A canonical set of NGS platforms as enums with convenient manipulation methods

public/java/src/org/broadinstitute/sting/utils/NGSPlatform.java

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+/*
+ * Copyright (c) 2011, 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.sting.utils;
+
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
+
+/**
+ * A canonical, master list of the standard NGS platforms.  These values
+ * can be obtained (efficiently) from a GATKSamRecord object with the
+ * getNGSPlatform method.
+ *
+ * @author Mark DePristo
+ * @since 2011
+ */
+public enum NGSPlatform {
+    ILLUMINA("ILLUMINA", "SLX", "SOLEXA"),
+    SOLID("SOLID"),
+    LS454("454"),
+    COMPLETE_GENOMICS("COMPLETE"),
+    PACBIO("PACBIO"),
+    ION_TORRENT("IONTORRENT"),
+    UNKNOWN("UNKNOWN");
+
+    /**
+     * Array of the prefix names in a BAM file for each of the platforms.
+     */
+    private final String[] BAM_PL_NAMES;
+
+    NGSPlatform(final String... BAM_PL_NAMES) {
+        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;
+    }
+
+    /**
+     * Returns a representative PL string for this platform
+     * @return
+     */
+    public final String getDefaultPlatform() {
+        return BAM_PL_NAMES[0];
+    }
+
+    /**
+     * Convenience constructor -- calculates the NGSPlatfrom from a SAMRecord.
+     * Note you should not use this function if you have a GATKSamRecord -- use the
+     * accessor method instead.
+     *
+     * @param read
+     * @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match
+     */
+    public static final NGSPlatform fromRead(SAMRecord read) {
+        return fromReadGroup(read.getReadGroup());
+    }
+
+    /**
+     * Returns the NGSPlatform corresponding to the PL tag in the read group
+     * @param rg
+     * @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match
+     */
+    public static final NGSPlatform fromReadGroup(SAMReadGroupRecord rg) {
+        return fromReadGroupPL(rg.getPlatform());
+    }
+
+    /**
+     * Returns the NGSPlatform corresponding to the PL tag in the read group
+     * @param plFromRG -- the PL field (or equivalent) in a ReadGroup object
+     * @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match
+     */
+    public static final NGSPlatform fromReadGroupPL(final String plFromRG) {
+        if ( plFromRG == null ) return UNKNOWN;
+
+        // todo -- algorithm could be implemented more efficiently, as the list of all
+        // todo -- names is known upfront, so a decision tree could be used to identify
+        // todo -- a prefix common to PL
+        final String pl = plFromRG.toUpperCase();
+        for ( final NGSPlatform ngsPlatform : NGSPlatform.values() ) {
+            for ( final String bamPLName : ngsPlatform.BAM_PL_NAMES ) {
+                if ( pl.contains(bamPLName) )
+                    return ngsPlatform;
+            }
+        }
+
+        return UNKNOWN;
+    }
+}