Code consolidation

BenLangmead · May 14, 2020 · 3945d8c · 3945d8c
1 parent 777cda3
commit 3945d8c
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Showing 149 changed files with 7,131 additions and 54,839 deletions.
diff --git a/Makefile b/Makefile
@@ -5,13 +5,7 @@
 prefix = /usr/local
 bindir = $(prefix)/bin
 
-SEQAN_DIR = ./SeqAn-1.1
-# treat SeqAn as a sysdir to suppress warnings
-SEQAN_INC = -isystem $(SEQAN_DIR)
-INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
-CPP = g++
-CXX = $(CPP)
-CC = gcc
+INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) -I third_party
 LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz
 HEADERS = $(wildcard *.h)
 BOWTIE_MM = 1
@@ -22,7 +16,7 @@ EXTRA_CXXFLAGS =
 CFLAGS += $(EXTRA_CFLAGS)
 CXXFLAGS += $(EXTRA_CXXFLAGS)
 WARNING_FLAGS = -Wall -Wno-unused-parameter -Wno-reorder \
-				-Wno-unused-local-typedefs
+		-Wno-unused-private-field
 
 RELEASE_DEPENDENCIES = $(if $(RELEASE_BUILD),static-libs)
 
@@ -205,7 +199,6 @@ GENERAL_LIST = $(wildcard scripts/*.sh) \
                $(wildcard genomes/NC_008253.fna) \
                $(wildcard reads/e_coli_1000.*) \
                $(wildcard reads/e_coli_1000_*) \
-               SeqAn-1.1 \
                bowtie \
                bowtie-build \
                bowtie-inspect \

diff --git a/SeqAn-1.1/GPL.txt b/SeqAn-1.1/GPL.txt
diff --git a/SeqAn-1.1/LGPL.txt b/SeqAn-1.1/LGPL.txt
diff --git a/SeqAn-1.1/README.txt b/SeqAn-1.1/README.txt
diff --git a/SeqAn-1.1/platform_linux_gcc.h b/SeqAn-1.1/platform_linux_gcc.h
diff --git a/SeqAn-1.1/platform_windows_mingw.h b/SeqAn-1.1/platform_windows_mingw.h
diff --git a/SeqAn-1.1/platform_windows_vs.h b/SeqAn-1.1/platform_windows_vs.h
diff --git a/SeqAn-1.1/seqan/basic.h b/SeqAn-1.1/seqan/basic.h