Remove GSA from extend_*
Use 'slim' structures
Use 'slim' structures

LSG now uses the `-end-pos` file produced by BEETL (instead of reconstructing the permutation with a scan of the BWT and of the GSA). Moreover, it now reads a SA without the sequence IDs (but only the suffix lengths) and sequence lengths (either of the LCP or of the GSA) are assumed to be 8-bit long.
Requires a customized version of BEETL (found in directory `thirdparty`).
Remove commented and dead code
Remove commented code
New version of extend_arc_labels (no LCP)
Let lsg output the termination time
Add operator== to arcInterval
Let interval manager work in a RLE-like fashion
Remove old commented code
Add two types of interval managers (plain and RLE)
Fix merge conflicts
Merge branch 'interval-manager-split' into develop
Clean repository
Fix command-line parameter conversion
Fix read lexical order reconstruction when the read length is specified
Allow to use only numeric IDs in the ASQG format (instead of FASTA IDs)
Make the filename of the reads optional (with basename as default)
Let lsg manage rev&compl reads
Fix edge "multiplexing"