Author: Andreas Tille <tille@debian.org>
Last-Update: 2015-04-15
Description: Spelling fixes

--- a/doc/murasaki.1
+++ b/doc/murasaki.1
@@ -193,7 +193,7 @@
 reference and may be useful as an alternative in the unlikely event
 you're dealing with an environment where the adaptive hasher is
 unsuitable (for example a sequence consisting of only A and T (leaving
-1 out of every 2 bits unitilized)).
+1 out of every 2 bits uninitialized)).
 .SS "\s-1MEMORY\s0 \s-1SCALING\s0"
 .IX Subsection "MEMORY SCALING"
 Murasaki can take a lot of memory. Storing the location of each seed
@@ -204,7 +204,7 @@
 is the hash table structure, where each bucket carries a small
 overhead and unused are simply wasted space. More hash table buckets
 (i.e. a longer hash table) decreases the expected number of
-collisions, leading to faster executation time. Therefore Murasaki
+collisions, leading to faster execution time. Therefore Murasaki
 tries to use as many buckets as possible by inspecting the available
 system memory and using as much as it can while still storing all the
 seed locations. If this automatic scaling is ineffective, setting the
@@ -216,7 +216,7 @@
 .IX Subsection "PARALLELIZATION"
 Murasaki is designed to run in parallel using \s-1MPI\s0. Consult the
 documentation for the specific variations of your \s-1MPI\s0 implementation,
-however in general the executation method looks like:
+however in general the execution method looks like:
 .PP
 .Vb 1
 \& mpirun [MPI options] murasaki [murasaki options] \-p[pattern] [seq1 ...]
@@ -338,7 +338,7 @@
 .IP "\-\-scorebyminimumpair <B>" 4
 .IX Item "--scorebyminimumpair <B>"
 Do anchor scoring by minimum pair when appropriate
-(default). Alternative is arithmatic mean (seldom useful, but
+(default). Alternative is arithmetic mean (seldom useful, but
 theoretically faster).
 =item \-\-rifts|\-/ <D>
 .Sp
@@ -360,7 +360,7 @@
 .IP "\-\-scorebyminimumpair <B>" 4
 .IX Item "--scorebyminimumpair <B>"
 Do anchor scoring by minimum pair when appropriate
-(default). Alternative is arithmatic mean (seldom useful, but
+(default). Alternative is arithmetic mean (seldom useful, but
 theoretically faster).
 .SS "Output options"
 .IX Subsection "Output options"
@@ -521,7 +521,7 @@
 .IX Item "--mpidistro|-L <B>"
 Toggles use of \s-1MPI\s0 to distribute sequence data over (if the sequence
 is available on local disk on each node then turning this off may
-potentially accerlate the intial sequence loading).
+potentially accerlate the initial sequence loading).
 .IP "\-\-waittoanchor|\-w <B>" 4
 .IX Item "--waittoanchor|-w <B>"
 Postpone actual anchor computation until all location sets have been
@@ -553,8 +553,8 @@
 .IP "\-\-memorybalance|\-a <B>" 4
 .IX Item "--memorybalance|-a <B>"
 .RS 4
-.IP "If yes (deafult): balance hash storage between nodes based on the amount of available ram." 4
-.IX Item "If yes (deafult): balance hash storage between nodes based on the amount of available ram."
+.IP "If yes (default): balance hash storage between nodes based on the amount of available ram." 4
+.IX Item "If yes (default): balance hash storage between nodes based on the amount of available ram."
 .IP "If no: distribute storage evently. This more likely to achieve optimal run times, but might not utilize memory as efficiently." 4
 .IX Item "If no: distribute storage evently. This more likely to achieve optimal run times, but might not utilize memory as efficiently."
 .RE
@@ -628,7 +628,7 @@
 .SS ".anchors files"
 .IX Subsection ".anchors files"
 These files are 1 anchor per line, with a 3\-tuple per sequence. Each
-touple represents the start and stop coordinates and strand of the
+tuple represents the start and stop coordinates and strand of the
 anchored interval on each sequence. The sequence order matches that of
 the order in the .seqs file. The coordinates are structured such that
 1 refers to the first base in the sequence, 2 to the second,
@@ -653,7 +653,7 @@
 This is an antiquated file format, but used by \s-1GMV\s0 to calculate
 statistics like TF-IDF scores, and has been kept around for that
 reason. The .anchors.details file has the same format and information
-as the .anchors file, however after the anchor touples are two more
+as the .anchors file, however after the anchor tuples are two more
 terms: a score, and a comma (,) delimited list of term and count pairs
 (written \*(L"term:count\*(R"). The score and count data might be varied
 depending on the \f(CW\*(C`\-\-histogram\*(C'\fR option choices.
@@ -699,7 +699,7 @@
 .PP
 The first line (always prefixed \*(L"R:\*(R") shows the repeating seed itself
 (where the . are the bases masked by the pattern). The subsequent
-lines show where these seeds occured in the input sequences (in the
+lines show where these seeds occurred in the input sequences (in the
 first (0) and second (1) sequences). Note that if there are no hits in
 a particular sequence, it doesn't include a blank line for that sequence. For example:
 .PP
--- a/doc/murasaki.html
+++ b/doc/murasaki.html
@@ -140,7 +140,7 @@
 reference and may be useful as an alternative in the unlikely event
 you're dealing with an environment where the adaptive hasher is
 unsuitable (for example a sequence consisting of only A and T (leaving
-1 out of every 2 bits unitilized)).</p>
+1 out of every 2 bits uninitialized)).</p>
 <p>
 </p>
 <h2><a name="memory_scaling">MEMORY SCALING</a></h2>
@@ -152,7 +152,7 @@
 is the hash table structure, where each bucket carries a small
 overhead and unused are simply wasted space. More hash table buckets
 (i.e. a longer hash table) decreases the expected number of
-collisions, leading to faster executation time. Therefore Murasaki
+collisions, leading to faster execution time. Therefore Murasaki
 tries to use as many buckets as possible by inspecting the available
 system memory and using as much as it can while still storing all the
 seed locations. If this automatic scaling is ineffective, setting the
@@ -165,7 +165,7 @@
 <h2><a name="parallelization">PARALLELIZATION</a></h2>
 <p>Murasaki is designed to run in parallel using MPI. Consult the
 documentation for the specific variations of your MPI implementation,
-however in general the executation method looks like:</p>
+however in general the execution method looks like:</p>
 <pre>
  mpirun [MPI options] murasaki [murasaki options] -p[pattern] [seq1 ...]</pre>
 <p>Murasaki in parallel divides the number of processors available (NP)
@@ -326,7 +326,7 @@
 
