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Support loading paired fastqs #831

Closed
wants to merge 8 commits into from
Closed

Support loading paired fastqs #831

wants to merge 8 commits into from

Commits on Oct 2, 2015

  1. add helper for loading paired fastq files

    @ryan-williams
    ryan-williams committed Oct 2, 2015
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  2. generalize stringency, fastqs use it from cmdline

    @ryan-williams
    ryan-williams committed Oct 2, 2015
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  3. support loading paired-fastq via loadAlignments 

    previous code path required -force_load_fastq flag
    @ryan-williams
    ryan-williams committed Oct 2, 2015
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  4. drop "/1" and "/2" from paired-fastq reads

    @ryan-williams
    ryan-williams committed Oct 2, 2015
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  5. support setting recordGroup from cmdline

    @ryan-williams
    ryan-williams committed Oct 2, 2015
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  6. "-concat" flag to merge two AlignmentRecord RDDs 

    useful for merging paired-fastq files and a corresponding "unpaired"
reads file
    @ryan-williams
    ryan-williams committed Oct 2, 2015
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  7. optimize imports

    @ryan-williams
    ryan-williams committed Oct 2, 2015
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  8. make flagstat safe for some null fields 

    previously crashed on fastq reads
    @ryan-williams
    ryan-williams committed Oct 2, 2015
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