The kmertable functionality from the main essaMEM repository has been added, and the indentation in the files sparseSA.* have been changed to 8 spaces. This commit (8f6082f) significantly bloats the number of changes.
Additionally this fixes some bugs:
A naming bug in the settings.cpp file.
A bug that caused the usage of suffix links in essaMEM to not return the entire set of MEMs.
Finally, suffixlinks and a kmertable are now being used to speed up the MEM-finding procedure. For the kmertable, k=10 is being used. This value can probably be further optimised.
The kmertable functionality from the main essaMEM repository has been added, and the indentation in the files sparseSA.* have been changed to 8 spaces. This commit (8f6082f) significantly bloats the number of changes.
Additionally this fixes some bugs:
Finally, suffixlinks and a kmertable are now being used to speed up the MEM-finding procedure. For the kmertable, k=10 is being used. This value can probably be further optimised.