[med-svn] [mummer] 05/06: fix more spelling issues

[Andreas Tille]

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tille pushed a commit to branch master
in repository mummer.

commit 0e6a90c2c9d7529394826c96092c93ae20b4232f
Author: Andreas Tille <tille at debian.org>
Date:   Sat Jul 23 21:54:04 2016 +0200

    fix more spelling issues
---
 debian/changelog              |  1 +
 debian/patches/spelling.patch | 64 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 65 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 16df108..5da9cff 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,7 @@ mummer (3.23+dfsg-1) UNRELEASED; urgency=medium
   * Moved packaging from SVN to Git
   * d/copyright: use Files-Excluded to clean up upstream source
   * cme fix dpkg-control
+  * fix more spelling issues
 
  -- Andreas Tille <tille at debian.org>  Sat, 23 Jul 2016 21:27:40 +0200
 
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index d5e86f1..8672d88 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -13,3 +13,67 @@ Description: Spelling
             "\n"
             "Options:\n"
             "-C       Check that fasta header labels alternately have \"Reverse\"\n"
+--- a/src/tigr/delta.hh
++++ b/src/tigr/delta.hh
+@@ -139,7 +139,7 @@ private:
+ 
+ 
+   //--------------------------------------------------- checkStream ------------
+-  //! \brief Check stream status and abort program if an error has occured
++  //! \brief Check stream status and abort program if an error has occurred
+   //!
+   //! \return void
+   //!
+--- a/src/tigr/postnuc.cc
++++ b/src/tigr/postnuc.cc
+@@ -9,7 +9,7 @@
+ //      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.
+@@ -372,16 +372,16 @@ int main
+ 	    {
+ 	      fprintf (stderr,
+ 		 "ERROR: A MUM was found with a start coordinate greater than\n"
+-                 "       the sequence length, a serious error has occured.\n"
++                 "       the sequence length, a serious error has occurred.\n"
+ 		 "       Please file a bug report\n");
+ 	      exit (EXIT_FAILURE);
+ 	    }
+ 
+-	  //-- If the match spans across a sequence boundry
++	  //-- If the match spans across a sequence boundary
+ 	  if ( sA + len - 1 > Af[Seqi].len || sA <= 0)
+ 	    {
+ 	      fprintf (stderr,
+-		 "WARNING: A MUM was found extending beyond the boundry of:\n"
++		 "WARNING: A MUM was found extending beyond the boundary of:\n"
+ 		 "         Reference sequence '>%s'\n\n"
+ 		 "Please check that the '-n' option is activated on 'mummer2'\n"
+ 		 "and try again, or file a bug report\n"
+--- a/src/kurtz/libbasedir/procopt.c
++++ b/src/kurtz/libbasedir/procopt.c
+@@ -295,7 +295,7 @@ Sint checkdoubleexclude(Uint numofopts,O
+       DEBUG2(2,"Exclude %s %s\n",opt[indi].optname,opt[indj].optname);
+       if(excludepairs[indi*numofopts+indj])
+       {
+-        ERROR2("option %s and option %s already specfied as excluded",
++        ERROR2("option %s and option %s already specified as excluded",
+                opt[indi].optname,opt[indj].optname);
+         return -1;
+       }
+--- a/src/kurtz/mm3src/procmaxmat.c
++++ b/src/kurtz/mm3src/procmaxmat.c
+@@ -269,7 +269,7 @@ static void showsequenceheader(Multiseq
+ 
+ /*
+   The following is one of three functions to further process 
+-  a MUM-candidate specfied by its length, its start position
++  a MUM-candidate specified by its length, its start position
+   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 

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