From a7dfcd368cda94d5847d3f2b42d4288399d77835 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Fri, 6 Nov 2009 14:06:40 +0000
Subject: [PATCH]  * samtools-0.1.6-21 (r508)  * fixed a potential bug in the
 indel caller towards the end of a chromosome

---
 bam_maqcns.c | 4 ++++
 bam_plcmd.c  | 2 +-
 bamtk.c      | 2 +-
 sam_view.c   | 7 +++++--
 4 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/bam_maqcns.c b/bam_maqcns.c
index 7aed741..71c2185 100644
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -399,6 +399,10 @@ bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, c
 		left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0;
 		right = pos + INDEL_WINDOW_SIZE;
 		if (types[0] < 0) right -= types[0];
+		// in case the alignments stand out the reference
+		for (i = pos; i < right; ++i)
+			if (ref[i] == 0) break;
+		right = i;
 	}
 	{ // the core part
 		char *ref2, *rs, *inscns = 0;
diff --git a/bam_plcmd.c b/bam_plcmd.c
index fff42f7..e2601ec 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -182,7 +182,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 	// call the consensus and indel
 	if (d->format & BAM_PLF_CNS) // call consensus
 		cns = bam_maqcns_call(n, pu, d->c);
-	if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref) { // call indels
+	if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // call indels
 		if (proposed_indels) // the first element gives the size of the array
 			r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
 		else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0);
diff --git a/bamtk.c b/bamtk.c
index a6bf524..b4af0ec 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.6-19 (r494)"
+#define PACKAGE_VERSION "0.1.6-21 (r508)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
diff --git a/sam_view.c b/sam_view.c
index 7e171b9..06dd01a 100644
--- a/sam_view.c
+++ b/sam_view.c
@@ -21,8 +21,11 @@ static void sol2sanger(bam1_t *b)
 			if (g_sol2sanger_tbl[l] >= 93) g_sol2sanger_tbl[l] = 93;
 		}
 	}
-	for (l = 0; l < b->core.l_qseq; ++l)
-		qual[l] = g_sol2sanger_tbl[qual[l]];
+	for (l = 0; l < b->core.l_qseq; ++l) {
+		int q = qual[l];
+		if (q > 127) q = 127;
+		qual[l] = g_sol2sanger_tbl[q];
+	}
 }
 
 static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
-- 
2.39.2