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Merge pull request #24 from broadinstitute/md_ngsplatform_unittests 

Expand NGSPlatform to meet SAM 1.4 spec, with full unit tests
This commit is contained in:
MauricioCarneiro 2013-02-09 09:27:03 -08:00
parent 7dbdc4ea6a b127fc6a1a
commit 3ff10ab277
2 changed files with 188 additions and 10 deletions
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31
public/java/src/org/broadinstitute/sting/utils/NGSPlatform.java
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@ -25,6 +25,7 @@
package org.broadinstitute.sting.utils;
import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/**
@ -36,22 +37,29 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
* @since 2011
*/
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"),
SOLID("SOLID"),
LS454("454"),
COMPLETE_GENOMICS("COMPLETE"),
PACBIO("PACBIO"),
ION_TORRENT("IONTORRENT"),
CAPILLARY("CAPILLARY"),
HELICOS("HELICOS"),
UNKNOWN("UNKNOWN");
/**
* Array of the prefix names in a BAM file for each of the platforms.
*/
private final String[] BAM_PL_NAMES;
protected final String[] BAM_PL_NAMES;
NGSPlatform(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;
}
@ -64,21 +72,24 @@ public enum NGSPlatform {
}
/**
* Convenience get -- get the NGSPlatfrom from a SAMRecord.
* Convenience get -- get the NGSPlatform from a GATKSAMRecord.
*
* Just gets the platform from the GATKReadGroupRecord associated with this read.
*
* @param read a GATKSAMRecord
* @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match
* @param read a non-null GATKSAMRecord
* @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match,
* if there is no read group for read, or there's no PL field for the read group
*/
public static NGSPlatform fromRead(GATKSAMRecord read) {
return read.getReadGroup().getNGSPlatform();
public static NGSPlatform fromRead(final GATKSAMRecord read) {
if ( read == null ) throw new IllegalArgumentException("read cannot be null");
final GATKSAMReadGroupRecord rg = read.getReadGroup();
return rg == null ? UNKNOWN : rg.getNGSPlatform();
}
/**
* 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, or UNKNOWN if there was no match
* @param plFromRG -- the PL field (or equivalent) in a ReadGroup object. Can be null => UNKNOWN
* @return an NGSPlatform object matching the PL field of the header, or UNKNOWN if there was no match or plFromRG is null
*/
public static NGSPlatform fromReadGroupPL(final String plFromRG) {
if ( plFromRG == null ) return UNKNOWN;
@ -100,10 +111,10 @@ public enum NGSPlatform {
/**
* checks whether or not the requested platform is listed in the set (and is not unknown)
*
* @param platform the read group string that describes the platform used
* @param platform the read group string that describes the platform used. can be null
* @return true if the platform is known (i.e. it's in the list and is not UNKNOWN)
*/
public static final boolean isKnown(final String platform) {
public static boolean isKnown(final String platform) {
return fromReadGroupPL(platform) != UNKNOWN;
}
}

167
public/java/test/org/broadinstitute/sting/utils/NGSPlatformUnitTest.java 100644
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@ -0,0 +1,167 @@
/*
* 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.sting.utils;
// the imports for unit testing.
