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Added an info log containing the SAM/BAM files that were eventually found from the commandline (useful for when there are files hiding inside bam.lists which may or may not have been constructed correctly...) 

Added a @hidden option controling the appearance of the full BamList in the log
This commit is contained in:
Yossi Farjoun 2014-01-15 11:02:04 -05:00
parent 3b6b7626aa
commit c79e8ca53e
2 changed files with 15 additions and 4 deletions
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14
public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
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@ -26,8 +26,10 @@
package org.broadinstitute.sting.gatk;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
@ -41,7 +43,9 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.ListFileUtils;
import java.security.PublicKey;
import java.util.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
/**
* @author aaron
@ -87,7 +91,11 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
engine.setArguments(getArgumentCollection());
// File lists can require a bit of additional expansion. Set these explicitly by the engine.
engine.setSAMFileIDs(ListFileUtils.unpackBAMFileList(getArgumentCollection().samFiles,parser));
final Collection<SAMReaderID> bamFileList=ListFileUtils.unpackBAMFileList(getArgumentCollection().samFiles,parser);
engine.setSAMFileIDs(bamFileList);
if(getArgumentCollection().showFullBamList){
logger.info(String.format("Adding the following input SAM Files: %s",bamFileList.toString()));
}
engine.setWalker(walker);
walker.setToolkit(engine);

5
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -34,7 +34,6 @@ import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.gatk.samples.PedigreeValidationType;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
@ -63,6 +62,10 @@ public class GATKArgumentCollection {
@Input(fullName = "input_file", shortName = "I", doc = "Input file containing sequence data (SAM or BAM)", required = false)
public List<String> samFiles = new ArrayList<String>();
@Hidden
@Argument(fullName = "showFullBamList",doc="Emit a log entry (level INFO) containing the full list of sequence data files to be included in the analysis (including files inside .bam.list files).")
public Boolean showFullBamList = false;
@Argument(fullName = "read_buffer_size", shortName = "rbs", doc="Number of reads per SAM file to buffer in memory", required = false, minValue = 0)
public Integer readBufferSize = null;