[med-svn] [hhsuite] 04/06: extend spelling patch

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository hhsuite.

commit ac8a7d28e7775a4c8aacb06f9dd7130ad18b79ec
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sun Jan 15 09:12:16 2017 +0000

    extend spelling patch
---
 debian/patches/spelling.patch | 53 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index 207b14b..d073dc8 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -13,3 +13,56 @@ Last-Update: Sat, 13 Aug 2016 07:27:28 +0200
  
      // If everything went fine we can resize our data memmbers
      probs.Resize(len);
+--- a/doc/hhsuite-userguide.tex
++++ b/doc/hhsuite-userguide.tex
+@@ -1575,7 +1575,7 @@
+  -neffmax ]1,20] skip further search iterations when diversity Neff of query MSA 
+                 becomes larger than neffmax (default=10.0)
+  -cpu <int>     number of CPUs to use (for shared memory SMPs) (default=2)      
+- -scores <file> write scores for all pairwise comparisions to file               
++ -scores <file> write scores for all pairwise comparisons to file               
+  -atab   <file> write all alignments in tabular layout to file                   
+  -maxres <int>  max number of HMM columns (def=20001)             
+  -maxmem [1,inf[ limit memory for realignment (in GB) (def=3.0)          
+@@ -1706,7 +1706,7 @@
+ Other options:                                                                   
+  -v <int>       verbose mode: 0:no screen output  1:only warings  2: verbose (def=2)
+  -cpu <int>     number of CPUs to use (for shared memory SMPs) (default=2)      
+- -scores <file> write scores for all pairwise comparisions to file               
++ -scores <file> write scores for all pairwise comparisons to file               
+  -atab   <file> write all alignments in tabular layout to file                   
+  -maxres <int>  max number of HMM columns (def=20001)             
+  -maxmem [1,inf[ limit memory for realignment (in GB) (def=3.0)          
+--- a/src/cs/crf_state-inl.h
++++ b/src/cs/crf_state-inl.h
+@@ -44,7 +44,7 @@
+     assert(len & 1);
+     if (nalph != Abc::kSize)
+         throw Exception("Alphabet size of serialized CRF state should be %d"
+-                        "but is acutally %d!", Abc::kSize, nalph);
++                        "but is actually %d!", Abc::kSize, nalph);
+ 
+     // If everything went fine we can resize our data memmbers
+     context_weights.Resize(len);
+--- a/src/hhblits.cpp
++++ b/src/hhblits.cpp
+@@ -457,7 +457,7 @@
+   printf("                becomes larger than neffmax (default=%.1f)\n", par.neffmax);
+   printf(" -cpu <int>     number of CPUs to use (for shared memory SMPs) (default=%i)      \n", par.threads);
+   if (all) {
+-	printf(" -scores <file> write scores for all pairwise comparisions to file               \n");
++	printf(" -scores <file> write scores for all pairwise comparisons to file               \n");
+ 	  printf(" -filter_matrices filter matrices for similarity to output at most 100 matrices\n");
+     printf(" -atab   <file> write all alignments in tabular layout to file                   \n");
+     printf(" -maxres <int>  max number of HMM columns (def=%5i)             \n", par.maxres);
+--- a/src/hhsearch.cpp
++++ b/src/hhsearch.cpp
+@@ -241,7 +241,7 @@
+   printf(" -v <int>       verbose mode: 0:no screen output  1:only warings  2: verbose (def=%i)\n", par.v);
+   printf(" -cpu <int>     number of CPUs to use (for shared memory SMPs) (default=%i)      \n", par.threads);
+   if (all) {
+-  printf(" -scores <file> write scores for all pairwise comparisions to file               \n");
++  printf(" -scores <file> write scores for all pairwise comparisons to file               \n");
+     printf(" -atab   <file> write all alignments in tabular layout to file                   \n");
+     printf(" -maxres <int>  max number of HMM columns (def=%5i)             \n", par.maxres);
+     printf(" -maxmem [1,inf[ limit memory for realignment (in GB) (def=%.1f)          \n", par.maxmem);

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