Add CRAM writer (alpha) #313
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #313 +/- ##
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+ Coverage 88.85% 89.28% +0.43%
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Files 93 97 +4
Lines 8091 8841 +750
Branches 465 481 +16
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+ Hits 7189 7894 +705
- Misses 437 466 +29
- Partials 465 481 +16 ☔ View full report in Codecov by Sentry. |
alumi
approved these changes
Jul 12, 2024
src/cljam/io/cram/data_series.clj
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| a map {<data series name> <encoder>}, where: | ||
| - <data series name>: a keyword representing the data series name | ||
| - <encoding>: a map representing the encoding of the data series | ||
| - <encoder>: a function that takes one argument to encode" |
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The encoder is actually an overloaded function that acts as both a single-argument function that performs encoding and a zero-argument function that returns the encoding result.
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Good catch! It slipped my mind when I was writing these docstrings. Thanks for pointing that out 🙏
Fixed in 800eecf.
niyarin
approved these changes
Jul 22, 2024
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This PR adds an implementation of the CRAM writer, based on CRAM v3.1.
Like the initial implementation of the CRAM reader, the current CRAM writer is quite naive and supports only a limited set of features. Additionally, its performance has not been tuned yet.
The structure of the CRAM writer mirrors that of the CRAM reader in many ways, making it easy to understand for those familiar with the CRAM reader's implementation.
The biggest difference can be found in
cljam.io.cram.writer, which scans and aggregates the records in slices and containers to calculate various header components. Some of these might be moved to separate namespaces in the future.Currently, the following features are not supported (roughly ordered by priority):
APdata seriesAlso, the PR contains the following commits for miscellaneous fixes within the CRAM reader:
:external-idto:content-idfor consistency with the CRAM writer:basescase forrecord-cigar