[med-svn] r22675 - in trunk/packages/hhsuite/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Sat Aug 13 05:48:32 UTC 2016
Author: tille
Date: 2016-08-13 05:48:31 +0000 (Sat, 13 Aug 2016)
New Revision: 22675
Added:
trunk/packages/hhsuite/trunk/debian/patches/spelling.patch
Modified:
trunk/packages/hhsuite/trunk/debian/changelog
trunk/packages/hhsuite/trunk/debian/patches/series
Log:
Fix spelling
Modified: trunk/packages/hhsuite/trunk/debian/changelog
===================================================================
--- trunk/packages/hhsuite/trunk/debian/changelog 2016-08-13 05:44:01 UTC (rev 22674)
+++ trunk/packages/hhsuite/trunk/debian/changelog 2016-08-13 05:48:31 UTC (rev 22675)
@@ -3,6 +3,7 @@
* Use system defined log2 and log10 to enable build using gcc-6.1
Closes: #831115
* cme fix dpkg-control
+ * fix spelling
-- Andreas Tille <tille at debian.org> Sat, 13 Aug 2016 07:27:28 +0200
Modified: trunk/packages/hhsuite/trunk/debian/patches/series
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/series 2016-08-13 05:44:01 UTC (rev 22674)
+++ trunk/packages/hhsuite/trunk/debian/patches/series 2016-08-13 05:48:31 UTC (rev 22675)
@@ -9,3 +9,4 @@
version_bump
add_Makefile_in_data.patch
gcc-6.1.patch
+spelling.patch
Added: trunk/packages/hhsuite/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/spelling.patch (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/patches/spelling.patch 2016-08-13 05:48:31 UTC (rev 22675)
@@ -0,0 +1,57 @@
+Description: Fix spelling
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 13 Aug 2016 07:27:28 +0200
+
+--- a/src/hhblits.C
++++ b/src/hhblits.C
+@@ -398,7 +398,7 @@ void help(char all=0)
+ printf(" -cpu <int> number of CPUs to use (for shared memory SMPs) (default=%i) \n",cpu);
+ #endif
+ 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[ max available memory in GB (def=%.1f) \n",par.maxmem);
+--- a/src/hhsearch.C
++++ b/src/hhsearch.C
+@@ -325,7 +325,7 @@ void help(char all=0)
+ if (all) {
+ printf(" -maxres <int> max number of HMM columns (def=%5i) \n",par.maxres);
+ printf(" -maxmem [1,inf[ max available memory in GB (def=%.1f) \n",par.maxmem);
+- 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(" -calm {0,..,3} empirical score calibration of 0:query 1:template 2:both \n");
+ printf(" default 3: neural network-based estimation of EVD params \n");
+ // printf(" -opt <file> parameter optimization mode (def=off): return sum of ranks \n");
+--- a/src/hhsuite-userguide.tex
++++ b/src/hhsuite-userguide.tex
+@@ -1542,7 +1542,7 @@ Other options:
+ -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=15002)
+ -maxmem [1,inf[ max available memory in GB (def=3.0)
+@@ -1663,7 +1663,7 @@ Other options:
+ -v <int> verbose mode: 0:no screen output 1:only warings 2: verbose
+ -maxres <int> max number of HMM columns (def=15002)
+ -maxmem [1,inf[ max available memory in GB (def=3.0)
+- -scores <file> write scores for all pairwise comparisions to file
++ -scores <file> write scores for all pairwise comparisons to file
+ -calm {0,..,3} empirical score calibration of 0:query 1:template 2:both
+ default 3: neural network-based estimation of EVD params
+
+--- a/src/cs/context_profile-inl.h
++++ b/src/cs/context_profile-inl.h
+@@ -36,7 +36,7 @@ void ContextProfile<Abc>::Read(FILE* fin
+ assert(len & 1);
+ if (nalph != Abc::kSize)
+ throw Exception("Alphabet size of serialized context profile 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
+ probs.Resize(len);
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