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Slice and Container ref seq IDs must match
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jmthibault79 committed Apr 4, 2019
1 parent c689122 commit 0c15db9
Showing 1 changed file with 4 additions and 2 deletions.
6 changes: 4 additions & 2 deletions CRAMv3.tex
Original file line number Diff line number Diff line change
Expand Up @@ -445,7 +445,8 @@ \section{\textbf{Container structure}}
\hline
itf8 & reference sequence id & reference sequence identifier or\linebreak{}
-1 for unmapped reads\linebreak{}
-2 for multiple reference sequences\tabularnewline
-2 for multiple reference sequences.\linebreak{}
All slices in this container must have a reference sequence id matching this value.\tabularnewline
\hline
itf8 & starting position on the reference & the alignment start position or\linebreak{}
0 for unmapped reads\tabularnewline
Expand Down Expand Up @@ -777,7 +778,8 @@ \subsection{\textbf{Slice header block}}
\hline
itf8 & reference sequence id & reference sequence identifier or\linebreak{}
-1 for unmapped reads\linebreak{}
-2 for multiple reference sequences\tabularnewline
-2 for multiple reference sequences.\linebreak{}
This value must match that of its enclosing container.\tabularnewline
\hline
itf8 & alignment start & the alignment start position.\linebreak{}
Ignored on read and set to 0 on write if the slice is multiple-reference
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