Merge pull request #770 from broadinstitute/pd_ngs_platform

Moved platform flow information into NGSPlatform

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java

@@ -55,11 +55,10 @@ import org.broadinstitute.gatk.engine.recalibration.ReadCovariates;
 import org.broadinstitute.gatk.engine.recalibration.RecalibrationArgumentCollection;
 import org.broadinstitute.gatk.utils.BaseUtils;
 import org.broadinstitute.gatk.utils.NGSPlatform;
+import org.broadinstitute.gatk.utils.SequencerFlowClass;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
-import java.util.EnumSet;
-
 /*
  * Copyright (c) 2009 The Broad Institute
  *
@@ -104,9 +103,6 @@ public class CycleCovariate implements StandardCovariate {
     public static final int CUSHION_FOR_INDELS = 4;
     private String default_platform = null;
 
-    private static final EnumSet<NGSPlatform> DISCRETE_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.ILLUMINA, NGSPlatform.SOLID, NGSPlatform.PACBIO, NGSPlatform.COMPLETE_GENOMICS);
-    private static final EnumSet<NGSPlatform> FLOW_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.LS454, NGSPlatform.ION_TORRENT);
-
     // Initialize any member variables using the command-line arguments passed to the walkers
     @Override
     public void initialize(final RecalibrationArgumentCollection RAC) {
@@ -126,7 +122,7 @@ public class CycleCovariate implements StandardCovariate {
         final NGSPlatform ngsPlatform = default_platform == null ? read.getNGSPlatform() : NGSPlatform.fromReadGroupPL(default_platform);
 
         // Discrete cycle platforms
-        if (DISCRETE_CYCLE_PLATFORMS.contains(ngsPlatform)) {
+        if (ngsPlatform.getSequencerType() == SequencerFlowClass.DISCRETE) {
             final int readOrderFactor = read.getReadPairedFlag() && read.getSecondOfPairFlag() ? -1 : 1;
             final int increment;
             int cycle;
@@ -149,7 +145,7 @@ public class CycleCovariate implements StandardCovariate {
         }
 
         // Flow cycle platforms
-        else if (FLOW_CYCLE_PLATFORMS.contains(ngsPlatform)) {
+        else if (ngsPlatform.getSequencerType() == SequencerFlowClass.FLOW) {
 
             final byte[] bases = read.getReadBases();
 

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java

@@ -28,6 +28,7 @@ package org.broadinstitute.gatk.utils;
 import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord;
 import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
+import java.util.Arrays;
 import java.util.LinkedList;
 import java.util.List;
 
@@ -42,38 +43,48 @@ import java.util.List;
 public enum NGSPlatform {
     // note the order of elements here determines the order of matching operations, and therefore the
     // efficiency of getting a NGSPlatform from a string.
-    ILLUMINA("ILLUMINA", "SLX", "SOLEXA"),
+    ILLUMINA(SequencerFlowClass.DISCRETE, "ILLUMINA", "SLX", "SOLEXA"),
-    SOLID("SOLID"),
+    SOLID(SequencerFlowClass.DISCRETE, "SOLID"),
-    LS454("454"),
+    LS454(SequencerFlowClass.FLOW, "454", "LS454"),
-    COMPLETE_GENOMICS("COMPLETE"),
+    COMPLETE_GENOMICS(SequencerFlowClass.DISCRETE, "COMPLETE"),
-    PACBIO("PACBIO"),
+    PACBIO(SequencerFlowClass.DISCRETE, "PACBIO"),
-    ION_TORRENT("IONTORRENT"),
+    ION_TORRENT(SequencerFlowClass.FLOW, "IONTORRENT"),
-    CAPILLARY("CAPILLARY"),
+    CAPILLARY(SequencerFlowClass.OTHER, "CAPILLARY"),
-    HELICOS("HELICOS"),
+    HELICOS(SequencerFlowClass.OTHER, "HELICOS"),
-    UNKNOWN("UNKNOWN");
+    UNKNOWN(SequencerFlowClass.OTHER, "UNKNOWN");
 
     /**
      * Array of the prefix names in a BAM file for each of the platforms.
      */
     protected final String[] BAM_PL_NAMES;
+    protected final SequencerFlowClass sequencerType;
 
-    NGSPlatform(final String... BAM_PL_NAMES) {
+    NGSPlatform(final SequencerFlowClass type, final String... BAM_PL_NAMES) {
         if ( BAM_PL_NAMES.length == 0 ) throw new IllegalStateException("Platforms must have at least one name");
 
         for ( int i = 0; i < BAM_PL_NAMES.length; i++ )
             BAM_PL_NAMES[i] = BAM_PL_NAMES[i].toUpperCase();
 
         this.BAM_PL_NAMES = BAM_PL_NAMES;
+        this.sequencerType = type;
     }
 
     /**
      * Returns a representative PL string for this platform
-     * @return
+     * @return a representative PL string
      */
     public final String getDefaultPlatform() {
         return BAM_PL_NAMES[0];
     }
 
+    /**
+     * The broad "type" of sequencer this platform represents (discrete or flow)
+     * @return a SequencerFlowClass
+     */
+    public final SequencerFlowClass getSequencerType() {
+        return sequencerType;
+    }
+
     /**
      * Convenience get -- get the NGSPlatform from a GATKSAMRecord.
      *
@@ -126,10 +137,9 @@ public enum NGSPlatform {
      * @return the list of platform names
      */
     public static String knownPlatformsString() {
-        final List<String> names = new LinkedList<String>();
+        final List<String> names = new LinkedList<>();
         for ( final NGSPlatform pl : values() ) {
-            for ( final String name : pl.BAM_PL_NAMES )
+            names.addAll(Arrays.asList(pl.BAM_PL_NAMES));
-                names.add(name);
         }
         return Utils.join(",", names);
     }

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequencerFlowClass.java

@@ -0,0 +1,38 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.utils;
+
+/**
+ * In broad terms, each sequencing platform can be classified by whether it flows nucleotides in some order
+ * such that homopolymers get sequenced in a single event (ie 454 or Ion) or it reads each position in the
+ * sequence one at a time, regardless of base composition (Illumina or Solid).  This information is primarily
+ * useful in the BQSR process
+ */
+public enum SequencerFlowClass {
+    DISCRETE,
+    FLOW,
+    OTHER //Catch-all for unknown platforms, as well as relics that GATK doesn't handle well (Capillary, Helicos)
+}