From 8f9081fe5d62916987b928753d13e06c08322236 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 29 Mar 2012 10:50:16 +0100
Subject: [PATCH] Compile cleanly from top-level Makefile. Check for out of
 bounds tids.

---
 misc/Makefile   | 3 +++
 misc/bamcheck.c | 4 ++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/misc/Makefile b/misc/Makefile
index 9434399..64aa9df 100644
--- a/misc/Makefile
+++ b/misc/Makefile
@@ -30,6 +30,9 @@ lib:
 bamcheck:bamcheck.o
 		$(CC) $(CFLAGS) -o $@ bamcheck.o -lm -lz -L.. -lbam
 
+bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
+		$(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
+
 ace2sam:ace2sam.o
 		$(CC) $(CFLAGS) -o $@ ace2sam.o -lz
 
diff --git a/misc/bamcheck.c b/misc/bamcheck.c
index 7b5fd02..03cf3b2 100644
--- a/misc/bamcheck.c
+++ b/misc/bamcheck.c
@@ -12,7 +12,7 @@
             considered, even small overlap is good enough to include the read in the stats.
 */
 
-#define BAMCHECK_VERSION "2012-03-22"
+#define BAMCHECK_VERSION "2012-03-29"
 
 #define _ISOC99_SOURCE
 #define _GNU_SOURCE
@@ -1240,7 +1240,7 @@ int main(int argc, char *argv[])
         {
             if ( stats->regions )
             {
-                if ( bam_line->core.tid >= stats->nregions ) continue;
+                if ( bam_line->core.tid >= stats->nregions || bam_line->core.tid<0 ) continue;
                 if ( !stats->is_sorted ) error("The BAM must be sorted in order for -t to work.\n");
 
                 regions_t *reg = &stats->regions[bam_line->core.tid];
-- 
2.39.2