From 7474afa7a349e1efb6fb8c0bde5a534b4a5079d5 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 23 Aug 2010 18:52:00 +0000
Subject: [PATCH] allow other objects access to the static method that resolves
 bam lists, and some renaming and improved documentation for the function.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4087 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/CommandLineExecutable.java        | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
index f93af2ad6..0042817fc 100644
--- a/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
+++ b/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
@@ -32,10 +32,6 @@ import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
-import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
-import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
-import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -145,18 +141,18 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      * @param argCollection Collection of arguments to preprocess.
      */
     private void processArguments( GATKArgumentCollection argCollection ) {
-        argCollection.samFiles = unpackList( argCollection.samFiles );
+        argCollection.samFiles = unpackBAMFileList( argCollection.samFiles );
     }
 
     /**
-     * Unpack the files to be processed, given a list of files.  That list of files can
-     * itself contain lists of other files to be read.
+     * Unpack the bam files to be processed, given a list of files.  That list of files can
+     * itself contain entries which are lists of other files to be read (note: you cannot have lists of lists of lists)
      *
-     * @param inputFiles
+     * @param inputFiles a list of files that represent either bam files themselves, or a file containing a list of bam files to process
      *
-     * @return
+     * @return a flattened list of the bam files provided 
      */
-    private static List<File> unpackList( List<File> inputFiles ) {
+    public static List<File> unpackBAMFileList( List<File> inputFiles ) {
         List<File> unpackedReads = new ArrayList<File>();
         for( File inputFile: inputFiles ) {
             if (inputFile.getName().toLowerCase().endsWith(".list") ) {