[med-svn] [lambda-align] 01/04: New upstream version 1.0.1

Sascha Steinbiss satta at debian.org
Tue Jan 10 15:17:35 UTC 2017 

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

commit be1268687a2a2c79fb76d26f7821964f8ea0b423
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Tue Jan 10 16:03:01 2017 +0100

    New upstream version 1.0.1
---
 .travis.yml                 | 11 ++++++-----
 CMakeLists.txt              | 20 ++++++++++++++++++++
 INFO                        | 17 +++++++++--------
 LICENSE-BSD.rst             |  2 +-
 LICENSE.rst                 |  6 +++---
 src/CMakeLists.txt          |  5 ++++-
 src/holders.hpp             |  6 +++---
 src/lambda.cpp              |  4 ++--
 src/lambda.hpp              |  8 ++++----
 src/lambda_indexer.cpp      |  4 ++--
 src/lambda_indexer.hpp      |  4 ++--
 src/lambda_indexer_misc.hpp |  4 ++--
 src/match.hpp               |  4 ++--
 src/misc.hpp                |  4 ++--
 src/options.hpp             | 22 ++++++++++++----------
 src/output.hpp              |  4 ++--
 16 files changed, 76 insertions(+), 49 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index a73ebe4..8710ee5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,15 +9,16 @@ before_install:
  - test $(uname) = "Linux" && wget -O - http://llvm.org/apt/llvm-snapshot.gpg.key | sudo apt-key add - || true
  - test $(uname) = "Linux" && sudo apt-get update -y || true
  - test $(uname) = "Linux" && sudo apt-get install -qq -y g++-4.9 g++-5 g++-6 clang-3.8 clang-3.9 cmake cmake-data zlib1g-dev libbz2-dev || true
- - test $(uname) = "Darwin" && sudo brew update || true
- - test $(uname) = "Darwin" && sudo brew tap homebrew/versions || true
- - test $(uname) = "Darwin" && sudo brew install gcc5 || true
- - test $(uname) = "Darwin" && sudo brew install gcc6 || true
+ - test $(uname) = "Darwin" && brew update || true
+ - test $(uname) = "Darwin" && brew tap homebrew/versions || true
+ - test $(uname) = "Darwin" && brew install gcc5 || true
+ - test $(uname) = "Darwin" && brew install gcc6 || true
 matrix:
   include:
     - os: linux
       compiler: gcc-4.9
       install: export CXX="g++-4.9"
+      env: CMAKE_ARGS="-DLAMBDA_STATIC_BUILD=1"
     - os: linux
       compiler: gcc-5
       install: export CXX="g++-5"
@@ -34,7 +35,7 @@ matrix:
     - os: osx
       compiler: gcc-4.9
       install: export CXX="g++-4.9"
-      env: CMAKE_ARGS="-DLAMBDA_FASTBUILD=1"
+      env: CMAKE_ARGS="-DLAMBDA_FASTBUILD=1 -DLAMBDA_STATIC_BUILD=1"
     - os: osx
       compiler: gcc-5
       install: export CXX="g++-5"
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 58969a9..8ed38ca 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -6,11 +6,23 @@ cmake_minimum_required (VERSION 3.0.0)
 string(ASCII 27 Esc)
 set(ColourBold  "${Esc}[1m")
 set(ColourReset "${Esc}[m")
+set(ColourRed   "${Esc}[31m")
+
 message ("${ColourBold}Compiler Detection${ColourReset}")
 
 project (lambda CXX)
 
 # ----------------------------------------------------------------------------
+# Make "Release" the default cmake build type
+# ----------------------------------------------------------------------------
+
+if (NOT CMAKE_BUILD_TYPE)
+    set (CMAKE_BUILD_TYPE Release CACHE STRING
+         "Choose the type of build, options are: Debug Release RelWithDebInfo"
+         FORCE)
+endif ()
+
+# ----------------------------------------------------------------------------
 # Begin of dependency detection
 # ----------------------------------------------------------------------------
 
@@ -34,6 +46,14 @@ endif ()
 add_subdirectory(src)
 
