From: Heng Li <lh3@live.co.uk>
Date: Fri, 2 Jul 2010 23:32:24 +0000 (+0000)
Subject: fixed a minor bug in idxstats
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=a5adc91ac9fb9f3c88b80a77b1eecfe8d5fb0551;p=samtools.git

fixed a minor bug in idxstats
---

diff --git a/bam.h b/bam.h
index fb71a49..8e26ea6 100644
--- a/bam.h
+++ b/bam.h
@@ -329,6 +329,7 @@ extern "C" {
 	  be destroyed in the first place.
 	 */
 	int sam_header_parse(bam_header_t *h);
+	int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
 
 	/*!
 	  @abstract       Parse @RG lines a update a header struct
diff --git a/bam_index.c b/bam_index.c
index 7a53d7f..4152f20 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -504,7 +504,7 @@ int bam_idxstats(int argc, char *argv[])
 	bam_index_t *idx;
 	bam_header_t *header;
 	bamFile fp;
-	int i, no_stats = 0;
+	int i;
 	if (argc < 2) {
 		fprintf(stderr, "Usage: samtools idxstats <in.bam>\n");
 		return 1;
@@ -522,12 +522,10 @@ int bam_idxstats(int argc, char *argv[])
 		k = kh_get(i, h, BAM_MAX_BIN);
 		if (k != kh_end(h))
 			printf("\t%llu\t%llu", (long long)kh_val(h, k).list[1].u, (long long)kh_val(h, k).list[1].v);
-		else no_stats = 1;
+		else printf("\t0\t0");
 		putchar('\n');
 	}
-	printf("*\t0");
-	if (!no_stats) printf("\t0\t%llu", (long long)idx->n_no_coor);
-	putchar('\n');
+	printf("*\t0\t0\t%llu\n", (long long)idx->n_no_coor);
 	bam_header_destroy(header);
 	bam_index_destroy(idx);
 	return 0;
diff --git a/misc/Makefile b/misc/Makefile
index 2c400f8..2f1578b 100644
--- a/misc/Makefile
+++ b/misc/Makefile
@@ -1,10 +1,10 @@
 CC=			gcc
 CXX=		g++
-CFLAGS=		-g -Wall -O2 -m64 #-arch ppc
+CFLAGS=		-g -Wall #-O2 #-m64 #-arch ppc
 CXXFLAGS=	$(CFLAGS)
 DFLAGS=		-D_FILE_OFFSET_BITS=64
 OBJS=		
-PROG=		md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
+PROG=		md5sum-lite md5fa maq2sam-short maq2sam-long wgsim afs2
 INCLUDES=	-I..
 SUBDIRS=	.
 
@@ -27,6 +27,9 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
 
 lib:
 
+afs2:afs2.o
+		$(CC) $(CFLAGS) -o $@ afs2.o -lm -lz -L.. -lbam
+
 wgsim:wgsim.o
 		$(CC) $(CFLAGS) -o $@ wgsim.o -lm
 
@@ -48,6 +51,9 @@ maq2sam-long:maq2sam.c
 md5fa.o:md5.h md5fa.c
 		$(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
 
+afs2.o:afs2.c ../bam.h
+		$(CC) $(CFLAGS) -c -I.. -o $@ afs2.c
+
 cleanlocal:
 		rm -fr gmon.out *.o a.out *.exe *.dSYM $(PROG) *~ *.a