CRAM: revert #1326 and fix tests and comments #1341
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- added comments clarifying the real situation - see samtools/hts-specs#396 - see samtools/hts-specs#398
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#1326 was based on a misunderstanding of values in the CRAM Container Header. samtools/hts-specs#398 is the companion PR for the spec. |
jmthibault79
commented
Apr 1, 2019
| @@ -159,7 +159,7 @@ void recordMetaData(final Slice slice) { | |||
| unAlignedRecords += slice.unmappedReadsCount; | |||
| } | |||
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| final long start = slice.byteOffsetFromContainer; | |||
| final long start = slice.byteOffsetFromCompressionHeaderStart; | |||
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it's a mouthful but it's correct
jmthibault79
commented
Apr 1, 2019
| } | ||
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| final Slice lastSlice = slices[lastSliceIndex]; | ||
| lastSlice.index = lastSliceIndex; | ||
| lastSlice.byteOffsetFromContainer = landmarks[lastSliceIndex]; | ||
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| // calculate a "final landmark" indicating the byte offset of the end of the container |
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no. containerBlocksByteSize is already equal to that "final landmark".
This is the section that reverts #1326
Codecov Report
@@ Coverage Diff @@
## master #1341 +/- ##
===============================================
- Coverage 67.848% 67.846% -0.003%
Complexity 8273 8273
===============================================
Files 562 562
Lines 33678 33675 -3
Branches 5653 5653
===============================================
- Hits 22850 22847 -3
Misses 8653 8653
Partials 2175 2175
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jmthibault79
commented
Apr 1, 2019
| final ReferenceContext refContext = new ReferenceContext(0); | ||
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| final Container container = new Container(refContext); | ||
| container.containerByteSize = slice0size; | ||
| container.containerBlocksByteSize = compressionHeaderSize + slice0size; |
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this is the change to the test (as well the similar line below)
jmthibault79
commented
Apr 1, 2019
| // a Slice of size 6262 bytes | ||
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| final int containerHeaderSize = 1234; | ||
| final int compressionHeaderSize = 7552; |
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the meaningful changes here are below, in createOneSliceContainer() / createTwoSliceContainer()
cmnbroad
requested changes
Apr 2, 2019
cmnbroad
approved these changes
Apr 3, 2019
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