Fix warnings identified with -fsanitize=address

samtools · Jul 17, 2018 · 26b2845 · 26b2845
1 parent c3c5569
commit 26b2845
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Showing 3 changed files with 16 additions and 15 deletions.
diff --git a/bam_sample.c b/bam_sample.c
@@ -1,7 +1,7 @@
 /*  bam_sample.c -- group data by sample.
 
     Copyright (C) 2010, 2011 Broad Institute.
-    Copyright (C) 2013, 2016 Genome Research Ltd.
+    Copyright (C) 2013, 2016-2018 Genome Research Ltd.
 
     Author: Heng Li <lh3@sanger.ac.uk>, Petr Danecek <pd3@sanger.ac.uk>
 
@@ -238,6 +238,7 @@ int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname)
     {
         // no suitable read group is available in this bam: ignore the whole file.
         free(file->fname);
+        if ( file->rg2idx ) khash_str2int_destroy_free(file->rg2idx);
         bsmpl->nfiles--;
         return -1;
     }

diff --git a/csq.c b/csq.c
@@ -3376,7 +3376,7 @@ int test_cds(args_t *args, bcf1_t *rec)
                         fprintf(args->out,"LOG\tWarning: Skipping overlapping variants at %s:%d\t%s>%s\n", chr,rec->pos+1,rec->d.allele[0],rec->d.allele[1]);
                 }
                 else ret = 1;   // prevent reporting as intron in test_tscript
-                free(child);
+                hap_destroy(child);
                 continue;
             }
             if ( child->type==HAP_SSS )
@@ -3390,7 +3390,7 @@ int test_cds(args_t *args, bcf1_t *rec)
                 csq.type.gene    = tr->gene->name;
                 csq.type.type = child->csq;
                 csq_stage(args, &csq, rec);
-                free(child);
+                hap_destroy(child);
                 ret = 1;
                 continue;
             }
@@ -3475,7 +3475,7 @@ int test_cds(args_t *args, bcf1_t *rec)
                             fprintf(args->out,"LOG\tWarning: Skipping overlapping variants at %s:%d, sample %s\t%s>%s\n",
                                     chr,rec->pos+1,args->hdr->samples[args->smpl->idx[ismpl]],rec->d.allele[0],rec->d.allele[ial]);
                     }
-                    free(child);
+                    hap_destroy(child);
                     continue;
                 }
                 if ( child->type==HAP_SSS )
@@ -3489,7 +3489,7 @@ int test_cds(args_t *args, bcf1_t *rec)
                     csq.type.gene    = tr->gene->name;
                     csq.type.type = child->csq;
                     csq_stage(args, &csq, rec);
-                    free(child);
+                    hap_destroy(child);
                     continue;
                 }
                 if ( parent->cur_rec!=rec )

diff --git a/vcfroh.c b/vcfroh.c
@@ -1,6 +1,6 @@
 /*  vcfroh.c -- HMM model for detecting runs of autozygosity.
 
-    Copyright (C) 2013-2017 Genome Research Ltd.
+    Copyright (C) 2013-2018 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -749,9 +749,9 @@ int estimate_AF_from_PL(args_t *args, bcf_fmt_t *fmt_pl, int ial, double *alt_fr
                 if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue;    /* missing value */ \
                 if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue;    /* all values are the same */ \
                 double prob[3], norm = 0; \
-                prob[0] = p[irr] < (type_t)256 ? args->pl2p[ p[irr] ] : args->pl2p[255]; \
-                prob[1] = p[ira] < (type_t)256 ? args->pl2p[ p[ira] ] : args->pl2p[255]; \
-                prob[2] = p[iaa] < (type_t)256 ? args->pl2p[ p[iaa] ] : args->pl2p[255]; \
+                prob[0] = p[irr] < 256 ? args->pl2p[ p[irr] ] : args->pl2p[255]; \
+                prob[1] = p[ira] < 256 ? args->pl2p[ p[ira] ] : args->pl2p[255]; \
+                prob[2] = p[iaa] < 256 ? args->pl2p[ p[iaa] ] : args->pl2p[255]; \
                 for (j=0; j<3; j++) norm += prob[j]; \
                 for (j=0; j<3; j++) prob[j] /= norm; \
                 af += 0.5*prob[1] + prob[2]; \
@@ -779,9 +779,9 @@ int estimate_AF_from_PL(args_t *args, bcf_fmt_t *fmt_pl, int ial, double *alt_fr
                 if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue;    /* missing value */ \
                 if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue;    /* all values are the same */ \
                 double prob[3], norm = 0; \
-                prob[0] = p[irr] < (type_t)256 ? args->pl2p[ p[irr] ] : args->pl2p[255]; \
-                prob[1] = p[ira] < (type_t)256 ? args->pl2p[ p[ira] ] : args->pl2p[255]; \
-                prob[2] = p[iaa] < (type_t)256 ? args->pl2p[ p[iaa] ] : args->pl2p[255]; \
+                prob[0] = p[irr] < 256 ? args->pl2p[ p[irr] ] : args->pl2p[255]; \
+                prob[1] = p[ira] < 256 ? args->pl2p[ p[ira] ] : args->pl2p[255]; \
+                prob[2] = p[iaa] < 256 ? args->pl2p[ p[iaa] ] : args->pl2p[255]; \
                 for (j=0; j<3; j++) norm += prob[j]; \
                 for (j=0; j<3; j++) prob[j] /= norm; \
                 af += 0.5*prob[1] + prob[2]; \
@@ -926,9 +926,9 @@ int process_line(args_t *args, bcf1_t *line, int ial)
                 type_t *p = (type_t*)fmt_pl->p + fmt_pl->n*ismpl; \
                 if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue;    /* missing value */ \
                 if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue;    /* all values are the same */ \
-                pdg[0] = p[irr] < (type_t)256 ? args->pl2p[ p[irr] ] : args->pl2p[255]; \
-                pdg[1] = p[ira] < (type_t)256 ? args->pl2p[ p[ira] ] : args->pl2p[255]; \
-                pdg[2] = p[iaa] < (type_t)256 ? args->pl2p[ p[iaa] ] : args->pl2p[255]; \
+                pdg[0] = p[irr] < 256 ? args->pl2p[ p[irr] ] : args->pl2p[255]; \
+                pdg[1] = p[ira] < 256 ? args->pl2p[ p[ira] ] : args->pl2p[255]; \
+                pdg[2] = p[iaa] < 256 ? args->pl2p[ p[iaa] ] : args->pl2p[255]; \
             }
             switch (fmt_pl->type) {
                 case BCF_BT_INT8:  BRANCH(int8_t); break;