From 8c076143212c03e3c41d1755680ce1db89827681 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 10 Jul 2013 16:16:28 -0400
Subject: [PATCH] QualifyMissingIntervals: support different formats

Problem
-------
Qualify Missing Intervals only accepted GATK formatted interval files for it's coding sequence and bait parameters.

Solution
-------
There is no reason for such limitation, I erased all the code that did the parsing and used IntervalUtils to parse it (therefore, now it handles any type of interval file that the GATK can handle).

ps: Also added an average depth column to the output
---
 .../walkers/diagnostics/missing/Metrics.java  |  1 +
 .../missing/QualifyMissingIntervals.java      | 48 +++++--------------
 2 files changed, 12 insertions(+), 37 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java
index 5e3da5f4f..9296cc89b 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java
@@ -91,6 +91,7 @@ final class Metrics {
     double gccontent() {return refs > 0 ? gccontent/refs : 0.0;}
     double baseQual() {return reads > 0 ? baseQual/reads : 0.0;}
     double mapQual() {return reads > 0 ? mapQual/reads : 0.0;}
+    double depth() {return refs > 0 ? (double) reads/refs : 0.0;}
 
     /**
      * Combines two metrics
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 d0db3ef98..609f11f97 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
@@ -61,14 +61,11 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.text.XReadLines;
 
-import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.PrintStream;
 import java.util.List;
 
@@ -115,10 +112,10 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
     protected PrintStream out;
 
     @Argument(shortName = "targets", required = true)
-    public File targetsFile;
+    public String targetsFile;
 
     @Argument(shortName = "cds", required = false)
-    public File cdsFile = null;
+    public String cdsFile = null;
 
     GATKReport simpleReport;
     GenomeLocSortedSet target;
@@ -129,13 +126,14 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
     }
 
     public void initialize() {
-        simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "IN", "GC", "BQ", "MQ", "TP", "CD", "LN");
+        // if cds file is not provided, just use the targets file (no harm done)
+        if (cdsFile == null)
+            cdsFile = targetsFile;
+
+        simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "IN", "GC", "BQ", "MQ", "DP", "TP", "CD", "LN");
         final GenomeLocParser parser = getToolkit().getGenomeLocParser();
-        target = new GenomeLocSortedSet(parser);
-        cds = new GenomeLocSortedSet(parser);
-        parseFile(targetsFile, target, parser);
-        if (cdsFile != null)
-            parseFile(cdsFile, cds, parser);
+        target = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, targetsFile));
+        cds = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, cdsFile));
     }
 
     public Metrics reduceInit() {
@@ -183,6 +181,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
                     metrics.gccontent(),
                     metrics.baseQual(),
                     metrics.mapQual(),
+                    metrics.depth(),
                     getPositionInTarget(interval),
                     cds.overlaps(interval),
                     interval.size()
@@ -192,31 +191,6 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
         out.close();
     }
 
-    private static GenomeLoc parseInterval(String s, GenomeLocParser parser) {
-        if (s.isEmpty()) {
-            return null;
-        }
-        String[] first = s.split(":");
-        if (first.length == 2) {
-            String[] second = first[1].split("\\-");
-            return parser.createGenomeLoc(first[0], Integer.decode(second[0]), Integer.decode(second[1]));
-        } else {
-            throw new UserException.BadInput("Interval doesn't parse correctly: " + s);
-        }
-    }
-
-    private void parseFile(File file, GenomeLocSortedSet set, GenomeLocParser parser) {
-        try {
-            for (String s : new XReadLines(file) ) {
-                GenomeLoc interval = parseInterval(s, parser);
-                if (interval != null)
-                    set.add(interval, true);
-            }
-        } catch (FileNotFoundException e) {
-            e.printStackTrace();
-        }
-    }
-
     private int getPositionInTarget(GenomeLoc interval) {
         final List<GenomeLoc> hits = target.getOverlapping(interval);
         int result = 0;