From eb7dbc14295962bbef4542969c3f594c1523ca4c Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 2 Apr 2018 10:43:41 -0400
Subject: [PATCH] optionally write XB to include alignment score

request from 4DN-DCIC
---
 bwamem.c       | 5 ++++-
 bwamem.h       | 1 +
 bwamem_extra.c | 4 ++++
 fastmap.c      | 3 ++-
 4 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/bwamem.c b/bwamem.c
index d7c00fe..da102b5 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -932,7 +932,10 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
 		if (p->alt_sc > 0)
 			ksprintf(str, "\tpa:f:%.3f", (double)p->score / p->alt_sc);
 	}
-	if (p->XA) { kputsn("\tXA:Z:", 6, str); kputs(p->XA, str); }
+	if (p->XA) {
+		kputsn((opt->flag&MEM_F_XB)? "\tXB:Z:" : "\tXA:Z:", 6, str);
+		kputs(p->XA, str);
+	}
 	if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
 	if ((opt->flag&MEM_F_REF_HDR) && p->rid >= 0 && bns->anns[p->rid].anno != 0 && bns->anns[p->rid].anno[0] != 0) {
 		int tmp;
diff --git a/bwamem.h b/bwamem.h
index 4e2b1d8..e40ebcc 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -20,6 +20,7 @@ typedef struct __smem_i smem_i;
 #define MEM_F_SOFTCLIP  0x200
 #define MEM_F_SMARTPE   0x400
 #define MEM_F_PRIMARY5  0x800
+#define MEM_F_XB        0x1000
 
 typedef struct {
 	int a, b;               // match score and mismatch penalty
diff --git a/bwamem_extra.c b/bwamem_extra.c
index d2e37f4..fb42abd 100644
--- a/bwamem_extra.c
+++ b/bwamem_extra.c
@@ -126,6 +126,10 @@ char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac
 			kputc("MIDSHN"[t.cigar[k]&0xf], &str);
 		}
 		kputc(',', &str); kputw(t.NM, &str);
+		if (opt->flag & MEM_F_XB) {
+			kputc(',', &str);
+			kputw(t.score, &str);
+		}
 		kputc(';', &str);
 		free(t.cigar);
 		kputsn(str.s, str.l, &aln[r]);
diff --git a/fastmap.c b/fastmap.c
index d89c495..9f37d4e 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -130,7 +130,7 @@ int main_mem(int argc, char *argv[])
 
 	aux.opt = opt = mem_opt_init();
 	memset(&opt0, 0, sizeof(mem_opt_t));
-	while ((c = getopt(argc, argv, "51paMCSPVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:")) >= 0) {
+	while ((c = getopt(argc, argv, "51paMCSPVYjuk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
 		else if (c == '1') no_mt_io = 1;
 		else if (c == 'x') mode = optarg;
@@ -148,6 +148,7 @@ int main_mem(int argc, char *argv[])
 		else if (c == 'Y') opt->flag |= MEM_F_SOFTCLIP;
 		else if (c == 'V') opt->flag |= MEM_F_REF_HDR;
 		else if (c == '5') opt->flag |= MEM_F_PRIMARY5;
+		else if (c == 'u') opt->flag |= MEM_F_XB;
 		else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1;
 		else if (c == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
 		else if (c == 'v') bwa_verbose = atoi(optarg);