[med-svn] [dnaclust] 04/04: Standards-Version: 4.1.0 (no changes needed), spelling, upload

[Andreas Tille]

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tille pushed a commit to branch master
in repository dnaclust.

commit dfb931652361f18ee683e42f344c504dabb4bba4
Author: Andreas Tille <tille at debian.org>
Date:   Sun Sep 24 08:20:00 2017 +0200

    Standards-Version: 4.1.0 (no changes needed), spelling, upload
---
 debian/changelog  | 6 ++++--
 debian/control    | 4 ++--
 debian/dnaclust.1 | 6 +++---
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 74163ae..e1fdc19 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-dnaclust (3-5) UNRELEASED; urgency=medium
+dnaclust (3-5) unstable; urgency=medium
 
   [ Steffen Moeller ]
   * debian/upstream/metadata: Added references to
@@ -9,8 +9,10 @@ dnaclust (3-5) UNRELEASED; urgency=medium
   * Do not parse d/changelog
   * Build-Depends: rename
     Closes: #876602
+  * Standards-Version: 4.1.0 (no changes needed)
+  * Spelling
 
- -- Andreas Tille <tille at debian.org>  Sun, 24 Sep 2017 08:15:30 +0200
+ -- Andreas Tille <tille at debian.org>  Sun, 24 Sep 2017 08:20:24 +0200
 
 dnaclust (3-4) unstable; urgency=medium
 
diff --git a/debian/control b/debian/control
index 85be5aa..2c673fe 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Build-Depends: debhelper (>= 10),
                libboost-dev,
                libboost-program-options-dev,
                rename
-Standards-Version: 3.9.8
+Standards-Version: 4.1.0
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/dnaclust.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/dnaclust.git
 Homepage: http://dnaclust.sourceforge.net/
@@ -24,4 +24,4 @@ Description: tool for clustering millions of short DNA sequences
  The input sequences to be clustered should be in Fasta format. The id
  of each sequence is based on the first word of the seqeunce in the Fasta
  format. The first word is the prefix of the header up to the first
- occurance of white space characters in the header. 
+ occurrence of white space characters in the header. 
diff --git a/debian/dnaclust.1 b/debian/dnaclust.1
index 40092ee..e5702d9 100644
--- a/debian/dnaclust.1
+++ b/debian/dnaclust.1
@@ -43,7 +43,7 @@ program\&.
 \fBdnaclust\fR
 is a tool for clustering large number of short DNA sequences\&. The clusters are created in such a way that the "radius" of each clusters is no more than the specified threshold\&.
 .PP
-The input sequences to be clustered should be in Fasta format\&. The id of each sequence is based on the first word of the seqeunce in the Fasta format\&. The first word is the prefix of the header up to the first occurance of white space characters in the header\&. The output is written to STDOUT\&. If you want the output to be written to a file, just redirect the output (See Examples)\&.
+The input sequences to be clustered should be in Fasta format\&. The id of each sequence is based on the first word of the seqeunce in the Fasta format\&. The first word is the prefix of the header up to the first occurrence of white space characters in the header\&. The output is written to STDOUT\&. If you want the output to be written to a file, just redirect the output (See Examples)\&.
 .PP
 The output has two modes: the default clustering mode, and clustering with multiple sequence alignment\&. In the clustering mode (without multiple alignment), each cluster will be printed on a separate line\&. The line will contain the ids of the sequences in the cluster\&. The first id in each line is the cluster center sequence id\&. Because of the way our clusters are constructed, the length of the cluster center sequence is always greater than or equal to the length of any of the seq [...]
 .PP
@@ -84,9 +84,9 @@ The default alignment is a one sided semi\-global alignment\&. i\&.e\&. gaps are
 .PP
 \fB\-\-multiple\-alignment\fR, \fB\-m\fR
 .RS 4
-Set the output format to show the multiple sequence alignment of each cluster\&. The gaps in the alignments are represented with the dash \*(Aq\-\*(Aq charachter\&.
+Set the output format to show the multiple sequence alignment of each cluster\&. The gaps in the alignments are represented with the dash \*(Aq\-\*(Aq character\&.
 .sp
-The format of the MSA output is as follows: The MSA of each cluster spans several lines\&. The MSA starts with a line containing charachter \*(Aq#\*(Aq followed by the number of sequences in that cluster\&. The aligned sequences (which may contain gaps) follow in the Fasta format\&. Each Fasta record will be composed of two lines\&. The header line and the sequence line\&. Since each aligned sequence is output on a single line, the output may contain very long lines\&. Please use \*(Aqle [...]
+The format of the MSA output is as follows: The MSA of each cluster spans several lines\&. The MSA starts with a line containing character \*(Aq#\*(Aq followed by the number of sequences in that cluster\&. The aligned sequences (which may contain gaps) follow in the Fasta format\&. Each Fasta record will be composed of two lines\&. The header line and the sequence line\&. Since each aligned sequence is output on a single line, the output may contain very long lines\&. Please use \*(Aqles [...]
 .RE
 .PP
 \fB\-\-no\-k\-mer\-filter\fR

-- 
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