Add test for #1598

Note this fails until samtools/htslib#1396 is merged

NEWS

@@ -4,6 +4,10 @@
   of a VCF or BCF file. Without any options, this is equivalent to
   `bcftools view --header-only --no-version` but more succinct and memorable.
 
+* The `-T, --targets-file` option had the following bug originating in HTSlib code:
+  when an uncompressed file with multiple columns CHR,POS,REF was provided, the
+  REF would be interpreted as 0 gigabases (#1598)
+
 Changes affecting specific commands:
 
 * bcftools annotate
@@ -89,7 +93,7 @@ Changes affecting specific commands:
 Changes affecting the whole of bcftools, or multiple commands:
 
 * New `--regions-overlap` and `--targets-overlap` options which address
-  a long-standing design problem with subsetting VCF files by region. 
+  a long-standing design problem with subsetting VCF files by region.
   BCFtools recognize two sets of options, one for streaming (`-t/-T`) and
   one for index-gumping (`-r/-R`). They behave differently, the first
   includes only records with POS coordinate within the regions, the other
@@ -117,11 +121,11 @@ Changes affecting specific commands:
       by using `-c INFO/END`.
 
     - add a new '.' modifier to control wheter missing values should be carried
-      over from a tab-delimited file or not. For example: 
+      over from a tab-delimited file or not. For example:
 
          -c TAG .. adds TAG if the source value is not missing. If TAG
                    exists in the target file, it will be overwritten
-    
+
         -c .TAG .. adds TAG even if the source value is missing. This
                    can overwrite non-missing values with a missing value
                    and can create empty VCF fields (`TAG=.`)
@@ -250,7 +254,7 @@ Changes affecting specific commands:
 * bcftools +fill-tags:
 
     - Generalization and better support for custom functions that allow
-      adding new INFO tags based on arbitrary `-i, --include` type of 
+      adding new INFO tags based on arbitrary `-i, --include` type of
       expressions. For example, to calculate a missing INFO/DP annotation
       from FORMAT/AD, it is possible to use:
 
@@ -314,7 +318,7 @@ Changes affecting specific commands:
 
     - Atomization of AD and QS tags now correctly updates occurrences of duplicate
       alleles within different haplotypes
-    
+
     - Fix a bug in atomization of Number=A,R tags
 
 * bcftools reheader:
@@ -326,7 +330,7 @@ Changes affecting specific commands:
     - A wider range of genotypes can be set by the plugin by allowing
       specifying custom genotypes. For example, to force a heterozygous
       genotype it is now possible to use expressions like:
-    
+
         c:'m|M'
         c:0/1
         c:0
@@ -338,7 +342,7 @@ Changes affecting specific commands:
     - Better handling of ambiguous keys such as INFO/AF and CSQ/AD. The
       `-p, --annot-prefix` option is now applied before doing anything else
       which allows its use with `-f, --format` and `-c, --columns` options.
-    
+
     - Some consequence field names may not constitute a valid tag name, such
       as "pos(1-based)". Newly field names are trimmed to exclude brackets.
 
@@ -468,7 +472,7 @@ Changes affecting specific commands:
 
 * bcftools csq:
 
-    - Fix a bug wich caused incorrect FORMAT/BCSQ formatting at sites with too 
+    - Fix a bug wich caused incorrect FORMAT/BCSQ formatting at sites with too
       many per-sample consequences
 
     - Fix a bug which incorrectly handled the --ncsq parameter and could clash

test/test.pl

@@ -306,6 +306,8 @@
 test_vcf_view($opts,in=>'view.filter.annovar',out=>'view.filter.annovar.2.out',args=>q[-H -i 'Gene.refGene~"NOD"'],reg=>'');
 test_vcf_view($opts,in=>'view.filter.annovar',out=>'view.filter.annovar.3.out',args=>q[-H -i 'LJB2_MutationTaster=="0.291000"'],reg=>'');
 test_vcf_view($opts,in=>'view-a',out=>'view-a.1.out',args=>q[-H -a]);
+test_vcf_view($opts,in=>'view.sites',out=>'view.sites.1.out',args=>'',tgts=>'view.sites.txt');
+test_vcf_view($opts,in=>'view.sites',out=>'view.sites.1.out',args=>'',tgts=>'view.sites.txt.gz');
 test_vcf_head($opts,in=>'mpileup.2.vcf',in_nheaders=>22);
 test_vcf_call($opts,in=>'mpileup',out=>'mpileup.1.out',args=>'-mv');
 test_vcf_call($opts,in=>'mpileup',out=>'mpileup.2.out',args=>'-mg0');
@@ -868,7 +870,7 @@ sub parse_params
         $$opts{path} = cygpath($$opts{path});
         $$opts{bin}  = cygpath($$opts{bin});
     }
-    
+
     return $opts;
 }
 sub _cmd
@@ -1540,7 +1542,7 @@ sub test_vcf_plugin
     if ( !$$opts{test_plugins} ) { return; }
     $ENV{BCFTOOLS_PLUGINS} = "$$opts{bin}/plugins";
     if ( !exists($args{args}) ) { $args{args} = ''; }
-    my $wpath = $$opts{path}; 
+    my $wpath = $$opts{path};
     if ($^O =~ /^msys/) {
         $wpath = `cygpath -w $$opts{path}`;
         $wpath =~ s/\r?\n//;

test/view.sites.1.out

@@ -0,0 +1,8 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=1,length=20000000>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	10001	.	G	C	40	.	.
+1	10002	.	T	A	50	.	.
+1	10003	.	A	G	60	.	.
+1	10004	.	A	T	70	.	.

test/view.sites.txt

@@ -0,0 +1,4 @@
+1	10001	G	A
+1	10002	T	A
+1	10003	G	C
+1	10004	A	C

test/view.sites.vcf

@@ -0,0 +1,8 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=1,length=20000000>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	10001	.	G	C	40	.	.
+1	10002	.	T	A	50	.	.
+1	10003	.	A	G	60	.	.
+1	10004	.	A	T	70	.	.