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public class NGSPlatformUnitTest extends BaseTest {
// example genome loc parser for this test, can be deleted if you don't use the reference
private GenomeLocParser genomeLocParser;
// example fasta index file, can be deleted if you don't use the reference
private IndexedFastaSequenceFile seq;
@BeforeClass
public void setup() throws FileNotFoundException {
// sequence
seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
genomeLocParser = new GenomeLocParser(seq);
}
@DataProvider(name = "TestPrimary")
public Object[][] makeTestPrimary() {
List<Object[]> tests = new ArrayList<Object[]>();
for ( final NGSPlatform pl : NGSPlatform.values() ) {
tests.add(new Object[]{pl, pl.BAM_PL_NAMES[0]});
}
return tests.toArray(new Object[][]{});
}
@Test(dataProvider = "TestPrimary")
public void testPrimary(final NGSPlatform pl, final String expectedPrimaryName) {
Assert.assertEquals(pl.getDefaultPlatform(), expectedPrimaryName, "Failed primary test for " + pl);
}
// make sure common names in BAMs are found
@DataProvider(name = "TestMappings")
public Object[][] makeTestMappings() {
List<Object[]> tests = new ArrayList<Object[]>();
final Map<String, NGSPlatform> expected = new HashMap<String, NGSPlatform>();
// VALID VALUES ACCORDING TO SAM SPEC: https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CC8QFjAA&url=http%3A%2F%2Fsamtools.sourceforge.net%2FSAM1.pdf&ei=Dm8WUbXAEsi10QHYqoDwDQ&usg=AFQjCNFkMtvEi6LeiKgpxQGtHTlqWKw2yw&bvm=bv.42080656,d.dmQ
expected.put("CAPILLARY", NGSPlatform.CAPILLARY);
expected.put("LS454", NGSPlatform.LS454);
expected.put("ILLUMINA", NGSPlatform.ILLUMINA);
expected.put("SOLID", NGSPlatform.SOLID);
expected.put("HELICOS", NGSPlatform.HELICOS);
expected.put("IONTORRENT", NGSPlatform.ION_TORRENT);
expected.put("PACBIO", NGSPlatform.PACBIO);
// other commonly seen values out in the wild
expected.put("SLX", NGSPlatform.ILLUMINA);
expected.put("SOLEXA", NGSPlatform.ILLUMINA);
expected.put("454", NGSPlatform.LS454);
expected.put("COMPLETE", NGSPlatform.COMPLETE_GENOMICS);
// unknown platforms should map to unknown
expected.put("MARKS_GENOMICS_TECH", NGSPlatform.UNKNOWN);
expected.put("RANDOM_PL_VALUE", NGSPlatform.UNKNOWN);
// critical -- a null platform maps to unknown
expected.put(null, NGSPlatform.UNKNOWN);
for ( final Map.Entry<String,NGSPlatform> one : expected.entrySet() ) {
tests.add(new Object[]{one.getKey(), one.getValue()});
if ( one.getKey() != null ) {
// make sure we're case insensitive
tests.add(new Object[]{one.getKey().toLowerCase(), one.getValue()});
tests.add(new Object[]{one.getKey().toUpperCase(), one.getValue()});
// make sure appending GENOMICS works (required for COMPLETE mapping
tests.add(new Object[]{one.getKey() + " GENOMICS", one.getValue()});
// make sure that random junk works correctly
tests.add(new Object[]{one.getKey() + " asdfa", one.getValue()});
}
}
return tests.toArray(new Object[][]{});
}
@Test(dataProvider = "TestMappings")
public void testMappings(final String plField, final NGSPlatform expected) {
Assert.assertEquals(NGSPlatform.fromReadGroupPL(plField), expected, "Failed primary test for " + plField + " mapping to " + expected);
}
@Test(dataProvider = "TestMappings")
public void testKnown(final String plField, final NGSPlatform expected) {
Assert.assertEquals(NGSPlatform.isKnown(plField), expected != NGSPlatform.UNKNOWN, "Failed isKnown test for " + plField + " mapping to " + expected);
}
/**
* A unit test that creates an artificial read for testing some code that uses reads
*/
@Test(dataProvider = "TestMappings")
public void testPLFromReadWithRG(final String plField, final NGSPlatform expected) {
final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
final String rgID = "ID";
final SAMReadGroupRecord rg = new SAMReadGroupRecord(rgID);
if ( plField != null )
rg.setPlatform(plField);
header.addReadGroup(rg);
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 10);
read.setAttribute("RG", rgID);
Assert.assertEquals(NGSPlatform.fromRead(read), expected);
}
@Test()
public void testPLFromReadWithRGButNoPL() {
final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
final String rgID = "ID";
final SAMReadGroupRecord rg = new SAMReadGroupRecord(rgID);
header.addReadGroup(rg);
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 10);
read.setAttribute("RG", rgID);
Assert.assertEquals(NGSPlatform.fromRead(read), NGSPlatform.UNKNOWN);
}
@Test
public void testReadWithoutRG() {
final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 10);
Assert.assertEquals(NGSPlatform.fromRead(read), NGSPlatform.UNKNOWN);
}
}