Fix for bug GSA-441: BAM file list with blank lines gives a confusing error

message. Lines containing only whitespace in .list files are now ignored. 
Also added support for comments in .list files: lines whose first
non-whitespace character is '#' are now also ignored.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5550 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java

@@ -134,6 +134,14 @@ public abstract class CommandLineProgram {
      */
     protected String getArgumentSourceName( Class source ) { return source.toString(); }
 
+    /**
+     * Sets the command-line parsing engine. Necessary for unit testing purposes.
+     * @param parser the new command-line parsing engine
+     */
+    public void setParser( ParsingEngine parser ) {
+        this.parser = parser;
+    }
+
     /**
      * this is the function that the inheriting class can expect to have called
      * when all the argument processing is done

java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java

@@ -71,6 +71,11 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      */
     private final Collection<Object> argumentSources = new ArrayList<Object>();
 
+    /**
+     * Lines starting with this String in .list files are considered comments.
+     */
+    public static final String LIST_FILE_COMMENT_START = "#";
+
     /**
      * this is the function that the inheriting class can expect to have called
      * when the command line system has initialized.
@@ -196,20 +201,25 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
 
     /**
      * 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)
+     * itself contain entries which are lists of other files to be read (note: you cannot have lists
+     * of lists of lists). Lines in .list files containing only whitespace or which begin with
+     * LIST_FILE_COMMENT_START are ignored.
      *
      * @param argCollection the command-line arguments from which to extract the BAM file list.
      * @return a flattened list of the bam files provided
      */
-    private List<SAMReaderID> unpackBAMFileList(GATKArgumentCollection argCollection) {
+    protected List<SAMReaderID> unpackBAMFileList(GATKArgumentCollection argCollection) {
         List<SAMReaderID> unpackedReads = new ArrayList<SAMReaderID>();
         for( String inputFileName: argCollection.samFiles ) {
             Tags inputFileNameTags = parser.getTags(inputFileName);
             inputFileName = expandFileName(inputFileName);
             if (inputFileName.toLowerCase().endsWith(".list") ) {
                 try {
-                    for(String fileName : new XReadLines(new File(inputFileName)))
+                    for ( String fileName : new XReadLines(new File(inputFileName), true) ) {
-                        unpackedReads.add(new SAMReaderID(fileName,parser.getTags(inputFileName)));
+                        if ( fileName.length() > 0 && ! fileName.startsWith(LIST_FILE_COMMENT_START) ) {
+                            unpackedReads.add(new SAMReaderID(fileName,parser.getTags(inputFileName)));
+                        }
+                    }
                 }
                 catch( FileNotFoundException ex ) {
                     throw new UserException.CouldNotReadInputFile(new File(inputFileName), "Unable to find file while unpacking reads", ex);

java/test/org/broadinstitute/sting/gatk/CommandLineExecutableUnitTest.java

@@ -0,0 +1,106 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.commandline.ParsingEngine;
+import org.broadinstitute.sting.commandline.Tags;
+import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
+import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
+
+
+/**
+ * Tests selected functionality in the CommandLineExecutable class
+ */
+public class CommandLineExecutableUnitTest extends BaseTest {
+
+    @Test
+    public void testIgnoreBlankLinesInBAMListFiles() throws Exception {
+        File tempListFile = createTempListFile("testIgnoreBlankLines",
+                                               "",
+                                               "testdata/exampleBAM.bam",
+                                               "         "
+                                              );
+
+        List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
+        expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags()));
+
+        performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
+    }
+
+    @Test
+    public void testCommentSupportInBAMListFiles() throws Exception {
+        File tempListFile = createTempListFile("testCommentSupport",
+                                               "#",
+                                               "testdata/exampleBAM.bam",
+                                               "#testdata/foo.bam",
+                                               "      # testdata/bar.bam"
+                                              );
+
+        List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
+        expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags()));
+
+        performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
+    }
+
+    private File createTempListFile( String tempFilePrefix, String... lines ) throws Exception {
+        File tempListFile = File.createTempFile(tempFilePrefix, ".list");
+        tempListFile.deleteOnExit();
+
+        PrintWriter out = new PrintWriter(tempListFile);
+        for ( String line : lines ) {
+            out.println(line);
+        }
+        out.close();
+
+        return tempListFile;
+    }
+
+    private void performBAMListFileUnpackingTest( File tempListFile, List<SAMReaderID> expectedUnpackedFileList ) throws Exception {
+        List<String> bamFiles = new ArrayList<String>();
+        bamFiles.add(tempListFile.getAbsolutePath());
+
+        GATKArgumentCollection argCollection = new GATKArgumentCollection();
+        argCollection.samFiles = bamFiles;
+
+        CommandLineGATK testInstance = new CommandLineGATK();
+        testInstance.setParser(new ParsingEngine(testInstance));
+
+        List<SAMReaderID> unpackedBAMFileList = testInstance.unpackBAMFileList(argCollection);
+
+        Assert.assertEquals(unpackedBAMFileList.size(), expectedUnpackedFileList.size(),
+                            "Unpacked BAM file list contains extraneous lines");
+        Assert.assertEquals(unpackedBAMFileList, expectedUnpackedFileList,
+                            "Unpacked BAM file list does not contain correct BAM file names");
+    }
+}