thomasKuilman
commented
9 years ago We were in the process of fixing this bug while you created this pull request; in the new version 2.0.2 downloadable from GitHub and within the next day or so from Bioconductor, the issue has been fixed. Thank you very much for bringing this to our attention.
Best regards,
Thomas Kuilman
Thomas Kuilman, PhD Department of Molecular Oncology Netherlands Cancer Institute 1066 CX Amsterdam The Netherlands
Phone: +31-20-5121841
On 24 Apr 2015, at 13:46, David A. Parry notifications@github.com<mailto:notifications@github.com> wrote:
Many BAM files (e.g. those sorted with picard) have a header line that looks like the following:
@HDhttps://github.com/HD VN:1.4 GO:none SO:coordinate
The original code to capture the sort order will not identify that these are coordinate sorted files and will capture "GO:none" instead, stopping the run. Using grep instead allows for the sort order to be captured correctly.
You can view, comment on, or merge this pull request online at:
https://github.com/PeeperLab/CopywriteR/pull/2
Commit Summary
- Detect sort mode for B/SAM files with GO tags
File Changes
- M R/CopywriteR.Rhttps://github.com/PeeperLab/CopywriteR/pull/2/files#diff-0 (2)
Patch Links:
- https://github.com/PeeperLab/CopywriteR/pull/2.patch
- https://github.com/PeeperLab/CopywriteR/pull/2.diff
� Reply to this email directly or view it on GitHubhttps://github.com/PeeperLab/CopywriteR/pull/2.
Many BAM files (e.g. those sorted with picard) have a header line that looks like the following:
@HD VN:1.4 GO:none SO:coordinate
The original code to capture the sort order will not identify that these are coordinate sorted files and will capture "GO:none" instead, stopping the run. Using grep instead allows for the sort order to be captured correctly.