[med-svn] [lambda-align] 06/06: Refresh patches

[Andreas Tille]

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

commit 78d8176660deef5e2b6c0f7e629fa51392cd063e
Author: Andreas Tille <tille at debian.org>
Date:   Sun Dec 18 09:21:05 2016 +0100

    Refresh patches
---
 debian/patches/cast-min-initializer.patch |  2 +-
 debian/patches/fix-documentation.patch    | 30 +++++++++++++++---------------
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/debian/patches/cast-min-initializer.patch b/debian/patches/cast-min-initializer.patch
index e61163a..7e0ec0b 100644
--- a/debian/patches/cast-min-initializer.patch
+++ b/debian/patches/cast-min-initializer.patch
@@ -7,7 +7,7 @@ Forwarded: https://github.com/seqan/lambda/issues/68
 Applied-Upstream: https://github.com/seqan/lambda/commit/cdb7e755af9829e26bf6e5f9ddbb07b5102038ef
 --- a/src/lambda.hpp
 +++ b/src/lambda.hpp
-@@ -701,8 +701,8 @@
+@@ -784,8 +784,8 @@ seedLooksPromising(LocalDataHolder<TGlob
          }
  
          effectiveLength = std::min({
diff --git a/debian/patches/fix-documentation.patch b/debian/patches/fix-documentation.patch
index 3fa5502..a62d8e7 100644
--- a/debian/patches/fix-documentation.patch
+++ b/debian/patches/fix-documentation.patch
@@ -2,20 +2,9 @@ Description: fix documentation strings
 Author: Sascha Steinbiss <satta at debian.org>
 Forwarded: https://github.com/seqan/lambda/pull/65
 Applied-Upstream: https://github.com/seqan/lambda/pull/65
---- 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 @@
+@@ -615,14 +615,14 @@ parseCommandLine(LambdaOptions & options
  //         "STR"));
  //     setValidValues(parser, "query-alphabet", "dna5 aminoacid");
  //     setDefaultValue(parser, "query-alphabet", "dna5");
@@ -32,7 +21,7 @@ Applied-Upstream: https://github.com/seqan/lambda/pull/65
  //     addOption(parser, ArgParseOption("sa", "seeding-alphabet",
  //         "alphabet to use during seeding (reduction possible)",
  //         ArgParseArgument::STRING,
-@@ -710,7 +710,7 @@
+@@ -754,7 +754,7 @@ parseCommandLine(LambdaOptions & options
      addSection(parser, "Scoring");
  
      addOption(parser, ArgParseOption("sc", "scoring-scheme",
@@ -41,14 +30,14 @@ Applied-Upstream: https://github.com/seqan/lambda/pull/65
          "[ignored for BlastN]",
          ArgParseArgument::INTEGER));
      setDefaultValue(parser, "scoring-scheme", "62");
-@@ -1033,12 +1033,14 @@
+@@ -1128,12 +1128,14 @@ parseCommandLine(LambdaIndexerOptions &
      // 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");
+     addUsageLine(parser, "[\\fIOPTIONS\\fP] \\-d DATABASE.fasta [-i INDEX.lambda]\\fP");
  
      sharedSetup(parser);
  
@@ -57,3 +46,14 @@ Applied-Upstream: https://github.com/seqan/lambda/pull/65
  
      addSection(parser, "Input Options");
      addOption(parser, ArgParseOption("d", "database",
+--- a/src/holders.hpp
++++ b/src/holders.hpp
+@@ -199,7 +199,7 @@ void printStats(StatsHolder const & stat
+                   << "\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";
+ 
+         std::cout << "Detailed Non-Wall-Clock times:\n"
+                   << " genSeeds: " << stats.timeGenSeeds << "\n"

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