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{{InBAMInputFile}}
{{OutBAMOutputFile}}
== Optional Parameters ==
=== Verbose (<code>--verbose</code>) ===
Use <code>--verbose</code> to turn on verbose mode.
=== Specify Log Filename (<code>--log</code>) ===
Use <code>--log</code> followed by the log filename to specify the log filename. Default is the output file basename with a <code>.log</code> extension
=== Add the HD Header (<code>--HD</code>) ===
Use <code>--HD</code> followed by the HD header line to add a HD header. Be sure to include "@HD" in the line you specify.
=== Add the RG Header (<code>--RG</code>) ===
Use <code>--RG</code> followed by the RG header line to add a RG header. Be sure to include "@RG" in the line you specify.
=== Add the PG Header (<code>--PG</code>) ===
Use <code>--PG</code> followed by the PG header line to add a PG header. Be sure to include "@PG" in the line you specify.
=== Add MD5 and UR tags to SQ Headers (<code>--fasta</code>) ===
Use <code>--fasta</code> followed by the fasta reference file name to compute MD5sums and update SQ tags with the M5 & UR values. Use the [[#Add the UR tag to SQ Headers (--UR)|<code>--UR</code>]] option to specify a different UR value.
=== Add the AS tag to SQ Headers (<code>--AS</code>) ===
Use <code>--AS</code> followed by the genome assembly identify to add the AS tag to the SQ Headers.
=== Add the UR tag to SQ Headers (<code>--UR</code>) ===
Use <code>--UR</code> followed by the URI of the sequence to add the UR tag to the SQ Headers.
The UR header will be automatically added with the [[#Add MD5 and UR tags to SQ Headers (--fasta)|<code>--fasta</code>]] option, so if [[#Add MD5 and UR tags to SQ Headers (--fasta)|<code>--fasta</code>]] is used, <code>--UR</code> only needs to be specified if it is different from [[#Add MD5 and UR tags to SQ Headers (--fasta)|<code>--fasta</code>]].
=== Add the SP tag to SQ Headers (<code>--SP</code>) ===
Use <code>--SP</code> followed by the species to add the SP tag to the SQ Headers.
{{PhoneHomeParameters}}
= Return Value =
= Return Value =
Returns 0.
Returns 0 on success, non-0 on failure.
= Example =
= Example =
