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-rw-r--r--kmer_counts_per_sequence.c23
1 files changed, 22 insertions, 1 deletions
diff --git a/kmer_counts_per_sequence.c b/kmer_counts_per_sequence.c
index ac7ff44..d871ae5 100644
--- a/kmer_counts_per_sequence.c
+++ b/kmer_counts_per_sequence.c
@@ -7,7 +7,28 @@
#include "kmer_utils.h"
-unsigned long position = 0;
+void help() {
+ printf("usage: kmer_counts_per_sequence input_file kmer [kmer-file] ...\n\n"
+ "count mers in each sequence of size k from a fasta file\n"
+ "\n"
+ " --input -i input fasta file to count\n"
+ " --kmer -k size of mers to count\n"
+ " --mer-file -m a file containing a list of mers you are interested\n"
+ " in opening. this will enable output your results in\n"
+ " a sparse format \n"
+ " --sparse -s output values in a sparse format. output is in the\n"
+ " order sequence_number, mer_index, value\n"
+ "\n"
+ "Report all bugs to mutantturkey@gmail.com\n"
+ "\n"
+ "Copyright 2014 Calvin Morrison, Drexel University.\n"
+ "\n"
+ "If you are using any dna-utils tool for a publication\n"
+ "please cite your usage:\n\n"
+ "dna-utils. Drexel University, Philadelphia USA, 2014;\n"
+ "software available at www.github.com/EESI/dna-utils/\n");
+}
+
int main(int argc, char **argv) {
// getdelim variables