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commit c9758816c355d353359e3c04131bc573e9962df4
Author: Afif Elghraoui <a...@ghraoui.name>
Date: Sun May 24 17:46:36 2015 -0700
Create manpage for last remaining function
It did not have command-line help, so this
page was written from scratch by reading
the source code.
---
debian/meryl.1 | 1 +
debian/meryl.manpages | 1 +
debian/simple.1 | 43 +++++++++++++++++++++++++++++++++++++++++++
3 files changed, 45 insertions(+)
diff --git a/debian/meryl.1 b/debian/meryl.1
index 137b00e..0565214 100644
--- a/debian/meryl.1
+++ b/debian/meryl.1
@@ -319,6 +319,7 @@ meryl \fB\-mergebatch\fR N \fB\-o\fR file
.RE
.fi
.SH SEE ALSO
+.BR simple (1),
.BR mapMers (1),
.BR mapMers-depth (1),
.BR kmer-mask (1)
diff --git a/debian/meryl.manpages b/debian/meryl.manpages
index a2a9a7d..396da3a 100644
--- a/debian/meryl.manpages
+++ b/debian/meryl.manpages
@@ -2,5 +2,6 @@ debian/kmer-mask.1
debian/mapMers.1
debian/mapMers-depth.1
debian/meryl.1
+debian/simple.1
debian/existDB.1
debian/positionDB.1
diff --git a/debian/simple.1 b/debian/simple.1
new file mode 100644
index 0000000..0bcf017
--- /dev/null
+++ b/debian/simple.1
@@ -0,0 +1,43 @@
+.\" (C) Copyright 2015 Afif Elghraoui <a...@ghraoui.name>,
+.TH SIMPLE "1" "May 2015" "simple 0~20150520+2004" "User Commands"
+.SH NAME
+simple \- the obvious array-based kmer counter
+.SH SYNOPSIS
+.B simple
+.RB [ \-f | \-r | \-C ]
+.RB [ \-c
+.IR compression ]
+.RB [ \-m
+.IR mersize ]
+.BI \-i \0input
+.BI \-o \0output
+.SH DESCRIPTION
+.B simple
+is a very simple mer counter.
+It allocates a gigantic 32-bit array, populates the array with mers, sorts,
+and writes the output.
+It will allocate 4 bytes per kmer.
+k=16 will require 16 GB to run.
+.SH OPTIONS
+.TP
+.BI \-i \0input
+.TP
+.BI \-o \0output
+.TP
+.BI \-m \0mersize
+the mer size.
+Default is 22
+.TP
+.B \-f
+forward kmer (this is the default)
+.TP
+.B \-r
+reverse kmer
+.TP
+.B \-C
+canonical kmer (lexicographically smaller of the forward and reverse kmer at
each location)
+.TP
+.BI \-c \0#
+mer compression
+.SH SEE ALSO
+.BR meryl (1)
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