[med-svn] [mummer] 01/01: More spelling fixes

[Andreas Tille]

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

tille pushed a commit to branch master
in repository mummer.

commit e100b0c6c5c91cf6351e88ca8e588cc0de6b75fb
Author: Andreas Tille <tille at debian.org>
Date:   Sat Jul 23 22:04:23 2016 +0200

    More spelling fixes
---
 debian/mummer.1               |  4 ++--
 debian/patches/spelling.patch | 40 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 42 insertions(+), 2 deletions(-)

diff --git a/debian/mummer.1 b/debian/mummer.1
index afc37f3..8558575 100644
--- a/debian/mummer.1
+++ b/debian/mummer.1
@@ -88,7 +88,7 @@ will be ordered as found in the <deltafile> input.
 .SH DESCRIPTION
 
 .SH OPTIONS
-All tools (exept for gaps) obey to the \-h, \-\-help, \-V and \-\-version options
+All tools (except for gaps) obey to the \-h, \-\-help, \-V and \-\-version options
 as one would expect. This help is excellent and makes these man pages basically obsolete.
 .br
 .B combineMUMs
@@ -285,7 +285,7 @@ sufficiently long maximal matches of a substring in
                   cluster, measured in amino acids (default 30)
   \-l|minmatch     Set the minimum length of a single match, measured in amino
                   acids (default 6)
-  \-m|masklen      Set the maximum bookend masking lenth, measured in amino
+  \-m|masklen      Set the maximum bookend masking length, measured in amino
                   acids (default 8)
   \-o
   \-\-coords        Automatically generate the original PROmer1.1 ".coords"
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index 8672d88..574d375 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -77,3 +77,43 @@ Description: Spelling
    in the subject sequence, the number of the query in which
    it matches as well as the start of the match in the query.
    The function \texttt{showmaximalmatch} simply shows the 
+--- a/src/tigr/postpro.cc
++++ b/src/tigr/postpro.cc
+@@ -6,7 +6,7 @@
+ //      Purpose: To translate the coordinates referencing the concatenated
+ //              reference sequences back to the individual sequences and deal
+ //             with any conflict that may have arisen (i.e. a MUM that spans
+-//            the boundry between two sequences). Then to extend each cluster
++//            the boundary between two sequences). Then to extend each cluster
+ //           via Smith-Waterman techniques to expand the alignment coverage.
+ //          Alignments which encounter each other will be fused to form one
+ //         encompasing alignment when appropriate.
+@@ -392,24 +392,24 @@ int main
+ 	  CurrFrameA = i + 1;
+ 	  assert ( CurrFrameA > 0  &&  CurrFrameA < 7 );
+ 
+-	  //-- If the match spans across a frame boundry
++	  //-- If the match spans across a frame boundary
+ 	  if ( CurrFrameA < 1  ||  CurrFrameA > 6  ||
+ 	       sA + len - 1 > (Af[Seqi].len - ((CurrFrameA - 1) % 3)) / 3 + 1 ||
+ 	       sA <= 0 )
+ 	    {
+ 	      fprintf (stderr,
+-                 "\nWARNING: A MUM was found extending beyond the boundry of:\n"
++                 "\nWARNING: A MUM was found extending beyond the boundary of:\n"
+                  "         Reference sequence '>%s', frame %d\n"
+                  "Please file a bug report\n"
+                  "Attempting to continue.\n", Af[Seqi].Id, CurrFrameA);
+               continue;
+ 	    }
+ 
+-          //-- If the match spans across a sequence boundry
++          //-- If the match spans across a sequence boundary
+           if ( sA + len - 1 > refLen (Af[Seqi].len) || sA <= 0 )
+             {
+               fprintf (stderr,
+-                 "\nWARNING: A MUM was found extending beyond the boundry of:\n"
++                 "\nWARNING: A MUM was found extending beyond the boundary of:\n"
+                  "         Reference sequence '>%s'\n"
+                  "Please file a bug report\n"
+                  "Attempting to continue.\n", Af[Seqi].Id);

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mummer.git