Add support for re-serializing (sharding and reassembling) CRAM containers. #1609
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cmnbroad
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Codecov Report
@@ Coverage Diff @@
## master #1609 +/- ##
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+ Coverage 69.838% 69.866% +0.028%
- Complexity 9666 9677 +11
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Files 703 704 +1
Lines 37690 37728 +38
Branches 6121 6124 +3
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+ Hits 26322 26359 +37
- Misses 8914 8916 +2
+ Partials 2454 2453 -1
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…iners to a new stream.
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@cmnbroad Questions / comments about mutability. If this is the only sane way to do this I can accept that it adds some more state.
| private final OutputStream outputStream; | ||
| private final String outputStreamIdentifier; | ||
| private final CramHeader cramHeader; | ||
| private final SAMFileHeader samFileHeader; |
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This field is assigned but never accessed.
| cramIndexer.finish(); | ||
| } | ||
| } catch (final IOException e) { | ||
| throw new RuntimeIOException(String.format("IOException closing stream for %s", outputStreamIdentifier)); |
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Is the output stream actually closed here? It seems like it's just flushed.
| * @param streamByteOffset the new stream byte offset counter for this container | ||
| * @return the updated global record counter | ||
| */ | ||
| public long relocateContainer(final long containerRecordCounter, final long streamByteOffset) { |
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Is it necessary to mutate the container? It was previously effectively immutable wasn't it? It seems like it would be nicer to copy it since I assume the container / slice objects are fairly lightweight and you could just pass through the reference to the heavy data?
Not a blocker if you think this is necessary for efficiency reasons / copying a container being very annoying.
| } | ||
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| void setGlobalRecordCounter(final long recordCounter) { | ||
| this.globalRecordCounter = recordCount; |
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again, unfortunate to make this mutable.
| // landmark 0 = byte length of the compression header | ||
| // landmarks after 0 = byte length of the compression header plus all slices before this one | ||
| landmarks.add(tempOutputStream.size()); | ||
| slice.byteOffsetOfContainer = containerByteOffset; |
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Why is this updated again here when it's already set by relocate?
| private final CompressionHeader compressionHeader; | ||
| private final SliceBlocks sliceBlocks; | ||
| private final long byteOffsetOfContainer; | ||
| public long byteOffsetOfContainer; |
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Why make this public? It seems like it's already updated through relocate.
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Fixes #1606.