Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix documentation for AT_DROPOUT and GC_DROPOUT in PanelMetricsBase.java #1977

Merged
merged 2 commits into from
Aug 22, 2024
Merged
Changes from 1 commit
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions src/main/java/picard/analysis/directed/PanelMetricsBase.java
Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ public class PanelMetricsBase extends MultilevelMetrics {
/** The number of PF aligned bases that mapped to a targeted region of the genome. */
public long ON_TARGET_BASES;

//metrics below here are derived after collection
// Metrics below here are derived after collection

/** The fraction of reads passing filter, PF_READS/TOTAL_READS. */
public double PCT_PF_READS;
Expand Down Expand Up @@ -151,15 +151,15 @@ public class PanelMetricsBase extends MultilevelMetrics {
/**
* A measure of how undercovered <= 50% GC regions are relative to the mean. For each GC bin [0..50]
* we calculate a = % of target territory, and b = % of aligned reads aligned to these targets.
* AT DROPOUT is then abs(sum(a-b when a-b < 0)). E.g. if the value is 5% this implies that 5% of total
* AT_DROPOUT is then sum(abs(b-a)) when b-a < 0. E.g. if the value is 5%, this implies that 5% of total
kockan marked this conversation as resolved.
Show resolved Hide resolved
* reads that should have mapped to GC<=50% regions mapped elsewhere.
*/
public double AT_DROPOUT;

/**
* A measure of how undercovered >= 50% GC regions are relative to the mean. For each GC bin [50..100]
* we calculate a = % of target territory, and b = % of aligned reads aligned to these targets.
* GC DROPOUT is then abs(sum(a-b when a-b < 0)). E.g. if the value is 5% this implies that 5% of total
* GC_DROPOUT is then sum(abs(b-a)) when b-a < 0. E.g. if the value is 5% this implies that 5% of total
* reads that should have mapped to GC>=50% regions mapped elsewhere.
*/
public double GC_DROPOUT;
Expand Down
Loading