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Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 13 Apr 2015 22:29:27 +0200
Description: Spelling
--- a/src/tigr/mgaps.cc
+++ b/src/tigr/mgaps.cc
@@ -694,7 +694,7 @@ static void Usage
"\n"
"Clusters MUMs based on diagonals and separation.\n"
"Input is from stdin in format produced by mummer.\n"
- "Ouput goes to stdout.\n"
+ "Output goes to stdout.\n"
"\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
--- 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);
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