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New Illumina FASTQ spec adds metadata to read name line #1585

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fnothaft opened this Issue Jun 30, 2017 · 1 comment

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fnothaft commented Jun 30, 2017

From http://support.illumina.com/content/dam/illumina-support/help/BaseSpaceHelp_v2/Content/Vault/Informatics/Sequencing_Analysis/BS/swSEQ_mBS_FASTQFiles.htm:

@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos> <read>:<is filtered>:<control number>:<sample number>

This causes trouble when grouping reads by fragment.

@fnothaft fnothaft added this to the 0.23.0 milestone Jun 30, 2017

@fnothaft fnothaft self-assigned this Jun 30, 2017

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heuermh Jul 1, 2017

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Lovely.

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heuermh commented Jul 1, 2017

Lovely.

fnothaft added a commit to fnothaft/adam that referenced this issue Jul 2, 2017

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.

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

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