Provide the queries that overlap with a reference, when the query is small.
../Java/Python/CompareOverlappingSmallQuery.py -i $formatType.inputFileName1
#if $formatType.FormatInputFileName1 == 'bed':
-f bed
#elif $formatType.FormatInputFileName1 == 'gff':
-f gff
#elif $formatType.FormatInputFileName1 == 'gff2':
-f gff2
#elif $formatType.FormatInputFileName1 == 'gff3':
-f gff3
#elif $formatType.FormatInputFileName1 == 'sam':
-f sam
#elif $formatType.FormatInputFileName1 == 'gtf':
-f gtf
#end if
-j $formatType2.inputFileName2
#if $formatType2.FormatInputFileName2 == 'bed':
-g bed
#elif $formatType2.FormatInputFileName2 == 'gff':
-g gff
#elif $formatType2.FormatInputFileName2 == 'gff2':
-g gff2
#elif $formatType2.FormatInputFileName2 == 'gff3':
-g gff3
#elif $formatType2.FormatInputFileName2 == 'sam':
-g sam
#elif $formatType2.FormatInputFileName2 == 'gtf':
-g gtf
#end if
-o $outputFileGff
#if $OptionDistance.Dist == 'Yes':
-d $OptionDistance.distance
#end if
#if $OptionMinOverlap.present == 'Yes':
-m $OptionMinOverlap.minOverlap
#end if
#if $OptionCollinearOrAntiSens.OptionCA == 'Collinear':
-c
#elif $OptionCollinearOrAntiSens.OptionCA == 'Antisense':
-a
#end if
$InvertMatch
$NotOverlapping