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.

Sign up for GitHub

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

Jump to bottom

Apostrophe char in bed "name" field produces incorrect output from teststrandbias.R #172

Open
grafitos opened this issue Mar 22, 2022 · 0 comments
Open

Apostrophe char in bed "name" field produces incorrect output from teststrandbias.R #172

grafitos opened this issue Mar 22, 2022 · 0 comments

Comments

@grafitos
Copy link

Hi,

Given the BED specification (https://samtools.github.io/hts-specs/BEDv1.pdf), page 3, apostrophe character can be used in name field.

Creating the input file /tmp/input:

SAMPLE_1 XXX_exon_11 chr1 16262627 16262627 T G 6650 56 3867 2716 35 21 T/C 0.0084 2;2 5.9 1 32.2 1 0.58923 0.85431 60 10.2 0.0084 0 0 2 1 1.3 51 6066 AAAAAAAAAAA TTTTTTTTTT chr1:16254573-16262773 SNV 0 0

And running cat /tmp/input | teststrandbias.R is OK.

But with this input file:

SAMPLE_1 XXX_exon_11_3'_UTR chr1 16262627 16262627 T G 6650 56 3867 2716 35 21 T/C 0.0084 2;2 5.9 1 32.2 1 0.58923 0.85431 60 10.2 0.0084 0 0 2 1 1.3 51 6066 AAAAAAAAAAA TTTTTTTTTT chr1:16254573-16262773 SNV 0 0

Running cat /tmp/input | teststrandbias.R produces no output.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@grafitos