static rc_t ref_walker_walk_alignment( struct ref_walker * self,
ReferenceIterator * ref_iter,
const PlacementRecord * rec,
ref_walker_data * rwd )
{
walker_rec * xrec = PlacementRecordCast ( rec, placementRecordExtension1 );
rwd->state = ReferenceIteratorState ( ref_iter, &rwd->seq_pos );
rwd->valid = ( ( rwd->state & align_iter_invalid ) == 0 );
rwd->reverse = xrec->reverse;
rwd->first = ( ( rwd->state & align_iter_first ) == align_iter_first );
rwd->last = ( ( rwd->state & align_iter_last ) == align_iter_last );
rwd->skip = ( ( rwd->state & align_iter_skip ) == align_iter_skip );
rwd->match = ( ( rwd->state & align_iter_match ) == align_iter_match );
rwd->bin_alignment_base = ( rwd->state & 0x0F );
rwd->ascii_alignment_base = _4na_to_ascii( rwd->state, rwd->reverse );
if ( !self->omit_quality )
rwd->quality = xrec->quality[ rwd->seq_pos ];
rwd->mapq = rec->mapq;
return self->on_alignment( rwd );
}
static rc_t walk_placements( walk_data * data, walk_funcs * funcs )
{
rc_t rc;
do
{
rc = ReferenceIteratorNextPlacement ( data->ref_iter, &data->rec );
if ( GetRCState( rc ) != rcDone )
{
if ( rc != 0 )
{
LOGERR( klogInt, rc, "ReferenceIteratorNextPlacement() failed" );
}
else
{
data->state = ReferenceIteratorState ( data->ref_iter, &data->seq_pos );
data->xrec = ( tool_rec * ) PlacementRecordCast ( data->rec, placementRecordExtension1 );
if ( funcs->on_placement != NULL )
rc = funcs->on_placement( data );
}
}
} while ( rc == 0 );
if ( GetRCState( rc ) == rcDone ) { rc = 0; }
return rc;
}
static void handle_base_pos( ReferenceIterator *ref_iter,
const PlacementRecord *rec,
uint8_t * qual,
bool nodebug )
{
INSDC_coord_zero seq_pos;
int32_t state = ReferenceIteratorState ( ref_iter, &seq_pos );
ext_rec *xrec = ( ext_rec * ) PlacementRecordCast ( rec, placementRecordExtension1 );
bool reverse = xrec->reverse;
if ( !nodebug )
OUTMSG(( "[%lu.%u ", rec->id, seq_pos ));
*qual = xrec->quality[ seq_pos ];
if ( ( state & align_iter_first ) == align_iter_first )
{
char mapq = ( rec->mapq + 33 );
OUTMSG(( "^%c", mapq ));
}
if ( ( state & align_iter_last ) == align_iter_last )
OUTMSG(( "$" ));
if ( ( state & align_iter_insert ) == align_iter_insert )
{
const INSDC_4na_bin *bases;
uint32_t n = ReferenceIteratorBasesInserted ( ref_iter, &bases );
char * s = dup_2_ascii( bases, n, reverse );
OUTMSG(( "+%u%s", n, s ));
free( s );
}
if ( ( state & align_iter_delete ) == align_iter_delete )
{
const INSDC_4na_bin *bases;
INSDC_coord_zero ref_pos;
uint32_t n = ReferenceIteratorBasesDeleted ( ref_iter, &ref_pos, &bases );
if ( bases != NULL )
{
char * s = dup_2_ascii( bases, n, reverse );
OUTMSG(( "-%u%s", n, s ));
free( s );
free( (void *) bases );
}
else
{
OUTMSG(( "-%u?", n ));
}
}
if ( ( state & align_iter_skip ) == align_iter_skip )
OUTMSG(( "*" ));
else
{
if ( ( state & align_iter_match ) == align_iter_match )
OUTMSG(( "%c", reverse ? ',' : '.' ));
else
OUTMSG(( "%c", _4na_to_ascii( state & 0x0F, reverse ) ));
}
if ( !nodebug )
OUTMSG(( "]" ));
}