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Interleaved FASTQ recognizes only /1 suffix pattern #1589

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heuermh opened this Issue Jul 6, 2017 · 1 comment

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heuermh commented Jul 6, 2017

FastqRecordConverter supports read suffixes with a few different patterns, [space]1, +1, _1, and /1. I've seen [space]1 and /1 in the wild.

InterleavedFastqInputFormat only recognizes /1, resulting in empty FragmentRDDs if the interleaved FASTQ file uses one of the other patterns.

fnothaft added a commit to fnothaft/adam that referenced this issue Jul 11, 2017

[ADAM-1585] Support additional Illumina FASTQ metadata.
Resolves bigdatagenomics#1585, bigdatagenomics#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.

heuermh added a commit that referenced this issue Jul 11, 2017

[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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fnothaft Jul 11, 2017

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Resolved by 7a11d9e.

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fnothaft commented Jul 11, 2017

Resolved by 7a11d9e.

@fnothaft fnothaft closed this Jul 11, 2017

@heuermh heuermh modified the milestone: 0.23.0 Jul 22, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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