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

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merged 1 commit into from Jul 11, 2017

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fnothaft commented Jul 2, 2017

Resolves #1585.

@fnothaft fnothaft added this to the 0.23.0 milestone Jul 2, 2017

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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.

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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.

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coveralls 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.

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.

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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.

AmplabJenkins commented Jul 2, 2017

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2172/
Test PASSed.

@heuermh

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

[ADAM-1585] Support additional Illumina FASTQ metadata.
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.
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Rebased and added code to address review comments. Resolves #1589 now as well.

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fnothaft commented Jul 11, 2017

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

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coveralls 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.

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.

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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.

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

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codacy/pr Not so good... This pull request quality could be better.
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coverage/coveralls Coverage increased (+0.1%) to 84.157%
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default Merged build finished.
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heuermh Jul 11, 2017

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Thank you, @fnothaft

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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

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