Debian Patches

Status for gatk-bwamem/1.0.4+dfsg3-1

Patch	Description	Author	Forwarded	Last update
build.patch	removing parts of build.gradle that are not useful for a Debian build	Pierre Gruet <pgt@debian.org>	not-needed	2022-03-06
use_bwa_from_component.patch	bwa headers are got through a component tarball, not by downloading anything. Also loading the JNI from the canonical path.	Pierre Gruet <pgt@debian.org>	not-needed	2022-03-30
fix_heap_block_overrun	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. ======================================================================	Nadiya Sitdykova	no	2017-06-30
fix_build_on_freebsd.patch	-lrt does not help only for Linux but also for freebsd This is a copy of the patch written for the bwa Debian package.	Andreas Tille <tille@debian.org>	yes	2015-07-10
simde	use the simde header library for greater compatibility This is a copy of the patch written for the bwa Debian package.	Michael R. Crusoe <crusoe@debian.org>	yes
hardening.patch	hardening by passing LDFLAGS	Pierre Gruet <pgt@debian.org>	not-needed	2022-07-04
missing_obj_files.patch	some .o files have to be added to libbwa.a to provide needed symbols for the shared library	Pierre Gruet <pgt@debian.org>	not-needed	2022-07-04