1 files changed, 0 insertions, 84 deletions
diff --git a/Library/Formula/bwa.rb b/Library/Formula/bwa.rb
deleted file mode 100644
index 5a66b4641..000000000
--- a/Library/Formula/bwa.rb
+++ /dev/null
@@ -1,84 +0,0 @@
-require 'formula'
-
-class Bwa < Formula
-  homepage 'http://bio-bwa.sourceforge.net/'
-  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);