[med-svn] [sga] 04/04: Drop backported GCC6 compatibility patch

[Afif Elghraoui]

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

commit 73da6d002e3226658aab6d3529bee1f1c94c667f
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon Aug 22 00:21:52 2016 -0700

    Drop backported GCC6 compatibility patch
---
 debian/patches/0007-gcc-6.patch | 50 -----------------------------------------
 debian/patches/series           |  1 -
 2 files changed, 51 deletions(-)

diff --git a/debian/patches/0007-gcc-6.patch b/debian/patches/0007-gcc-6.patch
deleted file mode 100644
index 7985552..0000000
--- a/debian/patches/0007-gcc-6.patch
+++ /dev/null
@@ -1,50 +0,0 @@
-Author: Matei David <matei at cs.toronto.edu>
-Date: Wed, 3 Feb 2016 23:28:04 -0500
-Bug-Debian: https://bugs.debian.org/811664
-Origin: https://github.com/jts/sga/pull/110/commits/2e6ba7572460b1cbf96bc74d385b4f3993164372
-Description: Fix compilation with gcc-6 (i.e. -std >= c++11)
-
---- 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 706a8ef..39bef58 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,4 +4,3 @@
 0004-Add-help-to-sga-bam2de.pl.patch
 0005-Remove-extensions-on-scripts-we-ship.patch
 0006-remove-google-addsense.patch
-0007-gcc-6.patch

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