Using samjs:

the first exon ends at "rotavirus:100", the second exon starts at "rotavirus:125"

• the first samtools get the reads in that region
• samjs remove the unmapped reads or the reads on a bad contig, we acceot the reads starting before exon1_end and ending after exon2_start. If the reads are paired we accept the reads where the left segment is before exon1_end and the right segment is after exon2_start.
• the last samtools count the reads

    $ samtools view -b S1.bam "rotavirus:100-1000" |\
     java -jar dist/samjs.jar -e 'function accept(rec){var exon1_end=100,exon2_start=125;if(rec.getReadUnmappedFlag() ) return false; if(rec.getReferenceName()!="rotavirus") return false; if(rec.getAlignmentStart() <= exon1_end && rec.getAlignmentEnd()>=exon2_start) return true; if(rec.getReadPairedFlag() && !rec.getMateUnmappedFlag() && Math.min(rec.getAlignmentStart(),rec.getMateAlignmentStart()) <=exon1_end && Math.max(rec.getAlignmentEnd(),rec.getMateAlignmentStart())>=exon2_start ) return true; return false;}accept(record)'  | \
    samtools view -c