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commit ca626401a2b084df3c5d3e74bfadfbe00c4f0607
Author: Afif Elghraoui <a...@ghraoui.name>
Date: Sat May 23 02:56:06 2015 -0700
Clean up existDB manpage
Fix formatting, add SYNOPSIS, DESCRIPTION, and SEE ALSO sections.
---
debian/existDB.1 | 76 +++++++++++++++++++++++++-------------------------------
1 file changed, 34 insertions(+), 42 deletions(-)
diff --git a/debian/existDB.1 b/debian/existDB.1
index 36cb211..2fe20a7 100644
--- a/debian/existDB.1
+++ b/debian/existDB.1
@@ -1,51 +1,43 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
.TH EXISTDB "1" "May 2015" "existDB 0~20150520+2004" "User Commands"
.SH NAME
-existDB \- manual page for existDB 0~20150520+2004
+existDB \- management of existDB files
+.SH SYNOPSIS
+.B existDB
+[\fB\-mersize\fR \fImersize\fR] \fB\-build\fR \fIsome.fasta\fR \fIprefix\fR |
+\fB\-describe\fR \fIprefix\fR |
+\fB\-testfiles\fR \fIsome.fasta\fR \fIprefix\fR |
+\fB\-testexistence\fR \fIsome.fasta\fR |
+\fB\-testexhaustive\fR \fIsome.fasta\fR \fIsome.meryl\fR
.SH DESCRIPTION
-usage: existDB [stuff]
-.HP
-\fB\-mersize\fR mersize
-.HP
-\fB\-\-\fR Use the specified mersize when building existDB tables.
-.HP
-\fB\-build\fR some.fasta prefix
-.HP
-\fB\-\-\fR Build an existDB on all mers in some.fasta and save
-.IP
-the tables into prefix.
-.HP
-\fB\-describe\fR prefix
-.HP
-\fB\-\-\fR Reports the state of some existDB file.
-.HP
-\fB\-testfiles\fR some.fasta prefix
+This program is part of libkmer.
+.SH OPTIONS
.TP
-\fB\-\-\fR Build an existDB table from some.fasta.
-Write that table to disk.
+\fB\-mersize\fR \fImersize\fR
+Use the specified \fImersize\fR when building existDB tables.
.TP
-Load the table back.
-Compare that each mer in some.fasta is present
-.IP
-in all three existDB tables created earlier.
-.HP
-\fB\-testexistence\fR some.fasta
-.HP
-\fB\-\-\fR Build an existDB table from some.fasta, check that every
+\fB\-build\fR \fIsome.fasta\fR \fIprefix\fR
+Build an existDB on all mers in \fIsome.fasta\fR and save the tables into
\fIprefix\fR.
+.TP
+\fB\-describe\fR \fIprefix\fR
+Reports the state of some existDB file.
.TP
-mer in some.fasta can be found in the table.
-Does not
-.IP
-guarantee that every mer in the table is found in the file.
-.HP
-\fB\-testexhaustive\fR some.fasta some.meryl
-.HP
-\fB\-\-\fR Build an existDB table from some.fasta, check _EVERY_ mer
+\fB\-testfiles\fR \fIsome.fasta\fR \fIprefix\fR
+Build an existDB table from \fIsome.fasta\fR.
+Write that table to disk.
+Load the table back.
+Compare that each mer in \fIsome.fasta\fR is present in all three existDB
+tables created earlier.
.TP
-for existance.
-Complain if a mer exists in the table but
+\fB\-testexistence\fR \fIsome.fasta\fR
+Build an existDB table from \fIsome.fasta\fR, check that every mer in
+\fIsome.fasta\fR can be found in the table.
+Does not guarantee that every mer in the table is found in the file.
.TP
-not in the meryl database.
-Assumes 'some.meryl' is the
-.IP
-mercount of some.fasta.
+\fB\-testexhaustive\fR \fIsome.fasta\fR \fIsome.meryl\fR
+Build an existDB table from \fIsome.fasta\fR, check _EVERY_ mer for existence.
+Complain if a mer exists in the table but not in the meryl database.
+Assumes \fIsome.meryl\fR is the mercount of \fIsome.fasta\fR.
+.SH SEE ALSO
+\fBmeryl\fR(1),
+\fBpositionDB\fR(1)
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