Created new mutations using mutatrix, automatized performance tests.

Author: Martinsos

apps/aligner/aligner.cpp

@@ -68,7 +68,7 @@ int main(int argc, char * const argv[]) {
                 " If N = 0 then all sequences will be calculated."
                 " Specifying small N can make total calculation much faster. [default: 0]\n");
         fprintf(stderr, "\t-k K  Sequences with score > K will be discarded."
-                " Smaller k, faster calculation.\n");
+                " Smaller k, faster calculation. If -1, no sequences will be discarded. [default: -1]\n");
         fprintf(stderr, "\t-p  If specified, alignment path will be found and printed. "
                 "This may significantly slow down the calculation.\n");
         fprintf(stderr, "\t-l  If specified, start locations will be found and printed. "

test_data/Chromosome_2890043_3890042_0/Chromosome_2890043_3890042_0.fasta

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:4a2942f217f05214cb2f8d4c474c83ccecabebe5656529751824b346ff1a789c
-size 1000051
+oid sha256:1c75ea6ff04064c522cc9ecb66b89093667316e9242457352b912f59dc03c48a
+size 1000031