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, 09:26, 7 October 2011
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| | --seqEquals : Convert any bases that match the reference to '=' (requires --ref). | | --seqEquals : Convert any bases that match the reference to '=' (requires --ref). |
| | </pre> | | </pre> |
| − | == input File (<code>--in</code>) ==
| |
| | | | |
| − | Use <code>--in</code> followed by your file name to specify the SAM/BAM input file.
| + | {{InBAMInputFile}} |
| − | | |
| − | 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.
| |
| − | | |
| − | 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).
| |
| − | | |
| − | {|border="1" cellspacing="0" cellpadding="2" | |
| − | |SAM/BAM/Uncompressed BAM from file
| |
| − | | <code>--in yourFileName</code>
| |
| − | |-
| |
| − | |SAM from stdin
| |
| − | | <code>--in -</code>
| |
| − | |-
| |
| − | |BAM from stdin
| |
| − | | <code>--in -.bam</code>
| |
| − | |-
| |
| − | |Uncompressed BAM from stdin
| |
| − | | <code>--in -.ubam</code>
| |
| − | |}
| |
| − | | |
| − | | |
| − | 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.
| |
| − | | |
| − | == output File (<code>--out</code>) ==
| |
| − | | |
| − | Use <code>--out</code> followed by your file name to specify the SAM/BAM output file.
| |
| − | | |
| − | The file extension is used to determine whether to write SAM/BAM/uncompressed BAM. A <code>-</code> is used to indicate stdout and the extension for file type (no extension is SAM).
| |
| − | | |
| − | {|border="1" cellspacing="0" cellpadding="2"
| |
| − | |SAM to file
| |
| − | | <code>--out yourFileName.sam</code>
| |
| − | |-
| |
| − | |BAM to file
| |
| − | | <code>--out yourFileName.bam</code>
| |
| − | |-
| |
| − | |Uncompressed BAM to file
| |
| − | | <code>--out yourFileName.ubam</code>
| |
| − | |-
| |
| − | |SAM to stdout
| |
| − | | <code>--out -</code>
| |
| − | |-
| |
| − | |BAM to stdout
| |
| − | | <code>--out -.bam</code>
| |
| − | |-
| |
| − | |Uncompressed BAM to stdout
| |
| − | | <code>--out -.ubam</code>
| |
| − | |}
| |
| − | | |
| − | | |
| − | 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.
| |
| | | | |
| | + | {{OutBAMOutputFile}} |
| | | | |
| | == Recover a corrupted BAM file (<code>--recover</code>) == | | == Recover a corrupted BAM file (<code>--recover</code>) == |
