r911: check before attempting adding

bwashm.c

@@ -13,15 +13,15 @@ int bwa_shm_stage(bwaidx_t *idx, const char *hint, const char *_tmpfn)
 {
 	const char *name;
 	uint8_t *shm, *shm_idx;
-	uint16_t *cnt, i;
+	uint16_t *cnt;
 	int shmid, to_init = 0, l;
-	char path[PATH_MAX + 1], *p, *tmpfn = (char*)_tmpfn;
+	char path[PATH_MAX + 1], *tmpfn = (char*)_tmpfn;
 
 	if (hint == 0 || hint[0] == 0) return -1;
 	for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
 	++name;
 
-	if ((shmid = shm_open("/bwactl", O_RDWR, 0444)) < 0) {
+	if ((shmid = shm_open("/bwactl", O_RDWR, 0)) < 0) {
 		shmid = shm_open("/bwactl", O_CREAT|O_RDWR|O_EXCL, 0644);
 		to_init = 1;
 	}
@@ -32,15 +32,6 @@ int bwa_shm_stage(bwaidx_t *idx, const char *hint, const char *_tmpfn)
 	if (to_init) {
 		memset(shm, 0, BWA_CTL_SIZE);
 		cnt[1] = 4;
-	} else {
-		for (i = 0, p = (char*)shm + 4; i < cnt[0]; ++i) {
-			if (strcmp(p + 8, name) == 0) break;
-			p += 9 + strlen(p + 8);
-		}
-		if (i < cnt[0]) {
-			fprintf(stderr, "[W::%s] index '%s' is already in shared memory\n", __func__, name);
-			return -1;
-		}
 	}
 
 	if (idx->mem == 0) bwa_idx2mem(idx);
@@ -106,7 +97,7 @@ bwaidx_t *bwa_idx_load_from_shm(const char *hint)
 	if (hint == 0 || hint[0] == 0) return 0;
 	for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
 	++name;
-	if ((shmid = shm_open("/bwactl", O_RDONLY, 0444)) < 0) return 0;
+	if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return 0;
 	shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
 	cnt = (uint16_t*)shm;
 	if (cnt[0] == 0) return 0;
@@ -118,20 +109,40 @@ bwaidx_t *bwa_idx_load_from_shm(const char *hint)
 	if (i == cnt[0]) return 0;
 
 	strcat(strcpy(path, "/bwaidx-"), name);
-	if ((shmid = shm_open(path, O_RDONLY, 0444)) < 0) return 0;
+	if ((shmid = shm_open(path, O_RDONLY, 0)) < 0) return 0;
 	shm_idx = mmap(0, l_mem, PROT_READ, MAP_SHARED, shmid, 0);
 	idx = calloc(1, sizeof(bwaidx_t));
 	bwa_mem2idx(l_mem, shm_idx, idx);
 	idx->is_shm = 1;
 	return idx;
 }
 
+int bwa_shm_test(const char *hint)
+{
+	int shmid;
+	uint16_t *cnt, i;
+	char *p, *shm;
+	const char *name;
+
+	if (hint == 0 || hint[0] == 0) return 0;
+	for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
+	++name;
+	if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return 0;
+	shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
+	cnt = (uint16_t*)shm;
+	for (i = 0, p = shm + 4; i < cnt[0]; ++i) {
+		if (strcmp(p + 8, name) == 0) return 1;
+		p += strlen(p) + 9;
+	}
+	return 0;
+}
+
 int bwa_shm_list(void)
 {
 	int shmid;
 	uint16_t *cnt, i;
 	char *p, *shm;
-	if ((shmid = shm_open("/bwactl", O_RDONLY, 0444)) < 0) return -1;
+	if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return -1;
 	shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
 	cnt = (uint16_t*)shm;
 	for (i = 0, p = shm + 4; i < cnt[0]; ++i) {
@@ -150,7 +161,7 @@ int bwa_shm_destroy(void)
 	char *p, *shm;
 	char path[PATH_MAX + 1];
 
-	if ((shmid = shm_open("/bwactl", O_RDONLY, 0444)) < 0) return -1;
+	if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return -1;
 	shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
 	cnt = (uint16_t*)shm;
 	for (i = 0, p = shm + 4; i < cnt[0]; ++i) {
@@ -186,13 +197,15 @@ int main_shm(int argc, char *argv[])
 		return 1;
 	}
 	if (optind < argc) {
-		bwaidx_t *idx;
-		idx = bwa_idx_load_from_disk(argv[optind], BWA_IDX_ALL);
-		if (bwa_shm_stage(idx, argv[optind], tmpfn) < 0) {
-			fprintf(stderr, "[E::%s] failed to stage the index in shared memory\n", __func__);
-			ret = 1;
-		}
-		bwa_idx_destroy(idx);
+		if (bwa_shm_test(argv[optind]) == 0) {
+			bwaidx_t *idx;
+			idx = bwa_idx_load_from_disk(argv[optind], BWA_IDX_ALL);
+			if (bwa_shm_stage(idx, argv[optind], tmpfn) < 0) {
+				fprintf(stderr, "[E::%s] failed to stage the index in shared memory\n", __func__);
+				ret = 1;
+			}
+			bwa_idx_destroy(idx);
+		} else fprintf(stderr, "[M::%s] index '%s' is already in shared memory\n", __func__, argv[optind]);
 	}
 	if (to_list) bwa_shm_list();
 	if (to_drop) bwa_shm_destroy();

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r907-dirty"
+#define PACKAGE_VERSION "0.7.10-r911-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);