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doc: update description of consenus tags for duplex
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nh13 authored Apr 29, 2024
1 parent a82cfe0 commit 7603c30
Showing 1 changed file with 5 additions and 3 deletions.
8 changes: 5 additions & 3 deletions src/main/scala/com/fulcrumgenomics/umi/ConsensusTags.scala
Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,11 @@ package com.fulcrumgenomics.umi
* Object that encapsulates the various consensus related tags that are added to consensus reads
* at both the per-read and per-base level.
*
* Currently only contains tags for single-strand consensus reads, but with a view to using the following
* names for consistency if/when we add duplex calling:
* Contains tags for both single-strand and duplex consensus reads. The first letter in the tag is `c` if
* it relates to the final consensus read, `a` if it relates to the top-strand of a duplex consensus read,
* and `b` if it relates to the bottom-strand of a duplex consensus read. The second letter in the tag is
* lower case if it is per-base, upper case if it is per-read.
*
* Value AB BA Final
* --------------------- -- -- -----
* per-read-depth aD bD cD
Expand All @@ -39,7 +42,6 @@ package com.fulcrumgenomics.umi
* per-base-error-count ae be ce
* per-base-bases ac bc bases
* per-base-quals aq bq quals
* The second letter in the tag is lower case if it is per-base, upper case if it is per-read.
*/
object ConsensusTags {
/** The default field in which to look for UMI sequences and qualities. */
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