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Clarify container header fields. Resolves #396 #398

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Apr 4, 2019
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Clarify container header fields. Resolves #396 #398

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9bc6025
Clarify container header fields. Resolves #396
jmthibault79 Mar 29, 2019
bd2c42c
landmarks[0] note
jmthibault79 Apr 1, 2019
835c877
clarify wording on block byte lengths
jmthibault79 Apr 2, 2019
180524d
more text clarification
cmnbroad Apr 3, 2019
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12 changes: 8 additions & 4 deletions CRAMv3.tex
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Original file line number Diff line number Diff line change
Expand Up @@ -440,7 +440,8 @@ \section{\textbf{Container structure}}
\textbf{Data type} & \textbf{Name} & \textbf{Value}
\tabularnewline
\hline
int32 & length & byte size of the container data (blocks)\tabularnewline
int32 & length & the sum of the lengths of all blocks in this container (headers and data);
equal to the total byte length of the container minus the byte length of this header structure\tabularnewline
\hline
itf8 & reference sequence id & reference sequence identifier or\linebreak{}
-1 for unmapped reads\linebreak{}
Expand All @@ -458,10 +459,13 @@ \section{\textbf{Container structure}}
\hline
ltf8 & bases & number of read bases\tabularnewline
\hline
itf8 & number of blocks & the number of blocks\tabularnewline
itf8 & number of blocks & the total number of blocks in this container\tabularnewline
\hline
itf8[ ] & landmarks & Each integer value of this array is a byte offset into the
blocks byte array. Landmarks are used for random access indexing.\tabularnewline
itf8[ ] & landmarks & the locations of slices in this container as byte offsets from the end of
this container header, used for random access indexing.
The landmark count must equal the slice count.\linebreak{}
Since the block before the first slice is the compression header,
landmarks[0] is equal to the byte length of the compression header.\tabularnewline
\hline
int & crc32 & CRC32 hash of the all the preceding bytes in the container.\tabularnewline
\hline
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