From 62c484b57a6a3db436e6bec074227e2706fd1932 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 9 Oct 2009 18:11:32 +0000
Subject: [PATCH] Fixes for GSA-201, where enumerated types in command line
 arguments had to be defined as all uppercase for the system to work.

Also a little playground walker that changes the sort order flag of a BAM file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1805 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/UpdateSAMSortOrderWalker.java     | 49 +++++++++++++++++++
 .../utils/cmdLine/ArgumentTypeDescriptor.java |  5 +-
 .../sting/utils/cmdLine/ParsingEngine.java    | 14 ++++++
 3 files changed, 67 insertions(+), 1 deletion(-)
 create mode 100644 java/src/org/broadinstitute/sting/playground/gatk/walkers/UpdateSAMSortOrderWalker.java

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/UpdateSAMSortOrderWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/UpdateSAMSortOrderWalker.java
new file mode 100644
index 000000000..27d4e3ce5
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/UpdateSAMSortOrderWalker.java
@@ -0,0 +1,49 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileWriterFactory;
+
+import java.io.File;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: aaron
+ * Date: Oct 9, 2009
+ * Time: 2:21:08 PM
+ */
+public class UpdateSAMSortOrderWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
+
+    @Argument(required=true, shortName="out_bam", doc="The samfile to output to")
+    public File SAM_FILE_OUTPUT_LOCATION;
+
+    @Argument(required=false, shortName="sortorder", doc="the sort order to emit in")
+    public SAMFileHeader.SortOrder SORT_ORDER=SAMFileHeader.SortOrder.coordinate;
+
+    @Override
+    public SAMRecord map(char[] ref, SAMRecord read) {
+        return read;
+    }
+
+    @Override
+    public SAMFileWriter reduceInit() {
+        SAMFileHeader header = GenomeAnalysisEngine.instance.getSAMFileHeader();
+        header.setSortOrder(SORT_ORDER);
+        SAMFileWriterFactory factory = new SAMFileWriterFactory();
+        return factory.makeBAMWriter(header,false,SAM_FILE_OUTPUT_LOCATION);
+    }
+
+    @Override
+    public SAMFileWriter reduce(SAMRecord value, SAMFileWriter sum) {
+        sum.addAlignment(value);
+        return sum;
+    }
+
+    public void onTraversalDone(SAMFileWriter result) {
+        result.close();
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentTypeDescriptor.java
index 5fa005759..b2af39842 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentTypeDescriptor.java
@@ -241,7 +241,10 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                 Method valueOf = primitiveToWrapperMap.get(type).getMethod("valueOf",String.class);
                 return valueOf.invoke(null,value.trim());
             } else if (type.isEnum()) {
-                return Enum.valueOf(type,value.toUpperCase().trim());
+                Object[] vals = type.getEnumConstants();
+                for (Object val : vals)
+                    if (String.valueOf(val).equalsIgnoreCase(value)) return val;
+                throw new UnknownEnumeratedValueException(value, type.getName());
             } else {
                 Constructor ctor = type.getConstructor(String.class);
                 return ctor.newInstance(value);
diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
index eadef98d4..2eeefb29d 100755
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
@@ -485,4 +485,18 @@ class ArgumentsAreMutuallyExclusiveException extends ArgumentException {
         return sb.toString();
     }
 
+}
+
+
+/**
+ * An exception for when an argument doesn't match an of the enumerated options for that var type
+ */
+class UnknownEnumeratedValueException extends ArgumentException {
+    public UnknownEnumeratedValueException(String argumentPassed, String typeName ) {
+        super( formatArguments(argumentPassed, typeName) );
+    }
+
+    private static String formatArguments(String argumentPassed, String typeName  ) {
+        return new String("Enumerated constant " + argumentPassed + " Not found in type " + typeName);
+    }
 }
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