 # ----------------------------------------------------------------------------
+# Warn if cmake build type is not "Release"
+# ----------------------------------------------------------------------------
+
+if (NOT CMAKE_BUILD_TYPE STREQUAL Release)
+    message (STATUS "${ColourRed}CMAKE_BUILD_TYPE is not \"Release\", your binaries will be slow.${ColourReset}")
+endif ()
+
+# ----------------------------------------------------------------------------
 # Add Tests
 # ----------------------------------------------------------------------------
 
diff --git a/INFO b/INFO
index 4e6dccb..ce05463 100644
--- a/INFO
+++ b/INFO
@@ -1,11 +1,12 @@
 Name: lambda
-Author: Hannes Hauswedell <hannes.hauswedell at molgen.mpg.de>
-Maintainer: Hannes Hauswedell <hannes.hauswedell at molgen.mpg.de>
+Author: Hannes Hauswedell <hannes.hauswedell at fu-berlin.de>
+Maintainer: Hannes Hauswedell <hannes.hauswedell at fu-berlin.de>
 License: GPL v3
-Copyright: 2013-2014, FU Berlin
+Copyright: 2013-2017, Hannes Hauswedell; 2016-2017 Knut Reinert, FU-Berlin
 Status: under development
-Description: NCBI-Blast compatible local aligner that is very fast.
- LAMBDA: the Local Aligner for Massive Biological DatA is a fast local
- aligner optimized for NGS data and protein searches, but it also works on
- DNA-DNA searches. It is faster than most of its competitors while still being
- rather sensitive.
+Description: Lambda is a biological sequence aligner optimized for many
+query sequences and searches in protein space. It is highly compatible
+to BLAST (bitscore and e-value statistics, tab seperated and verbose
+output formats), much faster than BLAST and many other comparable tools
+and supports many other input and output formats, including standards-
+conformant .sam and .bam and many compression types
diff --git a/LICENSE-BSD.rst b/LICENSE-BSD.rst
index 8b5eb0d..e1e746a 100644
--- a/LICENSE-BSD.rst
+++ b/LICENSE-BSD.rst
@@ -1,7 +1,7 @@
 BSD-License (3-clause)
 ======================
 
- | Copyright (c) 2006-2016, Knut Reinert, Freie Universität Berlin
+ | Copyright (c) 2016-2017, Knut Reinert, Freie Universität Berlin
  | All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
diff --git a/LICENSE.rst b/LICENSE.rst
index 6c89f88..1df6c54 100644
--- a/LICENSE.rst
+++ b/LICENSE.rst
@@ -2,7 +2,7 @@ lambda copyright
 ================
 ::
 
-  Copyright (c) 2013-2016, Hannes Hauswedell
+  Copyright (c) 2013-2017, Hannes Hauswedell
   All rights reserved.
 
 Lambda is *free software*: you can redistribute it and/or modify
@@ -21,7 +21,7 @@ rights and obligations implied.
 Some of the contributions to Lambda are alternatively or additionally
 ::
 
-  Copyright (c) 2016, Knut Reinert and Freie Universität Berlin
+  Copyright (c) 2016-2017, Knut Reinert and Freie Universität Berlin
 
 These are covered by the three clause BSD license as can be found in
 the file `LICENSE-BSD.rst <./LICENSE-BSD.rst>`__. In cases of doubt
@@ -38,7 +38,7 @@ SeqAn copyright
 ---------------
 ::
 
-  Copyright (c) 2006-2016, Knut Reinert and Freie Universität Berlin
+  Copyright (c) 2006-2017, Knut Reinert and Freie Universität Berlin
 
 SeqAn is published under the terms of the three clause BSD license as can
 be found in the file `include/seqan/LICENSE <./include/seqan/LICENSE>`__
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 8c18c27..9cedcd9 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -13,7 +13,7 @@
 # change this after every release
 set (SEQAN_APP_VERSION_MAJOR "1")
 set (SEQAN_APP_VERSION_MINOR "0")
-set (SEQAN_APP_VERSION_PATCH "0")
+set (SEQAN_APP_VERSION_PATCH "1")
 
 # don't change the following
 set (SEQAN_APP_VERSION "${SEQAN_APP_VERSION_MAJOR}.${SEQAN_APP_VERSION_MINOR}.${SEQAN_APP_VERSION_PATCH}")
@@ -134,6 +134,9 @@ message(   "     LAMBDA_STATIC_BUILD      ${LAMBDA_STATIC_BUILD}")
 message(STATUS "Run 'cmake -LH' to get a comment on each option.")
 message(STATUS "Remove CMakeCache.txt and re-run cmake with -DOPTIONNAME=ON|OFF to change an option.")
 
