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@output and @input arguments for table recalibration for use with Q 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4037 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-08-14 18:36:28 +00:00
parent 61064d7075
commit a36951f11a
1 changed files with 4 additions and 4 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -78,13 +78,13 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
///////////////////////////// /////////////////////////////
@ArgumentCollection private RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); @ArgumentCollection private RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
@Argument(fullName="recal_file", shortName="recalFile", required=false, doc="Filename for the input covariates table recalibration .csv file") @Input(fullName="recal_file", shortName="recalFile", required=false, doc="Filename for the input covariates table recalibration .csv file")
public String RECAL_FILE = "output.recal_data.csv"; public File RECAL_FILE = new File("output.recal_data.csv");
///////////////////////////// /////////////////////////////
// Command Line Arguments // Command Line Arguments
///////////////////////////// /////////////////////////////
@Argument(fullName="output_bam", shortName="outputBam", doc="The output BAM file", required=true) @Output(fullName="output_bam", shortName="outputBam", doc="The output BAM file", required=true)
private StingSAMFileWriter OUTPUT_BAM = null; private StingSAMFileWriter 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)
@ -159,7 +159,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
boolean sawEOF = false; boolean sawEOF = false;
try { try {
for ( String line : new XReadLines(new File( RECAL_FILE )) ) { for ( String line : new XReadLines(RECAL_FILE) ) {
lineNumber++; lineNumber++;
if ( EOF_MARKER.equals(line) ) { if ( EOF_MARKER.equals(line) ) {
sawEOF = true; sawEOF = true;