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Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 27 Jan 2017 13:18:48 +0100
Description: Do not use code copy of libssw
Forwarded: not-needed
--- a/seq_test/Makefile.am
+++ b/seq_test/Makefile.am
@@ -19,4 +19,4 @@ seq_test_SOURCES = seq_test.cpp \
../src/ReadFilter.cpp ../src/BamRecord.cpp \
../src/BWAWrapper.cpp \
../src/RefGenome.cpp ../src/SeqPlot.cpp ../src/BamHeader.cpp \
- ../src/FermiAssembler.cpp ../src/ssw_cpp.cpp ../src/ssw.c
+ ../src/FermiAssembler.cpp
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -2,7 +2,7 @@ lib_LTLIBRARIES = libseqlib.la
libseqlib_la_CPPFLAGS = -I/usr/include -I/usr/include/htslib -I/usr/include/fml `@PKG_CONFIG@ --cflags jsoncpp` -Wno-sign-compare
-libseqlib_la_SOURCES = FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp ssw_cpp.cpp ssw.c \
+libseqlib_la_SOURCES = FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp \
GenomicRegion.cpp RefGenome.cpp BamWriter.cpp BamReader.cpp \
BWAWrapper.cpp BamRecord.cpp FermiAssembler.cpp BamHeader.cpp
-libseqlib_la_LDFLAGS = -version-info @LIB_VERSION@ -lfml `@PKG_CONFIG@ --libs htslib` `@PKG_CONFIG@ --libs jsoncpp`
+libseqlib_la_LDFLAGS = -version-info @LIB_VERSION@ -lfml `@PKG_CONFIG@ --libs htslib` `@PKG_CONFIG@ --libs jsoncpp` -lssw
--- a/src/BamRecord.cpp
+++ b/src/BamRecord.cpp
@@ -5,7 +5,7 @@
#include <cctype>
#include <stdexcept>
-#include "SeqLib/ssw_cpp.h"
+#include <ssw_cpp.h>
#define TAG_DELIMITER "^"
#define CTAG_DELIMITER '^'
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