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One possible solution to cigarLen>65535 (DON'T MERGE; for discussion only) #938

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One possible solution to cigarLen>65535 (DON'T MERGE; for discussion only) #938

wants to merge 3 commits into from

Commits on Jul 19, 2017

  1. A solution for cigar longer than 65536 

    This approach was initially proposed in this thread (solution 1):

https://sourceforge.net/p/samtools/mailman/message/30672431/

It is reusing the bin field to store the higher 16 bits of cigarLen.
Importantly, this change is only applied to BAM files. Once the BAMRecord is
read into memory by new htsjdk, all the fields should be correctly populated.
    @lh3
    lh3 committed Jul 19, 2017
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  2. Don't call setIndexingBin(). It won't compile.

    @lh3
    lh3 committed Jul 19, 2017
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  3. make changes compile. "All tests passed". 

    It is silly to send a PR not compilable. Even for discussion purposes.
    @lh3
    lh3 committed Jul 19, 2017
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