Commit b32b65de authored by Mikaël Salson's avatar Mikaël Salson
Browse files

vidjil.cpp: Set default index to Kmer index.

The default index will be set to Aho-Corasick when we'll
consider that it is ready. For now, option -q (quick) can launch AC automaton
parent efdff7b7
......@@ -331,7 +331,7 @@ int main (int argc, char **argv)
int k = DEFAULT_K ;
int w = DEFAULT_W ;
IndexTypes indexType = AC_AUTOMATON;
IndexTypes indexType = KMER_INDEX;
int epsilon = DEFAULT_EPSILON ;
int minPts = DEFAULT_MINPTS ;
......@@ -398,7 +398,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while ((c = getopt(argc, argv, "A!x:X:hHadiI124g:G:V:D:J:k:r:vw:e:E:C:f:W:l:Fc:m:N:s:b:Sn:o:L%:y:z:uUK3=:t:#:")) != EOF)
while ((c = getopt(argc, argv, "A!x:X:hHadiI124g:G:V:D:J:k:r:vw:e:E:C:f:W:l:Fc:m:N:s:b:Sn:o:L%:y:z:uUK3E:t:#:q")) != EOF)
switch (c)
{
......@@ -423,6 +423,10 @@ int main (int argc, char **argv)
}
break;
case 'q':
indexType = AC_AUTOMATON;
break;
// Input
case '#':
read_header_separator = string(optarg);
......
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