From 39678b6a20fc56f46eb5aff3732d9cabeaa9dca0 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 10 Nov 2011 13:34:03 -0500
Subject: [PATCH] Check for reads with missing read groups and throw a
 UserException when encountered.  Mauricio said this wouldn't break
 integration tests.

---
 .../gatk/filters/MalformedReadFilter.java     | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
index 11bbf9e4c..46d28185b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
@@ -50,19 +50,20 @@ public class MalformedReadFilter extends ReadFilter {
 
     public boolean filterOut(SAMRecord read) {
         // slowly changing the behavior to blow up first and filtering out if a parameter is explicitly provided
-        if (!checkMismatchingBasesAndQuals(read)) {
-            if (!filterMismatchingBaseAndQuals)
-                throw new UserException.MalformedBAM(read, "BAM file has a read with mismatching number of bases and base qualities. Offender: " + read.getReadName() +"  [" + read.getReadLength() + " bases] [" +read.getBaseQualities().length +"] quals");
-            else
-                return true;
-        }
-
         return  !checkInvalidAlignmentStart(read) ||
                 !checkInvalidAlignmentEnd(read) ||
                 !checkAlignmentDisagreesWithHeader(this.header,read) ||
+                !checkHasReadGroup(read) ||
+                !checkMismatchingBasesAndQuals(read, filterMismatchingBaseAndQuals) ||
                 !checkCigarDisagreesWithAlignment(read);
     }
 
+    private static boolean checkHasReadGroup(SAMRecord read) {
+        if ( read.getReadGroup() == null )
+            throw new UserException.ReadMissingReadGroup(read);
+        return true;
+    }
+
     /**
      * Check for the case in which the alignment start is inconsistent with the read unmapped flag.
      * @param read The read to validate.
@@ -127,7 +128,9 @@ public class MalformedReadFilter extends ReadFilter {
      * @param read the read to validate
      * @return true if they have the same number. False otherwise.
      */
-    private static boolean checkMismatchingBasesAndQuals(SAMRecord read) {
+    private static boolean checkMismatchingBasesAndQuals(SAMRecord read, boolean filterMismatchingBaseAndQuals) {
+        if (!filterMismatchingBaseAndQuals)
+            throw new UserException.MalformedBAM(read, "BAM file has a read with mismatching number of bases and base qualities. Offender: " + read.getReadName() +"  [" + read.getReadLength() + " bases] [" +read.getBaseQualities().length +"] quals");
         return (read.getReadLength() == read.getBaseQualities().length);
     }
 }