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AssemblePairs-reference : option to fill in nt from reference for gapped stitch

Issue #13 resolved
Former user created an issue

We talked about this option before (stealing sequence from reference when stitched reads do not overlap) but it occurred to me that it really makes even more sense for TCR stitching.

Low priority.

Comments (8)

  2. Jason Vander Heiden

    Will add option to fill gap with reference sequence to AssemblePairs-reference. Maybe --fill?

  3. Former user Account Deleted

    I am thinking this is particularly useful in TCR, and it would be good to be able to specify to fill-in for TCR but not BCR

  4. Jason Vander Heiden

    Yeah, it should probably come with a warning that you run the risk of making chimeric BCR sequences.

  5. Jason Vander Heiden

    I added the --fill option to fill in the reference sequence. No extensive testing yet, but I checked several assemblies. Let me know if it's behaving for you.

  6. Former user Account Deleted

    wow ! i am super grateful. we will test.

    PS you wouldn't be procrastinating on writing your thesis intro, would you !?!?!?

  7. Jason Vander Heiden

    No problem, and thanks.

    PS: Maybe a little. At least it's Structured Procrastination...

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Type
enhancement
Priority
minor
Status
resolved
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