First commit: code of Khan et al.
Child table traversal for MEMs added (suffix link exclusive)
Changed:
-added parameters for adding suffix links and/or child tables or not
-fixed bug when combi of Suffix links and child table is used
-added debugging
-added resource information (time used for mapping)
-added child for MAM
-added prints back
-updated usage
-corrected usage statement
Corrected bug where ISA memory was not freed when suffix links are not used
*Added keeping track of number of MEMs, MAMs and MUMs (+print result)
*Added new sparsification optimization using -skip parameter (works best with child array and w/o suffix link array)
*Added MUMmer -L option
*Added MUMmer -r option
*Fixed bug in reading the option -skip (always returned 1)
*Added MUMmer -s option
*Added MUMmer -c option
*Added support for multiple query sequences
*Added additional files to the repository
*Fixed bug in findMUM when no matches were found, but the last would be printed (segmentation fault)
*fixed wrong order of arguments in usage example
*changed makefile to proper linux makefile; deleted Netbeans-generated Makefile
*updated new tar with correct Makefile
*bugfix:
-automatic choice of skip factor could result in skip factor being zero, leading to infinite loop
Thanks to Francisco Fernandes for pointing this out
bugfix in findMEM function. loop did not extend to end of query file, which resulted in rare bug. Thanks to Timo Beller for reporting the bug.
*added kmer table of suffix array intervals to speed up search