I am trying to run the Picard MergeSamFiles API directly from java .
File outputDir = bamFiles.get(0).getParentFile();
String baseName = FilenameUtils.getBaseName(bamFiles.get(0).getName());
File mergedBamFile = new File(outputDir, baseName+ "_merged.bam");
MergeSamFiles mergeSamFiles = new MergeSamFiles();
mergeSamFiles.INPUT = bamFiles;
mergeSamFiles.OUTPUT = mergedBamFile;
mergeSamFiles.USE_THREADING = true;
List<File> tmpDir = new ArrayList<File>(0);
tmpDir.add(outputDir);
mergeSamFiles.TMP_DIR = tmpDir;
mergeSamFiles.CREATE_INDEX = true;
mergeSamFiles.SORT_ORDER = SAMFileHeader.SortOrder.coordinate;
mergeSamFiles.VALIDATION_STRINGENCY = SAMFileReader.ValidationStringency.LENIENT;
if(mergeSamFiles.doWork() != 0 )
{
throw new IOException("Could not merge bam files using Picard " + bamFiles.toString());
}
return mergedBamFile;
I need the validation stringency to be lenient because is need to ignore "MAPQ should be 0 for unmapped read" which is an artifact of our version of BWA (0.5.9, last version that support colorspace.)
Picard however keeps crashing on "MAPQ should be 0 for unmapped read", as if the validation stringency still is set to strict. Am I missing something here? Debugging shows that the inherited variable VALIDATION_STRINGENCY is set to Lenient on the mergeSamFiles object.
2 answers
Hum, I think the variables like VALIDATION_STRINGENCY are filled using the java annotations (?)
try to set it the global way using setDefaultValidationStringency:
SAMFileReader.setDefaultValidationStringency(ValidationStringency.LENIENT);
if(mergeSamFiles.doWork() != 0 )
(....)
I don't know why but replacing the if statement with
String[] arguments = new String[] { "VALIDATION_STRINGENCY=LENIENT" };
mergeSamFiles.instanceMain(arguments);
seems to have solved the problem. Any info on why the solved the problem and what the preferred way is to use / run Picard API still is appreciated.
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