From: Heng Li <lh3@live.co.uk>
Date: Wed, 15 Apr 2009 13:31:32 +0000 (+0000)
Subject:  * samtools-0.1.2-28
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=5fa181a401f891a049e3c43d03917e9452d1d739;p=samtools.git

 * samtools-0.1.2-28
 * make samtools more robust to weird input such as empty file
---

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 5f20c1e..38680df 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -280,7 +280,7 @@ int bam_pileup(int argc, char *argv[])
 		fprintf(stderr, "        -l FILE   list of sites at which pileup is output\n");
 		fprintf(stderr, "        -f FILE   reference sequence in the FASTA format\n\n");
 		fprintf(stderr, "        -c        output the maq consensus sequence\n");
-		fprintf(stderr, "        -g        output in the extended GLT format (suppressing -c/-i/-s)\n");
+		fprintf(stderr, "        -g        output in the GLFv3 format (suppressing -c/-i/-s)\n");
 		fprintf(stderr, "        -T FLOAT  theta in maq consensus calling model (for -c/-g) [%f]\n", d->c->theta);
 		fprintf(stderr, "        -N INT    number of haplotypes in the sample (for -c/-g) [%d]\n", d->c->n_hap);
 		fprintf(stderr, "        -r FLOAT  prior of a difference between two haplotypes (for -c/-g) [%f]\n", d->c->het_rate);
@@ -292,7 +292,7 @@ int bam_pileup(int argc, char *argv[])
 	}
 	if (fn_fa) d->fai = fai_load(fn_fa);
 	free(fn_fa);
-	bam_maqcns_prepare(d->c);
+	if (d->format & (BAM_PLF_CNS|BAM_PLF_GLF)) bam_maqcns_prepare(d->c);
 	if (d->format & BAM_PLF_GLF) {
 		glf3_header_t *h;
 		h = glf3_header_init();
@@ -300,7 +300,7 @@ int bam_pileup(int argc, char *argv[])
 		glf3_header_write(d->fp, h);
 		glf3_header_destroy(h);
 	}
-	if (d->fai == 0)
+	if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)))
 		fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n");
 	if (fn_list) { // the input is SAM
 		tamFile fp;
@@ -322,6 +322,10 @@ int bam_pileup(int argc, char *argv[])
 		bamFile fp;
 		fp = (strcmp(argv[optind], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[optind], "r");
 		d->h = bam_header_read(fp);
+		if (d->h == 0) {
+			fprintf(stderr, "[bam_pileup] fail to read the BAM header. Abort!\n");
+			return 1;
+		}
 		if (fn_pos) d->hash = load_pos(fn_pos, d->h);
 		bam_pileup_file(fp, d->mask, pileup_func, d);
 		bam_close(fp);
diff --git a/bamtk.c b/bamtk.c
index 1c8c7b1..2bdc00a 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-27"
+#define PACKAGE_VERSION "0.1.2-28"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -51,6 +51,10 @@ int bam_view(int argc, char *argv[])
 	fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
 	assert(fp);
 	header = bam_header_read(fp);
+	if (header == 0) {
+		fprintf(stderr, "[bam_view] fail to read the BAM header. Abort!\n");
+		return 1;
+	}
 	if (is_bam) {
 		assert(fpout = bam_dopen(fileno(stdout), "w"));
 		bam_header_write(fpout, header);
@@ -82,7 +86,10 @@ int bam_view(int argc, char *argv[])
 		for (i = optind + 1; i < argc; ++i) {
 			int tid, beg, end;
 			bam_parse_region(header, argv[i], &tid, &beg, &end);
-			if (tid < 0) return 0;
+			if (tid < 0) {
+				fprintf(stderr, "[bam_view] fail to get the reference name. Abort!\n");
+				return 1;
+			}
 			if (is_bam) bam_fetch(fp, idx, tid, beg, end, fpout, view_auxb);
 			else bam_fetch(fp, idx, tid, beg, end, header, view_aux);
 		}