BWA 0.6.2

Closes #13009.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>

1 files changed, 71 insertions, 2 deletions

diff --git a/Library/Formula/bwa.rb b/Library/Formula/bwa.rb
index 552b76917..5a66b4641 100644
--- a/Library/Formula/bwa.rb
+++ b/Library/Formula/bwa.rb
@@ -2,14 +2,83 @@ require 'formula'
 
 class Bwa < Formula
   homepage 'http://bio-bwa.sourceforge.net/'
-  url 'http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.10.tar.bz2'
-  md5 '04962f916f761dc259d9fb2452b46c5d'
+  url 'http://downloads.sourceforge.net/project/bio-bwa/bwa-0.6.2.tar.bz2'
+  sha1 'fd3d0666a89d189b642d6f1c4cfa9c29123c12bc'
 
   head 'https://github.com/lh3/bwa.git'
 
+  # These inline functions cause undefined symbol errors with CLANG.
+  # Fixed upstream for next release. See:
+  # https://github.com/lh3/bwa/pull/11
+  def patches; DATA; end
+
   def install
     system "make", "CC=#{ENV.cc}", "CFLAGS=#{ENV.cflags}"
     bin.install "bwa"
     man1.install "bwa.1"
   end
 end
+
+__END__
+diff --git a/bwt.c b/bwt.c
+index fcc141e..966b718 100644
+--- a/bwt.c
++++ b/bwt.c
+@@ -95,7 +95,7 @@ static inline int __occ_aux(uint64_t y, int c)
+	return ((y + (y >> 4)) & 0xf0f0f0f0f0f0f0full) * 0x101010101010101ull >> 56;
+ }
+
+-inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c)
++bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c)
+ {
+	bwtint_t n, l, j;
+	uint32_t *p;
+@@ -121,7 +121,7 @@ inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c)
+ }
+
+ // an analogy to bwt_occ() but more efficient, requiring k <= l
+-inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol)
++void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol)
+ {
+	bwtint_t _k, _l;
+	_k = (k >= bwt->primary)? k-1 : k;
+@@ -158,7 +158,7 @@ inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint
+	((bwt)->cnt_table[(b)&0xff] + (bwt)->cnt_table[(b)>>8&0xff]		\
+	 + (bwt)->cnt_table[(b)>>16&0xff] + (bwt)->cnt_table[(b)>>24])
+
+-inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
++void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
+ {
+	bwtint_t l, j, x;
+	uint32_t *p;
+@@ -178,7 +178,7 @@ inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
+ }
+
+ // an analogy to bwt_occ4() but more efficient, requiring k <= l
+-inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4])
++void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4])
+ {
+	bwtint_t _k, _l;
+	_k = (k >= bwt->primary)? k-1 : k;
+diff --git a/bwt_lite.c b/bwt_lite.c
+index dd411e1..902e0fc 100644
+--- a/bwt_lite.c
++++ b/bwt_lite.c
+@@ -65,7 +65,7 @@ inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c)
+	if (c == 0) n -= 15 - (k&15); // corrected for the masked bits
+	return n;
+ }
+-inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4])
++void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4])
+ {
+	uint32_t x, b;
+	if (k == (uint32_t)(-1)) {
+@@ -80,7 +80,7 @@ inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4])
+	x -= 15 - (k&15);
+	cnt[0] += x&0xff; cnt[1] += x>>8&0xff; cnt[2] += x>>16&0xff; cnt[3] += x>>24;
+ }
+-inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4])
++void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4])
+ {
+	bwtl_occ4(bwt, k, cntk);
+	bwtl_occ4(bwt, l, cntl);