Adjust snp-ins-del code for the revised bcf_has_variant_type API

Author: daviesrob

plugins/smpl-stats.c

@@ -394,8 +394,9 @@ static void process_record(args_t *args, bcf1_t *rec, flt_stats_t *flt)
                     error("The GT index is out of range at %s:%"PRId64" in %s\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1,args->hdr->samples[j]);
 
                 if ( args->ac[als[j]]==1 ) { stats->nsingleton++; site_singleton = 1; }
-
-                if ( bcf_has_variant_type(rec, als[j], VCF_SNP|VCF_MNP, subset) )
+                int var_type = bcf_has_variant_type(rec, als[j], VCF_SNP|VCF_MNP|VCF_INDEL);
+                if ( var_type < 0 ) error("bcf_has_variant_type() failed");
+                if ( var_type & (VCF_SNP|VCF_MNP) )
                 {
                     int k = 0;
                     while ( rec->d.allele[0][k] && rec->d.allele[als[j]][k] )
@@ -410,7 +411,7 @@ static void process_record(args_t *args, bcf1_t *rec, flt_stats_t *flt)
                         k++;
                     }
                 }
-                else if ( bcf_has_variant_type(rec, als[j], VCF_INDEL, exact) ) has_indel = 1;
+                else if ( var_type == VCF_INDEL ) has_indel = 1;
             }
             if ( has_ts ) { stats->nts++; site_has_ts = 1; }
             if ( has_tv ) { stats->ntv++; site_has_tv = 1; }

vcfmerge.c

@@ -2753,7 +2753,8 @@ int can_merge(args_t *args)
                 id = line->d.id;
             else
             {
-                int var_type = bcf_get_variant_types(line);
+                int var_type = bcf_has_variant_types(line, VCF_ANY, bcf_match_overlap);
+                if (var_type < 0) error("bcf_has_variant_types() failed.");
                 if ( args->collapse==COLLAPSE_SNP_INS_DEL )
                 {
                     // need to distinguish between ins and del so strip the VCF_INDEL flag
@@ -2794,7 +2795,8 @@ int can_merge(args_t *args)
 
             bcf1_t *line = buf->lines[j]; // ptr to reader's buffer or gvcf buffer
 
-            int line_type = bcf_get_variant_types(line);
+            int line_type = bcf_has_variant_types(line, VCF_ANY, bcf_match_overlap);
+            if (line_type < 0) error("bcf_has_variant_types() failed.");
             line_type = line_type ? line_type<<2 : 2;
 
             // select relevant lines
@@ -2911,7 +2913,8 @@ void stage_line(args_t *args)
             {
                 if ( buf->rec[j].skip ) continue;   // done or not compatible
                 if ( args->collapse&COLLAPSE_ANY ) break;   // anything can be merged
-                int line_type = bcf_get_variant_types(buf->lines[j]);
+                int line_type = bcf_has_variant_types(buf->lines[j], VCF_ANY, bcf_match_overlap);
+                if (line_type < 0) error("bcf_has_variant_types() failed.");
                 if ( maux->var_types&snp_mask && line_type&VCF_SNP && (args->collapse&COLLAPSE_SNPS) ) break;
                 if ( maux->var_types&indel_mask && line_type&VCF_INDEL && (args->collapse&COLLAPSE_INDELS) ) break;
                 if ( maux->var_types&ins_mask && line_type&VCF_INS && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break;

vcfstats.c

@@ -706,8 +706,10 @@ static void do_indel_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
     for (i=1; i<line->n_allele; i++)
     {
         if ( args->first_allele_only && i>1 ) break;
-        if ( !bcf_has_variant_type(line,i,VCF_INDEL,exact) ) continue;
-        int len = line->d.var[i].n;
+        int is_indel = bcf_has_variant_type(line,i,VCF_INDEL);
+        if (is_indel < 0) error("bcf_has_variant_type() failed.");
+        if ( !is_indel ) continue;
+        int len = bcf_variant_length(line, i);
 
         #if IRC_STATS
         // Indel repeat consistency