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

[ADAM-1874] Dedupe samples when loading VCFs. #1876

Merged
merged 1 commit into from Jan 22, 2018

Conversation

4 participants
@fnothaft
Member

fnothaft commented Jan 16, 2018

Resolves #1874. While samples should be unique in a single VCF, we may load data from multiple VCFs that contain the same samples (e.g., VCFs from a single sequencing project where the VCFs are split by chromosome). This change dedupes sample IDs on load.

[ADAM-1874] Dedupe samples when loading VCFs.
Resolves #1874. While samples should be unique in a single VCF, we may load data
from multiple VCFs that contain the same samples (e.g., VCFs from a single
sequencing project where the VCFs are split by chromosome). This change dedupes
sample IDs on load.

@fnothaft fnothaft added this to the 0.24.0 milestone Jan 16, 2018

@fnothaft

This comment has been minimized.

Member

fnothaft commented Jan 21, 2018

Jenkins, test this please.

@coveralls

This comment has been minimized.

coveralls commented Jan 21, 2018

Coverage Status

Coverage increased (+0.1%) to 82.94% when pulling 1e5450c on fnothaft:issues/1874-dedupe-samples into 4223f56 on bigdatagenomics:master.

3 similar comments
@coveralls

This comment has been minimized.

coveralls commented Jan 21, 2018

Coverage Status

Coverage increased (+0.1%) to 82.94% when pulling 1e5450c on fnothaft:issues/1874-dedupe-samples into 4223f56 on bigdatagenomics:master.

@coveralls

This comment has been minimized.

coveralls commented Jan 21, 2018

Coverage Status

Coverage increased (+0.1%) to 82.94% when pulling 1e5450c on fnothaft:issues/1874-dedupe-samples into 4223f56 on bigdatagenomics:master.

@coveralls

This comment has been minimized.

coveralls commented Jan 21, 2018

Coverage Status

Coverage increased (+0.1%) to 82.94% when pulling 1e5450c on fnothaft:issues/1874-dedupe-samples into 4223f56 on bigdatagenomics:master.

@AmplabJenkins

This comment has been minimized.

AmplabJenkins commented Jan 21, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2582/
Test PASSed.

@fnothaft

This comment has been minimized.

Member

fnothaft commented Jan 22, 2018

Ping @heuermh for review/merge.

@heuermh heuermh merged commit 87c515b into bigdatagenomics:master Jan 22, 2018

2 checks passed

Codacy/PR Quality Review Good work! A positive pull request.
Details
default Merged build finished.
Details
@heuermh

This comment has been minimized.

Member

heuermh commented Jan 22, 2018

Thank you, @fnothaft!

@heuermh heuermh added this to Completed in Release 0.24.0 Feb 10, 2018

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