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Resolved #168: citing the manpage for cs

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Heng Li 2018-05-30 11:03:16 -04:00
parent 9f4309c376
commit 248158a3e1
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@ -253,7 +253,9 @@ similar to the `MD` SAM tag but is standalone and easier to parse.
If `--cs=long` is used, the `cs` string also contains identical sequences in
the alignment. The above example will become
`=CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA`. The long form of `cs` encodes both
reference and query sequences in one string.
reference and query sequences in one string. The `cs` tag also encodes intron
positions and splicing signals (see the [minimap2 manpage][manpage-cs] for
details).
#### <a name="paftools"></a>Working with the PAF format
@ -365,3 +367,4 @@ mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`.
[issue]: https://github.com/lh3/minimap2/issues
[k8]: https://github.com/attractivechaos/k8
[manpage]: https://lh3.github.io/minimap2/minimap2.html
[manpage-cs]: https://lh3.github.io/minimap2/minimap2.html#10