* 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 5f20c1ead0f156ce85eb3d771e0b2a0106e6bb53..38680df3357a42b80cf251a3b8c796e057d17d32 100644 (file)
--- 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 1c8c7b1c643f4a19e478124ec56b300b311e2c39..2bdc00aba337ac45524dc3dd5ef76de5a2fb83be 100644 (file)
--- 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);
                }