--simplifyBAM is now in the SAMFileWriterArgumentTypeDescriptor, as suggested by map. PrintReads has an integrationtest now that writes out a 1 MB bit of HiSeq normally, with compress 0, and with simplifyBAM on.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5521 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -118,10 +118,6 @@ public class GATKArgumentCollection {
     @Input(fullName = "DBSNP", shortName = "D", doc = "DBSNP file", required = false)
     public String DBSNPFile = null;
 
-    @Element(required = false)
-    @Argument(fullName = "simplifyBAM", shortName = "simplifyBAM", doc = "If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier", required = false)
-    public boolean simplifyBAM = false;
-
     /**
      * The override mechanism in the GATK, by default, populates the command-line arguments, then
      * the defaults from the walker annotations.  Unfortunately, walker annotations should be trumped
@@ -439,9 +435,6 @@ public class GATKArgumentCollection {
         if (enableLowMemorySharding != other.enableLowMemorySharding)
             return false;
 
-        if ( simplifyBAM != other.simplifyBAM )
-            return false;
-
         return true;
     }
 

java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java

@@ -48,6 +48,9 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
     public static final String COMPRESSION_FULLNAME = "bam_compression";
     public static final String COMPRESSION_SHORTNAME = "compress";
 
+    public static final String SIMPLIFY_BAM_FULLNAME = "simplifyBAM";
+    public static final String SIMPLIFY_BAM_SHORTNAME = SIMPLIFY_BAM_FULLNAME;
+
     public static final String CREATE_INDEX_FULLNAME = "index_output_bam_on_the_fly";
 
     /**
@@ -79,7 +82,8 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
     public List<ArgumentDefinition> createArgumentDefinitions( ArgumentSource source ) {
         return Arrays.asList( createBAMArgumentDefinition(source),
                               createBAMCompressionArgumentDefinition(source),
-                              createWriteIndexArgumentDefinition(source));
+                              createWriteIndexArgumentDefinition(source),
+                              createSimplifyBAMArgumentDefinition(source));
     }
 
     @Override
@@ -114,6 +118,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
             stub.setCompressionLevel(compressionLevel);
 
         stub.setIndexOnTheFly(argumentIsPresent(createWriteIndexArgumentDefinition(source),matches));
+        stub.setSimplifyBAM(argumentIsPresent(createSimplifyBAMArgumentDefinition(source),matches));
 
         // WARNING: Side effects required by engine!
         parsingEngine.addTags(stub,getArgumentTags(matches));
@@ -181,4 +186,20 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
                                        null,
                                        null );
     }
+
+    private ArgumentDefinition createSimplifyBAMArgumentDefinition(ArgumentSource source) {
+        return new ArgumentDefinition( ArgumentIOType.ARGUMENT,
+                                       boolean.class,
+                                       SIMPLIFY_BAM_FULLNAME,
+                                       SIMPLIFY_BAM_SHORTNAME,
+                                       "If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier",
+                                       false,
+                                       false,
+                                       false,
+                                       source.isHidden(),
+                                       null,
+                                       null,
+                                       null,
+                                       null );
+    }
 }

java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java

@@ -107,6 +107,11 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     BAQ baqHMM = new BAQ();
 
+    /**
+     * Should we simplify the BAM file while writing it out?
+     */
+    private boolean simplifyBAM = false;
+
     /**
      * Create a new stub given the requested SAM file and compression level.
      * @param engine source of header data, maybe other data about input files.
@@ -138,7 +143,11 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
     }
 
     public boolean simplifyBAM() {
-        return engine.getArguments().simplifyBAM;
+        return simplifyBAM;
+    }
+
+    public void setSimplifyBAM(boolean v) {
+        simplifyBAM = v;
     }
 
     public OutputStream getSAMOutputStream() {

java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java

@@ -0,0 +1,42 @@
+package org.broadinstitute.sting.gatk.walkers;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+import java.util.HashMap;
+
+public class PrintReadsIntegrationTest extends WalkerTest {
+    private static class PRTest {
+        final static String REF = hg18Reference;
+        final static String BAM = validationDataLocation + "HiSeq.1mb.bam";
+        String args;
+        String md5;
+
+        private PRTest(String args, String md5) {
+            this.args = args;
+            this.md5 = md5;
+        }
+    }
+
+    @DataProvider(name = "PRTest")
+    public Object[][] createData1() {
+        return new Object[][]{
+                {new PRTest("",  "dc8e5451dd29757c336013146010f73a")},
+                {new PRTest(" -compress 0",  "fde82269c78c9e91e57286433531b4af")},
+                {new PRTest(" -simplifyBAM",  "0531717b32a7e21c0de70b1526b0751f")} };
+    }
+
+    @Test(dataProvider = "PRTest")
+    public void testPrintReads(PRTest params) {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T PrintReads -R " + params.REF +
+                        " -I " + params.BAM +
+                        params.args +
+                        " -o %s",
+                Arrays.asList(params.md5));
+        executeTest("testVariantRecalibrator-"+params.args, spec).getFirst();
+    }
+}
+