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Fix clang build failure due to --verbosity option handling #2414

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Merged
merged 1 commit into from
May 29, 2025
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Fix clang build failure due to --verbosity option handling #2414

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3 changes: 3 additions & 0 deletions bcftools.h
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,9 @@ void error(const char *format, ...) HTS_NORETURN HTS_FORMAT(HTS_PRINTF_FMT, 1, 2
// newline will be added by the function.
void error_errno(const char *format, ...) HTS_NORETURN HTS_FORMAT(HTS_PRINTF_FMT, 1, 2);

// Set hts_verbose and return 0, or return -1 if str is not a valid integer
int apply_verbosity(const char *str);

// For on the fly index creation with --write-index
int init_index2(htsFile *fh, bcf_hdr_t *hdr, const char *fname, char **idx_fname, int idx_fmt);
int init_index(htsFile *fh, bcf_hdr_t *hdr, const char *fname, char **idx_fname);
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5 changes: 1 addition & 4 deletions consensus.c
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Expand Up @@ -1259,15 +1259,12 @@ int main_consensus(int argc, char *argv[])
{0,0,0,0}
};
int c;
char *tmp;
while ((c = getopt_long(argc, argv, "h?s:S:1Ii:e:H:f:o:m:c:M:p:a:v:",loptions,NULL)) >= 0)
{
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 1 : args->mark_del = optarg[0]; break;
case 2 :
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5 changes: 1 addition & 4 deletions mpileup.c
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Expand Up @@ -1469,13 +1469,10 @@ int main_mpileup(int argc, char *argv[])
{"verbosity",required_argument,NULL,'v'},
{NULL, 0, NULL, 0}
};
char *tmp;
while ((c = getopt_long(argc, argv, "Ag:f:r:R:q:Q:C:BDd:L:b:P:po:e:h:Im:F:EG:6O:xa:s:S:t:T:M:X:UW::v:",lopts,NULL)) >= 0) {
switch (c) {
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
case 16 :
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4 changes: 1 addition & 3 deletions plugins/check-sparsity.c
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Expand Up @@ -246,9 +246,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'n':
args->min_sites = strtol(optarg,&tmp,10);
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4 changes: 1 addition & 3 deletions plugins/contrast.c
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Expand Up @@ -499,9 +499,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 1 : args->force_samples = 1; break;
case 'f': args->max_AC_str = optarg; break;
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4 changes: 1 addition & 3 deletions plugins/gvcfz.c
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Expand Up @@ -347,9 +347,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'a': args->trim_alts = 1; break;
case 'e':
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4 changes: 1 addition & 3 deletions plugins/indel-stats.c
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Expand Up @@ -706,9 +706,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 1 :
MAX_LEN = strtod(optarg,&tmp);
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4 changes: 1 addition & 3 deletions plugins/isecGT.c
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Expand Up @@ -99,9 +99,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'o': args->output_fname = optarg; break;
case 'O':
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4 changes: 1 addition & 3 deletions plugins/mendelian2.c
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Expand Up @@ -832,9 +832,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'e':
if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
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4 changes: 1 addition & 3 deletions plugins/parental-origin.c
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Expand Up @@ -345,9 +345,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'e':
if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
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4 changes: 1 addition & 3 deletions plugins/prune.c
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Expand Up @@ -363,9 +363,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 1 : args->rand_missing = 1; break;
case 2 : args->af_tag = optarg; break;
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4 changes: 1 addition & 3 deletions plugins/remove-overlaps.c
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Expand Up @@ -244,9 +244,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'm': args->mark_expr = optarg; break;
case 'M': args->mark_tag = optarg; break;
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4 changes: 1 addition & 3 deletions plugins/scatter.c
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Expand Up @@ -372,9 +372,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'e':
if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
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5 changes: 1 addition & 4 deletions plugins/smpl-stats.c
