Fix "may be used uninitialized" warnings at low optimisation

These are probably false positives, but with low optimisation
the compiler isn't able to work out that the variables are always
set before use.  Fix by always assigning them.

plugins/split-vep.c

@@ -30,6 +30,7 @@
 #include <getopt.h>
 #include <unistd.h>     // for isatty
 #include <inttypes.h>
+#include <assert.h>
 #include <htslib/hts.h>
 #include <htslib/vcf.h>
 #include <htslib/bgzf.h>
@@ -606,7 +607,7 @@ static void parse_column_str(args_t *args)
         char keep = *ep;
         *ep = 0;
         int type = -1;
-        int idx_beg, idx_end;
+        int idx_beg = 0, idx_end = -1;
         if ( !strcmp("-",bp) )
         {
             kstring_t str = {0,0,0};
@@ -973,11 +974,12 @@ static void init_data(args_t *args)
     else
     {
         int len = strlen(sel_csq);
-        int severity, modifier = '=';
+        int severity = -1, modifier = '=';
         if ( sel_csq[len-1]=='+' ) { modifier = '+'; sel_csq[len-1] = 0; }
         else if ( sel_csq[len-1]=='-' ) { modifier = '-'; sel_csq[len-1] = 0; }
         if ( khash_str2int_get(args->csq2severity, sel_csq, &severity)!=0 )
             error("Error: the consequence \"%s\" is not recognised. Run \"bcftools +split-vep -S ?\" to see the default list.\n", sel_csq);
+        assert(severity >= 0);
         if ( modifier=='=' ) { args->min_severity = severity; args->max_severity = severity; }
         else if ( modifier=='+' ) { args->min_severity = severity; args->max_severity = INT_MAX; }
         else if ( modifier=='-' ) { args->min_severity = 0; args->max_severity = severity; }

read_consensus.c

@@ -521,7 +521,7 @@ static int create_haplotype_frequency_spectrum(read_cns_t *rcns)
             }
             else if ( cvar->vtype==ins )
             {
-                int len;
+                int len = 0;
                 ins_freq_t *ifrq = &rcns->ins_freq[cvar->pos - rcns->beg];
                 int iseq = cstate_seek_op_fwd(&cigar, cvar->pos+1, BAM_CINS, &len);
                 if ( iseq==-2 ) break;
@@ -533,7 +533,7 @@ static int create_haplotype_frequency_spectrum(read_cns_t *rcns)
             }
             else if ( cvar->vtype==del )
             {
-                int len;
+                int len = 0;
                 del_freq_t *dfrq = &rcns->del_freq[cvar->pos - rcns->beg];
                 int ret = cstate_seek_op_fwd(&cigar, cvar->pos+1, BAM_CDEL, &len);
                 if ( ret==-2 ) break;