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

[ADAM-1585] Support additional Illumina FASTQ metadata. #1586

Merged
merged 1 commit into from Jul 11, 2017

Conversation

@fnothaft
Copy link
Member

@fnothaft fnothaft commented Jul 2, 2017

Resolves #1585.

@fnothaft fnothaft added this to the 0.23.0 milestone Jul 2, 2017
@fnothaft
Copy link
Member Author

@fnothaft fnothaft commented Jul 2, 2017

As an aside, I was going to add a FASTQ with said metadata, but I don't have a FASTQ that I can share publically with it. I searched both ENA and SRA for reads with the metadata, but they appear to obliterate that metadata prior to upload.

@coveralls
Copy link

@coveralls coveralls commented Jul 2, 2017

Coverage Status

Coverage increased (+0.05%) to 83.1% when pulling 1488bdc on fnothaft:issues/1585-fastq-metadata into 0306717 on bigdatagenomics:master.

@AmplabJenkins
Copy link

@AmplabJenkins AmplabJenkins commented Jul 2, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2172/
Test PASSed.

Copy link
Member

@heuermh heuermh left a comment

See also #1589, the pattern here will also need to be added to InterleavedFastqInputFormat.

Resolves #1585, #1589. Adds regex to cover new metadata that Illumina added into
FASTQ name line. Also, adds a regex to the InterleavedFastqInputFormat that
checks for a wider range of supported first-of-read ending suffices.
@fnothaft fnothaft force-pushed the fnothaft:issues/1585-fastq-metadata branch from 1488bdc to 61202b2 Jul 11, 2017
@fnothaft
Copy link
Member Author

@fnothaft fnothaft commented Jul 11, 2017

Rebased and added code to address review comments. Resolves #1589 now as well.

@coveralls
Copy link

@coveralls coveralls commented Jul 11, 2017

Coverage Status

Coverage increased (+0.1%) to 84.157% when pulling 61202b2 on fnothaft:issues/1585-fastq-metadata into 97a8498 on bigdatagenomics:master.

@AmplabJenkins
Copy link

@AmplabJenkins AmplabJenkins commented Jul 11, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2196/
Test PASSed.

@heuermh heuermh merged commit 7a11d9e into bigdatagenomics:master Jul 11, 2017
2 of 3 checks passed
2 of 3 checks passed
codacy/pr Not so good... This pull request quality could be better.
Details
coverage/coveralls Coverage increased (+0.1%) to 84.157%
Details
default Merged build finished.
Details
@heuermh
Copy link
Member

@heuermh heuermh commented Jul 11, 2017

Thank you, @fnothaft

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018
@fnothaft fnothaft deleted the fnothaft:issues/1585-fastq-metadata branch Jan 9, 2018
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
Linked issues

Successfully merging this pull request may close these issues.

None yet

4 participants
You can’t perform that action at this time.