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| author | Calvin <calvin@calvin-ThinkPad-X220.(none)> | 2013-05-15 10:41:13 -0400 |
|---|---|---|
| committer | Calvin <calvin@calvin-ThinkPad-X220.(none)> | 2013-05-15 10:41:13 -0400 |
| commit | 75c8047886584b2beb81402ad2a6903857dfabda (patch) | |
| tree | 40f4208200efce89bab897aa39aab6b5329c48b6 /src/c/quikr.1 | |
| parent | 0773aaf89678b967588a902df1f5e6f9ccea393d (diff) | |
add -d flag for debugging so verbose doesn't take longer, use generate_kmers instead of a hacky awk
Diffstat (limited to 'src/c/quikr.1')
| -rw-r--r-- | src/c/quikr.1 | 4 |
1 files changed, 4 insertions, 0 deletions
diff --git a/src/c/quikr.1 b/src/c/quikr.1 index 9982d94..937109b 100644 --- a/src/c/quikr.1 +++ b/src/c/quikr.1 @@ -16,6 +16,7 @@ quikr \- Calculate estimated frequencies of bacteria in a sample. .RB [ \-o .IR output ] .RB [ \-v ] +.RB [ \-d ] .P .BR quikr " ..." .SH DESCRIPTION @@ -45,6 +46,9 @@ OTU_FRACTION_PRESENT a vector representing the percentage of database sequence's .TP .B \-v, --verbose verbose mode. +.TP +.B \-d, --debug +debug mode, this will save our sensing matrix and sample matrix (A and B matricies) in files called 'sensing.matrix' and 'count.matrix' for debugging purposes .SH EXAMPLES Use quikr to calculate the estimated frequencies for sample.fa, using rdp7.fasta as the sensing matrix we generated with quikr_train. This uses 6-mers by default, and a lambda value of 10000: .P |