--- a/test-data/expected_outcome3.vcf	Sun Sep 29 10:23:36 2024 +0000
+++ b/test-data/expected_outcome3.vcf	Thu Nov 14 07:25:22 2024 +0000
@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
-##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/6/outputs/dataset_85e708bb-74e2-4686-8dca-f0e9404b4e44.dat --allow-overwrite --minsupport 1 --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
-##fileDate="2024/09/28 23:19:48"
+##source=Sniffles2_2.5
+##command="/home/ross/miniconda3/envs/__sniffles@2.5.2/bin/sniffles -t 1 -i input.bam -v /tmp/tmpqwecq14c/job_working_directory/000/6/outputs/dataset_c8216b3d-5cba-4681-a3da-03306ae2e22a.dat --allow-overwrite --minsupport 1 --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
+##fileDate="2024/11/13 10:03:40"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>
@@ -106,14 +106,15 @@
 ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
 ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
 ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)">
-##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
+##FILTER=<ID=COV_CHANGE_DEL,Description="Coverage change filter for DEL">
+##FILTER=<ID=COV_CHANGE_DUP,Description="Coverage change filter for DUP">
 ##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS">
 ##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start">
 ##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center">
 ##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end">
 ##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream">
-##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter">
-##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic">
+##FILTER=<ID=MOSAIC_VAF,Description="Mosaic variant allele fraction filter">
+##FILTER=<ID=NOT_MOSAIC_VAF,Description="Variant allele fraction filter for non-mosaic">
 ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
 ##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs">
 ##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs">
@@ -138,8 +139,8 @@
 ##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="List of read support for all samples">
 ##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description="Number of reads that support the generated insertion (INS) consensus sequence">
 ##INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of supporting reads (if enabled with --output-rnames)">
-##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=VAF,Number=1,Type=Float,Description="Variant Allele Fraction">
 ##INFO=<ID=NM,Number=.,Type=Float,Description="Mean number of query alignment length adjusted mismatches of supporting reads">
 ##INFO=<ID=PHASE,Number=.,Type=String,Description="Phasing information derived from supporting reads, represented as list of: HAPLOTYPE,PHASESET,HAPLOTYPE_SUPPORT,PHASESET_SUPPORT,HAPLOTYPE_FILTER,PHASESET_FILTER">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
-21	21492142	Sniffles2.DEL.0S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492648;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;AF=1.000;STDEV_LEN=0.509;STDEV_POS=1.404	GT:GQ:DR:DV	1/1:60:0:48
+21	21492142	Sniffles2.DEL.0S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492647;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;STDEV_LEN=0.509;STDEV_POS=1.404;VAF=0.527	GT:GQ:DR:DV	0/1:60:43:48