From: Heng Li <lh3@live.co.uk>
Date: Tue, 5 May 2009 21:31:41 +0000 (+0000)
Subject:  * samtools-0.1.3-16 (r267)
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=964138e0a5d0948536b714f77d6188d4adc1c9b8;p=samtools.git

 * samtools-0.1.3-16 (r267)
 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
---

diff --git a/bamtk.c b/bamtk.c
index 31ef17c..3a89dfb 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.3-15 (r266)"
+#define PACKAGE_VERSION "0.1.3-16 (r267)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
diff --git a/sam_view.c b/sam_view.c
index f070b32..5bd679c 100644
--- a/sam_view.c
+++ b/sam_view.c
@@ -6,13 +6,13 @@
 
 static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
 
+#define __g_skip_aln(b) (((b)->core.qual < g_min_mapQ) || ((b->core.flag & g_flag_on) != g_flag_on) \
+						 || (b->core.flag & g_flag_off))
+
 // callback function for bam_fetch()
 static int view_func(const bam1_t *b, void *data)
 {
-	if (b->core.qual < g_min_mapQ) return 0;
-	if (g_flag_on && (b->core.flag & g_flag_on) == 0) return 0;
-	if (b->core.flag & g_flag_off) return 0;
-	samwrite((samfile_t*)data, b);
+	if (!__g_skip_aln(b)) samwrite((samfile_t*)data, b);
 	return 0;
 }
 
@@ -60,7 +60,8 @@ int main_samview(int argc, char *argv[])
 		bam1_t *b = bam_init1();
 		int r;
 		while ((r = samread(in, b)) >= 0) // read one alignment from `in'
-			samwrite(out, b); // write the alignment to `out'
+			if (!__g_skip_aln(b))
+				samwrite(out, b); // write the alignment to `out'
 		if (r < -1) fprintf(stderr, "[main_samview] truncated file.\n");
 		bam_destroy1(b);
 	} else { // retrieve alignments in specified regions