[med-svn] [lambda-align] 01/01: add patch to fix documentation issues

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository lambda-align.

commit 1b7f803a9e8557f342ed9940d33fa34035acaa81
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sat Aug 20 22:45:29 2016 +0000

    add patch to fix documentation issues
---
 debian/patches/fix-documentation.patch | 57 ++++++++++++++++++++++++++++++++++
 debian/patches/series                  |  1 +
 2 files changed, 58 insertions(+)

diff --git a/debian/patches/fix-documentation.patch b/debian/patches/fix-documentation.patch
new file mode 100644
index 0000000..66f7720
--- /dev/null
+++ b/debian/patches/fix-documentation.patch
@@ -0,0 +1,57 @@
+Description: fix documentation strings
+Author: Sascha Steinbiss <satta at debian.org>
+--- a/src/holders.hpp
++++ b/src/holders.hpp
+@@ -174,7 +174,7 @@
+                   << "\033[0m\n\n";
+ 
+         if (rem != stats.hitsFinal)
+-            std::cout << "WARNING: hits dont add up\n";
++            std::cout << "WARNING: hits don't add up\n";
+     }
+ 
+     if (options.verbosity >= 1)
+--- a/src/options.hpp
++++ b/src/options.hpp
+@@ -587,14 +587,14 @@
+ //         "STR"));
+ //     setValidValues(parser, "query-alphabet", "dna5 aminoacid");
+ //     setDefaultValue(parser, "query-alphabet", "dna5");
+-// 
++//
+ //     addOption(parser, ArgParseOption("da", "db-alphabet",
+ //         "original alphabet of the subject sequences",
+ //         ArgParseArgument::STRING,
+ //         "STR"));
+ //     setValidValues(parser, "db-alphabet", "dna5 aminoacid");
+ //     setDefaultValue(parser, "db-alphabet", "aminoacid");
+-// 
++//
+ //     addOption(parser, ArgParseOption("sa", "seeding-alphabet",
+ //         "alphabet to use during seeding (reduction possible)",
+ //         ArgParseArgument::STRING,
+@@ -710,7 +710,7 @@
+     addSection(parser, "Scoring");
+ 
+     addOption(parser, ArgParseOption("sc", "scoring-scheme",
+-        "'45' for Blosum45; '62' for Blosum62 (default);  '80' for Blosum80; "
++        "use '45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80; "
+         "[ignored for BlastN]",
+         ArgParseArgument::INTEGER));
+     setDefaultValue(parser, "scoring-scheme", "62");
+@@ -1033,12 +1033,14 @@
+     // Setup ArgumentParser.
+     ArgumentParser parser("lambda_indexer");
+ 
++    setShortDescription(parser, "indexer for creating lambda-compatible databases");
++
+     // Define usage line and long description.
+     addUsageLine(parser, "[\\fIOPTIONS\\fP] \\-d DATABASE.fasta\\fP");
+ 
+     sharedSetup(parser);
+ 
+-    addDescription(parser, "This is the indexer_binary for creating a lambda-compatible databases.");
++    addDescription(parser, "This is the indexer_binary for creating lambda-compatible databases.");
+ 
+     addSection(parser, "Input Options");
+     addOption(parser, ArgParseOption("d", "database",
diff --git a/debian/patches/series b/debian/patches/series
index 12aa523..f232c0f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 cmake-seqan-modules.patch
 do-not-install-separate-license-files.patch
+fix-documentation.patch

-- 
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