From 588fb8af5daea7d029cde0193d92ac1c7cee21e9 Mon Sep 17 00:00:00 2001
From: graphenn <graphenn@dnachron.com>
Date: Tue, 7 Jun 2022 23:11:00 +0800
Subject: [PATCH] Fixed clang compiling warnings

---
 .gitignore | 2 +-
 Makefile   | 2 +-
 bwt.h      | 8 ++++----
 bwt_lite.c | 2 +-
 bwt_lite.h | 6 +++---
 5 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/.gitignore b/.gitignore
index d71e3e2..9deb9b3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,4 @@ bwa
 depend.mk
 tags
 bwt_gen/libbwtgen.a
-
+.vscode
diff --git a/Makefile b/Makefile
index 32966c2..9fe6490 100644
--- a/Makefile
+++ b/Makefile
@@ -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`
diff --git a/bwt.h b/bwt.h
index c9cc4ed..b99b951 100644
--- a/bwt.h
+++ b/bwt.h
@@ -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);
diff --git a/bwt_lite.c b/bwt_lite.c
index dd411e1..12fe408 100644
--- a/bwt_lite.c
+++ b/bwt_lite.c
@@ -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];
diff --git a/bwt_lite.h b/bwt_lite.h
index 0096b93..4fadcce 100644
--- a/bwt_lite.h
+++ b/bwt_lite.h
@@ -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