From 3e3236dfc400b1157726af61468914f5ebcbdc8a Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 7 Mar 2013 11:00:15 -0500
Subject: [PATCH] r337: mem - always read even number of reads

In the old code, we may read odd number of reads from an interleaved fastq.
---
 bwa.c     | 2 +-
 fastmap.c | 5 +++++
 main.c    | 2 +-
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/bwa.c b/bwa.c
index 76b54ae..991b23a 100644
--- a/bwa.c
+++ b/bwa.c
@@ -55,7 +55,7 @@ bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_)
 			kseq2bseq1(ks2, &seqs[n]);
 			size += seqs[n++].l_seq;
 		}
-		if (size >= chunk_size) break;
+		if (size >= chunk_size && (n&1) == 0) break;
 	}
 	if (size == 0) { // test if the 2nd file is finished
 		if (ks2 && kseq_read(ks2) >= 0)
diff --git a/fastmap.c b/fastmap.c
index e6c2b1e..9204399 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -106,6 +106,11 @@ int main_mem(int argc, char *argv[])
 	}
 	while ((seqs = bseq_read(opt->chunk_size * opt->n_threads, &n, ks, ks2)) != 0) {
 		int64_t size = 0;
+		if ((opt->flag & MEM_F_PE) && (n&1) == 1) {
+			if (bwa_verbose >= 2)
+				fprintf(stderr, "[W::%s] odd number of reads in the PE mode; last read dropped\n", __func__);
+			n = n>>1<<1;
+		}
 		if (!copy_comment)
 			for (i = 0; i < n; ++i) {
 				free(seqs[i].comment); seqs[i].comment = 0;
diff --git a/main.c b/main.c
index d9a87f1..f7b3a03 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.0-r336-beta"
+#define PACKAGE_VERSION "0.7.0-r337-beta"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);