Multiple encodings for ReadDatastores #12
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Codecov Report
@@ Coverage Diff @@
## master #12 +/- ##
==========================================
- Coverage 94.24% 93.21% -1.04%
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Files 5 6 +1
Lines 365 398 +33
==========================================
+ Hits 344 371 +27
- Misses 21 27 +6
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Codecov Report
@@ Coverage Diff @@
## master #12 +/- ##
==========================================
- Coverage 94.24% 93.21% -1.04%
==========================================
Files 5 6 +1
Lines 365 398 +33
==========================================
+ Hits 344 371 +27
- Misses 21 27 +6
Continue to review full report at Codecov.
|
Codecov Report
@@ Coverage Diff @@
## master #12 +/- ##
==========================================
- Coverage 94.24% 93.21% -1.04%
==========================================
Files 5 6 +1
Lines 365 398 +33
==========================================
+ Hits 344 371 +27
- Misses 21 27 +6
Continue to review full report at Codecov.
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Fixup sequence buffer creation Add inline statements typo Tests edit Test 2 bit lrseq Add size check to buffered short read datastore creation Fixup sequence buffer Update tests Fixup sequence buffer Fixup tests Add resize test to long reads Push preview Fixup docs Docs fixup Docs fixup Doctest fixup Doctests fixup Doctest fixup Doctest fixup pwd doctests Fixup doctests Doctest fixup Fixup doctests Doctests fixup Fixup doctests Doctest fixup Docs edit Export max_read_length Export stream
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Types of changes
This PR implements the following changes:
(Please tick any or all of the following that are applicable)
📋 Additional detail
In v0.1, all ReadDatastores only support the storage of
LongSequence{DNAAlphabet{4}}.This pull request allows you to also have datastores of
LongSequence{DNAAlphabet{2}}.Some additional improvements are also implemented. For example, the buffering behaviour when streaming sequences from a datastore has been improved:
Previously, a bug meant buffers were refreshed a long time before they needed to be.
In addition, an arbitrary chunk size option was used which HAD to be bigger than the largest long read in a datastore or else there would be a crash.
With this PR, a buffered long read datastore will resize the buffer when it needs to load a sequence that is bigger than the buffer. For ShortRead datastores, such a buffer size check and resizing only needs to be done once at creation.
☑️ Checklist
docs/src/.[UNRELEASED]section of the manually curatedCHANGELOG.mdfile for this repository.