Merge branch 'CollectQualityYieldMetricsFlowSpace-dev' of github.com:…

…Ultimagen/picard into CollectQualityYieldMetricsFlowSpace-dev
broadinstitute · Jan 28, 2024 · 4cc0e00 · 4cc0e00
2 parents b1586b9 + e17dcc8
commit 4cc0e00
Showing 1 changed file with 47 additions and 2 deletions.
diff --git a/src/main/java/picard/analysis/CollectQualityYieldMetricsSNVQ.java b/src/main/java/picard/analysis/CollectQualityYieldMetricsSNVQ.java
@@ -243,10 +243,10 @@ public void acceptRecord(final SAMRecord rec, final ReferenceSequence ref) {
                             }
                         } else if (q >= 30) {
                             metrics.Q20_SNVQ++;
-                            metrics.Q30_BASES++;
+                            metrics.Q30_SNVQ++;
                             if ( isPfRead ) {
                                 metrics.PF_Q20_SNVQ++;
-                                metrics.PF_Q30_BASES++;
+                                metrics.PF_Q30_SNVQ++;
                             }
                         } else if (q >= 20) {
                             metrics.Q20_SNVQ++;
@@ -386,6 +386,42 @@ public QualityYieldMetrics(final boolean useOriginalQualities) {
         @MergeByAdding
         public long PF_Q40_BASES = 0;
 
+        /**
+         * The percentage of SNVQ values in all reads that achieve quality score 20 or higher
+         */
+        @MergingIsManual
+        public double PCT_Q20_BASES = 0;
+
+        /**
+         * The percentage of SNVQ values in all reads that achieve quality score 30 or higher
+         */
+        @MergingIsManual
+        public double PCT_Q30_BASES = 0;
+
+        /**
+         * The percentage of SNVQ values in all reads that achieve quality score 40 or higher
+         */
+        @MergingIsManual
+        public double PCT_Q40_BASES = 0;
+
+        /**
+         * The percentage of SNVQ values in all reads that achieve quality score 20 or higher and pass filter
+         */
+        @MergingIsManual
+        public double PCT_PF_Q20_BASES = 0;
+
+        /**
+         * The percentage of SNVQ values in all reads that achieve quality score 30 or higher and pass filter
+         */
+        @MergingIsManual
+        public double PCT_PF_Q30_BASES = 0;
+
+        /**
+         * The percentage of SNVQ values in all reads that achieve quality score 40 or higher and pass filter
+         */
+        @MergingIsManual
+        public double PCT_PF_Q40_BASES = 0;
+
         /**
          * The total number of SNVQ values in all reads
          */
@@ -478,6 +514,15 @@ public void calculateDerivedFields() {
             super.calculateDerivedFields();
             this.READ_LENGTH = this.TOTAL_READS == 0 ? 0 : (int) (this.TOTAL_BASES / this.TOTAL_READS);
 
+            this.PCT_Q20_BASES = this.TOTAL_BASES == 0 ? 0 : (double)this.Q20_BASES / this.TOTAL_BASES;
+            this.PCT_Q30_BASES = this.TOTAL_BASES == 0 ? 0 : (double)this.Q30_BASES / this.TOTAL_BASES;
+            this.PCT_Q40_BASES = this.TOTAL_BASES == 0 ? 0 : (double)this.Q40_BASES / this.TOTAL_BASES;
+
+            this.PCT_PF_Q20_BASES = this.PF_BASES == 0 ? 0 : (double)this.PF_Q20_BASES / this.PF_BASES;
+            this.PCT_PF_Q30_BASES = this.PF_BASES == 0 ? 0 : (double)this.PF_Q30_BASES / this.PF_BASES;
+            this.PCT_PF_Q40_BASES = this.PF_BASES == 0 ? 0 : (double)this.PF_Q40_BASES / this.PF_BASES;
+
+
             this.PCT_Q20_SNVQ = this.TOTAL_SNVQ == 0 ? 0 : (double)this.Q20_SNVQ / this.TOTAL_SNVQ;
             this.PCT_Q30_SNVQ = this.TOTAL_SNVQ == 0 ? 0 : (double)this.Q30_SNVQ / this.TOTAL_SNVQ;
             this.PCT_Q40_SNVQ = this.TOTAL_SNVQ == 0 ? 0 : (double)this.Q40_SNVQ / this.TOTAL_SNVQ;