From 6a0952948dd30bdc8151d4950ec51f5740c3cdbe Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 15 Oct 2014 14:44:08 -0400
Subject: [PATCH] shared memory

---
 Makefile | 2 +-
 bwa.c    | 4 ++--
 bwa.h    | 8 ++++++--
 main.c   | 3 +++
 4 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/Makefile b/Makefile
index 9bccbf6..8a10df6 100644
--- a/Makefile
+++ b/Makefile
@@ -4,7 +4,7 @@ CFLAGS=		-g -Wall -Wno-unused-function -O2
 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
 AR=			ar
 DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
-LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
+LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwashm.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
 AOBJS=		QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
 			is.o bwtindex.o bwape.o kopen.o pemerge.o \
 			bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
diff --git a/bwa.c b/bwa.c
index e2e1376..65e3c16 100644
--- a/bwa.c
+++ b/bwa.c
@@ -263,11 +263,11 @@ void bwa_idx_destroy(bwaidx_t *idx)
 		if (idx->bwt) bwt_destroy(idx->bwt);
 		if (idx->bns) bns_destroy(idx->bns);
 		if (idx->pac) free(idx->pac);
-	} else free((uint8_t*)idx->mem);
+	} else if (!idx->is_shm) free(idx->mem);
 	free(idx);
 }
 
-int bwa_mem2idx(int64_t l_mem, const uint8_t *mem, bwaidx_t *idx)
+int bwa_mem2idx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx)
 {
 	int64_t k = 0, x;
 	int i;
diff --git a/bwa.h b/bwa.h
index 7e2c153..094d79b 100644
--- a/bwa.h
+++ b/bwa.h
@@ -10,13 +10,17 @@
 #define BWA_IDX_PAC 0x4
 #define BWA_IDX_ALL 0x7
 
+#define BWA_SHM_KEY  5291
+#define BWA_SHM_SIZE 0x10000
+
 typedef struct {
 	bwt_t    *bwt; // FM-index
 	bntseq_t *bns; // information on the reference sequences
 	uint8_t  *pac; // the actual 2-bit encoded reference sequences with 'N' converted to a random base
 
+	int    is_shm;
 	int64_t l_mem;
-	const uint8_t *mem;
+	uint8_t  *mem;
 } bwaidx_t;
 
 typedef struct {
@@ -43,7 +47,7 @@ extern "C" {
 	bwaidx_t *bwa_idx_load(const char *hint, int which);
 	void bwa_idx_destroy(bwaidx_t *idx);
 	int bwa_idx2mem(bwaidx_t *idx);
-	int bwa_mem2idx(int64_t l_mem, const uint8_t *mem, bwaidx_t *idx);
+	int bwa_mem2idx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx);
 
 	void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line);
 	char *bwa_set_rg(const char *s);
diff --git a/main.c b/main.c
index 9108c49..30ac54d 100644
--- a/main.c
+++ b/main.c
@@ -22,6 +22,7 @@ int bwa_bwtsw2(int argc, char *argv[]);
 
 int main_fastmap(int argc, char *argv[]);
 int main_mem(int argc, char *argv[]);
+int main_shm(int argc, char *argv[]);
 
 int main_pemerge(int argc, char *argv[]);
 	
@@ -43,6 +44,7 @@ static int usage()
 	fprintf(stderr, "         sampe         generate alignment (paired ended)\n");
 	fprintf(stderr, "         bwasw         BWA-SW for long queries\n");
 	fprintf(stderr, "\n");
+	fprintf(stderr, "         shm           manage indices in shared memory\n");
 	fprintf(stderr, "         fa2pac        convert FASTA to PAC format\n");
 	fprintf(stderr, "         pac2bwt       generate BWT from PAC\n");
 	fprintf(stderr, "         pac2bwtgen    alternative algorithm for generating BWT\n");
@@ -81,6 +83,7 @@ int main(int argc, char *argv[])
 	else if (strcmp(argv[1], "bwasw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
 	else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1);
 	else if (strcmp(argv[1], "mem") == 0) ret = main_mem(argc-1, argv+1);
+	else if (strcmp(argv[1], "shm") == 0) ret = main_shm(argc-1, argv+1);
 	else if (strcmp(argv[1], "pemerge") == 0) ret = main_pemerge(argc-1, argv+1);
 	else {
 		fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);