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Expand Up @@ -446,15 +446,12 @@ int run(int argc, char **argv)
{NULL,0,NULL,0}
};
int c, i;
char *tmp;
while ((c = getopt_long(argc, argv, "o:s:i:e:r:R:t:T:v:",loptions,NULL)) >= 0)
{
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'e':
if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
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4 changes: 1 addition & 3 deletions plugins/split-vep.c
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Expand Up @@ -1588,9 +1588,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 2 : args->record_cmd_line = 0; break;
case 1 : args->column_types = optarg; break;
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4 changes: 1 addition & 3 deletions plugins/split.c
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Expand Up @@ -668,9 +668,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 1 : args->hts_opts = hts_readlist(optarg,0,&args->nhts_opts); break;
case 'k': args->keep_tags = optarg; break;
Expand Down
4 changes: 1 addition & 3 deletions plugins/trio-dnm2.c
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Expand Up @@ -1685,9 +1685,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 1 : args->force_ad = 1; break;
case 2 : free(args->dnm_score_tag); args->dnm_score_tag = strdup(optarg); break;
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5 changes: 1 addition & 4 deletions plugins/trio-stats.c
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Expand Up @@ -728,15 +728,12 @@ int run(int argc, char **argv)
{NULL,0,NULL,0}
};
int c, i;
char *tmp;
while ((c = getopt_long(argc, argv, "P:p:o:s:i:e:r:R:t:T:a:d:v:",loptions,NULL)) >= 0)
{
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'd':
{
Expand Down
4 changes: 1 addition & 3 deletions plugins/variant-distance.c
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Expand Up @@ -260,9 +260,7 @@ int run(int argc, char **argv)
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'd':
if ( !strcasecmp("nearest",optarg) ) args->direction = DIR_NEAREST;
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5 changes: 1 addition & 4 deletions reheader.c
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Expand Up @@ -699,15 +699,12 @@ int main_reheader(int argc, char *argv[])
{"verbosity",required_argument,NULL,'v'},
{0,0,0,0}
};
char *tmp;
while ((c = getopt_long(argc, argv, "s:h:o:f:T:v:",loptions,NULL)) >= 0)
{
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 1 : args->n_threads = strtol(optarg, 0, 0); break;
case 'T': break; // unused - was temp file prefix
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4 changes: 1 addition & 3 deletions vcfannotate.c
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Expand Up @@ -3739,9 +3739,7 @@ int main_vcfannotate(int argc, char *argv[])
{
switch (c) {
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'f': args->force = 1; break;
case 'k': args->keep_sites = 1; break;
Expand Down
4 changes: 1 addition & 3 deletions vcfcall.c
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Expand Up @@ -1154,9 +1154,7 @@ int main_vcfcall(int argc, char *argv[])
error("Unsupported index format '%s'\n", optarg);
break;
case 10:
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
default: usage(&args);
}
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4 changes: 1 addition & 3 deletions vcfcnv.c
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Expand Up @@ -1303,9 +1303,7 @@ int main_vcfcnv(int argc, char *argv[])
while ((c = getopt_long(argc, argv, "h?r:R:t:T:s:o:p:l:T:c:b:P:x:e:O:W::f:a:L:d:k:v:",loptions,NULL)) >= 0) {
switch (c) {
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'L':
args->lrr_smooth_win = strtol(optarg,&tmp,10);
Expand Down
4 changes: 1 addition & 3 deletions vcfconvert.c
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Expand Up @@ -1729,9 +1729,7 @@ int main_vcfconvert(int argc, char *argv[])
while ((c = getopt_long(argc, argv, "?h:r:R:s:S:t:T:i:e:g:G:o:O:c:f:H:W::v:",loptions,NULL)) >= 0) {
switch (c) {
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'e':
if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
Expand Down
4 changes: 1 addition & 3 deletions vcffilter.c
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Expand Up @@ -545,9 +545,7 @@ int main_vcffilter(int argc, char *argv[])
while ((c = getopt_long(argc, argv, "e:i:t:T:r:R:h?s:m:M:o:O:g:G:S:W::v:",loptions,NULL)) >= 0) {
switch (c) {
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'g':
args->snp_gap = strtol(optarg,&tmp,10);
Expand Down
4 changes: 1 addition & 3 deletions vcfgtcheck.c
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Expand Up @@ -1255,9 +1255,7 @@ int main_vcfgtcheck(int argc, char *argv[])
while ((c = getopt_long(argc, argv, "hg:p:s:S:p:P:Hr:R:at:T:G:c:u:e:E:i:o:O:v:",loptions,NULL)) >= 0) {
switch (c) {
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'o': args->output_fname = optarg; break;
case 'O':
Expand Down
5 changes: 1 addition & 4 deletions vcfhead.c
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Expand Up @@ -61,14 +61,11 @@ int main_vcfhead(int argc, char *argv[])
uint64_t nheaders = 0;
uint64_t nrecords = 0;

