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Left shift indels as far as they can go in the read.
Left shift indels as far as they can go in the read.
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== Recover a corrupted BAM file (<code>--recover</code>) ==
== Recover a corrupted BAM file (<code>--recover</code>) ==
See [[#BAM File Recovery |BAM File Recovery]].
See [[#BAM File Recovery |BAM File Recovery]].
== Sequence Representation Parameters (<code>--seqOrig</code>, <code>--seqBases</code>, <code>--seqEquals</code>, <code>--refFile</code>) ==
== Sequence Representation Parameters (<code>--seqOrig</code>, <code>--seqBases</code>, <code>--seqEquals</code>, <code>--refFile</code>) ==
