From a05dcac35e7715f0ebd113ff5e1c2fb2bbc0dce9 Mon Sep 17 00:00:00 2001
From: Maarten-vd-Sande <Maarten-vd-Sande@users.noreply.github.com>
Date: Sat, 11 Jul 2020 11:51:09 +0200
Subject: [PATCH] [ci skip] Merge PR 23102

Merge PR #23102, commits were:
 * bwa-mem2: skip osx due to https://github.com/intel/safestringlib/issues/14
 * bwa-mem2: fix source,patch,make,multi,license,doi
 * try as libs
 * try/use makefile patch
 * allow zlib
 * use cpp compiler
 * more lint
 * some lint
 * try building from source
 * ignore some lint
 * add libgcc
 * rename to bwa-mem2
 * rename bwamem2 to bwa-mem2
 * move all related files
 * noarch generic
 * Merge branch 'master' into bwamem2
 * add bwa-mem2
---
 ...7692aeb857d5b9241a08bbd68f2c6be01811.patch | 22 +++++++++
 recipes/bwa-mem2/Makefile.patch               | 15 +++++++
 recipes/bwa-mem2/build.sh                     |  6 +++
 recipes/bwa-mem2/meta.yaml                    | 45 +++++++++++++++++++
 4 files changed, 88 insertions(+)
 create mode 100644 recipes/bwa-mem2/771c7692aeb857d5b9241a08bbd68f2c6be01811.patch
 create mode 100644 recipes/bwa-mem2/Makefile.patch
 create mode 100644 recipes/bwa-mem2/build.sh
 create mode 100644 recipes/bwa-mem2/meta.yaml

diff --git a/recipes/bwa-mem2/771c7692aeb857d5b9241a08bbd68f2c6be01811.patch b/recipes/bwa-mem2/771c7692aeb857d5b9241a08bbd68f2c6be01811.patch
new file mode 100644
index 0000000000000..2156e02f4680b
--- /dev/null
+++ b/recipes/bwa-mem2/771c7692aeb857d5b9241a08bbd68f2c6be01811.patch
@@ -0,0 +1,22 @@
+From 08e70563012725edc8d130c24237b25f9ba1262f Mon Sep 17 00:00:00 2001
+From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com>
+Date: Thu, 9 Jul 2020 17:51:39 +0200
+Subject: [PATCH] Fix version to be correct
+
+---
+ src/main.cpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/main.cpp b/src/main.cpp
+index 0fb8211..cd34830 100644
+--- a/src/main.cpp
++++ b/src/main.cpp
+@@ -32,7 +32,7 @@ Contacts: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@
+ #include "main.h"
+ 
+ #ifndef PACKAGE_VERSION
+-#define PACKAGE_VERSION "2.0pre2"
++#define PACKAGE_VERSION "2.0"
+ #endif
+ 
+ 
diff --git a/recipes/bwa-mem2/Makefile.patch b/recipes/bwa-mem2/Makefile.patch
new file mode 100644
index 0000000000000..ac988b78b9ceb
--- /dev/null
+++ b/recipes/bwa-mem2/Makefile.patch
@@ -0,0 +1,15 @@
+diff --git a/Makefile b/Makefile
+index ad06b39..8213cbd 100644
+--- a/Makefile
++++ b/Makefile
+@@ -39,7 +39,7 @@ ARCH_FLAGS=   -msse4.1
+ MEM_FLAGS=     -DSAIS=1
+-CPPFLAGS=      -DENABLE_PREFETCH -DV17=1 $(MEM_FLAGS) 
++CPPFLAGS+=      -DENABLE_PREFETCH -DV17=1 $(MEM_FLAGS) 
+ INCLUDES=   -Isrc -Iext/safestringlib/include
+-LIBS=          -lpthread -lm -lz -L. -lbwa  -Lext/safestringlib -lsafestring
++LIBS+=          -lpthread -lm -lz -L. -lbwa  -Lext/safestringlib -lsafestring
+ OBJS=          src/fastmap.o src/bwtindex.o src/utils.o src/kthread.o \
+                        src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o \
+                        src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o \
+
diff --git a/recipes/bwa-mem2/build.sh b/recipes/bwa-mem2/build.sh
new file mode 100644
index 0000000000000..4aecd0e742daa
--- /dev/null
+++ b/recipes/bwa-mem2/build.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+LIBS="${LDFLAGS}" make CC="${CC}" CXX="${CXX}" multi
+
+mkdir -p $PREFIX/bin
+cp bwa-mem2* $PREFIX/bin
diff --git a/recipes/bwa-mem2/meta.yaml b/recipes/bwa-mem2/meta.yaml
new file mode 100644
index 0000000000000..88e145cacdec2
--- /dev/null
+++ b/recipes/bwa-mem2/meta.yaml
@@ -0,0 +1,45 @@
+{% set version = "2.0" %}
+
+package:
+  name: bwa-mem2
+  version: {{ version }}
+
+source:
+  - url: https://github.com/bwa-mem2/bwa-mem2/releases/download/v{{ version }}/Source_code_including_submodule.tar.gz
+    sha256: 23a8aa9d295ed1e042aec255157313b0ddf45ae2271a9b878b5e05a4c1026d38
+    patches:
+      - Makefile.patch
+      - 771c7692aeb857d5b9241a08bbd68f2c6be01811.patch
+
+build:
+  number: 0
+  # Compilation fails on OSX:
+  #   ext/safestringlib/include/safe_mem_lib.h:100:16: error: conflicting types for 'memset_s'
+  #   extern errno_t memset_s(void *dest, rsize_t dmax, uint8_t value);
+  #   /Applications/Xcode-9.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/string.h:145:9: note: previous declaration is here
+  #   errno_t memset_s(void *__s, rsize_t __smax, int __c, rsize_t __n) __OSX_AVAILABLE_STARTING(__MAC_10_9, __IPHONE_7_0);
+  # Cause: https://github.com/intel/safestringlib/issues/14
+  skip: True  # [osx]
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+  host:
+    - zlib
+
+test:
+  commands:
+    - bwa-mem2 version
+    - bwa-mem2.sse41 version
+    - bwa-mem2.avx2 version
+    - bwa-mem2.avx512bw version
+
+about:
+  home: https://github.com/bwa-mem2/bwa-mem2
+  license: MIT
+  license_file: LICENSE
+  summary: The next version of bwa-mem 
+
+extra:
+  identifiers:
+    - doi:10.1109/IPDPS.2019.00041