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, 16:02, 6 January 2014
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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. |
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− | 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. |
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| === 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. |
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− | 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. |
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| {{PhoneHomeParameters}} | | {{PhoneHomeParameters}} |