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A convenience argument - for Mark - so that you don't have to specify all the output file names 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1442 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-08-20 00:49:12 +00:00
parent 5725de56dc
commit 1d74143ef4
1 changed files with 14 additions and 8 deletions
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22
java/src/org/broadinstitute/sting/playground/gatk/walkers/VennCallSetsWalker.java
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@ -18,6 +18,8 @@ import java.io.PrintWriter;
*/ */
@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="callset1",type=AllelicVariant.class),@RMD(name="callset2",type=AllelicVariant.class)}) @Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="callset1",type=AllelicVariant.class),@RMD(name="callset2",type=AllelicVariant.class)})
public class VennCallSetsWalker extends RefWalker<Integer, Integer> { public class VennCallSetsWalker extends RefWalker<Integer, Integer> {
@Argument(fullName="outputPrefix", shortName="prefix", doc="File prefix for output; turns on ALL output options below", required=false)
private String PREFIX = null;
@Argument(fullName="union_out", shortName="union", doc="File to which union of sets should be written", required=false) @Argument(fullName="union_out", shortName="union", doc="File to which union of sets should be written", required=false)
String UNION_OUT = null; String UNION_OUT = null;
@Argument(fullName="intersect_out", shortName="intersect", doc="File to which intersection of sets should be written", required=false) @Argument(fullName="intersect_out", shortName="intersect", doc="File to which intersection of sets should be written", required=false)
@ -37,18 +39,22 @@ public class VennCallSetsWalker extends RefWalker<Integer, Integer> {
*/ */
public void initialize() { public void initialize() {
try { try {
if ( UNION_OUT != null ) { if ( UNION_OUT != null )
union_writer = new PrintWriter(UNION_OUT); union_writer = new PrintWriter(UNION_OUT);
} else if ( PREFIX != null )
if ( INTERSECTION_OUT != null ) { union_writer = new PrintWriter(PREFIX + ".union.calls");
if ( INTERSECTION_OUT != null )
intersect_writer = new PrintWriter(INTERSECTION_OUT); intersect_writer = new PrintWriter(INTERSECTION_OUT);
} else if ( PREFIX != null )
if ( SET1_OUT != null ) { intersect_writer = new PrintWriter(PREFIX + ".intersect.calls");
if ( SET1_OUT != null )
set1_writer = new PrintWriter(SET1_OUT); set1_writer = new PrintWriter(SET1_OUT);
} else if ( PREFIX != null )
if ( SET2_OUT != null ) { set1_writer = new PrintWriter(PREFIX + ".set1Only.calls");
if ( SET2_OUT != null )
set2_writer = new PrintWriter(SET2_OUT); set2_writer = new PrintWriter(SET2_OUT);
} else if ( PREFIX != null )
set2_writer = new PrintWriter(PREFIX + ".set2Only.calls");
} catch (FileNotFoundException e) { } catch (FileNotFoundException e) {
throw new StingException(String.format("Could not open file(s) for writing")); throw new StingException(String.format("Could not open file(s) for writing"));
} }