[med-svn] [augustus] 03/06: update manpages from upstream

[Sascha Steinbiss]

This is an automated email from the git hooks/post-receive script.

satta pushed a commit to branch master
in repository augustus.

commit fdb868d576e03b9491c8d9cd6ce7957cd07f7df2
Author: Sascha Steinbiss <satta at debian.org>
Date:   Fri Jul 28 21:01:02 2017 +0200

    update manpages from upstream
---
 debian/manpages                      |  2 +-
 debian/mansrc/augustus.1.adoc        |  2 +-
 debian/mansrc/fastBlockSearch.1.adoc | 31 +++++++++++++------------------
 debian/mansrc/prepareAlign.1.adoc    | 11 ++++-------
 4 files changed, 19 insertions(+), 27 deletions(-)

diff --git a/debian/manpages b/debian/manpages
index ec7cf6b..317f75d 100644
--- a/debian/manpages
+++ b/debian/manpages
@@ -1 +1 @@
-mansrc/*.1
+debian/mansrc/*.1
diff --git a/debian/mansrc/augustus.1.adoc b/debian/mansrc/augustus.1.adoc
index d120299..0039e37 100644
--- a/debian/mansrc/augustus.1.adoc
+++ b/debian/mansrc/augustus.1.adoc
@@ -31,7 +31,7 @@ SPECIES is an identifier for the species. Use *--species=help* to see a list.
   predict genes independently on each strand, allow overlapping genes on opposite strands.
   This option is turned off by default.
 
-*--hintsfile=hintsfilename*::
+*--hintsfile=hintsfilenam*e::
   When this option is used the prediction considering hints (extrinsic information) is turned on.
   hintsfilename contains the hints in gff format.
 
diff --git a/debian/mansrc/fastBlockSearch.1.adoc b/debian/mansrc/fastBlockSearch.1.adoc
index 967674a..5eaf20f 100644
--- a/debian/mansrc/fastBlockSearch.1.adoc
+++ b/debian/mansrc/fastBlockSearch.1.adoc
@@ -8,27 +8,16 @@ fastBlockSearch - search loci matching protein block profiles
 
 *fastBlockSearch* [options] seqs.fa fam.prfl
 
-## DESCRIPTION
-
-Searches hits (matches) of the blocks in the profile given by fam.prfl within
-the genomic sequences in the file seqs.fa.
-Hits are sorted by increasing score, so the last displayed hit is the best one
-found in the region. The format is similar to that of the blockscore file (which
-is optionally generated by msa2prfl.pl): It shows coordinate, strand, mean odds-
-ratio score, and specificity of score, and the motif.
-From the output users can choose regions with matching blocks to perform gene
-prediction with AUGUSTUS-PPX using the same block profile.
-
-## OPTIONS
-
-*--cutoff=c*::
-  This minimum for the average log score of the motifs found can be used to adjust the sensitivity of the block search.
-  The standard cutoff is 0.7, which is very sensitive but can give many false positive hits for smaller profiles.
+## DESCRIPTION  
+  Searches hits (matches) of the blocks in the profile given by fam.prfl within the genomic sequences in the file seqs.fa.
+  Hits are sorted increasingly by score, so the last displayed hit is the best one found in the region. The format is similar
+  to that of the blockscore file (which is optionally generated by msa2prfl.pl): It shows coordinate, strand,
+  mean odds-ratio score, and specificity of score, and the motif. 
+  From the output users can chose regions with matching blocks to perform gene prediction with AUGUSTUS-PPX using the same block profile.
 
 ## EXAMPLE
-
   > fastBlockSearch --cutoff=1.1 chr4.103M.fa PF00225_seed.prfl
-
+  
   Hits found in chr4 103000000 105000000
   Score:207.987
   Mult. score:4.83391
@@ -45,6 +34,12 @@ prediction with AUGUSTUS-PPX using the same block profile.
   1117399 unknown_B[1,7]  -       3.59083 5.03059 .CLDRVF
   1119420 unknown_A[0,8]  -       4.64107 6.44285 RVRPLNSR.
 
+## OPTIONS
+
+*--cutoff=c*::
+  This minimum for the average log score of the motifs found can be used to adjust the sensitivity of the block search.
+  The standard cutoff is 0.7, which is very sensitive but can give many false positive hits for smaller profiles.
+
 ## AUTHORS
 
 Oliver Keller
diff --git a/debian/mansrc/prepareAlign.1.adoc b/debian/mansrc/prepareAlign.1.adoc
index 818c5f4..34da081 100644
--- a/debian/mansrc/prepareAlign.1.adoc
+++ b/debian/mansrc/prepareAlign.1.adoc
@@ -9,14 +9,11 @@ prepareAlign - prepare an alignment for block profile creation by deleting gap-r
 *prepareAlign* < input.fa  > output.fa
 
 ## DESCRIPTION
+   An input multiple alignment of proteins is read from standard input. prepareAlign removes rows from it
+   with the aim of producing fully conserved blocks in the remaining alignment which is then output to standard output.
 
-An input multiple alignment of proteins is read from standard input.
-prepareAlign removes rows from it with the aim of producing fully conserved
-blocks in the remaining alignment which is then output to standard output.
-
-When an alignment contains many sequences and too many gaps, e.g. a full PFAM
-alignment, trying to run msa2prfl.pl results in the message "No blocks found in
-MSA". Then use "prepareAlign" first to eliminate sequences.
+   When an alignment contains many sequences and too many gaps, e.g. a full PFAM alignment, trying to run msa2prfl.pl
+   results in the message "No blocks found in MSA". Then use "prepareAlign" first to eliminate sequences.
 
 ## AUTHORS
 

-- 
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