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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
This commit is contained in:
aaron 2010-08-23 18:52:00 +00:00
parent ccda4f6ec1
commit 7474afa7a3
1 changed files with 6 additions and 10 deletions
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16
java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
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@ -32,10 +32,6 @@ import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.gatk.walkers.Walker; 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.File;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
@ -145,18 +141,18 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
* @param argCollection Collection of arguments to preprocess. * @param argCollection Collection of arguments to preprocess.
*/ */
private void processArguments( GATKArgumentCollection argCollection ) { 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 * Unpack the bam files to be processed, given a list of files. That list of files can
* itself contain lists of other files to be read. * 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>(); List<File> unpackedReads = new ArrayList<File>();
for( File inputFile: inputFiles ) { for( File inputFile: inputFiles ) {
if (inputFile.getName().toLowerCase().endsWith(".list") ) { if (inputFile.getName().toLowerCase().endsWith(".list") ) {