build.gradle | 97 2 + 95 - 0 !
1 file changed, 2 insertions(+), 95 deletions(-)

 removing parts of build.gradle that are not useful for a debian build

src/main/c/Makefile | 25 9 + 16 - 0 !
src/main/c/jnibwa.c | 12 6 + 6 - 0 !
src/main/c/jnibwa.h | 2 1 + 1 - 0 !
src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c | 1 0 + 1 - 0 !
src/main/java/org/broadinstitute/hellbender/utils/bwa/BwaMemIndex.java | 36 1 + 35 - 0 !
5 files changed, 17 insertions(+), 59 deletions(-)

 bwa headers are got through a component tarball, not by
 downloading anything.
 Also loading the JNI from the canonical path.

bwa-apache2/ksw.c | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 allocate more memory so the heap block overrun wouldn't 
happen (when qlen = 0). Issue was spotted by valgrind during 
investigation of bug https://github.com/lh3/bwa/issues/108
 This is a copy of the patch written for the bwa Debian package.

bwa-apache2/Makefile | 3 3 + 0 - 0 !
1 file changed, 3 insertions(+)

 -lrt does not help only for linux but also for freebsd
 This is a copy of the patch written for the bwa Debian package.

bwa-apache2/bntseq.c | 8 7 + 1 - 0 !
1 file changed, 7 insertions(+), 1 deletion(-)

 fix cve-2019-10269.
 This is a copy of the patch written for the bwa Debian package.

bwa-apache2/ksw.c | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 use the simde header library for greater compatibility
 This is a copy of the patch written for the bwa Debian package.

bwa-apache2/rle.h | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix package to build with gcc-10
 This is a copy of the patch written for the bwa Debian package.
Bug-Debian: https://bugs.debian.org/957059

bwa-apache2/bwashm.c | 4 4 + 0 - 0 !
1 file changed, 4 insertions(+)

 enable building on gnu/hurd
 This is a copy of the patch written for the bwa Debian package.

bwa-apache2/Makefile | 4 2 + 2 - 0 !
src/main/c/Makefile | 6 3 + 3 - 0 !
2 files changed, 5 insertions(+), 5 deletions(-)

 hardening by passing ldflags

bwa-apache2/Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 some .o files have to be added to libbwa.a to provide needed
 symbols for the shared library