From 5ed47988b83de0c17cc9b1065522a4aa14f8818b Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 24 Oct 2013 17:13:25 -0400
Subject: [PATCH] Changed the parameter names from cds to baits

Making the usage more clear since the parameter is being used over and over to define baited
regions. Updated the headers accordingly and made it more readable.
---
 .../missing/QualifyMissingIntervals.java      | 25 +++++++++----------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
index 52a92d9ff..54fc6e97e 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
@@ -126,11 +126,10 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
     public String targetsFile;
 
     /**
-     * List of coding sequence intervals (exons) if different from the targets file, to distinguish intervals
-     * that overlap the cds and intervals that don't.
+     * List of baits to distinguish untargeted intervals from those that are targeted but not covered
      */
-    @Argument(shortName = "cds", required = false)
-    public String cdsFile = null;
+    @Argument(shortName = "baits", required = false)
+    public String baitsFile = null;
 
     /**
      * This value will be used to determine whether or not an interval had too high or too low GC content to be
@@ -183,8 +182,8 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
     }
 
     GATKReport simpleReport;
-    GenomeLocSortedSet target;
-    GenomeLocSortedSet cds;
+    GenomeLocSortedSet targets;
+    GenomeLocSortedSet baits;
 
     public boolean isReduceByInterval() {
         return true;
@@ -192,13 +191,13 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
 
     public void initialize() {
         // if cds file is not provided, just use the targets file (no harm done)
-        if (cdsFile == null)
-            cdsFile = targetsFile;
+        if (baitsFile == null)
+            baitsFile = targetsFile;
 
-        simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "IN", "GC", "BQ", "MQ", "DP", "TP", "TS", "CD", "LN", "DS");
+        simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "INTERVAL", "GC", "BQ", "MQ", "DP", "POS_IN_TARGET", "TARGET_SIZE", "BAITED", "MISSING_SIZE", "INTERPRETATION");
         final GenomeLocParser parser = getToolkit().getGenomeLocParser();
-        target = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, targetsFile));
-        cds = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, cdsFile));
+        targets = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, targetsFile));
+        baits = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, baitsFile));
     }
 
     public Metrics reduceInit() {
@@ -241,7 +240,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
         for (Pair<GenomeLoc, Metrics> r : results) {
             final GenomeLoc interval = r.getFirst();
             final Metrics metrics = r.getSecond();
-            final List<GenomeLoc> overlappingIntervals = target.getOverlapping(interval);
+            final List<GenomeLoc> overlappingIntervals = targets.getOverlapping(interval);
 
             simpleReport.addRow(
                     interval.toString(),
@@ -251,7 +250,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
                     metrics.depth(),
                     getPositionInTarget(interval, overlappingIntervals),
                     getTargetSize(overlappingIntervals),
-                    cds.overlaps(interval),
+                    baits.overlaps(interval),
                     interval.size(),
                     interpret(metrics, interval)
             );