From 8d6b859bf8cadf5cd8438630f5bfb4fe931ae36d Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Thu, 7 Apr 2011 17:26:08 -0400
Subject: [PATCH] speed up multi-threading

---
 bwtaln.c     | 15 +--------------
 bwtsw2_aux.c | 14 +-------------
 2 files changed, 2 insertions(+), 27 deletions(-)

diff --git a/bwtaln.c b/bwtaln.c
index bd2aad2..66310d3 100644
--- a/bwtaln.c
+++ b/bwtaln.c
@@ -13,9 +13,7 @@
 #include "utils.h"
 
 #ifdef HAVE_PTHREAD
-#define THREAD_BLOCK_SIZE 1024
 #include <pthread.h>
-static pthread_mutex_t g_seq_lock = PTHREAD_MUTEX_INITIALIZER;
 #endif
 
 gap_opt_t *gap_init_opt()
@@ -98,18 +96,7 @@ void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt[2], int n_seqs, bwa_seq_t *seq
 	for (i = 0; i != n_seqs; ++i) {
 		bwa_seq_t *p = seqs + i;
 #ifdef HAVE_PTHREAD
-		if (opt->n_threads > 1) {
-			pthread_mutex_lock(&g_seq_lock);
-			if (p->tid < 0) { // unassigned
-				int j;
-				for (j = i; j < n_seqs && j < i + THREAD_BLOCK_SIZE; ++j)
-					seqs[j].tid = tid;
-			} else if (p->tid != tid) {
-				pthread_mutex_unlock(&g_seq_lock);
-				continue;
-			}
-			pthread_mutex_unlock(&g_seq_lock);
-		}
+		if (i % opt->n_threads != tid) continue;
 #endif
 		p->sa = 0; p->type = BWA_TYPE_NO_MATCH; p->c1 = p->c2 = 0; p->n_aln = 0; p->aln = 0;
 		seq[0] = p->seq; seq[1] = p->rseq;
diff --git a/bwtsw2_aux.c b/bwtsw2_aux.c
index 96d0d0a..8ba6455 100644
--- a/bwtsw2_aux.c
+++ b/bwtsw2_aux.c
@@ -309,10 +309,6 @@ typedef struct {
 	bsw2seq1_t *seq;
 } bsw2seq_t;
 
-#ifdef HAVE_PTHREAD
-static pthread_mutex_t g_dbwtsw_lock = PTHREAD_MUTEX_INITIALIZER;
-#endif
-
 static int fix_cigar(const char *qname, const bntseq_t *bns, bsw2hit_t *p, int n_cigar, uint32_t *cigar)
 {
 	// FIXME: this routine does not work if the query bridge three reference sequences
@@ -469,15 +465,7 @@ static void bsw2_aln_core(int tid, bsw2seq_t *_seq, const bsw2opt_t *_opt, const
 		l = p->l;
 
 #ifdef HAVE_PTHREAD
-		if (_opt->n_threads > 1) {
-			pthread_mutex_lock(&g_dbwtsw_lock);
-			if (p->tid < 0) p->tid = tid;
-			else if (p->tid != tid) {
-				pthread_mutex_unlock(&g_dbwtsw_lock);
-				continue;
-			} // in pinciple else should not happen
-			pthread_mutex_unlock(&g_dbwtsw_lock);
-		}
+		if (x % _opt->n_threads != tid) continue;
 #endif
 
 		// set opt->t