From c84f0deb1d8e946f8fb25fa6f0390af5e0689fff Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 10 Jun 2013 13:42:00 -0400
Subject: [PATCH 1/2] Don't crash if cds file is not provided

CDS file should be optional.
---
 .../walkers/diagnostics/missing/QualifyMissingIntervals.java | 5 +++--
 1 file changed, 3 insertions(+), 2 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 62716d6d2..cdcf32dcc 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
@@ -117,7 +117,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
     public File targetsFile;
 
     @Argument(shortName = "cds", required = false)
-    public File cdsFile;
+    public File cdsFile = null;
 
     GATKReport simpleReport;
     GenomeLocSortedSet target;
@@ -133,7 +133,8 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
         target = new GenomeLocSortedSet(parser);
         cds = new GenomeLocSortedSet(parser);
         parseFile(targetsFile, target, parser);
-        parseFile(cdsFile, cds, parser);
+        if (cdsFile != null)
+            parseFile(cdsFile, cds, parser);
     }
 
     public Metrics reduceInit() {

From 1d67d07cf118ca74a8a8b7987c68c6a252b47c29 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 10 Jun 2013 15:17:40 -0400
Subject: [PATCH 2/2] better docs for Qualify Missing Intervals

now that it's available to the public, better give'em good docs!
---
 .../walkers/diagnostics/missing/QualifyMissingIntervals.java   | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

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 cdcf32dcc..d0db3ef98 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
@@ -87,7 +87,7 @@ import java.util.List;
  *
  * <h3>Input</h3>
  * <p>
- *  A reference file
+ *  A reference file (for GC content), the input bam file (for base and mapping quality calculation), the missing intervals (in the -L), the baits/targets used to sequence (in the -targets) and a bed file with the coding sequence intervals of the genome (in the -cds)
  * </p>
  *
  * <h3>Output</h3>
@@ -100,6 +100,7 @@ import java.util.List;
  * java -Xmx2g -jar GenomeAnalysisTK.jar \
  *   -T QualifyMissingIntervals \
  *   -R ref.fasta \
+ *   -I input.bam \
  *   -o output.grp \
  *   -L input.intervals \
  *   -cds cds.intervals \