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Refactoring the variant calling code into its own directory

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commit b8106e880ad2749059bb94b6c4e35ea046995b4b 1 parent d8bac6d
@jts authored
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2  src/Algorithm/HapgenProcess.cpp
@@ -15,7 +15,7 @@
#include "StdAlnTools.h"
#include "HaplotypeBuilder.h"
#include "MultiAlignment.h"
-#include "DindelRealignWindow.h"
+
//
//
//
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6 src/Algorithm/Makefile.am
@@ -7,6 +7,7 @@ libalgorithm_a_CPPFLAGS = \
-I$(top_srcdir)/SQG \
-I$(top_srcdir)/SuffixTools \
-I$(top_srcdir)/Thirdparty \
+ -I$(top_srcdir)/GraphDiff \
-I$(top_srcdir)/Concurrency
libalgorithm_a_SOURCES = \
@@ -28,7 +29,6 @@ libalgorithm_a_SOURCES = \
LRCorrectionAlgorithm.h LRCorrectionAlgorithm.cpp \
LRCorrectionProcess.h LRCorrectionProcess.cpp \
StringThreader.h StringThreader.cpp \
- GraphCompare.h GraphCompare.cpp \
HapgenProcess.h HapgenProcess.cpp \
ExtensionDP.h ExtensionDP.cpp \
VariationBubbleBuilder.h VariationBubbleBuilder.cpp \
@@ -38,10 +38,6 @@ libalgorithm_a_SOURCES = \
MetagenomeBuilder.h MetagenomeBuilder.cpp \
HapgenUtil.h HapgenUtil.cpp \
BuilderCommon.h BuilderCommon.cpp \
- VCFTester.h VCFTester.cpp \
- DindelUtil.h DindelUtil.cpp \
- DindelRealignWindow.h DindelRealignWindow.cpp \
- DindelHMM.h DindelHMM.cpp \
ReadCoherentHaplotypeBuilder.h ReadCoherentHaplotypeBuilder.cpp \
OverlapHaplotypeBuilder.h OverlapHaplotypeBuilder.cpp \
KmerOverlaps.h KmerOverlaps.cpp
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0  src/Algorithm/DindelHMM.cpp → src/GraphDiff/DindelHMM.cpp
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0  src/Algorithm/DindelHMM.h → src/GraphDiff/DindelHMM.h
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0  src/Algorithm/DindelRealignWindow.cpp → src/GraphDiff/DindelRealignWindow.cpp
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0  src/Algorithm/DindelRealignWindow.h → src/GraphDiff/DindelRealignWindow.h
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0  src/Algorithm/DindelUtil.cpp → src/GraphDiff/DindelUtil.cpp
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0  src/Algorithm/DindelUtil.h → src/GraphDiff/DindelUtil.h
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0  src/Algorithm/GraphCompare.cpp → src/GraphDiff/GraphCompare.cpp
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0  src/Algorithm/GraphCompare.h → src/GraphDiff/GraphCompare.h
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0  src/Algorithm/VCFTester.cpp → src/GraphDiff/VCFTester.cpp
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0  src/Algorithm/VCFTester.h → src/GraphDiff/VCFTester.h
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2  src/Makefile.am
@@ -1,2 +1,2 @@
AUTOMAKE_OPTIONS = foreign
-SUBDIRS = bin Thirdparty Util SQG Bigraph Algorithm StringGraph Concurrency SuffixTools Scaffold SGA
+SUBDIRS = bin Thirdparty Util SQG Bigraph Algorithm StringGraph Concurrency SuffixTools Scaffold GraphDiff SGA
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2  src/SGA/Makefile.am
@@ -9,10 +9,12 @@ sga_CPPFLAGS = \
-I$(top_srcdir)/Algorithm \
-I$(top_srcdir)/SQG \
-I$(top_srcdir)/Scaffold \
+ -I$(top_srcdir)/GraphDiff \
-I$(top_srcdir)/Thirdparty
sga_LDADD = \
$(top_builddir)/Scaffold/libscaffold.a \
+ $(top_builddir)/GraphDiff/libgraphdiff.a \
$(top_builddir)/StringGraph/libstringgraph.a \
$(top_builddir)/Concurrency/libconcurrency.a \
$(top_builddir)/Algorithm/libalgorithm.a \
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1  src/configure.ac
@@ -95,6 +95,7 @@ AC_CONFIG_FILES([Makefile
StringGraph/Makefile
Concurrency/Makefile
SuffixTools/Makefile
+ GraphDiff/Makefile
Scaffold/Makefile
SGA/Makefile])
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