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, 16:50, 6 January 2014
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| | </pre> | | </pre> |
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| − | == Input File (1st Parameter) == | + | == Required Parameters == |
| − | | + | {{InBAMInputFile|noParam=1st}} |
| − | The 1st argumentis the input SAM/BAM file. The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user, unless your input file is stdin.
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| − | | |
| − | A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).
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| − | | |
| − | {|border="1" cellspacing="0" cellpadding="2" | |
| − | |SAM/BAM/Uncompressed BAM from file
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| − | | <code>yourFileName</code>
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| − | |-
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| − | |SAM from stdin
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| − | | <code>-</code>
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| − | |-
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| − | |BAM from stdin
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| − | | <code>-.bam</code>
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| − | |-
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| − | |Uncompressed BAM from stdin
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| − | | <code>-.ubam</code>
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| − | |}
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| − | | |
| − | Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported.
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| | == Phone Home Parameters == | | == Phone Home Parameters == |
