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sci-biology/STAR: unbundle htslib properly
Closes: https://bugs.gentoo.org/833770 Signed-off-by: David Seifert <soap@gentoo.org>
This commit is contained in:
David Seifert
@@ -17,6 +17,7 @@ RDEPEND="sci-libs/htslib:="
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DEPEND="${RDEPEND}"
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BDEPEND="virtual/pkgconfig"
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PATCHES=( "${FILESDIR}"/${PN}-2.7.10a-fix-build-system.patch )
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DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf )
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pkg_pretend() {
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@@ -27,6 +28,13 @@ pkg_setup() {
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[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
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}
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src_prepare() {
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default
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# remove bundled htslib
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rm -r source/htslib || die
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}
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src_configure() {
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tc-export CC CXX PKG_CONFIG
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}
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195
sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch
Normal file
195
sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch
Normal file
@@ -0,0 +1,195 @@
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--- a/source/bam_cat.c
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+++ b/source/bam_cat.c
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@@ -52,8 +52,8 @@
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#include <stdlib.h>
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#include <unistd.h>
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-#include "htslib/htslib/bgzf.h"
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-#include "htslib/htslib/sam.h"
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+#include <htslib/bgzf.h>
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+#include <htslib/sam.h>
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#include <cstring>
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#define BUF_SIZE 0x10000
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--- a/source/bam_cat.h
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+++ b/source/bam_cat.h
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@@ -1,7 +1,7 @@
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#ifndef CODE_bam_cat
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#define CODE_bam_cat
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-#include "htslib/htslib/sam.h"
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+#include <htslib/sam.h>
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int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam);
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--- a/source/BAMfunctions.cpp
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+++ b/source/BAMfunctions.cpp
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@@ -1,5 +1,5 @@
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#include "BAMfunctions.h"
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-#include "htslib/htslib/kstring.h"
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+#include <htslib/kstring.h>
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string bam_cigarString (bam1_t *b) {//output CIGAR string
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--- a/source/bamRemoveDuplicates.cpp
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+++ b/source/bamRemoveDuplicates.cpp
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@@ -1,7 +1,7 @@
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#include <unordered_map>
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#include "bamRemoveDuplicates.h"
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#include <iostream>
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-#include "htslib/htslib/sam.h"
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+#include <htslib/sam.h>
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#include "IncludeDefine.h"
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#include SAMTOOLS_BGZF_H
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#include "ErrorWarning.h"
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--- a/source/IncludeDefine.h
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+++ b/source/IncludeDefine.h
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@@ -30,8 +30,8 @@
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#define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ )
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//external libs
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-#define SAMTOOLS_BGZF_H "htslib/htslib/bgzf.h"
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-#define SAMTOOLS_SAM_H "htslib/htslib/sam.h"
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+#define SAMTOOLS_BGZF_H <htslib/bgzf.h>
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+#define SAMTOOLS_SAM_H <htslib/sam.h>
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using namespace std;
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--- a/source/Makefile
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+++ b/source/Makefile
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@@ -12,11 +12,7 @@
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CXX ?= g++
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# pre-defined flags
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-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
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-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
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-LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
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-LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
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-LDFLAGS_gdb := $(LDFLAGS_shared)
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+LIBS := -pthread -lhts -lz
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DATE_FMT = --iso-8601=seconds
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ifdef SOURCE_DATE_EPOCH
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@@ -27,7 +23,7 @@
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BUILD_PLACE ?= $(HOSTNAME):$(shell pwd)
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-COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(BUILD_DATE) $(BUILD_PLACE)"'
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+COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE=""'
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GIT_CHECK := $(shell git status 1> /dev/null 2> /dev/null && echo 0)
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@@ -41,13 +37,13 @@
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# Defaults, can be overridden by make arguments or environment
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CXXFLAGS ?= -pipe -Wall -Wextra
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-CFLAGS ?= -pipe -Wall -Wextra -O3
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+CFLAGS ?= -pipe -Wall -Wextra
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CXXFLAGS_SIMD ?= -mavx2
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# Unconditionally set essential flags and optimization options
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CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) $(GIT_BRANCH_COMMIT_DIFF)
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-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
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-CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common)
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+CXXFLAGS_main := $(CXXFLAGS_common)
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+CXXFLAGS_gdb := $(CXXFLAGS_common)
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##########################################################################################################
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OBJECTS = SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o \
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@@ -130,7 +126,7 @@
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ifneq ($(MAKECMDGOALS),clean_solo)
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ifneq ($(MAKECMDGOALS),STARforMac)
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ifneq ($(MAKECMDGOALS),STARforMacGDB)
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-Depend.list: $(SOURCES) parametersDefault.xxd htslib
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+Depend.list: $(SOURCES) parametersDefault.xxd
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echo $(SOURCES)
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'rm' -f ./Depend.list
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$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
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@@ -142,57 +138,43 @@
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endif
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endif
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-htslib : htslib/libhts.a
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-
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-htslib/libhts.a :
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- $(MAKE) -C htslib lib-static
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-
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parametersDefault.xxd: parametersDefault
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xxd -i parametersDefault > parametersDefault.xxd
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STAR$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
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-STAR$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
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STAR$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
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- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
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+ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
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STARstatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
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-STARstatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
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STARstatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
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- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
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+ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
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STARlong$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
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-STARlong$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
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STARlong$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
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- $(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
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+ $(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
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STARlongStatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
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-STARlongStatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
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STARlongStatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
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- $(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
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+ $(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
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POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS)
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-POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
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POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS)
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- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
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+ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
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gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS)
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-gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
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gdb : Depend.list parametersDefault.xxd $(OBJECTS)
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- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
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+ $(CXX) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS)
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gdb-long : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
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-gdb-long : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
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gdb-long : Depend.list parametersDefault.xxd $(OBJECTS)
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- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
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+ $(CXX) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS)
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STARforMacStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
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-STARforMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
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STARforMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
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- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
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+ $(CXX) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS)
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STARlongForMacStatic : CXXFLAGS := -D'COMPILE_FOR_LONG_READS' $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
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-STARlongForMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
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STARlongForMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
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- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
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+ $(CXX) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS)
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--- a/source/signalFromBAM.h
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+++ b/source/signalFromBAM.h
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@@ -1,6 +1,6 @@
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#ifndef CODE_signalFromBAM
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#define CODE_signalFromBAM
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-#include "htslib/htslib/sam.h"
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+#include <htslib/sam.h>
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#include <fstream>
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#include <string>
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#include "Stats.h"
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--- a/source/STAR.cpp
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+++ b/source/STAR.cpp
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@@ -29,7 +29,7 @@
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#include "twoPassRunPass1.h"
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-#include "htslib/htslib/sam.h"
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+#include <htslib/sam.h>
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#include "parametersDefault.xxd"
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void usage(int usageType) {
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