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Fix vcfconvert ALT parsing, null deref, and sample compression #2528

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Fix vcfconvert ALT parsing, null deref, and sample compression #2528

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14 changes: 7 additions & 7 deletions vcfconvert.c
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Original file line number Diff line number Diff line change
Expand Up @@ -204,8 +204,8 @@ static int _set_chrom_pos_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
if ( *se!='_' ) return -1;
kputsn(ss,se-ss,&args->str);
ss = ++se;
while ( se < tsv->se && *se!='_' && isspace_c(*tsv->se) ) se++;
if ( se < tsv->se && *se!='_' && isspace_c(*tsv->se) ) return -1;
while ( se < tsv->se && *se!='_' && !isspace_c(*se) ) se++;
if ( se < tsv->se && *se!='_' && !isspace_c(*se) ) return -1;
kputc(',',&args->str);
kputsn(ss,se-ss,&args->str);

Expand Down Expand Up @@ -920,7 +920,7 @@ static void vcf_to_gensample(args_t *args)
free(files);

if ( gen_fname && (strlen(gen_fname)<3 || strcasecmp(".gz",gen_fname+strlen(gen_fname)-3)) ) gen_compressed = 0;
if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0;
if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 1;

if (gen_fname) fprintf(stderr, "Gen file: %s\n", gen_fname);
if (sample_fname) fprintf(stderr, "Sample file: %s\n", sample_fname);
Expand Down Expand Up @@ -1045,7 +1045,7 @@ static void vcf_to_haplegendsample(args_t *args)

if ( hap_fname && (strlen(hap_fname)<3 || strcasecmp(".gz",hap_fname+strlen(hap_fname)-3)) ) hap_compressed = 0;
if ( legend_fname && (strlen(legend_fname)<3 || strcasecmp(".gz",legend_fname+strlen(legend_fname)-3)) ) legend_compressed = 0;
if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0;
if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 1;

if (hap_fname) fprintf(stderr, "Hap file: %s\n", hap_fname);
if (legend_fname) fprintf(stderr, "Legend file: %s\n", legend_fname);
Expand Down Expand Up @@ -1081,7 +1081,7 @@ static void vcf_to_haplegendsample(args_t *args)

// open haps and legend outputs
BGZF *hout = hap_fname ? bgzf_open(hap_fname, hap_compressed ? "wg" : "wu") : NULL;
if ( hap_compressed && args->n_threads ) bgzf_thread_pool(hout, args->files->p->pool, args->files->p->qsize);
if ( hout && hap_compressed && args->n_threads ) bgzf_thread_pool(hout, args->files->p->pool, args->files->p->qsize);
BGZF *lout = legend_fname ? bgzf_open(legend_fname, legend_compressed ? "wg" : "wu") : NULL;
if (legend_fname) {
str.l = 0;
Expand Down Expand Up @@ -1194,7 +1194,7 @@ static void vcf_to_hapsample(args_t *args)
free(files);

if ( hap_fname && (strlen(hap_fname)<3 || strcasecmp(".gz",hap_fname+strlen(hap_fname)-3)) ) hap_compressed = 0;
if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0;
if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 1;

if (hap_fname) fprintf(stderr, "Hap file: %s\n", hap_fname);
if (sample_fname) fprintf(stderr, "Sample file: %s\n", sample_fname);
Expand Down Expand Up @@ -1232,7 +1232,7 @@ static void vcf_to_hapsample(args_t *args)

// open haps output
BGZF *hout = hap_fname ? bgzf_open(hap_fname, hap_compressed ? "wg" : "wu") : NULL;
if ( hap_compressed && args->n_threads ) bgzf_thread_pool(hout, args->files->p->pool, args->files->p->qsize);
if ( hout && hap_compressed && args->n_threads ) bgzf_thread_pool(hout, args->files->p->pool, args->files->p->qsize);

int no_alt = 0, non_biallelic = 0, filtered = 0, nok = 0;
while ( bcf_sr_next_line(args->files) )
Expand Down