From a74523a68d77cf0d1b76b3de0a05b90af43eea10 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Thu, 9 Jun 2011 17:17:13 -0400
Subject: [PATCH] increase maximum barcode length limit to 63bp

---
 bwaseqio.c | 4 ++--
 bwtaln.h   | 4 +++-
 main.c     | 2 +-
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/bwaseqio.c b/bwaseqio.c
index 94271b9..12ac765 100644
--- a/bwaseqio.c
+++ b/bwaseqio.c
@@ -149,8 +149,8 @@ bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int mode, int tri
 	int n_seqs, l, i, is_comp = mode&BWA_MODE_COMPREAD, is_64 = mode&BWA_MODE_IL13, l_bc = mode>>24;
 	long n_trimmed = 0, n_tot = 0;
 
-	if (l_bc > 15) {
-		fprintf(stderr, "[%s] the maximum barcode length is 15.\n", __func__);
+	if (l_bc > BWA_MAX_BCLEN) {
+		fprintf(stderr, "[%s] the maximum barcode length is %d.\n", __func__, BWA_MAX_BCLEN);
 		return 0;
 	}
 	if (bs->is_bam) return bwa_read_bam(bs, n_needed, n, is_comp, trim_qual); // l_bc has no effect for BAM input
diff --git a/bwtaln.h b/bwtaln.h
index f659ac8..02f54f7 100644
--- a/bwtaln.h
+++ b/bwtaln.h
@@ -22,6 +22,8 @@
 #define BWA_AVG_ERR 0.02
 #define BWA_MIN_RDLEN 35 // for read trimming
 
+#define BWA_MAX_BCLEN 63 // maximum barcode length; 127 is the maximum
+
 #ifndef bns_pac
 #define bns_pac(pac, k) ((pac)[(k)>>2] >> ((~(k)&3)<<1) & 3)
 #endif
@@ -75,7 +77,7 @@ typedef struct {
 	// for multi-threading only
 	int tid;
 	// barcode
-	char bc[16]; // null terminated; up to 15 bases
+	char bc[BWA_MAX_BCLEN+1]; // null terminated; up to BWA_MAX_BCLEN bases
 	// NM and MD tags
 	uint32_t full_len:20, nm:12;
 	char *md;
diff --git a/main.c b/main.c
index 4f70bb5..b22552e 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.5.9-r18-dev"
+#define PACKAGE_VERSION "0.5.9-r19-dev"
 #endif
 
 static int usage()