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Remove inline declarations to allow build, rename output binary #4

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8 changes: 4 additions & 4 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ OBJS= utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o \
bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
bwtsw2_chain.o bamlite.o bam2bam.o bgzf.o \
insert_size.o
PROG= bwa
PROG= network-aware-bwa
INCLUDES=
LIBS= -lm -lz -lpthread -Lbwt_gen -lbwtgen
LIBS+= `pkg-config --libs libzmq`
Expand All @@ -33,9 +33,9 @@ all:$(PROG)

install: all
install -d $(prefix)/bin
install -m 775 bwa $(prefix)/bin/
install -m 775 network-aware-bwa $(prefix)/bin/
install -d $(prefix)/share/man/man1
install -m 644 bwa.1 $(prefix)/share/man/man1/
install -m 644 network-aware-bwa.1 $(prefix)/share/man/man1/

lib-recur all-recur clean-recur cleanlocal-recur install-recur:
@target=`echo $@ | sed s/-recur//`; \
Expand All @@ -49,7 +49,7 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:

lib:

bwa:lib-recur $(OBJS) main.o
network-aware-bwa:lib-recur $(OBJS) main.o
$(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS)


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8 changes: 4 additions & 4 deletions bwt.c
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Expand Up @@ -89,7 +89,7 @@ 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;
Expand All @@ -115,7 +115,7 @@ 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;
if (k == l) {
Expand Down Expand Up @@ -156,7 +156,7 @@ 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;
Expand All @@ -176,7 +176,7 @@ 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;
if (k == l) {
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8 changes: 4 additions & 4 deletions bwt.h
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Expand Up @@ -95,14 +95,14 @@ extern "C" {

void bwt_bwtupdate_core(bwt_t *bwt);

inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k);

// more efficient version of bwt_occ/bwt_occ4 for retrieving two close Occ values
void bwt_gen_cnt_table(bwt_t *bwt);
inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);

int bwt_match_exact(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *sa_begin, bwtint_t *sa_end);
int bwt_match_exact_alt(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *k0, bwtint_t *l0);
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6 changes: 3 additions & 3 deletions bwt_lite.c
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Expand Up @@ -52,7 +52,7 @@ bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq)
}
return b;
}
inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c)
uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c)
{
uint32_t n, b;
if (k == bwt->seq_len) return bwt->L2[c+1] - bwt->L2[c];
Expand All @@ -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)) {
Expand All @@ -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);
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6 changes: 3 additions & 3 deletions bwt_lite.h
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Expand Up @@ -17,9 +17,9 @@ extern "C" {
#endif

bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq);
inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c);
inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]);
inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]);
uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c);
void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]);
void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]);
void bwtl_destroy(bwtl_t *bwt);

#ifdef __cplusplus
Expand Down