I/O API refactoring #84
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@@ Coverage Diff @@
## master #84 +/- ##
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- Coverage 83% 81.9% -1.1%
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Files 63 60 -3
Lines 4142 4140 -2
Branches 432 432
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- Hits 3438 3391 -47
- Misses 272 317 +45
Partials 432 432
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| @@ -136,38 +140,3 @@ | |||
| #"(?i)\.bcf$" :bcf | |||
| #"(?i)\.bed" :bed | |||
| (throw (IllegalArgumentException. "Invalid file type")))) | |||
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| (defn ^Closeable reader | |||
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How about leaving reader/writer functions here?
It's true that they're unnecessary for developing apps, but I think those versatile functions are still useful for REPL.
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That causes cyclic load. cljam.io.sam loads cljam.io.util for cljam.io.sam/reader, and cljam.io.util loads cljam.io.sam for cljam.io.util/reader. If reader/writer are realy necessary, I have to reconsider namespace allocation.
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Thank you for pointing that out. OK, Let's remove them.
| @@ -136,38 +140,3 @@ | |||
| #"(?i)\.bcf$" :bcf | |||
| #"(?i)\.bed" :bed | |||
| (throw (IllegalArgumentException. "Invalid file type")))) | |||
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| (defn ^Closeable reader | |||
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Thank you for pointing that out. OK, Let's remove them.
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Merged. Thank you! 👍 |
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Thank you for review! |
Breaking refactoring of I/O API.
Old
cljam.iois not user-friendly, moving tocljam.io.protocols. Basically, this namespace should not be used directly on other projects. It can be used in cljam project or for advanced usage.Public namespaces related to a format and its binary equivalent are integrated. For example,
cljam.io.samsupports SAM and BAM,cljam.io.vcfsupports VCF and BCF,cljam.io.sequencesupports FASTA and TwoBit.These have read/write functions wrapping
cljam.io.protocols. Only commonly-used functions are wrapped. A user justrequirea single namespace that handles a format.