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== Optional Parameters for [[#Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]] ==
== Optional Parameters for [[#Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]] ==
=== Check First (<code>--checkFirst</code>) ===
=== Check First (<code>--checkFirst</code>) ===
Only applicable if [[Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]] is also provided.
Only applicable if [[#Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]] is also provided.
When specified along with [Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]], the output for each record processed also includes "NotFirst" if it is not marked as FirstFragment in the flags.
When specified along with [[#Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]], the output for each record processed also includes "NotFirst" if it is not marked as FirstFragment in the flags.
=== Check Strand (<code>--checkStrand</code>) ===
=== Check Strand (<code>--checkStrand</code>) ===
Only applicable if [Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]] is also provided.
Only applicable if [[#Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]] is also provided.
When specified along with [Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]], the output for each record processed also includes "Reverse" if it is marked as the reverse strand in the flags.
When specified along with [[#Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]], the output for each record processed also includes "Reverse" if it is marked as the reverse strand in the flags.
{{PhoneHomeParameters}}
{{PhoneHomeParameters}}
