From 7b62fbb4ba82eb68edb15d59f3d2c3af0a24e040 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 2 Oct 2014 15:34:49 -0400
Subject: [PATCH] r880: bug in writing .ann file

---
 bntseq.c       |  2 +-
 bwa-postalt.js | 31 +++++++++----------------------
 main.c         |  2 +-
 3 files changed, 11 insertions(+), 24 deletions(-)

diff --git a/bntseq.c b/bntseq.c
index 93cdba1..75e5813 100644
--- a/bntseq.c
+++ b/bntseq.c
@@ -226,7 +226,7 @@ static uint8_t *add1(const kseq_t *seq, bntseq_t *bns, uint8_t *pac, int64_t *m_
 	}
 	p = bns->anns + bns->n_seqs;
 	p->name = strdup((char*)seq->name.s);
-	p->anno = seq->comment.s? strdup((char*)seq->comment.s) : strdup("(null)");
+	p->anno = seq->comment.l > 0? strdup((char*)seq->comment.s) : strdup("(null)");
 	p->gi = 0; p->len = seq->seq.l;
 	p->offset = (bns->n_seqs == 0)? 0 : (p-1)->offset + (p-1)->len;
 	p->n_ambs = 0;
diff --git a/bwa-postalt.js b/bwa-postalt.js
index c50ae26..ab29c9e 100644
--- a/bwa-postalt.js
+++ b/bwa-postalt.js
@@ -289,30 +289,9 @@ function bwa_postalt(args)
 		if (buf2.length && (buf2[0][0] != t[0] || (buf2[0][1]&0xc0) != (t[1]&0xc0))) {
 			for (var i = 0; i < buf2.length; ++i)
 				print(buf2[i].join("\t"));
-			buf2 = [];
+			buf2 = []; buf3 = [];
 		}
 
-		// test primary and if so whether it overlaps with ALT regions
-		if (idx_pri[t[2]] != null) {
-			var start = t[3], end = start;
-			while ((m = re_cigar.exec(t[5])) != null)
-				if (m[2] == 'M' || m[2] == 'D' || m[2] == 'N')
-					end += parseInt(m[1]);
-			var ovlp = idx_pri[t[2]](start, end);
-			if (ovlp.length > 0) {
-				var score = (m = /\tAS:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 1;
-				for (var i = 0; i < ovlp.length; ++i)
-					buf3.push([t[2], start, end, ovlp[i][2]]);
-			}
-		}
-
-		// parse the XA tag
-		if ((m = /\tXA:Z:(\S+)/.exec(line)) == null) {
-			buf2.push(t);
-			continue;
-		}
-		var XA_strs = m[1].split(";");
-
 		// parse the reported hit
 		var hits = [];
 		var NM = (m = /\tNM:i:(\d+)/.exec(line)) == null? '0' : m[1];
@@ -322,6 +301,13 @@ function bwa_postalt(args)
 			buf2.push(t);
 			continue;
 		}
+
+		// parse the XA tag
+		if ((m = /\tXA:Z:(\S+)/.exec(line)) == null) {
+			buf2.push(t);
+			continue;
+		}
+		var XA_strs = m[1].split(";");
 		hits.push(h);
 
 		// parse hits in the XA tag
@@ -356,6 +342,7 @@ function bwa_postalt(args)
 			}
 			if (i == 0 && n_rpt_lifted == 1) rpt_lifted = lifted[0].slice(0);
 			if (lifted.length) ++n_lifted, hits[i].lifted = lifted;
+			buf3.push(hits[i]);
 		}
 		if (n_lifted == 0) {
 			buf2.push(t);
diff --git a/main.c b/main.c
index b162ab0..a680b92 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r878-dirty"
+#define PACKAGE_VERSION "0.7.10-r880-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);