNextReference( ref_iter, NULL, NULL, &ref_obj );
if ( rc == 0 && ref_obj != NULL )
{
if ( self->use_seq_name )
rc = ReferenceObj_Name( ref_obj, &rwd->ref_name );
else
rc = ReferenceObj_SeqId( ref_obj, &rwd->ref_name );
if ( rc == 0 )
{
INSDC_coord_zero first_pos;
INSDC_coord_len len;
rc_t rc_w = ReferenceIteratorNextWindow ( ref_iter, &first_pos, &len );
while ( rc == 0 && rc_w == 0 )
{
rc_t rc_p = ReferenceIteratorNextPos ( ref_iter, !self->no_skip );
if ( rc_p == 0 )
{
rc = ReferenceIteratorPosition ( ref_iter, &rwd->pos, &rwd->depth, &rwd->bin_ref_base );
if ( rwd->depth > 0 && rc == 0 )
{
rc_t rc_sg = 0;
rwd->ascii_ref_base = _4na_to_ascii( rwd->bin_ref_base, false );
if ( self->on_enter_ref_pos != NULL )
rc = self->on_enter_ref_pos( rwd );
while ( rc_sg == 0 && rc == 0 )
{
rc_sg = ReferenceIteratorNextSpotGroup ( ref_iter, &rwd->spot_group, &rwd->spot_group_len );
if ( rc_sg == 0 )
{
rc_t rc_pr = 0;
if ( self->on_enter_spot_group != NULL )
rc = self->on_enter_spot_group( rwd );
while ( rc == 0 && rc_pr == 0 )
{
const PlacementRecord * rec;
rc_pr = ReferenceIteratorNextPlacement ( ref_iter, &rec );
if ( rc_pr == 0 && self->on_alignment != NULL )
rc = ref_walker_walk_alignment( self, ref_iter, rec, rwd );
}
if ( self->on_exit_spot_group != NULL )
rc = self->on_exit_spot_group( rwd );
}
}
if ( self->on_exit_ref_pos != NULL )
rc = self->on_exit_ref_pos( rwd );
}
rc = Quitting();
}
}
}
}
}
/* free cur_id_vector */
ReferenceIteratorRelease ( ref_iter );
}
return rc;
}
static rc_t ref_walker_prepare_1_src( struct ref_walker * self, const char * name )
{
VPath * path = NULL;
const VPath * local_cache = NULL;
const KFile * remote_file = NULL;
rc_t rc = VFSManagerResolveSpec ( self->vfs_mgr, name, &path, &remote_file, &local_cache, true );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc, "cannot resolve '$(n)' via VFSManager", "n=%s", name ) );
}
else
{
char buffer[ 4096 ];
size_t num_read;
rc = VPathReadPath ( path, buffer, sizeof buffer, &num_read );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc, "cannot read path from vpath for '$(n)'", "n=%s", name ) );
}
else
{
if ( rc == 0 )
{
int path_type = ( VDBManagerPathType ( self->vmgr, "%s", buffer ) & ~ kptAlias );
if ( path_type == kptDatabase )
{
const ReferenceList * reflist;
uint32_t options = ( ereferencelist_usePrimaryIds |
ereferencelist_useSecondaryIds |
ereferencelist_useEvidenceIds );
rc = ReferenceList_MakePath( &reflist, self->vmgr, name, options, 0, NULL, 0 );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc, "cannot create ReferenceList for '$(n)'", "n=%s", name ) );
}
else
{
uint32_t count;
rc = ReferenceList_Count( reflist, &count );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc, "ReferenceList_Count() for '$(n)' failed", "n=%s", name ) );
}
else
{
uint32_t idx;
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const ReferenceObj * refobj;
rc = ReferenceList_Get( reflist, &refobj, idx );
if ( rc != 0 )
{
LOGERR( klogInt, rc, "ReferenceList_Get() failed" );
}
else
{
const char * seqid;
rc = ReferenceObj_SeqId( refobj, &seqid );
if ( rc == 0 )
{
INSDC_coord_len seqlen;
rc = ReferenceObj_SeqLength( refobj, &seqlen );
if ( rc == 0 )
{
rc = add_region( &self->regions, seqid, 0, seqlen - 1 );
}
}
ReferenceObj_Release( refobj );
}
}
}
ReferenceList_Release( reflist );
}
}
}
}
KFileRelease( remote_file );
VPathRelease ( local_cache );
VPathRelease ( path );
}
return rc;
}
rc_t walk_0( walk_data * data, walk_funcs * funcs )
{
rc_t rc;
data->ref_start = 0;
data->ref_len = 0;
data->ref_name = NULL;
data->ref_obj = NULL;
data->ref_window_start = 0;
data->ref_window_len = 0;
data->ref_pos = 0;
data->depth = 0;
data->ref_base = 0;
data->spotgroup = NULL;
data->spotgroup_len = 0;
data->rec = NULL;
data->xrec = NULL;
data->state = 0;
data->seq_pos = 0;
do
{
rc = ReferenceIteratorNextReference( data->ref_iter, &data->ref_start, &data->ref_len, &data->ref_obj );
if ( GetRCState( rc ) != rcDone )
{
if ( rc != 0 )
{
LOGERR( klogInt, rc, "ReferenceIteratorNextReference() failed" );
}
else if ( data->ref_obj != NULL )
{
if ( data->options->use_seq_name )
rc = ReferenceObj_Name( data->ref_obj, &data->ref_name );
else
rc = ReferenceObj_SeqId( data->ref_obj, &data->ref_name );
if ( data->options->skiplist != NULL )
skiplist_enter_ref( data->options->skiplist, data->ref_name );
if ( rc != 0 )
{
if ( data->options->use_seq_name )
{
LOGERR( klogInt, rc, "ReferenceObj_Name() failed" );
}
else
{
LOGERR( klogInt, rc, "ReferenceObj_SeqId() failed" );
}
}
else
{
rc = ReferenceObj_SeqLength( data->ref_obj, &data->ref_len );
if ( rc != 0 )
{
LOGERR( klogInt, rc, "ReferenceObj_SeqLength() failed" );
}
else
{
if ( funcs->on_enter_ref != NULL )
rc = funcs->on_enter_ref( data );
if ( rc == 0 )
rc = walk_ref_window( data, funcs );
if ( rc == 0 && funcs->on_exit_ref != NULL )
rc = funcs->on_exit_ref( data );
}
}
}
}
} while ( rc == 0 );
if ( GetRCState( rc ) == rcDone ) { rc = 0; }
if ( GetRCState( rc ) == rcCanceled ) { rc = 0; }
return rc;
}
