Updates to the bundle script:

1. Add the symbolic 'current' link for the new bundle dir
2. Don't gzip and copy .out files
3. Don't call chr20 SNPs on the example BAM because it's now just a few reads on chr1

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala

@@ -44,7 +44,7 @@ class GATKResourcesBundle extends QScript {
   var exampleFASTA: Reference = _
   var refs: List[Reference] = _
 
-  class Resource(val file: File, val name: String, val ref: Reference, val useName: Boolean = true, val makeSites: Boolean = true ) {
+  class Resource(val file: File, val name: String, val ref: Reference, val useName: Boolean = true, val makeSites: Boolean = true, val makeCallsIfBam: Boolean = true ) {
     def destname(target: Reference): String = {
       if ( useName )
         return name + "." + target.name + "." + getExtension(file)
@@ -68,6 +68,7 @@ class GATKResourcesBundle extends QScript {
 
   def isVCF(file: File) = file.getName.endsWith(".vcf")
   def isBAM(file: File) = file.getName.endsWith(".bam")
+  def isOUT(file: File) = file.getName.endsWith(".out")
   def isFASTA(file: File) = file.getName.endsWith(".fasta")
 
   var RESOURCES: List[Resource] = Nil
@@ -94,7 +95,7 @@ class GATKResourcesBundle extends QScript {
     addResource(new Resource(DATAROOT + "dbsnp_132_b37.vcf", "dbsnp_132", b37, true, false))
 
     addResource(new Resource(exampleFASTA.file, "exampleFASTA", exampleFASTA, false))
-    addResource(new Resource("public/testdata/exampleBAM.bam", "exampleBAM", exampleFASTA, false))
+    addResource(new Resource("public/testdata/exampleBAM.bam", "exampleBAM", exampleFASTA, false, false, false))
   }
 
   def initializeStandardDataFiles() = {
@@ -172,7 +173,7 @@ class GATKResourcesBundle extends QScript {
     // exampleFASTA file
     //
     addResource(new Resource(exampleFASTA.file, "exampleFASTA", exampleFASTA, false))
-    addResource(new Resource("public/testdata/exampleBAM.bam", "exampleBAM", exampleFASTA, false))
+    addResource(new Resource("public/testdata/exampleBAM.bam", "exampleBAM", exampleFASTA, false, false, false))
   }
 
   def createBundleDirectories(dir: File) = {
@@ -184,6 +185,15 @@ class GATKResourcesBundle extends QScript {
     }
   }
 
+  def createCurrentLink(bundleDir: File) = {
+
+    val currentLink = new File(BUNDLE_ROOT + "/current")
+
+    if ( currentLink.exists ) currentLink.delete()
+
+    add(new linkFile(bundleDir, currentLink))
+  }
+
   def script = {
     if ( TEST )
       initializeTestDataFiles();
@@ -201,8 +211,10 @@ class GATKResourcesBundle extends QScript {
         } else if ( isBAM(resource.file) ) {
           val f = copyBundleFile(resource, resource.ref)
           add(new IndexBAM(f))
-          @Output val outvcf: File = swapExt(f.getParent, f, ".bam", ".vcf")
+	  if ( resource.makeCallsIfBam ) {
-          add(new UG(resource.file, resource.ref.file, outvcf))
+            @Output val outvcf: File = swapExt(f.getParent, f, ".bam", ".vcf")
+            add(new UG(resource.file, resource.ref.file, outvcf))
+	  }
         } else if ( isVCF(resource.file) ) {
           for ( destRef <- refs ) {
             val out = destFile(BUNDLE_DIR, destRef, resource.destname(destRef))
@@ -240,6 +252,9 @@ class GATKResourcesBundle extends QScript {
           //throw new ReviewedStingException("Unknown file type: " + resource)
         }
       }
+
+      createCurrentLink(BUNDLE_DIR)
+
     } else {
       createBundleDirectories(DOWNLOAD_DIR)
       createDownloadsFromBundle(BUNDLE_DIR, DOWNLOAD_DIR)
@@ -249,7 +264,6 @@ class GATKResourcesBundle extends QScript {
 
   def createDownloadsFromBundle(in: File, out: File) {
     Console.printf("Visiting %s%n", in)
-    // todo -- ignore some of the other files too (e.g. *.out); will test next time we make a bundle
     if (! in.getName.startsWith(".")) {
       if ( in.isDirectory ) {
         out.mkdirs
@@ -261,7 +275,7 @@ class GATKResourcesBundle extends QScript {
         if ( isBAM(in) ) {
           add(new cpFile(in, out))
           add(new md5sum(out))
-        } else {
+        } else if ( !isOUT(in) ) {
           add(new GzipFile(in, out + ".gz"))
           add(new md5sum(out + ".gz"))
         }
@@ -299,6 +313,10 @@ class GATKResourcesBundle extends QScript {
     def commandLine = "cp %s %s".format(in.getAbsolutePath, out.getAbsolutePath)
   }
 
+  class linkFile(@Input val in: File, @Output val out: File) extends CommandLineFunction {
+    def commandLine = "ln -s %s %s".format(in.getAbsolutePath, out.getAbsolutePath)
+  }
+
   class md5sum(@Input val in: File) extends CommandLineFunction {
     @Output val o: File = new File(in.getAbsolutePath + ".md5")
     def commandLine = "md5sum %s > %s".format(in.getAbsolutePath, o)