First stab at generating MASC-PCR primers for specific variants.#7
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glebkuznetsov wants to merge 5 commits into
Open
First stab at generating MASC-PCR primers for specific variants.#7glebkuznetsov wants to merge 5 commits into
glebkuznetsov wants to merge 5 commits into
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This new code attempts to re-use the existing code as much as possible. Thus the pipeline is setup to create a modified genome and then reuse Mauve alignment and other functions where possible. It should be possible to refactor this to get rid of the need for Mauve by manually building the lookup tables (LUTs).
…Size Fix bug in ioutil#getPrimerPairProductSize.
This new code attempts to re-use the existing code as much as possible. Thus the pipeline is setup to create a modified genome and then reuse Mauve alignment and other functions where possible. It should be possible to refactor this to get rid of the need for Mauve by manually building the lookup tables (LUTs).
…mascpcr into specific_variant_pipeline
Previously we were not properly searching the space of possible primers. Now I'm more confident we are.
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This new code attempts to re-use the existing code as much as possible.
Thus the pipeline is setup to create a modified genome and then reuse
Mauve alignment and other functions where possible.
It should be possible to refactor this to get rid of the need for Mauve
by manually building the lookup tables (LUTs).