Add test for splitting multi allelic calls

test/data/fake_chrM_multiallelic.vcf

@@ -39,5 +39,6 @@ chrM	150	.	T	C	5149.77	.	AC=2;AF=1.00;AN=2;DP=130;ExcessHet=3.0103;FS=0.000;MLEA
 chrM	152	.	T	C	5149.77	.	AC=2;AF=1.00;AN=2;DP=126;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.63;SOR=0.711	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,113:113:99:1|1:150_T_C:5178,352,0
 chrM	195	.	C	T,*	690.21	.	AC=0,1;AF=0.00,0.500;AN=2;BaseQRankSum=-1.150e+00;ClippingRankSum=0.00;DP=17;ExcessHet=3.9794;FS=8.872;MQ=39.83;MQRankSum=-9.210e-01;QD=21.57;ReadPosRankSum=-4.390e-01;SOR=2.038	GT:AD:DP:GQ:PL	0/2:9,0,8:17:99:303,330,1227,0,897,873
 chrM	410	.	A	C,G	4849.13	.	AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.910;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=6.027;MQ=52.15;MQRankSum=-4.344e+00;QD=22.98;ReadPosRankSum=0.687;SOR=1.420	GT:AD:DP:GQ:PL	0/1:33,35,8:76:99:836,0,820,685,673,1584
+chrM	1581	.	A	C,G	492.77	.	AC=1,1;AF=0.5,0.5;AN=2;DP=15;ExcessHet=3.0103;FS=0;MLEAC=1,1;MLEAF=0.5,0.5;MQ=48.09;QD=32.85;SOR=5.549	GT:AD:DP:GQ:PL	1/2:0,11,4:15:85:521,117,85,404,0,392
 chrM	2261	.	C	T,CATTTT	4096.90	.	AC=2,0;AF=1.00,0.00;AN=2;DP=37;ExcessHet=3.0103;FS=0.000;MQ=60.00;QD=29.45;SOR=4.768	GT:AD:DP:GQ:PL	1/1:0,37,0:37:99:1248,110,0,1248,110,1248
 chrM	2354	.	C	T	3755.77	.	AC=2;AF=1.00;AN=2;DP=117;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.95;SOR=1.054	GT:AD:DP:GQ:PL	1/1:0,114:114:99:3784,341,0

test/test-integration.yml

@@ -14,7 +14,7 @@
     - path: 16699289/varda/16699289_coverage.varda
     - path: 16699289/varda/16699289_variants.varda
 
-- name: test-trim-alt-exclude-uncalled
+- name: test-integration-trim-alt-exclude-uncalled
   tags:
     - integration
   command: >
@@ -36,7 +36,7 @@
           - "chrM\t152\t.\tT\t."
           - "chrM\t195\t.\tC\tT"
 
-- name: test-multiallelic
+- name: test-integration-multiallelic
   tags:
     - integration
   command: >
@@ -58,6 +58,11 @@
           - "chrM\t410\t.\tA\tC"
           - "chrM\t2261\t.\tC\tT"
     - path: 16699289/varda/16699289_single.vcf
+      must_not_contain:
+          - "chrM\t1581\t.\tA\tC,G"
+      contains:
+          - "chrM\t1581\t.\tA\tC"
+          - "chrM\t1581\t.\tA\tG"
     - path: 16699289/varda/16699289_no_alt_star.vcf
       must_not_contain:
           - "chrM\t195\t.\tC\t*"