TODO

TODO
====
7. output site files for different category of annotation.
   e.g. LOF file, NonSyn file...
8. Support different terms: e.g missense, non-sense ... instead of synonymous, nonsynonymous
9. Support custom input file formats
10. Support ANNOVAR type annotation

MIGHT-DO
========
1. vcfVersion checker 
2. joining sift and polyphen-2.
3. output format are configurable (user specify) - will add ANNOVAR support.
5. customized output

DONE
====
1. improve performance of     void findInRangeGene(int*
   start, int* end, const std::string& chr, int* pos) {
6. Triplet -> AA consider reverse strand
7. Support indel
2. output to VCF format
3. output statistics
* 3. output basis statisitcs:
 *    freq of each annotation  .anno.freq
 *    freq of each base change .base.freq
 *    freq of codon change     .codon.freq
 *    freq of indel length     .indel.freq
 */

4. support various input formats (partly done on gene file)
   support GENCODE (have script to convert GENOCODE to refFlat)

9. output frequency of uniq annotation type and duplicated annotation type
6. write a log file, parameter, start time, end time, how
   many gene, how many variant