From 2e445262f22998738eb9d016602c4ebca96ff91f Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 12 Jul 2010 22:53:53 +0000
Subject: [PATCH] Promotion to . for variable numbers of arguments

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3773 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broad/tribble/vcf/VCFCompoundHeaderLine.java  |  3 +++
 .../sting/utils/genotype/vcf/VCFUtils.java        | 15 +++++++++++++--
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broad/tribble/vcf/VCFCompoundHeaderLine.java b/java/src/org/broad/tribble/vcf/VCFCompoundHeaderLine.java
index c9a4030b5..3b8ca07a1 100644
--- a/java/src/org/broad/tribble/vcf/VCFCompoundHeaderLine.java
+++ b/java/src/org/broad/tribble/vcf/VCFCompoundHeaderLine.java
@@ -54,6 +54,9 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
     public String getDescription() { return description; }
     public VCFHeaderLineType getType() { return type; }
 
+    //
+    public void setNumberToUnbounded() { this.count = UNBOUNDED; }
+
     // our type of line, i.e. format, info, etc
     private final SupportedHeaderLineType lineType;
 
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
index e74664018..80e0ec10c 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
@@ -165,8 +165,19 @@ public class VCFUtils {
                         VCFCompoundHeaderLine compOther = (VCFCompoundHeaderLine)other;
 
                         // if the names are the same, but the values are different, we need to quit
-                        if (! (compLine).equalsExcludingDescription(compOther) )
-                            throw new IllegalStateException("Incompatible header types, collision between these two types: " + line + " " + other );
+                        if (! (compLine).equalsExcludingDescription(compOther) ) {
+                            if ( compLine.getType().equals(compOther.getType()) ) {
+                                // The Number entry is an Integer that describes the number of values that can be
+                                // included with the INFO field. For example, if the INFO field contains a single
+                                // number, then this value should be 1. However, if the INFO field describes a pair
+                                // of numbers, then this value should be 2 and so on. If the number of possible
+                                // values varies, is unknown, or is unbounded, then this value should be '.'.
+                                logger.warn("Promoting header field Number to . due to number differences in header lines: " + line + " " + other);
+                                compOther.setNumberToUnbounded();
+                            } else {
+                                throw new IllegalStateException("Incompatible header types, collision between these two types: " + line + " " + other );
+                            }
+                        }
                         if ( ! compLine.getDescription().equals(compOther) )
                             if ( logger != null ) logger.warn(String.format("Allowing unequal description fields through: keeping " + compOther + " excluding " + compLine));
                     } else {