Added slow5 parser #220
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Added slow5 parser #220
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Linter should be failing due to metadata being a lot. For coverage, we're going to have to add a ton of test files, which will be fun. |
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https://pkg.go.dev/github.com/bmkessler/streamvbyte + https://pkg.go.dev/github.com/klauspost/compress/zstd should be useful for blow5 compression native to golang. |
…f a plain string.. (#264) * Replaced the Seqhash sequencetype with Struct type argument instead of a plain string.. * Cleared the linting errors for Go > 1.16 where ioutils package has been depreciated Co-authored-by: Tim <TimothyStiles@users.noreply.github.com>
* fix: Use SliceStable to sort potential changes Fixes golang/go#55009 Co-authored-by: Tim <TimothyStiles@users.noreply.github.com>
* created config for gitpod. * removed non-existent vscode extennsions. * fixed yml spacing.
…everal other tutorials. (#267) * drafted intro and io tutorials. Added templates for README and several other tutorials. * added logic for tutorial workspace setup detection. * added todos to unwritten tutorial placeholders.
* added explicit wait for tutorial startup * added comment with issue explaining vscode -r bug.
* Install Go Analysis Tools Co-authored-by: Tim <TimothyStiles@users.noreply.github.com>
* Open tutorial README in Gitpod * Install godef
New go modules requires version.
* added transform tests * added benchmarks * runs 8-10X faster than previous implementation Co-authored-by: Tim <TimothySStiles@gmail.com> Co-authored-by: Timothy Stiles <tim@stiles.io>
* add more fasta.Parser API * add uniprot fasta creation * add maxLineSize argument to Parser * no EOF newline now invalidates fasta * parse now uses parseall behind the scenes. * fixed fasta.Build to output proper whitespace. * return to EOF as parse error state, fix some other stuff * fix Concurrent functions, ensure they close their readers Co-authored-by: Timothy Stiles <tim@stiles.io>
#288) * initial implementation of global alignment via NeedlemanWunsch * test coverage 100% * added wikipedia link for Needleman-Wunsch * added corner case tests at the suggestion of Daniel Liu @daniel_c0deb0t via twitter
Co-authored-by: Timothy Stiles <tim@stiles.io>
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@TimothyStiles Turns out I actually need this. I haven't implemented blow5, but slow5 is implemented here |
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This PR will add a slow5 and blow5 format parser, from https://github.com/hasindu2008/slow5tools
This won't implement the fast5 -> slow5 functionality, but will be able to read and write those files for downstream use.