Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

header parsing can't handle ">" in description #105

Open
brentp opened this issue May 22, 2019 · 3 comments
Open

header parsing can't handle ">" in description #105

brentp opened this issue May 22, 2019 · 3 comments

Comments

@brentp
Copy link
Contributor

brentp commented May 22, 2019

e.g. this header from the genome in a bottle truth set fails:

##INFO=<ID=DistPASSHG2gt49Minlt1000,Number=1,Type=String,Description="TRUE if Distance to the closest non-matching PASS variant >49bp in HG002 in either direction is less than 1000bp, suggesting possible complex or compound heterozygous variant or inaccurate call">
@brentp
Copy link
Contributor Author

brentp commented May 22, 2019

with this header as input, svtyper truncates the description and puts e.g. Description="" (note the double quote")

##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of SV:DEL=Deletion, CON=Contraction, INS=Insertion, DUP=Duplication, INV=Inversion">

@brentp
Copy link
Contributor Author

brentp commented May 22, 2019

It seems to also fail if there are = in the readme, e.g.:

##INFO=<ID=REPTYPE,Number=1,Type=String,Description="Type of SV, with designation of uniqueness of new or deleted sequence:SIMPLEDEL=Deletion of at least some unique sequence, SIMPLEINS=Insertion of at least some unique sequence, CONTRAC=Contraction, or deletion of sequence entirely similar to remaining sequence, DUP=Duplication, or insertion of sequence entirely similar to pre-existing sequence, INV=Inversion, SUBSINS=Insertion of new sequence with alteration of some pre-existing sequence, SUBSDEL=Deletion of sequence with alteration of some remaining sequence">

@brentp
Copy link
Contributor Author

brentp commented May 23, 2019

the vcf file that's the source of all of the is available here: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant