[med-svn] [seer] 02/03: Update manpages

Thu Mar 23 13:13:40 UTC 2017

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tille pushed a commit to branch master
in repository seer.

commit e775c09db2e447ac48dd92b95ffb6c64440e602c
Author: Andreas Tille <tille at debian.org>
Date:   Thu Mar 23 14:12:55 2017 +0100

    Update manpages
---
 debian/mans/blast_top_hits.1 |  5 ++---
 debian/mans/combineKmers.1   |  3 +--
 debian/mans/filter_seer.1    |  3 +--
 debian/mans/kmds.1           | 12 +++++-------
 debian/mans/map_back.1       |  6 ++++--
 debian/mans/seer.1           | 10 ++++------
 6 files changed, 17 insertions(+), 22 deletions(-)

diff --git a/debian/mans/blast_top_hits.1 b/debian/mans/blast_top_hits.1
index 15ce157..4ecb915 100644
--- a/debian/mans/blast_top_hits.1
+++ b/debian/mans/blast_top_hits.1
@@ -1,9 +1,8 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
-.TH BLAST_TOP_HITS "1" "March 2016" "blast_top_hits 1.1.0" "User Commands"
+.TH BLAST_TOP_HITS "1" "March 2017" "blast_top_hits 1.1.2" "User Commands"
 .SH NAME
 blast_top_hits \- reduces a blast or blat output file to the top hit for each query sequence only
 .SH SYNOPSIS
-.B blast_top_hits.pl
+.B blast_top_hits
 \fI\,--input blast_out --mode blast <options>\/\fR
 .SH DESCRIPTION
 Reduces a blast or blat output file to the top hit for each query sequence only.
diff --git a/debian/mans/combineKmers.1 b/debian/mans/combineKmers.1
index 51aaa5a..8dee120 100644
--- a/debian/mans/combineKmers.1
+++ b/debian/mans/combineKmers.1
@@ -1,5 +1,4 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
-.TH COMBINEKMERS "1" "March 2016" "combineKmers 1.1.0" "User Commands"
+.TH COMBINEKMERS "1" "March 2017" "combineKmers 1.1.2" "User Commands"
 .SH NAME
 combineKmers \- basic algorithm to combine kmer counts across samples
 .P
diff --git a/debian/mans/filter_seer.1 b/debian/mans/filter_seer.1
index f0c272b..77f075e 100644
--- a/debian/mans/filter_seer.1
+++ b/debian/mans/filter_seer.1
@@ -1,5 +1,4 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
-.TH FILTER_SEER "1" "March 2016" "filter_seer 1.1.0" "User Commands"
+.TH FILTER_SEER "1" "March 2017" "filter_seer 1.1.2" "User Commands"
 .SH NAME
 filter_seer \- post filtering of significant kmers
 .SH DESCRIPTION
diff --git a/debian/mans/kmds.1 b/debian/mans/kmds.1
index c02e1c9..60eaa38 100644
--- a/debian/mans/kmds.1
+++ b/debian/mans/kmds.1
@@ -1,5 +1,4 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
-.TH KMDS "1" "March 2016" "kmds 1.1.0" "User Commands"
+.TH KMDS "1" "March 2017" "kmds 1.1.2" "User Commands"
 .SH NAME
 kmds \- control for population structure
 .SH DESCRIPTION
@@ -9,7 +8,7 @@ This program belongs to seer(1) (Sequence Element (kmer) Enrichment Analysis).
 .SH OPTIONS
 1) filter and subsample with \fB\-\-no_mds\fR and \fB\-\-size\fR
 .P
-2) combine, and do metric multidimensional scaling with \fB\-\-combine_mds\fR
+2) combine, and do metric multidimensional scaling with \fB\-\-mds_concat\fR
 .SS "Required options:"
 .TP
 \fB\-k\fR [ \fB\-\-kmers\fR ] arg
@@ -54,12 +53,11 @@ minimum kmer frequency
 .TP
 \fB\-\-min_words\fR arg
 minimum kmer occurrences. Overrides \fB\-\-maf\fR
-.TP
-\fB\-\-chisq\fR arg (=10e\-5)
-p\-value threshold for initial chi squared test. Set
-to 1 to show all
 .SS "Other options:"
 .TP
+\fB\-\-version\fR
+prints version and exits
+.TP
 \fB\-h\fR [ \fB\-\-help\fR ]
 full help message
 .SH EXAMPLE
diff --git a/debian/mans/map_back.1 b/debian/mans/map_back.1
index ca1c85a..e18a4b6 100644
--- a/debian/mans/map_back.1
+++ b/debian/mans/map_back.1
@@ -1,5 +1,4 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
-.TH MAP_BACK "1" "March 2016" "map_back 1.1.0" "User Commands"
+.TH MAP_BACK "1" "March 2017" "map_back 1.1.2" "User Commands"
 .SH NAME
 map_back \- context of significant kmers
 .SH DESCRIPTION
@@ -20,6 +19,9 @@ file
 \fB\-\-threads\fR arg (=1)
 number of threads. Suggested: 4
 .TP
+\fB\-\-version\fR
+prints version and exits
+.TP
 \fB\-h\fR [ \fB\-\-help\fR ]
 full help message
 .SH AUTHOR
diff --git a/debian/mans/seer.1 b/debian/mans/seer.1
index 888a132..4454604 100644
--- a/debian/mans/seer.1
+++ b/debian/mans/seer.1
@@ -1,5 +1,4 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
-.TH SEER "1" "March 2016" "seer 1.1.0" "User Commands"
+.TH SEER "1" "March 2017" "seer 1.1.2" "User Commands"
 .SH NAME
 seer \- sequence element enrichment analysis
 .SH DESCRIPTION
@@ -44,10 +43,6 @@ minimum kmer frequency
 \fB\-\-min_words\fR arg
 minimum kmer occurrences. Overrides \fB\-\-maf\fR
 .TP
-\fB\-\-positive_only\fR
-only test words with a predicted positive effect
-direction
-.TP
 \fB\-\-chisq\fR arg (=10e\-5)
 p\-value threshold for initial chi squared test. Set
 to 1 to show all
@@ -61,6 +56,9 @@ to show all
 print lists of samples significant kmers were found
 in
 .TP
+\fB\-\-version\fR
+prints version and exits
+.TP
 \fB\-h\fR [ \fB\-\-help\fR ]
 full help message
 .SH EXAMPLES

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