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== Sequence Representation Parameters (<code>--seqOrig</code>, <code>--seqBases</code>, <code>--seqEquals</code>) ==
== Recover a corrupted BAM file (<code>--recover</code>) ==
See [[#BAM File Recovery |BAM File Recovery]].
== Sequence Representation Parameters (<code>--seqOrig</code>, <code>--seqBases</code>, <code>--seqEquals</code>, <code>--refFile</code>) ==
The sequence parameters options specify how to represent the sequence if the reference is specified (refFile option).
The sequence parameters options specify how to represent the sequence if the reference is specified (refFile option).
Sequence with Bases: AATAACTAGATAGGG
Sequence with Bases: AATAACTAGATAGGG
Sequence with Equals: AA======G===GGG
Sequence with Equals: AA======G===GGG
= BAM File Recovery =
= BAM File Recovery =
