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

VIRUSBreakend summary.tsv file has misformatted header line #504

Closed
toddajohnson opened this issue Jun 17, 2021 · 0 comments
Closed

VIRUSBreakend summary.tsv file has misformatted header line #504

toddajohnson opened this issue Jun 17, 2021 · 0 comments

Comments

@toddajohnson
Copy link

The header line in the final VIRUSBreakend 2.12.0 summary.tsv file has one less header label than there are columns, with column 14 label as alternate_kmer_count#rname. It looks like the virusbreakend code needs a field separator inserted between the two header input sources, and probably, the leading "#" removed:
grep taxid_genus $file_summary_references_tsv | tr -d '\n' > $file_summary_coverage_tsv.tmp head -1 $prefix_adjusted.merged.bam.coverage | tr -d '\n' >> $file_summary_coverage_tsv.tmp

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

2 participants