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Add tab5/6 as native output format for AlignmentRecordRDD #1377

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heuermh opened this issue Jan 25, 2017 · 1 comment
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Add tab5/6 as native output format for AlignmentRecordRDD #1377

heuermh opened this issue Jan 25, 2017 · 1 comment
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@heuermh
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@heuermh heuermh commented Jan 25, 2017

From BenLangmead/bowtie2#75:

--tab5 Each read or pair is on a single line. An unpaired read line is [name]\t[seq]\t[qual]\n. A paired-end read line is [name]\t[seq1]\t[qual1]\t[seq2]\t[qual2]\n. An input file can be a mix of unpaired and paired-end reads and Bowtie 2 recognizes each according to the number of fields, handling each as it should.

--tab6 is similar except, for paired-end reads, the second end can have a different name from the first: [name1]\t[seq1]\t[qual1]\t[name2]\t[seq2]\t[qual2]\n.

@heuermh
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@heuermh heuermh commented Mar 8, 2017

No hurry on this since bowtie2 may implement interleaved FASTQ.

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