zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

@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
This commit is contained in:
depristo 2010-08-14 18:36:28 +00:00
parent 61064d7075
commit a36951f11a
1 changed files with 4 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
View File

@ -78,13 +78,13 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
/////////////////////////////
@ArgumentCollection private RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
@Argument(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";
@Input(fullName="recal_file", shortName="recalFile", required=false, doc="Filename for the input covariates table recalibration .csv file")
public File RECAL_FILE = new File("output.recal_data.csv");
/////////////////////////////
// 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;
@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)
@ -159,7 +159,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
boolean sawEOF = false;
try {
for ( String line : new XReadLines(new File( RECAL_FILE )) ) {
for ( String line : new XReadLines(RECAL_FILE) ) {
lineNumber++;
if ( EOF_MARKER.equals(line) ) {
sawEOF = true;