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| author | Calvin Morrison <mutantturkey@gmail.com> | 2014-03-24 17:20:14 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2014-03-24 17:20:14 -0400 |
| commit | 4cab49ac3934a8fa568c7aee8484bd710f83c4e3 (patch) | |
| tree | 08f486b7a3f499743b2e36bca8de29892d1ed050 /src/c | |
| parent | d2a7c2a428a5c5ead81d87610d6b04a0e179295d (diff) | |
update documentation
Diffstat (limited to 'src/c')
| -rw-r--r-- | src/c/quikr.1 | 5 | ||||
| -rw-r--r-- | src/c/quikr.c | 1 |
2 files changed, 5 insertions, 1 deletions
diff --git a/src/c/quikr.1 b/src/c/quikr.1 index 4418a7f..7d0baf6 100644 --- a/src/c/quikr.1 +++ b/src/c/quikr.1 @@ -36,6 +36,9 @@ specify what size of kmer to use. (default value is 6) .B \-l, --lambda lambda value to use. (default value is 10000) .TP +.B \-r, --rare-percent +remove mers from classification if their values are less than the x percentile of values in the sample (default value is 10000) +.TP .B \-o, --output OTU_FRACTION_PRESENT a vector representing the percentage of database sequence's presence in sample. (csv output) .TP @@ -52,7 +55,7 @@ quikr -i sample.fa -s rdp_sensing_matrix.gz -o frequencies.txt \fBmultifasta_to_otu\fP(1), \fBquikr_train\fP(1). .SH AUTHORS .B quikr -was written by Gail Rosen <gailr@ece.drexel.edu>, Calvin Morrison +was written by Gail Rosen <gailr@ece.drexel.edu>, Calvin Morrison <mutantturkey@gmail.com>, David Koslicki, Simon Foucart, and Jean-Luc Bouchot. .SH REPORTING BUGS .TP diff --git a/src/c/quikr.c b/src/c/quikr.c index 01c5f63..de1f39a 100644 --- a/src/c/quikr.c +++ b/src/c/quikr.c @@ -115,6 +115,7 @@ int main(int argc, char **argv) { if(verbose) { printf("kmer: %u\n", kmer); + printf("rare: %lf\n", rare_percent); printf("lambda: %llu\n", lambda); printf("fasta: %s\n", input_fasta_filename); printf("sensing matrix: %s\n", sensing_matrix_filename); |