Replaced ulong/long by Gt[US]sainindextype.
Optimed the generation of the program code for different cases.
Determine unique symbol only when necessary.
Added line stating that file is generated.
Use sequential readint where possible.
Added parser for DNA sequences to gt dev sain.
Introduce BareEncseq class with constructor (=parser).
Introduce GtSainSpecialrange and add length of range.
Implement compare_Sstarstrings and assignSstarnames as templates.
Implement assignSstarlength as template.
Reordered code to eliminate forward declarations.
implement sorting on bare encoded sequences.
Fixed bugs: incorrect order of wildcard ranges

- and missing ISSPECIAL convertions.
Move gt_suftab_lightweightcheck into own file.
Renaming of file related to bare encoded sequence.
Added lightweightcheck for -fastadna input.
Fixed warnings related to exhaustive switch.
Fixed remaining problems so that lightweightcheck works.
use a shared copy of the D.mel genome in LTRd tests
Merge pull request #142 from satta/ltrd_test_redundancy

use a shared copy of the D.mel genome in LTRd tests