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Description: bwa headers are got through a component tarball, not by
downloading anything.
Also loading the JNI from the canonical path.
Author: Pierre Gruet <pgt@debian.org>
Forwarded: not-needed
Last-Update: 2022-03-30
--- a/src/main/java/org/broadinstitute/hellbender/utils/bwa/BwaMemIndex.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/bwa/BwaMemIndex.java
@@ -435,41 +435,7 @@
if ( !nativeLibLoaded ) {
synchronized(BwaMemIndex.class) {
if ( !nativeLibLoaded ) {
- final String libNameOverride = System.getProperty("LIBBWA_PATH");
- if ( libNameOverride != null ) {
- System.load(libNameOverride);
- }
- else {
- final String osName = System.getProperty("os.name", "unknown").toUpperCase();
- final String osArch = System.getProperty("os.arch");
- final String libName;
- if ( !"x86_64".equals(osArch) && !"amd64".equals(osArch) ) {
- throw new IllegalStateException(
- "We have pre-built fermi-lite binaries only for x86_64 and amd64. "+
- "Your os.arch is "+osArch+"."+
- "Set property LIBBWA_PATH to point to a native library for your architecture.");
- }
- if ( osName.startsWith("MAC") ) libName = "/libbwa.Darwin.dylib";
- else if ( osName.startsWith("LINUX") ) libName = "/libbwa.Linux.so";
- else {
- throw new IllegalStateException(
- "We have pre-built fermi-lite binaries only for Linux and Mac. "+
- "Your os.name is "+osName+"."+
- "Set property LIBBWA_PATH to point to a native library for your operating system.");
- }
- try ( final InputStream is = BwaMemIndex.class.getResourceAsStream(libName) ) {
- if ( is == null ) {
- throw new IllegalStateException("Can't find resource "+libName);
- }
- final File tmpFile = File.createTempFile("libbwa.",".jnilib");
- tmpFile.deleteOnExit();
- Files.copy(is, tmpFile.toPath(), StandardCopyOption.REPLACE_EXISTING);
- System.load(tmpFile.getPath());
- }
- catch (IOException ioe ) {
- throw new IllegalStateException("Misconfiguration: Unable to load fermi-lite native library "+libName, ioe);
- }
- }
+ System.loadLibrary("bwa");
nativeLibLoaded = true;
}
}
--- a/src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c
+++ b/src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c
@@ -2,7 +2,6 @@
#include <fcntl.h>
#include <stdlib.h>
#include "jnibwa.h"
-#include "bwa/bwa_commit.h"
char * jstring_to_chars(JNIEnv* env, jstring in) {
--- a/src/main/c/Makefile
+++ b/src/main/c/Makefile
@@ -7,33 +7,26 @@
CC=gcc
#OS-dependent extension lookup
-UNAME := $(shell uname)
-ifeq ($(UNAME),Darwin)
-LIB_EXT=Darwin.dylib
-else
-LIB_EXT=Linux.so
-endif
+LIB_EXT=so
-BWA_MEM_COMMIT=cb950614ce7217788780b9a8d445c64cd4d8f62e
JNI_BASE_NAME=org_broadinstitute_hellbender_utils_bwa_BwaMemIndex
all: libbwa.$(LIB_EXT)
-libbwa.$(LIB_EXT): $(JNI_BASE_NAME).o jnibwa.o bwa/libbwa.a
+libbwa.$(LIB_EXT): $(JNI_BASE_NAME).o jnibwa.o bwaComponent/libbwa.a
$(CC) -ggdb -dynamiclib -shared -o $@ $^ -lm -lz -lpthread
-bwa:
- git clone https://github.com/lh3/bwa && cd bwa && git checkout $(BWA_MEM_COMMIT) && echo '#define BWA_COMMIT "'$(BWA_MEM_COMMIT)'"' > bwa_commit.h
- sed -i.bak -e's/\(LOBJS=.*\)/\1 bwtindex.o rle.o rope.o bwt.o is.o/g' bwa/Makefile
+bwaComponent:
+ sed -i.bak -e's/\(LOBJS=.*\)/\1 bwtindex.o rle.o rope.o bwt.o is.o/g' bwaComponent/Makefile
-bwa/libbwa.a: bwa
- $(MAKE) CFLAGS="$(CFLAGS)" -C bwa libbwa.a
+bwaComponent/libbwa.a: bwaComponent
+ $(MAKE) CFLAGS="$(CFLAGS)" -C bwaComponent libbwa.a
-$(JNI_BASE_NAME).o: $(JNI_BASE_NAME).c jnibwa.h bwa
+$(JNI_BASE_NAME).o: $(JNI_BASE_NAME).c jnibwa.h bwaComponent
-jnibwa.o: jnibwa.c jnibwa.h bwa
+jnibwa.o: jnibwa.c jnibwa.h bwaComponent
clean:
- rm -rf bwa *.o *.$(LIB_EXT)
+ rm -rf bwaComponent *.o *.$(LIB_EXT)
.PHONY: all clean
--- a/src/main/c/jnibwa.c
+++ b/src/main/c/jnibwa.c
@@ -15,12 +15,12 @@
#include <errno.h>
#include "jnibwa.h"
-#include "bwa/kstring.h"
-#include "bwa/bntseq.h"
-#include "bwa/bwt.h"
-#include "bwa/utils.h"
-#include "bwa/rle.h"
-#include "bwa/rope.h"
+#include "bwaComponent/kstring.h"
+#include "bwaComponent/bntseq.h"
+#include "bwaComponent/bwt.h"
+#include "bwaComponent/utils.h"
+#include "bwaComponent/rle.h"
+#include "bwaComponent/rope.h"
static inline void kput32( int32_t val, kstring_t* str ) {
--- a/src/main/c/jnibwa.h
+++ b/src/main/c/jnibwa.h
@@ -5,7 +5,7 @@
#ifndef JNIBWA_H_
#define JNIBWA_H_
-#include "bwa/bwamem.h"
+#include "bwaComponent/bwamem.h"
int jnibwa_createReferenceIndex( char const* refFileName, char const* indexPrefix, char const* algoName);
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