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

Fixes to FASTA code to properly handle indices. #241

Merged
merged 1 commit into from May 12, 2014

Conversation

Projects
None yet
3 participants
@fnothaft
Member

fnothaft commented May 12, 2014

The current FASTA code has problems with some files, as the Spark indexing system seems to encode the line numbers in long values that overflow the Long-->Int conversion in our code. This PR appears to fix this. Additionally, this adds *.fa as a suffix that triggers conversion of FASTA to ADAM.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins May 12, 2014

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/321/

AmplabJenkins commented May 12, 2014

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/321/

massie added a commit that referenced this pull request May 12, 2014

Merge pull request #241 from fnothaft/fasta-long
Fixes to FASTA code to properly handle indices.

@massie massie merged commit 3859a15 into bigdatagenomics:master May 12, 2014

1 check passed

default Merged build finished.
Details
@massie

This comment has been minimized.

Show comment
Hide comment
@massie

massie May 12, 2014

Member

Thanks, Frank!

Member

massie commented May 12, 2014

Thanks, Frank!

@fnothaft fnothaft deleted the fnothaft:fasta-long branch Jul 10, 2014

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment