#208 SAM Output "YT:Z"

[Anonymous]

This output is not described in any of the documentation, though it is displayed on the documentation page. It would be useful to have what these codes mean on the documentation page and what each means.

if(alignedConcordant()) {
o.append("CP");
} else if(alignedDiscordant()) {
o.append("DP");
} else if(alignedUnpairedMate()) {
o.append("UP");
} else if(alignedUnpaired()) {
o.append("UU");
}

[Ben Langmead]

Thank you! I added documentation for this to the manual. The new manual text (also below) will be present in the next release.

Best,
Ben

--

[`YT:Z`]: #bowtie2-build-opt-fields-yt

YT:Z:<S>

</td><td>

Value of `UU` indicates the read was not part of a pair. Value of `CP`
indicates the read was part of a pair and the pair aligned concordantly.
Value of `DP` indicates the read was part of a pair and the pair aligned
discordantly. Value of `UP` indicates the read was part of a pair but the
pair failed to aligned either concordantly or discordantly.