Add test for breakend detection

Depends on samtools/htslib#1858

Author: pd3

test/norm.breakend.1.1.out

@@ -0,0 +1,8 @@
+##fileformat=VCFv4.5
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=MATEID,Number=A,Type=String,Description="ID of mate breakend">
+##contig=<ID=chrA,length=500>
+##contig=<ID=chrB,length=500>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+chrA	321	bnd_V	T	]chrB:123]AGTNNNNNCAT	6	PASS	MATEID=bnd_U
+chrB	123	bnd_U	C	CAGTNNNNNCA[chrA:321[	6	PASS	MATEID=bnd_V

test/norm.breakend.1.fa

@@ -0,0 +1,13 @@
+>chrA
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+ACTGACTGACTGACTGACTGCCCCCACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGA
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+ACTGACTGACTGACTGACTGTTTTTACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGA
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
+>chrB
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+ACTGACTGACTGACTGACTGCCCCCACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGA
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+ACTGACTGACTGACTGACTGTTTTTACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGAACTGA
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

test/norm.breakend.1.vcf

@@ -0,0 +1,7 @@
+##fileformat=VCFv4.5
+##INFO=<ID=MATEID,Number=A,Type=String,Description="ID of mate breakend">
+##contig=<ID=chrA,length=500>
+##contig=<ID=chrB,length=500>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+chrA	321	bnd_V	T	]chrB:123]AGTNNNNNCAT	6	PASS	MATEID=bnd_U
+chrB	123	bnd_U	C	CAGTNNNNNCA[chrA:321[	6	PASS	MATEID=bnd_V

test/test.pl

@@ -271,6 +271,7 @@
 run_test(\&test_vcf_query,$opts,in=>'query.header',out=>'query.98.2.out',args=>q[-HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]']);
 run_test(\&test_vcf_query,$opts,in=>'query.filter-or',out=>'query.filter-or.1.out',args=>q[-f'[%SAMPLE %DP\\n]' -i'DP=1 || DP=2']);
 run_test(\&test_vcf_query,$opts,in=>'query.filter-or',out=>'query.filter-or.2.out',args=>q[-f'[%SAMPLE %DP\\n]' -i'DP=1 |  DP=2']);
+run_test(\&test_vcf_norm,$opts,in=>'norm.breakend.1',fai=>'norm.breakend.1',out=>'norm.breakend.1.1.out',args=>'-m -');
 run_test(\&test_vcf_norm,$opts,in=>'norm.sort',out=>'norm.sort.1.out',args=>'-m -');
 run_test(\&test_vcf_norm,$opts,in=>'norm.sort',out=>'norm.sort.2.out',args=>'-m - -S lex');
 run_test(\&test_vcf_norm,$opts,in=>'norm.join-missing-ploidy',out=>'norm.join-missing-ploidy.1.out',args=>'-m +both');