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

Index bam files with-c flag if contig size exceeds 2 ** 29 #9570

Merged
merged 4 commits into from
May 4, 2020

Conversation

FredericBGA
Copy link
Contributor

@FredericBGA FredericBGA commented Mar 27, 2020

This is 98% based on @mvdbeek work (mvdbeek@e386b8d). Thank you!

Should close #6956

The limit seems to be 2**29 -1 (I still have issues with 2**30):
biostar

@FredericBGA
Copy link
Contributor Author

sorry, I will send another commit, the binary.py is not merged! This is the file based on my 19.05 version.

@galaxybot galaxybot added this to the 20.05 milestone Mar 27, 2020
@mvdbeek mvdbeek self-assigned this Apr 20, 2020
@mvdbeek
Copy link
Member

mvdbeek commented May 4, 2020

@galaxybot test this

@mvdbeek
Copy link
Member

mvdbeek commented May 4, 2020

Thank you @FredericBGA!

@mvdbeek mvdbeek merged commit 6a4a64a into galaxyproject:dev May 4, 2020
@mvdbeek mvdbeek changed the title index with -c flag for large bam (one region larger than 2**29 - 1) Index with bam files with-c flag is contig size exceeds 2 ** 29 Jun 2, 2020
@mvdbeek mvdbeek changed the title Index with bam files with-c flag is contig size exceeds 2 ** 29 Index bam files with-c flag is contig size exceeds 2 ** 29 Jun 2, 2020
@mvdbeek mvdbeek changed the title Index bam files with-c flag is contig size exceeds 2 ** 29 Index bam files with-c flag if contig size exceeds 2 ** 29 Jun 2, 2020
@dannon
Copy link
Member

dannon commented Jul 28, 2020

It looks like this has added bam_csi_index download links to all (old, too) bam files, even if they don't have the metadata (seen on usegalaxy.org). This shouldn't be available, right?

@bgruening
Copy link
Member

@dannon it seems that we also can not display BAM files anymore.

@dannon
Copy link
Member

dannon commented Jul 30, 2020

@bgruening Yeah, I'm seeing the same thing. I'll spend some time on this tomorrow to try to sort out what's going on with the display.

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

Successfully merging this pull request may close these issues.

BAM indexes for very large contigs
6 participants