From dd46d843fb186b4b9bd377cba0374b326865f460 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 6 Jun 2012 11:04:55 -0400
Subject: [PATCH] IR should skip Ion reads just like it does with 454 reads;
 Tim has confirmed that official platform name for Ion.

---
 .../gatk/walkers/indels/IndelRealigner.java   |  5 +++--
 .../sting/utils/sam/ReadUtils.java            | 21 ++++++++++++++-----
 2 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 8f939fc49..e12f26fcc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -532,8 +532,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 read.getMappingQuality() == 0 ||
                 read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ||
                 ConstrainedMateFixingManager.iSizeTooBigToMove(read, MAX_ISIZE_FOR_MOVEMENT) ||
-                ReadUtils.is454Read(read);
-        // TODO -- it would be nice if we could use indels from 454 reads as alternate consenses
+                ReadUtils.is454Read(read) ||
+                ReadUtils.isIonRead(read);
+        // TODO -- it would be nice if we could use indels from 454/Ion reads as alternate consenses
     }
 
     private void cleanAndCallMap(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 4e2fd1446..d2d5e6bc5 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -211,7 +211,7 @@ public class ReadUtils {
     }
 
     /**
-     * is the read a 454 read ?
+     * is the read a 454 read?
      *
      * @param read the read to test
      * @return checks the read group tag PL for the default 454 tag
@@ -221,7 +221,17 @@ public class ReadUtils {
     }
 
     /**
-     * is the read a SOLiD read ?
+     * is the read an IonTorrent read?
+     *
+     * @param read the read to test
+     * @return checks the read group tag PL for the default ion tag
+     */
+    public static boolean isIonRead(SAMRecord read) {
+        return isPlatformRead(read, "IONTORRENT");
+    }
+
+    /**
+     * is the read a SOLiD read?
      *
      * @param read the read to test
      * @return checks the read group tag PL for the default SOLiD tag
@@ -231,7 +241,7 @@ public class ReadUtils {
     }
 
     /**
-     * is the read a SLX read ?
+     * is the read a SLX read?
      *
      * @param read the read to test
      * @return checks the read group tag PL for the default SLX tag
@@ -241,10 +251,11 @@ public class ReadUtils {
     }
 
     /**
-     * checks if the read has a platform tag in the readgroup equal to 'name' ?
+     * checks if the read has a platform tag in the readgroup equal to 'name'.
+     * Assumes that 'name' is upper-cased.
      *
      * @param read the read to test
-     * @param name the platform name to test
+     * @param name the upper-cased platform name to test
      * @return whether or not name == PL tag in the read group of read
      */
     public static boolean isPlatformRead(SAMRecord read, String name) {