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bam: add example for paired end deduplication sorting #93

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kortschak opened this issue Apr 12, 2017 · 1 comment
Open

bam: add example for paired end deduplication sorting #93

kortschak opened this issue Apr 12, 2017 · 1 comment

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@kortschak
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This will look like the SortByCoordinate example for Merger but have a different less and ensure that pairs passed to the fn match QNAME.

@kortschak
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I had the thought that this would work. Further thinking shows I'm wrong. The only way to get this to work is to have a pair-ordered sort/grouping (how I did this in biogo/boom). The general algorithm is here. This would require that we add a pair-based merger.

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