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 walk_ref_pos( walk_data * data, walk_funcs * funcs )
{
rc_t rc;
do
{
rc = ReferenceIteratorNextPos ( data->ref_iter, !data->options->no_skip );
if ( GetRCState( rc ) != rcDone )
{
if ( rc != 0 )
{
LOGERR( klogInt, rc, "ReferenceIteratorNextPos() failed" );
}
else
{
rc = ReferenceIteratorPosition ( data->ref_iter, &data->ref_pos, &data->depth, &data->ref_base );
if ( rc != 0 )
{
LOGERR( klogInt, rc, "ReferenceIteratorPosition() failed" );
}
else if ( data->depth > 0 )
{
bool skip = false;
if ( data->options->skiplist != NULL )
skip = skiplist_is_skip_position( data->options->skiplist, data->ref_pos + 1 );
if ( !skip )
{
if ( funcs->on_enter_ref_pos != NULL )
rc = funcs->on_enter_ref_pos( data );
if ( rc == 0 )
rc = walk_spot_group( data, funcs );
if ( rc == 0 && funcs->on_exit_ref_pos != NULL )
rc = funcs->on_exit_ref_pos( data );
}
}
}
if ( rc == 0 ) { rc = Quitting(); }
}
} while ( rc == 0 );
if ( GetRCState( rc ) == rcDone ) { rc = 0; }
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;
}
