Use int64_t to prevent count overflow in view -c; on behalf of Joshua…

… Randall: Set y2range in quals2.png plot

bam2bcf.c

@@ -87,9 +87,9 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
 		if (min_dist > p->qpos) min_dist = p->qpos;
 		if (min_dist > CAP_DIST) min_dist = CAP_DIST;
 		r->anno[1<<2|is_diff<<1|0] += baseQ;
-		r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
+		r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;	// FIXME: signed int is not enough for thousands of samples
 		r->anno[2<<2|is_diff<<1|0] += mapQ;
-		r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
+		r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;		// FIXME: signed int is not enough for thousands of samples
 		r->anno[3<<2|is_diff<<1|0] += min_dist;
 		r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
 	}

misc/plot-bamcheck

@@ -349,6 +349,7 @@ sub plot_qualities
                 set size 0.4,0.8
                 unset ytics
                 set y2tics mirror
+				set yrange [0:$yrange]
                 unset ylabel
                 set xlabel "Cycle (rev reads)"
                 set label "$$args{title}" at screen 0.5,0.95 center

sam_view.c

@@ -14,7 +14,7 @@ KHASH_SET_INIT_STR(rg)
 // data passed to the bam_fetch callback is encapsulated in this struct.
 typedef struct {
 	bam_header_t *header;
-	int *count;
+	int64_t *count;  // int does overflow for very big BAMs
 } count_func_data_t;
 
 typedef khash_t(rg) *rghash_t;
@@ -128,7 +128,7 @@ int main_samview(int argc, char *argv[])
 {
 	int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0;
 	int of_type = BAM_OFDEC, is_long_help = 0, n_threads = 0;
-	int count = 0;
+	int64_t count = 0;
 	samfile_t *in = 0, *out = 0;
 	char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0, *q;
 
@@ -274,7 +274,7 @@ int main_samview(int argc, char *argv[])
 
 view_end:
 	if (is_count && ret == 0) {
-		printf("%d\n", count);
+		printf("%ld\n", count); // compilers on some platforms may complain about printing int64_t with %ld
 	}
 	// close files, free and return
 	free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);