close $fh_out;
push @args, "-n $options->{ 'mismatches' }";
+push @args, "-v $options->{ 'mismatches' }"; # DANGER: using seed mismatches as alignment mismatches - may work, may not!
push @args, "-f" if $type eq "FASTA";
if ( defined $options->{ 'max_hits' } ) {
my ( $record, @scores );
- $record->{ 'Q_ID' } = $entry->[ 0 ];
- $record->{ 'STRAND' } = $entry->[ 1 ];
- $record->{ 'S_ID' } = $entry->[ 2 ];
- $record->{ 'S_BEG' } = $entry->[ 3 ];
- $record->{ 'SEQ' } = $entry->[ 4 ];
- $record->{ 'SCORES' } = $entry->[ 5 ];
- $record->{ 'MISMATCH' } = $entry->[ 6 ];
+ $record->{ 'Q_ID' } = $entry->[ 0 ];
+ $record->{ 'STRAND' } = $entry->[ 1 ];
+ $record->{ 'S_ID' } = $entry->[ 2 ];
+ $record->{ 'S_BEG' } = $entry->[ 3 ];
+ $record->{ 'SEQ' } = $entry->[ 4 ];
+ $record->{ 'SCORES' } = $entry->[ 5 ];
+ $record->{ 'MAP_COUNT' } = $entry->[ 6 ];
+ $record->{ 'DESCRIPTOR' } = $entry->[ 7 ];
$record->{ 'SEQ_LEN' } = length $entry->[ 4 ];
$record->{ 'S_END' } = $record->{ 'S_BEG' } + $record->{ 'SEQ_LEN' } - 1;