static rc_t print_edge( struct rna_splice_log * sl,
INSDC_coord_zero pos,
bool const reverse_complement,
bool const add_newline )
{
rc_t rc;
INSDC_coord_len from_ref_obj, to_read;
uint8_t buffer[ EDGE_LEN + 1 ];
INSDC_coord_zero rd_pos = 0;
uint32_t pre_len = PRE_POST_LEN;
uint32_t post_len = PRE_POST_LEN;
if ( pos >= PRE_POST_LEN )
rd_pos = ( pos - PRE_POST_LEN ); /* in the rare case the delete is at the very beginning of the alignment */
else
pre_len = pos; /* rd_pos is still 0, what we want*/
to_read = pre_len + post_len + 2;
rc = ReferenceObj_Read( sl->ref_obj, rd_pos, to_read, buffer, &from_ref_obj );
if ( rc == 0 )
{
uint8_t complement[ EDGE_LEN + 1 ];
uint8_t to_write[ EDGE_LEN + 5 ];
uint8_t * ref_bytes = buffer;
if ( from_ref_obj < to_read )
post_len -= ( to_read - from_ref_obj );
if ( reverse_complement )
{
copy_read_and_reverse_complement( complement, buffer, from_ref_obj );
ref_bytes = complement;
}
memmove( to_write, ref_bytes, pre_len );
to_write[ pre_len ] = '\t';
to_write[ pre_len + 1 ] = ref_bytes[ pre_len ];
to_write[ pre_len + 2 ] = ref_bytes[ pre_len + 1 ];
to_write[ pre_len + 3 ] = '\t';
memmove( &( to_write[ pre_len + 4 ] ), &( ref_bytes[ pre_len + 2 ] ), post_len );
if ( add_newline )
to_write[ pre_len + post_len + 4 ] = '\n';
else
to_write[ pre_len + post_len + 4 ] = '\t';
rc = write_to_file( sl, to_write, pre_len + post_len + 5 );
}
return rc;
}
LIB_EXPORT rc_t CC ReferenceIteratorPosition ( const ReferenceIterator *self,
INSDC_coord_zero *pos, uint32_t * depth, INSDC_4na_bin * base )
{
rc_t rc = 0;
if ( self == NULL )
rc = RC( rcAlign, rcIterator, rcAccessing, rcSelf, rcNull );
else
{
/* return position, many records our record-list, and the base at this position */
if ( pos != NULL )
{
*pos = self->current_pos;
}
if ( depth != NULL )
{
*depth = self->depth;
}
if ( base != NULL )
{
uint32_t written;
*base = 0;
/* problem! how to get the base if depth == 0 */
if ( self->current_rec != NULL )
{
rc = ReferenceObj_Read( self->current_rec->ref, self->current_pos, 1, base, &written );
}
else if ( self->refobj != NULL )
{
rc = ReferenceObj_Read( self->refobj, self->current_pos, 1, base, &written );
}
}
}
return rc;
}
LIB_EXPORT uint32_t CC ReferenceIteratorBasesDeleted ( const ReferenceIterator *self,
INSDC_coord_zero *pos, const INSDC_4na_bin **bases )
{
uint32_t res = align_iter_invalid;
if ( bases != NULL )
{
*bases = NULL;
}
if ( self != NULL )
{
/* PlacementRecordCast returns NULL if self->current_rec is NULL */
AlignmentIterator * al_iter = PlacementRecordCast ( self->current_rec, placementRecordExtension0 );
if ( al_iter != NULL )
{
INSDC_coord_zero temp_pos;
res = AlignmentIteratorBasesDeleted( al_iter, &temp_pos );
if ( ( res & align_iter_invalid ) != align_iter_invalid )
{
if ( pos != NULL ) { *pos = temp_pos; }
/* where to get the reference-bases from ? PlacementRecord.ref ! */
if ( res > 0 && bases != NULL )
{
uint8_t * buffer = malloc( res );
if ( buffer != NULL )
{
INSDC_coord_len written;
rc_t rc = ReferenceObj_Read( self->current_rec->ref, temp_pos, res, buffer, &written );
if ( rc == 0 )
{
*bases = buffer;
}
}
}
}
}
}
return res;
}