[med-svn] [sga] 01/05: To stupid if there is no default layout - I was simply missing commits from Gert in debian/unstable

[Andreas Tille]

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tille pushed a commit to branch debian/unstable
in repository sga.

commit 961dbd3c8194b8a34c60520cfd5c2e18912743cb
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jul 5 16:20:04 2016 +0200

    To stupid if there is no default layout - I was simply missing commits from Gert in debian/unstable
---
 debian/changelog                |  8 +++----
 debian/patches/0007-gcc-6.patch | 49 +++++++++++++++++++++++++++++++++++++++++
 debian/patches/series           |  2 +-
 3 files changed, 53 insertions(+), 6 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index fa6cbf0..60ab798 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,9 @@
 sga (0.10.14-2) UNRELEASED; urgency=medium
 
-  * Team upload.
-  * d/p/0007: Fix compilation with gcc-6, Closes:  #811664
-  * d/control: Update standards version to 3.9.8 
-  * d/control: Use secure git url 
+  * Fix gcc-6 issue (thanks to Matei David)
+    Closes: #811664
 
- -- Gert Wollny <gw.fossdev at gmail.com>  Tue, 05 Jul 2016 14:01:46 +0000
+ -- Andreas Tille <tille at debian.org>  Tue, 05 Jul 2016 15:51:28 +0200
 
 sga (0.10.14-1) unstable; urgency=medium
 
diff --git a/debian/patches/0007-gcc-6.patch b/debian/patches/0007-gcc-6.patch
new file mode 100644
index 0000000..b383886
--- /dev/null
+++ b/debian/patches/0007-gcc-6.patch
@@ -0,0 +1,49 @@
+Author: Matei David
+Last-Update: 2016-02-04
+Origin: https://github.com/jts/sga/pull/110/commits/2e6ba7572460b1cbf96bc74d385b4f3993164372
+Description: Fix gcc6 issues - made code C++14 friendly
+
+--- a/src/SGA/rmdup.cpp
++++ b/src/SGA/rmdup.cpp
+@@ -232,7 +232,7 @@ std::string parseDupHits(const StringVec
+     while(!done)
+     {
+         // Parse a line from the current file
+-        bool valid = getline(*reader_vec[currReaderIdx], line);
++        bool valid = static_cast<bool>(getline(*reader_vec[currReaderIdx], line));
+         ++numRead;
+         // Deal with switching the active reader and the end of files
+         if(!valid || numRead == buffer_size)
+--- a/src/SuffixTools/STCommon.h
++++ b/src/SuffixTools/STCommon.h
+@@ -96,7 +96,7 @@ struct SAElem
+         // Masks
+         static const uint8_t ID_BITS = 36; // Allows up to 68 billion IDs
+         static const uint8_t POS_BITS = 64 - ID_BITS;
+-        static const uint64_t HIGH_MASK = ~0 << POS_BITS;
++        static const uint64_t HIGH_MASK = ~0llu << POS_BITS;
+         static const uint64_t LOW_MASK = ~HIGH_MASK;
+ };
+ 
+--- a/src/Util/ClusterReader.cpp
++++ b/src/Util/ClusterReader.cpp
+@@ -67,7 +67,7 @@ bool ClusterReader::generate(ClusterVect
+ bool ClusterReader::readCluster(ClusterRecord& record)
+ {
+     std::string line;
+-    bool good = getline(*m_pReader, line);
++    bool good = static_cast<bool>(getline(*m_pReader, line));
+     if(!good || line.empty())
+         return false;
+     std::stringstream parser(line);
+--- a/src/Util/StdAlnTools.cpp
++++ b/src/Util/StdAlnTools.cpp
+@@ -119,7 +119,7 @@ std::string StdAlnTools::expandCigar(con
+     char code;
+     while(parser >> length)
+     {
+-        bool success = parser >> code;
++        bool success = static_cast<bool>(parser >> code);
+         expanded.append(length, code);
+         assert(success);
+         (void)success;
diff --git a/debian/patches/series b/debian/patches/series
index f69845a..706a8ef 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,4 +4,4 @@
 0004-Add-help-to-sga-bam2de.pl.patch
 0005-Remove-extensions-on-scripts-we-ship.patch
 0006-remove-google-addsense.patch
-0007-fix-gcc-6.patch
+0007-gcc-6.patch

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