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Reverting Eric's previous change because it killed the PG tag in the output bam file header. Added a new -compress command line argument to set the compression level of the output bam file. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2555 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-11 19:02:56 +00:00
parent dfa3c3b875
commit 11f91b3c95
1 changed files with 19 additions and 4 deletions
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23
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
/////////////////////////////
@Argument(fullName="output_bam", shortName="outputBam", doc="output BAM file", required=true)
private SAMFileWriter OUTPUT_BAM = null;
private String OUTPUT_BAM_FILE = null;
@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)
private int PRESERVE_QSCORES_LESS_THAN = 5;
@ -79,6 +79,8 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
private int SMOOTHING = 1;
@Argument(fullName="max_quality_score", shortName="maxQ", required = false, doc="The integer value at which to cap the quality scores, default is 40")
private int MAX_QUALITY_SCORE = 40;
@Argument(fullName="compression_level", shortName="compress", required = false, doc="Compression level parameter passed to SAMFileWriter, higher value means more compression at added cost in run time, default is 5")
private int COMPRESSION_LEVEL = 5;
/////////////////////////////
// Debugging-only Arguments
@ -94,7 +96,8 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
private static final String versionString = "v2.2.7"; // Major version, minor version, and build number
private static final String versionString = "v2.2.8"; // 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 static final long RANDOM_SEED = 1032861495;
@ -245,6 +248,13 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
programRecord.setCommandLine( commandLineString );
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), COMPRESSION_LEVEL );
}
}
/**
@ -434,7 +444,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
* @return The FileWriter
*/
public SAMFileWriter reduce( SAMRecord read, SAMFileWriter output ) {
if ( output != null ) {
if( output != null ) {
output.addAlignment(read);
} else {
out.println(read.format());
@ -444,7 +454,12 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
}
/**
* Close the output 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();
}
}
}