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Add alignment string position support #44

Merged
merged 8 commits into from
Mar 4, 2021
Merged

Add alignment string position support #44

merged 8 commits into from
Mar 4, 2021

Commits on Mar 3, 2021

  1. print(op): don't throw Exception, print ? instead 

    otherwise Anchors with invalid operation (and these anchors are
created temporarily during traceback) would throw upon printing
    @alyst
    alyst committed Mar 3, 2021
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  2. count(pairwisealn): add @inbounds

    @alyst
    alyst committed Mar 3, 2021
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  3. AlnAnchor: drop Tuple-based ctor (use splatting)

    @alyst
    alyst committed Mar 3, 2021
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  4. check_aln_anchors(): optimize anchors access

    @alyst
    alyst committed Mar 3, 2021
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  5. refactor seq2ref/ref2seq() 

    - add position getters for AlignmentAnchor
- convert findanchor() from generated function to normal one with
  position getter as a param (in Julia constant propagation we trust)
- generic pos2pos() function that gets called by seq2ref/ref2seq()
    @alyst
    alyst committed Mar 3, 2021
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  6. Alignment: expand docstring

    @alyst
    alyst committed Mar 3, 2021
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  7. alignment position support (seq2aln, ref2aln etc) 

    - add alnpos to each anchor
- add mapping to/from alnpos
- add alnpos support to traceback
    @alyst
    alyst committed Mar 3, 2021
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  8. count_aligned(): optimize with alnpos

    @alyst
    alyst committed Mar 3, 2021
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