If you have encountered an error, please include:

[x] minimal conf and lua files that you are using. conf.toml.txt

# SimpleRepeat
[[annotation]]
file    = "test.bed.gz"
columns = [4       ]
names   = ["repeat"]
ops     = ["concat"]

[x] urls or actual files for annotations in conf file. test.bed.gz
```
chr1    874777  874888  trf-1
chr1    874778  874888  trf
```
line 2 is the real Simple Tandem Repeat Information tag I want to annotated.

[x] minimal query file. test.vcf.gz

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
1       874778  1164669 G       GCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA       .       .       ALLELEID=1153717;CLNDISDB=MedGen:CN517202;CLNDN=not_provided;CLNHGVS=NC_000001.10:g.874817_874864dup;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;CLNVC=Duplication;CLNVCSO=SO:1000035;CLNVI=Invitae:1613992;GENEINFO=SAMD11:148398;MC=SO:0001575|splice_donor_variant;ORIGIN=1
1       874778  1108252 G       GCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCACCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA       .       .       ALLELEID=1089348;CLNDISDB=MedGen:CN517202;CLNDN=not_provided;CLNHGVS=NC_000001.10:g.874817CCCCTCATCACCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATC[3];CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Likely_benign;CLNVC=Microsatellite;CLNVCSO=SO:0000289;CLNVI=Invitae:3807250;GENEINFO=SAMD11:148398;MC=SO:0001575|splice_donor_variant;ORIGIN=1
1       874778  769497  GCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA       G       .       .       ALLELEID=777163;CLNDISDB=MedGen:CN517202;CLNDN=not_provided;CLNHGVS=NC_000001.10:g.874817_874864del;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;CLNVC=Deletion;CLNVCSO=SO:0000159;CLNVI=Invitae:1680099;GENEINFO=SAMD11:148398;MC=SO:0001575|splice_donor_variant;ORIGIN=1;RS=568340123

get from tabix -h https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz 1:874778-874778 |bgzip > test.vcf.gz There're deletion or duplication of seq CCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA at 1:874779-874826

[x] the command you used to invoke vcfanno

vcfanno -ends -permissive-overlap conf.toml.txt test.vcf

[x] the full error message

============================================= vcfanno version 0.3.2 [built with go1.14.4]

vcfanno

vcfanno.go:115: found 1 sources from 1 files vcfanno.go:156: falling back to non-bgzip vcfanno.go:248: annotated 3 variants in 0.00 seconds (1962.4 / second)

annotated vcf result:

1 874778 1164669 G GCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA . . ALLELEID=1153717;CLNDISDB=MedGen:CN517202;CLNDN=not_provided;CLNHGVS=NC_000001.10:g.874817_874864dup;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;CLNVC=Duplication;CLNVCSO=SO:1000035;CLNVI=Invitae:1613992;GENEINFO=SAMD11:148398;MC=SO:0001575|splice_donor_variant;ORIGIN=1;repeat=trf-1 1 874778 1108252 G GCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCACCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA . . ALLELEID=1089348;CLNDISDB=MedGen:CN517202;CLNDN=not_provided;CLNHGVS=NC_000001.10:g.874817CCCCTCATCACCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATC[3];CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Likely_benign;CLNVC=Microsatellite;CLNVCSO=SO:0000289;CLNVI=Invitae:3807250;GENEINFO=SAMD11:148398;MC=SO:0001575|splice_donor_variant;ORIGIN=1;repeat=trf-1 1 874778 769497 GCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA G . . ALLELEID=777163;CLNDISDB=MedGen:CN517202;CLNDN=not_provided;CLNHGVS=NC_000001.10:g.874817_874864del;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;CLNVC=Deletion;CLNVCSO=SO:0000159;CLNVI=Invitae:1680099;GENEINFO=SAMD11:148398;MC=SO:0001575|splice_donor_variant;ORIGIN=1;RS=568340123;repeat=trf-1,trf;left_repeat=trf-1;right_repeat=trf-1,trf


For convenient, I use `0-base` to describe start coordinates.
I want annoate **`trf`** tag of region `1 874778 874888` to the insertion (duplication) like `1:874778G>GCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA` but failed.
I guess positon of this variant from `vcf` is treated as `1 874777 874778` or `1 874778 874778` without overlap with  `1 874778 874888`.
`-ends` and `-permissive-overlap` has no effect.
Extend region to `1 874777 874888` can annotate insertion of this position (`trf-1` as example), but with cons that extend annotate variants overlap with `1 874777 874778`.
Can we have a more appropriate way?

brentp / vcfanno

can annotate region info properly extend for insertion？ #149

see: https://github.com/brentp/vcfanno