+# deactivate the version check until all issues are resolved
+add_definitions (-DSEQAN_DISABLE_VERSION_CHECK="YES")
+
 # ----------------------------------------------------------------------------
 # Compiler specifics
 # ----------------------------------------------------------------------------
diff --git a/src/holders.hpp b/src/holders.hpp
index d397855..cf0541a 100644
--- a/src/holders.hpp
+++ b/src/holders.hpp
@@ -1,8 +1,8 @@
 // ==========================================================================
 //                                  lambda
 // ==========================================================================
-// Copyright (c) 2013-2016, Hannes Hauswedell <h2 @ fsfe.org>
-// Copyright (c) 2016, Knut Reinert and Freie Universität Berlin
+// Copyright (c) 2013-2017, Hannes Hauswedell <h2 @ fsfe.org>
+// Copyright (c) 2016-2017, Knut Reinert and Freie Universität Berlin
 // All rights reserved.
 //
 // This file is part of Lambda.
@@ -174,7 +174,7 @@ void printStats(StatsHolder const & stats, LambdaOptions const & options)
                   << "\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)
diff --git a/src/lambda.cpp b/src/lambda.cpp
index 88288e4..5fc0427 100644
--- a/src/lambda.cpp
+++ b/src/lambda.cpp
@@ -1,8 +1,8 @@
 // ==========================================================================
 //                                  lambda
 // ==========================================================================
-// Copyright (c) 2013-2016, Hannes Hauswedell <h2 @ fsfe.org>
-// Copyright (c) 2016, Knut Reinert and Freie Universität Berlin
+// Copyright (c) 2013-2017, Hannes Hauswedell <h2 @ fsfe.org>
+// Copyright (c) 2016-2017, Knut Reinert and Freie Universität Berlin
 // All rights reserved.
 //
 // This file is part of Lambda.
diff --git a/src/lambda.hpp b/src/lambda.hpp
index c83ca44..2dcefb6 100644
--- a/src/lambda.hpp
+++ b/src/lambda.hpp
@@ -1,8 +1,8 @@
 // ==========================================================================
 //                                  lambda
 // ==========================================================================
-// Copyright (c) 2013-2016, Hannes Hauswedell <h2 @ fsfe.org>
-// Copyright (c) 2016, Knut Reinert and Freie Universität Berlin
+// Copyright (c) 2013-2017, Hannes Hauswedell <h2 @ fsfe.org>
+// Copyright (c) 2016-2017, Knut Reinert and Freie Universität Berlin
 // All rights reserved.
 //
 // This file is part of Lambda.
@@ -701,8 +701,8 @@ seedLooksPromising(LocalDataHolder<TGlobalHolder, TScoreExtension> const & lH,
         }
 
