static void walk_counter_state( ReferenceIterator *ref_iter, int32_t state, bool reverse,
pileup_counters * counters )
{
if ( ( state & align_iter_invalid ) == align_iter_invalid )
return;
if ( ( state & align_iter_skip ) != align_iter_skip )
{
if ( ( state & align_iter_match ) == align_iter_match )
(counters->matches)++;
else
{
char c = _4na_to_ascii( state, false );
switch( c )
{
case 'A' : ( counters->mismatches[ 0 ] )++; break;
case 'C' : ( counters->mismatches[ 1 ] )++; break;
case 'G' : ( counters->mismatches[ 2 ] )++; break;
case 'T' : ( counters->mismatches[ 3 ] )++; break;
}
}
}
if ( reverse )
(counters->reverse)++;
else
(counters->forward)++;
if ( ( state & align_iter_insert ) == align_iter_insert )
{
const INSDC_4na_bin *bases;
uint32_t n = ReferenceIteratorBasesInserted ( ref_iter, &bases );
(counters->inserts) += n;
count_indel_fragment( &(counters->insert_fragments), bases, n );
}
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 )
{
(counters->deletes) += n;
count_indel_fragment( &(counters->delete_fragments), bases, n );
free( (void *) bases );
}
}
if ( ( state & align_iter_first ) == align_iter_first )
( counters->starting)++;
if ( ( state & align_iter_last ) == align_iter_last )
( counters->ending)++;
}
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(( "]" ));
}
