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--useBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --refFile)
--useBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --refFile)
--useEquals : Convert any bases that match the reference to '=' (requires --refFile)
--useEquals : Convert any bases that match the reference to '=' (requires --refFile)
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{{PhoneHomeParamDesc}}
== Required Parameters==
{{InBAMInputFile}}
{{InBAMInputFile}}
{{OutBAMOutputFile}}
{{OutBAMOutputFile}}
== Optional Parameters ==
{{refFile}}
{{refFile}}
== Left Shift Indels in the CIGAR (<code>--lshift</code>) ==
=== Left Shift Indels in the CIGAR (<code>--lshift</code>) ===
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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{{paramsParameter}}
== 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]].
= Return Value =
= Return Value =
Returns the SamStatus for the reads/writes (0 is success).
Returns the SamStatus for the reads/writes (0 for success, non-0 for failure).
= Example Output =
= Example Output =
