Making several esoteric arguments in the BQSR @Hidden. Adding basic support for Complete Genomics machine cycle.

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java

@@ -159,10 +159,11 @@ public class CycleCovariate implements StandardCovariate {
     */
 
     // todo -- this should be put into a common place in the code base
-    private static List<String> PACBIO_NAMES = Arrays.asList("PACBIO");
     private static List<String> ILLUMINA_NAMES = Arrays.asList("ILLUMINA", "SLX", "SOLEXA");
     private static List<String> SOLID_NAMES = Arrays.asList("SOLID");
     private static List<String> LS454_NAMES = Arrays.asList("454");
+    private static List<String> COMPLETE_GENOMICS_NAMES = Arrays.asList("COMPLETE");
+    private static List<String> PACBIO_NAMES = Arrays.asList("PACBIO");
 
     private static boolean isPlatform(SAMRecord read, List<String> names) {
         String pl = read.getReadGroup().getPlatform().toUpperCase();
@@ -176,11 +177,10 @@ public class CycleCovariate implements StandardCovariate {
     public void getValues(SAMRecord read, Comparable[] comparable) {
 
         //-----------------------------
-        // ILLUMINA and SOLID
+        // Illumina, Solid, PacBio, and Complete Genomics
         //-----------------------------
 
-
+        if( isPlatform(read, ILLUMINA_NAMES) || isPlatform(read, SOLID_NAMES) || isPlatform(read, PACBIO_NAMES) || isPlatform(read, COMPLETE_GENOMICS_NAMES) ) {
-        if( isPlatform(read, ILLUMINA_NAMES) || isPlatform(read, SOLID_NAMES) || isPlatform(read, PACBIO_NAMES)) {
             final int init;
             final int increment;
             if( !read.getReadNegativeStrandFlag() ) {
@@ -222,6 +222,11 @@ public class CycleCovariate implements StandardCovariate {
                 cycle += increment;
             }
         }
+
+        //-----------------------------
+        // 454
+        //-----------------------------
+
         else if ( isPlatform(read, LS454_NAMES) ) { // Some bams have "LS454" and others have just "454"
 
             final int readLength = read.getReadLength();

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java

@@ -245,8 +245,7 @@ public class RecalDataManager {
                 readGroup.setPlatform( RAC.DEFAULT_PLATFORM );
                 ((GATKSAMRecord)read).setReadGroup( readGroup );
             } else {
-                throw new UserException.MalformedBAM(read, "The input .bam file contains reads with no read group. First observed at read with name = " + read.getReadName() +
+                throw new UserException.MalformedBAM(read, "The input .bam file contains reads with no read group. First observed at read with name = " + read.getReadName() );
-                                         " Users must set both the default read group using the --default_read_group <String> argument and the default platform using the --default_platform <String> argument." );
             }
         }
 
@@ -271,8 +270,7 @@ public class RecalDataManager {
                 }
                 readGroup.setPlatform( RAC.DEFAULT_PLATFORM );
             } else {
-                throw new UserException.MalformedBAM(read, "The input .bam file contains reads with no platform information. First observed at read with name = " + read.getReadName() +
+                throw new UserException.MalformedBAM(read, "The input .bam file contains reads with no platform information. First observed at read with name = " + read.getReadName() );
-                                         " Users must set the default platform using the --default_platform <String> argument." );
             }
         }
     }

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Hidden;
 
 /**
  * Created by IntelliJ IDEA.
@@ -41,22 +42,29 @@ public class RecalibrationArgumentCollection {
     //////////////////////////////////
     // Shared Command Line Arguments
     //////////////////////////////////
+    @Hidden
     @Argument(fullName="default_read_group", shortName="dRG", required=false, doc="If a read has no read group then default to the provided String.")
     public String DEFAULT_READ_GROUP = null;
+    @Hidden
     @Argument(fullName="default_platform", shortName="dP", required=false, doc="If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.")
     public String DEFAULT_PLATFORM = null;
+    @Hidden
     @Argument(fullName="force_read_group", shortName="fRG", required=false, doc="If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group.")
     public String FORCE_READ_GROUP = null;
+    @Hidden
     @Argument(fullName="force_platform", shortName="fP", required=false, doc="If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.")
     public String FORCE_PLATFORM = null;
+    @Hidden
     @Argument(fullName = "window_size_nqs", shortName="nqs", doc="The window size used by MinimumNQSCovariate for its calculation", required=false)
     public int WINDOW_SIZE = 5;
 
     /**
      * This window size tells the module in how big of a neighborhood around the current base it should look for the minimum base quality score.
      */
+    @Hidden
     @Argument(fullName = "homopolymer_nback", shortName="nback", doc="The number of previous bases to look at in HomopolymerCovariate", required=false)
     public int HOMOPOLYMER_NBACK = 7;
+    @Hidden
     @Argument(fullName = "exception_if_no_tile", shortName="throwTileException", doc="If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1", required=false)
     public boolean EXCEPTION_IF_NO_TILE = false;