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

Base recalibrator now uses -o and deprecates -outputBam 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4189 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-09-01 22:13:50 +00:00
parent 33400074fa
commit b28f63a948
2 changed files with 10 additions and 12 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
View File

@ -82,13 +82,14 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
@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");
@Output
private PrintStream out;
/////////////////////////////
// Command Line Arguments
/////////////////////////////
@Output(fullName="output_bam", shortName="outputBam", doc="The output BAM file", required=true)
@Argument(fullName="output_bam", shortName="outputBam", doc="Please use --out instead", required=false)
@Deprecated
protected String outbam;
@Output(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)
@ -501,10 +502,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
public SAMFileWriter reduce( SAMRecord read, SAMFileWriter output ) {
if( output != null ) {
output.addAlignment(read);
} else {
out.println(read.format());
}
return output;
}

10
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -69,7 +69,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
" -I " + bam +
( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" )
? " -L 1:10,800,000-10,810,000" : " -L 1:10,100,000-10,300,000" ) +
" -outputBam %s" +
" -o %s" +
" --no_pg_tag" +
" --solid_recal_mode SET_Q_ZERO" +
" -recalFile " + paramsFile,
@ -120,7 +120,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
" -I " + bam +
( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" )
? " -L 1:10,800,000-10,810,000" : " -L 1:10,100,000-10,300,000" ) +
" -outputBam %s" +
" -o %s" +
" --no_pg_tag" +
" -maxQ 70" +
" --solid_recal_mode SET_Q_ZERO" +
@ -175,7 +175,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
"-R " + b36KGReference +
" -T TableRecalibration" +
" -I " + bam +
" -outputBam %s" +
" -o %s" +
" --no_pg_tag" +
" -U" +
" -L 1:10,000,000-20,000,000" +
@ -289,7 +289,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
" -T TableRecalibration" +
" -I " + bam +
" -L 1:10,100,000-10,300,000" +
" -outputBam %s" +
" -o %s" +
" --no_pg_tag" +
" --solid_recal_mode SET_Q_ZERO" +
" --default_read_group DefaultReadGroup" +
@ -343,7 +343,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
"-R " + b36KGReference +
" -T TableRecalibration" +
" -I " + bam +
" -outputBam %s" +
" -o %s" +
" --no_pg_tag" +
" --solid_recal_mode DO_NOTHING" +
" -recalFile " + paramsFile +