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, 17:00, 6 January 2014
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| == Optional Parmaeters == | | == Optional Parmaeters == |
| === output File (<code>--out</code>) === | | === output File (<code>--out</code>) === |
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| Use <code>--out</code> (optional) to specify the name of the output file. | | Use <code>--out</code> (optional) to specify the name of the output file. |
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| It is output in [[Diff Format]] by default. Specify the filename with a .bam, .sam, .ubam extension to output in [[SAM/BAM Format]]. | | It is output in [[Diff Format]] by default. Specify the filename with a .bam, .sam, .ubam extension to output in [[SAM/BAM Format]]. |
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| === Fields to Diff (<code>--all</code>, <code>--flag</code>, <code>--mapQual</code>, <code>--mate</code>, <code>--isize</code>, <code>--seq</code>, <code>--baseQual</code>, <code>--tags</code>, <code>--everyTag</code>, <code>--noCigar</code>, <code>--noPos</code>, )=== | | === Fields to Diff (<code>--all</code>, <code>--flag</code>, <code>--mapQual</code>, <code>--mate</code>, <code>--isize</code>, <code>--seq</code>, <code>--baseQual</code>, <code>--tags</code>, <code>--everyTag</code>, <code>--noCigar</code>, <code>--noPos</code>, )=== |
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| '''OR use <code>--all</code> to diff all SAM/BAM record fields. | | '''OR use <code>--all</code> to diff all SAM/BAM record fields. |
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| === Only print different fields (<code>--onlyDiffs</code>)=== | | === Only print different fields (<code>--onlyDiffs</code>)=== |
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| Specify <code>--onlyDiffs</code> to only print the fields that are different, otherwise for any diff all the fields that are compared are printed. The read name is always printed. | | Specify <code>--onlyDiffs</code> to only print the fields that are different, otherwise for any diff all the fields that are compared are printed. The read name is always printed. |
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| === Maximum Number of Records That Can be Allocated (<code>--recPoolSize</code>)=== | | === Maximum Number of Records That Can be Allocated (<code>--recPoolSize</code>)=== |