From 10d143c35c1b6bf8cb0d405c40ef7337f63784f8 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 23 Jul 2012 11:28:17 -0400 Subject: [PATCH] Adding error model header names in the BQSR recal plot. Making the downsampling of points look a little nicer. --- .../sting/gatk/walkers/bqsr/EventType.java | 14 ++++++++++---- .../sting/gatk/walkers/bqsr/RecalDataManager.java | 4 +--- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/EventType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/EventType.java index 6d004edb1..2650f0f8d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/EventType.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/EventType.java @@ -3,16 +3,18 @@ package org.broadinstitute.sting.gatk.walkers.bqsr; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; public enum EventType { - BASE_SUBSTITUTION(0, "M"), - BASE_INSERTION(1, "I"), - BASE_DELETION(2, "D"); + BASE_SUBSTITUTION(0, "M", "Base Substitution"), + BASE_INSERTION(1, "I", "Base Insertion"), + BASE_DELETION(2, "D", "Base Deletion"); public final int index; private final String representation; + private final String longRepresentation; - private EventType(int index, String representation) { + private EventType(int index, String representation, String longRepresentation) { this.index = index; this.representation = representation; + this.longRepresentation = longRepresentation; } public static EventType eventFrom(int index) { @@ -40,4 +42,8 @@ public enum EventType { public String toString() { return representation; } + + public String prettyPrint() { + return longRepresentation; + } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java index 876ce585a..f40a62d53 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java @@ -410,9 +410,7 @@ public class RecalDataManager { final int covariateKey = (Integer)keys.get(2); values.add(covariate.formatKey(covariateKey)); values.add(covariateNameMap.get(covariate)); - - final EventType event = EventType.eventFrom((Integer)keys.get(3)); - values.add(event); + values.add(EventType.eventFrom((Integer)keys.get(3)).prettyPrint()); return values; }