Update TODO to reflect closed functionality holes

I updated the TODO file to reflect that GERMLINE_GAP_D_MASK is now
being filled by one or another method.
Change masking method

I modified the default masking method when using fasta2tab on files.
Now the GERMLINE_GAP_D_MASK field is simply copied from SEQUENCE.
Merge branch 'master' of jdagilliland.com:git/hershberg_lab/fasta2tab

I merged the README file that I added with my program changes.