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Changed the OUTPUT_BAM_FILE argument from String to SAMFileWriter and removed the call to close(). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2551 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-01-10 03:45:54 +00:00
parent 7893aaefe9
commit 80af0f2f54
1 changed files with 2 additions and 14 deletions
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16
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -71,7 +71,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
// Command Line Arguments // Command Line Arguments
///////////////////////////// /////////////////////////////
@Argument(fullName="output_bam", shortName="outputBam", doc="output BAM file", required=true) @Argument(fullName="output_bam", shortName="outputBam", doc="output BAM file", required=true)
private String OUTPUT_BAM_FILE = null; private SAMFileWriter OUTPUT_BAM = null;
@Argument(fullName="preserve_qscores_less_than", shortName="pQ", @Argument(fullName="preserve_qscores_less_than", shortName="pQ",
doc="Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases", required=false) doc="Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases", required=false)
private int PRESERVE_QSCORES_LESS_THAN = 5; private int PRESERVE_QSCORES_LESS_THAN = 5;
@ -95,7 +95,6 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*"); private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*"); private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
private static final String versionString = "v2.2.6"; // Major version, minor version, and build number private static final String versionString = "v2.2.6"; // Major version, minor version, and build number
private SAMFileWriter OUTPUT_BAM = null;// The File Writer that will write out the recalibrated bam
private Random coinFlip; // Random number generator is used to remove reference bias in solid bams private Random coinFlip; // Random number generator is used to remove reference bias in solid bams
private static final long RANDOM_SEED = 1032861495; private static final long RANDOM_SEED = 1032861495;
@ -246,12 +245,6 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
programRecord.setCommandLine( commandLineString ); programRecord.setCommandLine( commandLineString );
header.addProgramRecord( programRecord ); header.addProgramRecord( programRecord );
} }
// Create the SAMFileWriter that we will be using to output the reads
if( OUTPUT_BAM_FILE != null ) {
final SAMFileWriterFactory factory = new SAMFileWriterFactory();
OUTPUT_BAM = factory.makeBAMWriter( header, true, new File(OUTPUT_BAM_FILE), 5 ); // BUGBUG: Bam compression hardcoded to 5
}
} }
/** /**
@ -451,12 +444,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
} }
/** /**
* Close the output bam file
* @param output The SAMFileWriter that outputs the bam file * @param output The SAMFileWriter that outputs the bam file
*/ */
public void onTraversalDone(SAMFileWriter output) { public void onTraversalDone(SAMFileWriter output) { }
if ( output != null ) {
output.close();
}
}
} }