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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]
= Parameters =
= Parameters =
</pre>
</pre>
== 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>
For multiple tags: <code>Tag:Type;Tag:Type;Tag:Type</code>...
{{noeofBGZFParameter}}
{{paramsParameter}}
{{PhoneHomeParameters}}
= 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 =
