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