Fix memory leaks:

* When downloading a remote FASTA index
* When indexing a BAM, we can't open the FAI file
* When indexing a BCF, we can't open the index file
* Parsing a VCF header with no sample line
* Encountering multiple adjacent tabs in a SAM header

diff --git a/bam_index.c b/bam_index.c
index d6b94e2413e1dab2d2dc4ce2c91e471854ddd35a..f916e0461dca145499303db8edb011e6db86f793 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -464,6 +464,7 @@ bam_index_t *bam_index_load(const char *fn)
                strcat(strcpy(fnidx, fn), ".bai");
                fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n");
                download_from_remote(fnidx);
+        free(fnidx);
                idx = bam_index_load_local(fn);
        }
        if (idx == 0) fprintf(stderr, "[bam_index_load] fail to load BAM index.\n");
@@ -494,6 +495,7 @@ int bam_index_build2(const char *fn, const char *_fnidx)
        if (fpidx == 0) {
                fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
                free(fnidx);
+        bam_index_destroy(idx);
                return -1;
        }
        bam_index_save(idx, fpidx);

diff --git a/bcftools/index.c b/bcftools/index.c
index 014856d2dd560cc288c9bdc3afbd3bf600ba1ea6..a7db24f671d6761dbc1558ec0a8af775814a2c98 100644 (file)
--- a/bcftools/index.c
+++ b/bcftools/index.c
@@ -259,6 +259,7 @@ int bcf_idx_build2(const char *fn, const char *_fnidx)
        if (fpidx == 0) {
                fprintf(stderr, "[bcf_idx_build2] fail to create the index file.\n");
                free(fnidx);
+        bcf_idx_destroy(idx);
                return -1;
        }
        bcf_idx_save(idx, fpidx);

diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index bc110847dab9e2b97d0248ddfef92312de561ce1..e8526a38706357c4aa2d067fcf9c64dadd8978f6 100644 (file)
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -30,7 +30,12 @@ bcf_hdr_t *vcf_hdr_read(bcf_t *bp)
        memset(&smpl, 0, sizeof(kstring_t));
        while (ks_getuntil(v->ks, '\n', &v->line, &dret) >= 0) {
                if (v->line.l < 2) continue;
-               if (v->line.s[0] != '#') return 0; // no sample line
+               if (v->line.s[0] != '#') {
+            free(meta.s);
+            free(smpl.s);
+            free(h);
+            return 0; // no sample line
+        }
                if (v->line.s[0] == '#' && v->line.s[1] == '#') {
                        kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
                } else if (v->line.s[0] == '#') {

diff --git a/sam_header.c b/sam_header.c
index a1b518101ad20aefb297c240a68756da8eebc371..ddc2c38569f4ee0430439bc10a6e34240939ed5d 100644 (file)
--- a/sam_header.c
+++ b/sam_header.c
@@ -366,6 +366,7 @@ static HeaderLine *sam_header_line_parse(const char *headerLine)
     while (*to && *to=='\t') to++;
     if ( to-from != 1 ) {
         debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
+        free(hline);
                return 0;
        }
     from = to;