2014-04-01

1. add a count for the number of mapped reads to each exon in the output
2. add a count for the total bases mapped in each exon to the output
3. use the count of the total bases mapped to the templates to select the best pairs rather than the total number of reads mapped
4. enforce continuous coverage within each exon by adding several constraints
5. reads that cross exon borders should only be counted in the exon in which the majority of the read lies

dict 1:

key: allele id
value: dict 2

dict 2:

key: exon
value: dict 3

dict 3:

key: short read id + sequence
value: list 4

list 4: alignment start , alignment length, alignment end