 <dd>
 <p>Do anchor scoring by minimum pair when appropriate
-(default). Alternative is arithmatic mean (seldom useful, but
+(default). Alternative is arithmetic mean (seldom useful, but
 theoretically faster).
 =item --rifts|-/ &lt;D&gt;</p>
 <p>Allow anchors to skip D sequences (default 0).</p>
@@ -357,7 +357,7 @@
 
 <dd>
 <p>Do anchor scoring by minimum pair when appropriate
-(default). Alternative is arithmatic mean (seldom useful, but
+(default). Alternative is arithmetic mean (seldom useful, but
 theoretically faster).</p>
 </dd>
 </dl>
@@ -606,7 +606,7 @@
 <dt><strong><a name="memorybalance_a_b" class="item">--memorybalance|-a &lt;B&gt;</a></strong></dt>
 
 <dl>
-<dt><strong>If yes (deafult): balance hash storage between nodes based on
+<dt><strong>If yes (default): balance hash storage between nodes based on
 the amount of available ram.</strong></dt>
 
 <dt><strong><a name="if_no_distribute_storage_evently_this_more_likely_to_achieve_optimal_run_times_but_might_not_utilize_memory_as_efficiently" class="item">If no: distribute storage evently. This more likely to achieve
@@ -697,7 +697,7 @@
 </p>
 <h2><a name="_anchors_files">.anchors files</a></h2>
 <p>These files are 1 anchor per line, with a 3-tuple per sequence. Each
-touple represents the start and stop coordinates and strand of the
+tuple represents the start and stop coordinates and strand of the
 anchored interval on each sequence. The sequence order matches that of
 the order in the .seqs file. The coordinates are structured such that
 1 refers to the first base in the sequence, 2 to the second,
@@ -719,7 +719,7 @@
 <p>This is an antiquated file format, but used by <em>GMV</em> to calculate
 statistics like TF-IDF scores, and has been kept around for that
 reason. The .anchors.details file has the same format and information
-as the .anchors file, however after the anchor touples are two more
+as the .anchors file, however after the anchor tuples are two more
 terms: a score, and a comma (,) delimited list of term and count pairs
 (written &quot;term:count&quot;). The score and count data might be varied
 depending on the <a href="#histogram"><code>--histogram</code></a> option choices.</p>
@@ -764,7 +764,7 @@
  1: 2480929222 -1874514626 2543723555 -2550045172</pre>
 <p>The first line (always prefixed &quot;R:&quot;) shows the repeating seed itself
 (where the . are the bases masked by the pattern). The subsequent
-lines show where these seeds occured in the input sequences (in the
+lines show where these seeds occurred in the input sequences (in the
 first (0) and second (1) sequences). Note that if there are no hits in
 a particular sequence, it doesn't include a blank line for that sequence. For example:</p>
 <pre>
--- a/doc/murasaki.pod
+++ b/doc/murasaki.pod
@@ -65,7 +65,7 @@
 reference and may be useful as an alternative in the unlikely event
 you're dealing with an environment where the adaptive hasher is
 unsuitable (for example a sequence consisting of only A and T (leaving
-1 out of every 2 bits unitilized)).
+1 out of every 2 bits uninitialized)).
 
