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Fixed clang compiling warnings #3

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Fixed clang compiling warnings #3

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2 changes: 1 addition & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,4 @@ bwa
depend.mk
tags
bwt_gen/libbwtgen.a

.vscode
2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -2,7 +2,7 @@ CC= gcc
CXX= g++
# CFLAGS= -ggdb -O0 -Wall -DUSE_MMAP
# CFLAGS= -ggdb -O2 -Wall -DUSE_MMAP
CFLAGS= -ggdb -O2 -Wall
CFLAGS= -g -O2 -Wall -Wno-unused-function
# CFLAGS= -ggdb -O0 -Wall
CFLAGS+= `pkg-config --cflags libzmq`
# CFLAGS+= `pkg-config --cflags libczmq`
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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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2 changes: 1 addition & 1 deletion 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];
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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
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