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, 14:07, 6 January 2014
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| NOTE: Does not reorder the BAM file after modifying the position, so the resulting file may not be sorted by coordinate. | | NOTE: Does not reorder the BAM file after modifying the position, so the resulting file may not be sorted by coordinate. |
| + | |
| + | = Usage = |
| + | ./bam revert --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--cigar] [--qual] [--keepTags] [--rmBQ] [--rmTags <Tag:Type[;Tag:Type]*>] [--noeof] [--params] |
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| = Parameters = | | = Parameters = |
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| --params : print the parameter settings | | --params : print the parameter settings |
| </pre> | | </pre> |
| + | {{PhoneHomeParamDesc}} |
| + | |
| + | == Required Parameters== |
| + | {{InBAMInputFile}} |
| + | {{OutBAMOutputFile}} |
| + | |
| + | ==Optional Parameters== |
| + | === Revert the CIGAR & Position (<code>--cigar</code>) === |
| + | Update the cigar and the base position of reads to the values in the OC (cigar) & OP (base position) tags. |
| + | |
| + | By default, the OC & OP tags are removed. Use [[Keep Tags Used for Reverting (<code>--keepTags</code>)|<code>--keepTags</code>]] to keep the OC & OP tags. |
| + | |
| + | === Revert the Quality (<code>--qual</code>) === |
| + | Update the quality of reads to the value in the OQ tag. |
| + | |
| + | By default, the OQ tag is removed. Use [[Keep Tags Used for Reverting (<code>--keepTags</code>)|<code>--keepTags</code>]] to keep the OQ tag. |
| + | |
| + | === Keep Tags Used for Reverting (<code>--keepTags</code>) === |
| + | Keep the tags that are used for reverting. The default (no option) is to remove the tags after they are used. |
| + | |
| + | === Remove BQ Tag (<code>--rmBQ</code>) === |
| + | Use the <code>--rmBQ</code> option to remove the BQ Tag. |
| | | |
| + | === Remove Tags (<code>--rmTags</code>) === |
| + | Use <code>--rmTags</code> followed by a list of tags separated by ';' to remove the specified tags. The tags should be formatted as: <code>Tag:Type"</code> |
| | | |
− | = Usage =
| + | For multiple tags: <code>Tag:Type;Tag:Type;Tag:Type</code>... |
− | ./bam revert --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--cigar] [--qual] [--keepTags] [--rmBQ] [--rmTags <Tag:Type[;Tag:Type]*>] [--noeof] [--params]
| + | |
| + | {{noeofBGZFParameter}} |
| + | {{paramsParameter}} |
| + | |
| + | {{PhoneHomeParameters}} |
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| = Return Value = | | = Return Value = |
− | Returns the SamStatus for the reads/writes. | + | Returns the SamStatus for the reads/writes (0 for success, non-0 for failure). |
| | | |
| = Example Output = | | = Example Output = |