 =head2 MEMORY SCALING
 
@@ -77,7 +77,7 @@
 is the hash table structure, where each bucket carries a small
 overhead and unused are simply wasted space. More hash table buckets
 (i.e. a longer hash table) decreases the expected number of
-collisions, leading to faster executation time. Therefore Murasaki
+collisions, leading to faster execution time. Therefore Murasaki
 tries to use as many buckets as possible by inspecting the available
 system memory and using as much as it can while still storing all the
 seed locations. If this automatic scaling is ineffective, setting the
@@ -90,7 +90,7 @@
 
 Murasaki is designed to run in parallel using MPI. Consult the
 documentation for the specific variations of your MPI implementation,
-however in general the executation method looks like:
+however in general the execution method looks like:
 
  mpirun [MPI options] murasaki [murasaki options] -p[pattern] [seq1 ...]
 
@@ -233,7 +233,7 @@
 =item --scorebyminimumpair <B>
 
 Do anchor scoring by minimum pair when appropriate
-(default). Alternative is arithmatic mean (seldom useful, but
+(default). Alternative is arithmetic mean (seldom useful, but
 theoretically faster).
 =item --rifts|-/ <D>
 
@@ -260,7 +260,7 @@
 =item --scorebyminimumpair <B>
 
 Do anchor scoring by minimum pair when appropriate
-(default). Alternative is arithmatic mean (seldom useful, but
+(default). Alternative is arithmetic mean (seldom useful, but
 theoretically faster).
 
 =back
@@ -486,7 +486,7 @@
 
 =over
 
-=item If yes (deafult): balance hash storage between nodes based on
+=item If yes (default): balance hash storage between nodes based on
 the amount of available ram.
 
 =item If no: distribute storage evently. This more likely to achieve
@@ -577,7 +577,7 @@
 =head2 .anchors files
 
 These files are 1 anchor per line, with a 3-tuple per sequence. Each
-touple represents the start and stop coordinates and strand of the
+tuple represents the start and stop coordinates and strand of the
 anchored interval on each sequence. The sequence order matches that of
 the order in the .seqs file. The coordinates are structured such that
 1 refers to the first base in the sequence, 2 to the second,
@@ -601,7 +601,7 @@
 This is an antiquated file format, but used by L<GMV> to calculate
 statistics like TF-IDF scores, and has been kept around for that
 reason. The .anchors.details file has the same format and information
-as the .anchors file, however after the anchor touples are two more
+as the .anchors file, however after the anchor tuples are two more
 terms: a score, and a comma (,) delimited list of term and count pairs
 (written "term:count"). The score and count data might be varied
 depending on the C<--histogram> option choices.
@@ -648,7 +648,7 @@
 
 The first line (always prefixed "R:") shows the repeating seed itself
 (where the . are the bases masked by the pattern). The subsequent
-lines show where these seeds occured in the input sequences (in the
+lines show where these seeds occurred in the input sequences (in the
 first (0) and second (1) sequences). Note that if there are no hits in
 a particular sequence, it doesn't include a blank line for that sequence. For example:
 
--- a/doc/murasaki.txt
+++ b/doc/murasaki.txt
@@ -58,7 +58,7 @@
     are available for reference and may be useful as an alternative in the
     unlikely event you're dealing with an environment where the adaptive
     hasher is unsuitable (for example a sequence consisting of only A and T
-    (leaving 1 out of every 2 bits unitilized)).
+    (leaving 1 out of every 2 bits uninitialized)).
 
   MEMORY SCALING
     Murasaki can take a lot of memory. Storing the location of each seed in
@@ -69,7 +69,7 @@
     hash table structure, where each bucket carries a small overhead and
     unused are simply wasted space. More hash table buckets (i.e. a longer
     hash table) decreases the expected number of collisions, leading to
-    faster executation time. Therefore Murasaki tries to use as many buckets
+    faster execution time. Therefore Murasaki tries to use as many buckets
     as possible by inspecting the available system memory and using as much
     as it can while still storing all the seed locations. If this automatic
     scaling is ineffective, setting the hash table size directly via the
@@ -81,7 +81,7 @@
   PARALLELIZATION
     Murasaki is designed to run in parallel using MPI. Consult the
     documentation for the specific variations of your MPI implementation,
-    however in general the executation method looks like:
+    however in general the execution method looks like:
 
      mpirun [MPI options] murasaki [murasaki options] -p[pattern] [seq1 ...]
 