char *tmp;
int c, nargs;
while ((c = getopt_long(argc, argv, "h:n:s:v:", loptions, NULL)) >= 0)
switch (c) {
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'h': all_headers = 0; nheaders = strtoull(optarg, NULL, 0); break;
case 'n': nrecords = strtoull(optarg, NULL, 0); break;
Expand Down
4 changes: 1 addition & 3 deletions vcfindex.c
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Expand Up @@ -249,9 +249,7 @@ int main_vcfindex(int argc, char *argv[])
switch (c)
{
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'c': tbi = 0; break;
case 't': tbi = 1; min_shift = 0; break;
Expand Down
4 changes: 1 addition & 3 deletions vcfisec.c
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Expand Up @@ -573,9 +573,7 @@ int main_vcfisec(int argc, char *argv[])
while ((c = getopt_long(argc, argv, "hc:r:R:p:n:w:t:T:Cf:o:O:i:e:l:W::v:",loptions,NULL)) >= 0) {
switch (c) {
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'o': args->output_fname = optarg; break;
case 'O':
Expand Down
8 changes: 4 additions & 4 deletions vcfmerge.c
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Expand Up @@ -2725,6 +2725,8 @@ void gvcf_flush(args_t *args, int done)

static inline int is_gvcf_block(args_t *args, bcf1_t *line)
{
maux_t *ma;

if ( line->rlen<=1 ) return 0;
if ( strlen(line->d.allele[0])==line->rlen ) return 0;
if ( line->n_allele==1 ) goto is_gvcf;
Expand All @@ -2739,7 +2741,7 @@ static inline int is_gvcf_block(args_t *args, bcf1_t *line)
return 0;

is_gvcf:
maux_t *ma = args->maux;
ma = args->maux;
if ( !ma->gvcf )
{
args->do_gvcf = 1;
Expand Down Expand Up @@ -3607,9 +3609,7 @@ int main_vcfmerge(int argc, char *argv[])
while ((c = getopt_long(argc, argv, "hm:f:r:R:o:O:i:M:l:g:F:0L:W::v:",loptions,NULL)) >= 0) {
switch (c) {
case 'v':
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'L':
args->local_alleles = strtol(optarg,&tmp,10);
Expand Down
5 changes: 1 addition & 4 deletions vcfquery.c
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Expand Up @@ -301,7 +301,6 @@ int main_vcfquery(int argc, char *argv[])
{"verbosity",required_argument,NULL,4},
{0,0,0,0}
};
char *tmp;
while ((c = getopt_long(argc, argv, "hlr:R:F:f:a:s:S:Ht:T:c:v:i:e:o:uN",loptions,NULL)) >= 0) {
switch (c) {
case 'o': args->fn_out = optarg; break;
Expand Down Expand Up @@ -354,9 +353,7 @@ int main_vcfquery(int argc, char *argv[])
break;
case 3 : args->force_samples = 1; break;
case 4 :
int verbose = strtol(optarg,&tmp,10);
if ( *tmp || verbose<0 ) error("Could not parse argument: --verbosity %s\n", optarg);
if ( verbose > 3 ) hts_verbose = verbose;
if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
break;
case 'h':
case '?': usage(); break;
Expand Down
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