From bfd5e1840fa275fdf8abad6f397c35283d52ad0d Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 15 Oct 2014 15:44:06 -0400
Subject: [PATCH] shm works on small files, but not large ones

I don't know why. SHMMAX, SHMALL and SHMMNI are large enough.
---
 bwa.c     | 21 +++++++++++++++------
 bwa.h     |  2 ++
 fastmap.c |  6 +++++-
 3 files changed, 22 insertions(+), 7 deletions(-)

diff --git a/bwa.c b/bwa.c
index 65e3c16..431cc49 100644
--- a/bwa.c
+++ b/bwa.c
@@ -227,7 +227,7 @@ bwt_t *bwa_idx_load_bwt(const char *hint)
 	return bwt;
 }
 
-bwaidx_t *bwa_idx_load(const char *hint, int which)
+bwaidx_t *bwa_idx_load_from_disk(const char *hint, int which)
 {
 	bwaidx_t *idx;
 	char *prefix;
@@ -256,6 +256,11 @@ bwaidx_t *bwa_idx_load(const char *hint, int which)
 	return idx;
 }
 
+bwaidx_t *bwa_idx_load(const char *hint, int which)
+{
+	return bwa_idx_load_from_disk(hint, which);
+}
+
 void bwa_idx_destroy(bwaidx_t *idx)
 {
 	if (idx == 0) return;
@@ -263,7 +268,10 @@ 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 if (!idx->is_shm) free(idx->mem);
+	} else {
+		free(idx->bwt); free(idx->bns->anns); free(idx->bns);
+		if (!idx->is_shm) free(idx->mem);
+	}
 	free(idx);
 }
 
@@ -273,19 +281,20 @@ int bwa_mem2idx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx)
 	int i;
 
 	// generate idx->bwt
-	x = sizeof(bwt_t); idx->bwt = (bwt_t*)(mem + k); k += x;
+	x = sizeof(bwt_t); idx->bwt = malloc(x); memcpy(idx->bwt, mem + k, x); k += x;
 	x = idx->bwt->n_sa * sizeof(bwtint_t); idx->bwt->sa = (bwtint_t*)(mem + k); k += x;
 	x = idx->bwt->bwt_size * 4; idx->bwt->bwt = (uint32_t*)(mem + k); k += x;
 
 	// generate idx->bns and idx->pac
-	x = sizeof(bntseq_t); idx->bns = (bntseq_t*)(mem + k); k += x;
+	x = sizeof(bntseq_t); idx->bns = malloc(x); memcpy(idx->bns, mem + k, x); k += x;
 	x = idx->bns->n_holes * sizeof(bntamb1_t); idx->bns->ambs = (bntamb1_t*)(mem + k); k += x;
-	x = idx->bns->n_seqs  * sizeof(bntann1_t); idx->bns->anns = (bntann1_t*)(mem + k); k += x;
+	x = idx->bns->n_seqs  * sizeof(bntann1_t); idx->bns->anns = malloc(x); memcpy(idx->bns->anns, mem + k, x); k += x;
 	for (i = 0; i < idx->bns->n_seqs; ++i) {
 		idx->bns->anns[i].name = (char*)(mem + k); k += strlen(idx->bns->anns[i].name) + 1;
 		idx->bns->anns[i].anno = (char*)(mem + k); k += strlen(idx->bns->anns[i].anno) + 1;
 	}
-	idx->pac = (uint8_t*)(mem + k);
+	idx->pac = (uint8_t*)(mem + k); k += idx->bns->l_pac/4+1;
+	assert(k == l_mem);
 
 	idx->l_mem = k; idx->mem = mem;
 	return 0;
diff --git a/bwa.h b/bwa.h
index 094d79b..5d40aae 100644
--- a/bwa.h
+++ b/bwa.h
@@ -44,6 +44,8 @@ extern "C" {
 	char *bwa_idx_infer_prefix(const char *hint);
 	bwt_t *bwa_idx_load_bwt(const char *hint);
 
+	bwaidx_t *bwa_idx_load_from_shm(const char *hint);
+	bwaidx_t *bwa_idx_load_from_disk(const char *hint, int which);
 	bwaidx_t *bwa_idx_load(const char *hint, int which);
 	void bwa_idx_destroy(bwaidx_t *idx);
 	int bwa_idx2mem(bwaidx_t *idx);
diff --git a/fastmap.c b/fastmap.c
index 43ddfd3..e949da3 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -230,7 +230,11 @@ int main_mem(int argc, char *argv[])
 	} else update_a(opt, &opt0);
 	bwa_fill_scmat(opt->a, opt->b, opt->mat);
 
-	if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
+	idx = bwa_idx_load_from_shm(argv[optind]);
+	if (idx == 0) {
+		if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
+	} else if (bwa_verbose >= 3)
+		fprintf(stderr, "[M::%s] load the bwa index from shared memory\n", __func__);
 	if (ignore_alt)
 		for (i = 0; i < idx->bns->n_seqs; ++i)
 			idx->bns->anns[i].is_alt = 0;