@@ -200,7 +200,7 @@
 
     --scorebyminimumpair <B>
         Do anchor scoring by minimum pair when appropriate (default).
-        Alternative is arithmatic mean (seldom useful, but theoretically
+        Alternative is arithmetic mean (seldom useful, but theoretically
         faster). =item --rifts|-/ <D>
 
         Allow anchors to skip D sequences (default 0).
@@ -221,7 +221,7 @@
 
     --scorebyminimumpair <B>
         Do anchor scoring by minimum pair when appropriate (default).
-        Alternative is arithmatic mean (seldom useful, but theoretically
+        Alternative is arithmetic mean (seldom useful, but theoretically
         faster).
 
   Output options
@@ -372,7 +372,7 @@
 
     --memorybalance|-a <B>
 
-        If yes (deafult): balance hash storage between nodes based on the
+        If yes (default): balance hash storage between nodes based on the
         amount of available ram.
         If no: distribute storage evently. This more likely to achieve
         optimal run times, but might not utilize memory as efficiently.
@@ -428,7 +428,7 @@
 
   .anchors files
     These files are 1 anchor per line, with a 3-tuple per sequence. Each
-    touple represents the start and stop coordinates and strand of the
+    tuple represents the start and stop coordinates and strand of the
     anchored interval on each sequence. The sequence order matches that of
     the order in the .seqs file. The coordinates are structured such that 1
     refers to the first base in the sequence, 2 to the second, etc. Negative
@@ -450,7 +450,7 @@
     This is an antiquated file format, but used by GMV to calculate
     statistics like TF-IDF scores, and has been kept around for that reason.
     The .anchors.details file has the same format and information as the
-    .anchors file, however after the anchor touples are two more terms: a
+    .anchors file, however after the anchor tuples are two more terms: a
     score, and a comma (,) delimited list of term and count pairs (written
     "term:count"). The score and count data might be varied depending on the
     "--histogram" option choices.
@@ -493,7 +493,7 @@
 
     The first line (always prefixed "R:") shows the repeating seed itself
     (where the . are the bases masked by the pattern). The subsequent lines
-    show where these seeds occured in the input sequences (in the first (0)
+    show where these seeds occurred in the input sequences (in the first (0)
     and second (1) sequences). Note that if there are no hits in a
     particular sequence, it doesn't include a blank line for that sequence.
     For example:
--- a/src/murasaki.cc
+++ b/src/murasaki.cc
@@ -303,7 +303,7 @@
   if(opt.getOptSource("quickhash")!=OPT_SRC_MANUAL){
     int target=(opt.hashPref==OpenHash_t ? 0:3);
     if(opt.quick_hash!=target){
-      cout << "Auto> Switching hash function to "<<target<<" to accomodate "<<opt.hashPref_s()<<endl;
+      cout << "Auto> Switching hash function to "<<target<<" to accommodate "<<opt.hashPref_s()<<endl;
       opt.quick_hash=target;
     }
   }
--- a/src/options.cc
+++ b/src/options.cc
@@ -930,7 +930,7 @@
   --bigfirst|-I    = assign hashers to large memory nodes first\n\
   --hostbalance|-l = if yes (default): spread out hashers evenly among hosts\n\
                      if no: ignore host name when assigning jobs\n\
-  --memorybalance|-a = if yes (deafult): balance hash storage between nodes\n\
+  --memorybalance|-a = if yes (default): balance hash storage between nodes\n\
                        based on the amount of available ram.\n\
                        if no: distribute storage evently.\n\
   --distmerge|-< = if yes (default): during the merge step, send seeds to\n\
--- a/filter.pl
+++ b/filter.pl
@@ -1682,7 +1682,7 @@
  "--nobins" turns off binning and plots a raw (likely bumpy) histogram
  "--showall=crop" sends all data to gnuplot even on logscale plots (by
     default for logscale plots values <=1 at the extreme right end are
-    chopped off because they dont show up in gnuplot (1 is the baseline)
+    chopped off because they don't show up in gnuplot (1 is the baseline)
     but they  do affect the visible range, and thus causes some scrunching.
  "--showall=scale" manually sets to the X and Y ranges to the range of the
     data (so 1's are visibly different from 0's).
--- a/simpal.pl
+++ b/simpal.pl
@@ -272,7 +272,7 @@
 maxLoop -- specifies max separation for the ends of the palindromes
 maxDistance -- specifies the maximum difference in palindrome length
                when comparing palindromes
-tolerance -- max permissable misses in palindromes between sequences
+tolerance -- max permissible misses in palindromes between sequences
 
 Setting either to -1 means no limit