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-rw-r--r--src/align_detector.c1
1 files changed, 1 insertions, 0 deletions
diff --git a/src/align_detector.c b/src/align_detector.c
index ec2b16b7..104445c1 100644
--- a/src/align_detector.c
+++ b/src/align_detector.c
@@ -290,6 +290,7 @@ int main(int argc, char *argv[])
if ( make_zero_sum(fh, groups, n_groups, "all", level) ) return 1;
fprintf(fh, "method inversion 5 0.1\n");
+ fprintf(fh, "skipemptycons\n");
fprintf(fh, "end\n");
fclose(fh);