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Alignment and reference sequence from CIGAR and MD #110

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Alignment and reference sequence from CIGAR and MD #110

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Commits on Sep 2, 2018

  1. Use CIGAR field and MD aux field to reconstruct alignments from BAM r… 

    …ecords
    @ingolia
    ingolia committed Sep 2, 2018
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Commits on Sep 4, 2018

  1. rustfmt

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    ingolia committed Sep 4, 2018
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Commits on Sep 5, 2018

  1. Unmangle table

    @ingolia
    ingolia committed Sep 5, 2018
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Commits on Sep 23, 2018

  1. Moved MD accessor convenience function onto record

    @ingolia
    ingolia committed Sep 23, 2018
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  2. Fix up tests and fmt

    @ingolia
    ingolia committed Sep 23, 2018
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Commits on Sep 24, 2018

  1. Simplified Cigar/MD reconstruction interface

    @ingolia
    ingolia committed Sep 24, 2018
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  2. Reference sequence reconstruction method on Record

    @ingolia
    ingolia committed Sep 24, 2018
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Commits on Sep 28, 2018

  1. Better MDString newtype using standard traits

    @ingolia
    ingolia committed Sep 28, 2018
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  2. Use Iter over MatchDesc rather than reified vector

    @ingolia
    ingolia committed Sep 28, 2018
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  3. Generic over MatchDesc iterator type

    @ingolia
    ingolia committed Sep 28, 2018
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  4. Moved to iterator access to Cigar information

    @ingolia
    ingolia committed Sep 28, 2018
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  5. fmt

    @ingolia
    ingolia committed Sep 28, 2018
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Commits on Sep 29, 2018

  1. Moved all read sequence lookup functions onto CigarMDPos and removed … 

    …all other iterators & position representations. Updated record interface accordingly.
    @ingolia
    ingolia committed Sep 29, 2018
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  2. fmt

    @ingolia
    ingolia committed Sep 29, 2018
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  3. Collecting into an Alignment now goes through FromIterator

    @ingolia
    ingolia committed Sep 29, 2018
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  4. Alignment reconstruction on the Record

    @ingolia
    ingolia committed Sep 29, 2018
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