From 31313481f6bcddd29ac7f9c61bf1d102835988d4 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 6 Jul 2009 18:41:55 +0000
Subject: [PATCH] Temporary patch to filter out bad alignments that aren't
 quite fully reported as bad.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1176 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/datasources/providers/LocusView.java       | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
index 49b805fcd..40fa2a003 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
@@ -178,6 +178,14 @@ public abstract class LocusView extends LocusContextIterator implements View {
                 TraversalStatistics.nBadAlignments++;
                 result = true;
                 why = "No alignment start";
+            } else if (rec.getAlignmentEnd() != -1 && rec.getAlignmentEnd() < rec.getAlignmentStart() ) {
+                TraversalStatistics.nBadAlignments++;
+                result = true;
+                why = "Alignment ends before it starts";
+            } else if (rec.getAlignmentStart() != -1 && rec.getAlignmentBlocks().size() == 0) {
+                TraversalStatistics.nBadAlignments++;
+                result = true;
+                why = "Alignment cigar string is invalid";
             } else if (rec.getDuplicateReadFlag()) {
                 TraversalStatistics.nDuplicates++;
                 result = true;