vcfanno: panic: intervals out of order within file: starts at: 4294967295 and 0

Hi Brent,

I am annotating SVs using vcfanno and receive an error panic: intervals out of order within file: starts at: 4294967295 and 0 from source: 0 (full error below). Given that 4294967295 = 2^32 - 1 this might be an overflow or something?

The 4 annotation bed files I use were used before and did not throw an error then. You can find them here https://mega.nz/#!jNUHHQiC!zU8fxxFUu_0WR98eXYfJuDQhBLVhBTHFu-_C4nzB7Ok

My toml annotation file looks like (paths modified):

[[annotation]]
file="GRCh38_full_annotation.bed.gz"
columns = [4]
ops = ["uniq"]
names = ["GENE"]

[[annotation]]
file="GRCh38_exons.bed.gz"
columns = [4]
ops = ["uniq"]
names = ["CODING"]

[[annotation]]
file="GRCh38_genomicSuperDups.bed.bgz"
columns = [4]
ops = ["uniq"]
names = ["SEGDUP"]

[[annotation]]
file="dgv_GRCh38.bed.bgz"
columns = [4]
ops = ["uniq"]
names = ["DGV"]

Command: vcfanno vcfanno_conf.toml SVs.vcf > SVs_annotated.vcf

I cannot share my vcf here publicly but can email it to you if that helps.

Output:

=============================================
vcfanno version 0.3.0 [built with go1.11]

see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:115: found 4 sources from 4 files
bix.go:221: chromosome chr14_GL000194v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr14_GL000225v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr14_KI270722v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr14_KI270725v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr14_KI270726v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr17_GL000205v2_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr17_KI270730v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_full_annotation.bed.gz
bix.go:221: chromosome chr17_KI270730v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_exons.bed.gz
bix.go:221: chromosome chr17_KI270730v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr17_KI270729v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_full_annotation.bed.gz
bix.go:221: chromosome chr17_KI270729v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_exons.bed.gz
bix.go:221: chromosome chr17_KI270729v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr1_KI270708v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_full_annotation.bed.gz
bix.go:221: chromosome chr1_KI270708v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_exons.bed.gz
bix.go:221: chromosome chr1_KI270708v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr1_KI270709v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_full_annotation.bed.gz
bix.go:221: chromosome chr1_KI270709v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_exons.bed.gz
bix.go:221: chromosome chr1_KI270709v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr1_KI270711v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr1_KI270712v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr22_KI270732v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_full_annotation.bed.gz
bix.go:221: chromosome chr22_KI270732v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_exons.bed.gz
bix.go:221: chromosome chr22_KI270732v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr22_KI270734v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr22_KI270733v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr22_KI270736v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_full_annotation.bed.gz
bix.go:221: chromosome chr22_KI270735v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_full_annotation.bed.gz
bix.go:221: chromosome chr22_KI270736v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_exons.bed.gz
bix.go:221: chromosome chr22_KI270735v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_exons.bed.gz
bix.go:221: chromosome chr22_KI270736v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr22_KI270735v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr22_KI270738v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_full_annotation.bed.gz
bix.go:221: chromosome chr22_KI270738v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_exons.bed.gz
bix.go:221: chromosome chr22_KI270737v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_full_annotation.bed.gz
bix.go:221: chromosome chr22_KI270737v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_exons.bed.gz
bix.go:221: chromosome chr22_KI270738v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr22_KI270737v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr2_KI270715v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_full_annotation.bed.gz
bix.go:221: chromosome chr2_KI270715v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_exons.bed.gz
bix.go:221: chromosome chr2_KI270715v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_genomicSuperDups.bed.bgz
bix.go:221: chromosome chr2_KI270715v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr5_GL000208v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_full_annotation.bed.gz
bix.go:221: chromosome chr5_GL000208v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_exons.bed.gz
bix.go:221: chromosome chr5_GL000208v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr9_KI270717v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_full_annotation.bed.gz
bix.go:221: chromosome chr9_KI270717v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_exons.bed.gz
bix.go:221: chromosome chr9_KI270717v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr9_KI270719v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chr9_KI270718v1_random not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chrEBV not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_full_annotation.bed.gz
bix.go:221: chromosome chrEBV not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_exons.bed.gz
bix.go:221: chromosome chrEBV not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/GRCh38_genomicSuperDups.bed.bgz
bix.go:221: chromosome chrEBV not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
bix.go:221: chromosome chrM not found in /home/wdecoster/databases/Homo_sapiens/GRCh38_recommended/dgv_GRCh38.bed.bgz
panic: intervals out of order within file: starts at: 4294967295 and 0 from source: 0

goroutine 41432 [running]:
github.com/brentp/irelate.(*merger).Next(0xc00014c000, 0x10000007938e0, 0x1900, 0x1900, 0xc003cba000)
	/home/brentp/go/src/github.com/brentp/irelate/irelate.go:278 +0xba4
github.com/brentp/irelate.(*irelate).Next(0xc0004143c0, 0x190, 0x190, 0xc003cba000, 0x190)
	/home/brentp/go/src/github.com/brentp/irelate/irelate.go:159 +0xc1
github.com/brentp/irelate.PIRelate.func3.1(0xc001341ce0, 0x7df100, 0xc0004160f0, 0xc000415e00, 0x5, 0x5)
	/home/brentp/go/src/github.com/brentp/irelate/parallel.go:250 +0xf5
created by github.com/brentp/irelate.PIRelate.func3
	/home/brentp/go/src/github.com/brentp/irelate/parallel.go:242 +0x10f