From ee59a131094ec3d0576bd72ed6421fc15b655397 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sun, 24 Feb 2013 12:17:29 -0500
Subject: [PATCH] simplified bwamem.h

Hide mem_seed_t and mem_chain_t. Don't expose unnecessary routines.
---
 bwamem.c      | 17 +++++++++++++----
 bwamem.h      | 44 ++++++++------------------------------------
 bwamem_pair.c |  9 +++++++++
 3 files changed, 30 insertions(+), 40 deletions(-)

diff --git a/bwamem.c b/bwamem.c
index 7daa5d2..b6741d2 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -155,6 +155,19 @@ const bwtintv_v *smem_next(smem_i *itr, int split_len, int split_width)
  * Chaining while finding SMEMs *
  ********************************/
 
+typedef struct {
+	int64_t rbeg;
+	int32_t qbeg, len;
+} mem_seed_t;
+
+typedef struct {
+	int n, m;
+	int64_t pos;
+	mem_seed_t *seeds;
+} mem_chain_t;
+
+typedef struct { size_t n, m; mem_chain_t *a;  } mem_chain_v;
+
 #include "kbtree.h"
 
 #define chain_cmp(a, b) (((b).pos < (a).pos) - ((a).pos < (b).pos))
@@ -398,10 +411,6 @@ void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a) // IMPORT
 	free(z.a);
 }
 
-/************************
- * Pick paired-end hits *
- ************************/
-
 /****************************************
  * Construct the alignment from a chain *
  ****************************************/
diff --git a/bwamem.h b/bwamem.h
index ce27c6e..27a3dc1 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -11,11 +11,6 @@
 struct __smem_i;
 typedef struct __smem_i smem_i;
 
-typedef struct {
-	int64_t rbeg;
-	int32_t qbeg, len;
-} mem_seed_t;
-
 #define MEM_F_HARDCLIP  0x1
 #define MEM_F_PE        0x2
 #define MEM_F_NOPAIRING 0x4
@@ -35,12 +30,6 @@ typedef struct {
 	int8_t mat[25]; // scoring matrix; mat[0] == 0 if unset
 } mem_opt_t;
 
-typedef struct {
-	int n, m;
-	int64_t pos;
-	mem_seed_t *seeds;
-} mem_chain_t;
-
 typedef struct {
 	int64_t rb, re;
 	int score, qb, qe, seedcov, sub, csub; // sub: suboptimal score; csub: suboptimal inside the chain
@@ -60,43 +49,26 @@ typedef struct {
 	int score, sub;
 } bwahit_t;
 
-typedef struct { size_t n, m; mem_chain_t *a;  } mem_chain_v;
 typedef struct { size_t n, m; mem_alnreg_t *a; } mem_alnreg_v;
 
-extern int mem_verbose;
-
 #ifdef __cplusplus
 extern "C" {
 #endif
 
-smem_i *smem_itr_init(const bwt_t *bwt);
-void smem_itr_destroy(smem_i *itr);
-void smem_set_query(smem_i *itr, int len, const uint8_t *query);
-const bwtintv_v *smem_next(smem_i *itr, int split_len, int split_width);
+	smem_i *smem_itr_init(const bwt_t *bwt);
+	void smem_itr_destroy(smem_i *itr);
+	void smem_set_query(smem_i *itr, int len, const uint8_t *query);
+	const bwtintv_v *smem_next(smem_i *itr, int split_len, int split_width);
 
-mem_opt_t *mem_opt_init(void);
-void mem_fill_scmat(int a, int b, int8_t mat[25]);
+	mem_opt_t *mem_opt_init(void);
+	void mem_fill_scmat(int a, int b, int8_t mat[25]);
 
-mem_chain_v mem_chain(const mem_opt_t *opt, const bwt_t *bwt, int len, const uint8_t *seq);
-int mem_chain_flt(const mem_opt_t *opt, int n_chn, mem_chain_t *chains);
-void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain_t *c, mem_alnreg_v *a);
-uint32_t *mem_gen_cigar(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar);
+	int mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int n, bseq1_t *seqs);
 
-int mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int n, bseq1_t *seqs);
-
-void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *regs, mem_pestat_t pes[4]);
+	void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *regs, mem_pestat_t pes[4]);
 
 #ifdef __cplusplus
 }
 #endif
 
-static inline int mem_infer_dir(int64_t l_pac, int64_t b1, int64_t b2, int64_t *dist)
-{
-	int64_t p2;
-	int r1 = (b1 >= l_pac), r2 = (b2 >= l_pac);
-	p2 = r1 == r2? b2 : (l_pac<<1) - 1 - b2; // p2 is the coordinate of read 2 on the read 1 strand
-	*dist = p2 > b1? p2 - b1 : b1 - p2;
-	return (r1 == r2? 0 : 1) ^ (p2 > b1? 0 : 3);
-}
-
 #endif
diff --git a/bwamem_pair.c b/bwamem_pair.c
index 57a128a..51f51c9 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -15,6 +15,15 @@
 #define MAPPING_BOUND 3.0
 #define MAX_STDDEV    4.0
 
+static inline int mem_infer_dir(int64_t l_pac, int64_t b1, int64_t b2, int64_t *dist)
+{
+	int64_t p2;
+	int r1 = (b1 >= l_pac), r2 = (b2 >= l_pac);
+	p2 = r1 == r2? b2 : (l_pac<<1) - 1 - b2; // p2 is the coordinate of read 2 on the read 1 strand
+	*dist = p2 > b1? p2 - b1 : b1 - p2;
+	return (r1 == r2? 0 : 1) ^ (p2 > b1? 0 : 3);
+}
+
 static int cal_sub(const mem_opt_t *opt, mem_alnreg_v *r)
 {
 	int j;