         effectiveLength = std::min({
-                            length(lH.gH.qrySeqs[m.qryId]) - effectiveQBegin,
-                            length(lH.gH.subjSeqs[m.subjId]) - effectiveSBegin,
+                            static_cast<uint64_t>(length(lH.gH.qrySeqs[m.qryId]) - effectiveQBegin),
+                            static_cast<uint64_t>(length(lH.gH.subjSeqs[m.subjId]) - effectiveSBegin),
                             effectiveLength});
 //         std::cout << effectiveQBegin << "\t" << effectiveSBegin << "\t"
 //                   << effectiveLength << "\n";
diff --git a/src/lambda_indexer.cpp b/src/lambda_indexer.cpp
index d53f0df..5bf68f6 100644
--- a/src/lambda_indexer.cpp
+++ b/src/lambda_indexer.cpp
@@ -1,8 +1,8 @@
 // ==========================================================================
 //                                  lambda
 // ==========================================================================
-// Copyright (c) 2013-2016, Hannes Hauswedell <h2 @ fsfe.org>
-// Copyright (c) 2016, Knut Reinert and Freie Universität Berlin
+// Copyright (c) 2013-2017, Hannes Hauswedell <h2 @ fsfe.org>
+// Copyright (c) 2016-2017, Knut Reinert and Freie Universität Berlin
 // All rights reserved.
 //
 // This file is part of Lambda.
diff --git a/src/lambda_indexer.hpp b/src/lambda_indexer.hpp
index 54fc759..1638744 100644
--- a/src/lambda_indexer.hpp
+++ b/src/lambda_indexer.hpp
@@ -1,8 +1,8 @@
 // ==========================================================================
 //                                  lambda
 // ==========================================================================
-// Copyright (c) 2013-2016, Hannes Hauswedell <h2 @ fsfe.org>
-// Copyright (c) 2016, Knut Reinert and Freie Universität Berlin
+// Copyright (c) 2013-2017, Hannes Hauswedell <h2 @ fsfe.org>
+// Copyright (c) 2016-2017, Knut Reinert and Freie Universität Berlin
 // All rights reserved.
 //
 // This file is part of Lambda.
diff --git a/src/lambda_indexer_misc.hpp b/src/lambda_indexer_misc.hpp
index 94d3864..023fd16 100644
--- a/src/lambda_indexer_misc.hpp
+++ b/src/lambda_indexer_misc.hpp
@@ -1,8 +1,8 @@
 // ==========================================================================
 //                                  lambda
 // ==========================================================================
-// Copyright (c) 2013-2016, Hannes Hauswedell <h2 @ fsfe.org>
-// Copyright (c) 2016, Knut Reinert and Freie Universität Berlin
+// Copyright (c) 2013-2017, Hannes Hauswedell <h2 @ fsfe.org>
+// Copyright (c) 2016-2017, Knut Reinert and Freie Universität Berlin
 // All rights reserved.
 //
 // This file is part of Lambda.
diff --git a/src/match.hpp b/src/match.hpp
index bc664b5..96a0f89 100644
--- a/src/match.hpp
+++ b/src/match.hpp
@@ -1,8 +1,8 @@
 // ==========================================================================
 //                                  lambda
 // ==========================================================================
-// Copyright (c) 2013-2016, Hannes Hauswedell <h2 @ fsfe.org>
-// Copyright (c) 2016, Knut Reinert and Freie Universität Berlin
+// Copyright (c) 2013-2017, Hannes Hauswedell <h2 @ fsfe.org>
+// Copyright (c) 2016-2017, Knut Reinert and Freie Universität Berlin
 // All rights reserved.
 //
 // This file is part of Lambda.
diff --git a/src/misc.hpp b/src/misc.hpp
index bd6de73..da14379 100644
--- a/src/misc.hpp
+++ b/src/misc.hpp
@@ -1,8 +1,8 @@
 // ==========================================================================
 //                                  lambda
 // ==========================================================================
-// Copyright (c) 2013-2016, Hannes Hauswedell <h2 @ fsfe.org>
-// Copyright (c) 2016, Knut Reinert and Freie Universität Berlin
+// Copyright (c) 2013-2017, Hannes Hauswedell <h2 @ fsfe.org>
+// Copyright (c) 2016-2017, Knut Reinert and Freie Universität Berlin
 // All rights reserved.
 //
 // This file is part of Lambda.
diff --git a/src/options.hpp b/src/options.hpp
index 7441cf9..b70b56a 100644
--- a/src/options.hpp
+++ b/src/options.hpp
@@ -1,8 +1,8 @@
 // ==========================================================================
 //                                  lambda
 // ==========================================================================
-// Copyright (c) 2013-2016, Hannes Hauswedell <h2 @ fsfe.org>
-// Copyright (c) 2016, Knut Reinert and Freie Universität Berlin
+// Copyright (c) 2013-2017, Hannes Hauswedell <h2 @ fsfe.org>
+// Copyright (c) 2016-2017, Knut Reinert and Freie Universität Berlin
 // All rights reserved.
 //
 // This file is part of Lambda.
@@ -321,13 +321,13 @@ sharedSetup(ArgumentParser & parser)
                                 std::string(SEQAN_REVISION) + ")";
     setVersion(parser, versionString);
     setDate(parser, __DATE__);
-    setShortCopyright(parser, "2013-2016 Hannes Hauswedell, released under the GNU GPL v3 (or later); "
-                              "2016 Knut Reinert and Freie Universität Berlin, released under the 3-clause-BSDL");
+    setShortCopyright(parser, "2013-2017 Hannes Hauswedell, released under the GNU GPL v3 (or later); "
+                              "2016-2017 Knut Reinert and Freie Universität Berlin, released under the 3-clause-BSDL");
 
     setCitation(parser, "Hauswedell et al (2014); doi: 10.1093/bioinformatics/btu439");
 
     setLongCopyright(parser,
-        " Copyright (c) 2013-2016, Hannes Hauswedell\n"
+        " Copyright (c) 2013-2017, Hannes Hauswedell\n"
         " All rights reserved.\n"
         "\n"
         " Lambda is free software: you can redistribute it and/or modify\n"
@@ -343,7 +343,7 @@ sharedSetup(ArgumentParser & parser)
         " You should have received a copy of the GNU General Public License\n"
         " along with Lambda.  If not, see <http://www.gnu.org/licenses/>.\n"
         "\n"
-        " Copyright (c) 2016 Knut Reinert and Freie Universität Berlin\n"
+        " Copyright (c) 2016-2017 Knut Reinert and Freie Universität Berlin\n"
         " All rights reserved.\n"
         "\n"
         " Redistribution and use in source and binary forms, with or without\n"
@@ -587,14 +587,14 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
 //         "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 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
     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 @@ parseCommandLine(LambdaIndexerOptions & options, int argc, char const ** argv)
     // 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/src/output.hpp b/src/output.hpp
index f0d9a2f..cad8fb5 100644
--- a/src/output.hpp
+++ b/src/output.hpp
@@ -1,8 +1,8 @@
 // ==========================================================================
 //                                  lambda
 // ==========================================================================
-// Copyright (c) 2013-2016, Hannes Hauswedell <h2 @ fsfe.org>
-// Copyright (c) 2016, Knut Reinert and Freie Universität Berlin
+// Copyright (c) 2013-2017, Hannes Hauswedell <h2 @ fsfe.org>
+// Copyright (c) 2016-2017, Knut Reinert and Freie Universität Berlin
 // All rights reserved.
 //
 // This file is part of Lambda.

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