Clarify the name tokeniser uncomp_len calculation (PR #803)#803
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jkbonfield merged 1 commit intosamtools:masterfrom Mar 24, 2025
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Clarify the name tokeniser uncomp_len calculation (PR #803)#803jkbonfield merged 1 commit intosamtools:masterfrom
jkbonfield merged 1 commit intosamtools:masterfrom
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Changed PDFs as of bece1f7: CRAMcodecs (diff). |
cmnbroad
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Jan 7, 2025
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Looks good - thanks! |
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This includes all visible read name bytes plus 1 termination byte per name (e.g. '\0'). Fixes samtools#802
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Changed PDFs as of 4982e03: CRAMcodecs (diff). |
zaeleus
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CRAMcodecs.tex
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| the number of read names. This is followed the array elements | ||
| themselves. Note the uncompressed size is calculated as the sum of |
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The serialised data stream starts with two unsigned little endian 32-bit integers... This is followed the array elements themselves.
This is unrelated to the length calculation, but note there is also a 1 byte flag between the 2 integers and the data stream:
| Bytes | Type | Name |
|---|---|---|
| 4 | uint32 | uncomp_length |
| 4 | uint32 | num_reads |
| 1 | uint8 | use_arith |
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Agreed. It also had a poor and nebulous "array elements" term which I expanded on.
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This includes all visible read name bytes plus 1 termination byte per name (e.g. '\0'). Fixes samtools#802 Also clarify the name tokeniser serialisation description. Acknowledge the 1-byte "use_arith" field and replace the nebulous "array elements" with a more descriptive text about token streams.
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Changed PDFs as of 7de0ae0: CRAMcodecs (diff). |
This includes all visible read name bytes plus 1 termination byte per name (e.g. '\0'). Fixes samtools#802 Also clarify the name tokeniser serialisation description. Acknowledge the 1-byte "use_arith" field and replace the nebulous "array elements" with a more descriptive text about token streams.
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Changed PDFs as of 7b61997: CRAMcodecs (diff). |
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This includes all visible read name bytes plus 1 termination byte per name (e.g. '\0').
Fixes #802