diff --git a/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java b/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java index 2b8d18a31..b7744d796 100644 --- a/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java +++ b/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java @@ -23,20 +23,22 @@ */ package htsjdk.samtools; +import htsjdk.samtools.util.Log; + import java.io.Serializable; import java.math.BigInteger; import java.security.MessageDigest; -import java.util.ArrayList; -import java.util.Collections; -import java.util.HashMap; -import java.util.Iterator; -import java.util.List; -import java.util.Map; +import java.util.*; +import java.util.stream.Collector; +import java.util.stream.Collectors; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlTransient; +import static htsjdk.samtools.SAMSequenceRecord.*; +import static java.util.stream.Collectors.toList; + /** * Collection of SAMSequenceRecords. */ @@ -64,6 +66,8 @@ public SAMSequenceDictionary(final List list) { return Collections.unmodifiableList(mSequences); } + private static Log log = Log.getInstance(SAMSequenceDictionary.class); + public SAMSequenceRecord getSequence(final String name) { return mSequenceMap.get(name); } @@ -135,7 +139,7 @@ public long getReferenceLength() { } return len; } - + /** * @return true is the dictionary is empty */ @@ -146,7 +150,7 @@ public boolean isEmpty() { private static String DICT_MISMATCH_TEMPLATE = "SAM dictionaries are not the same: %s."; /** * Non-comprehensive {@link #equals(Object)}-assertion: instead of calling {@link SAMSequenceRecord#equals(Object)} on constituent - * {@link SAMSequenceRecord}s in this dictionary against its pair in the target dictionary, in order, call + * {@link SAMSequenceRecord}s in this dictionary against its pair in the target dictionary, in order, call * {@link SAMSequenceRecord#isSameSequence(SAMSequenceRecord)}. * Aliases are ignored. * @@ -154,7 +158,7 @@ public boolean isEmpty() { */ public void assertSameDictionary(final SAMSequenceDictionary that) { if (this == that) return; - + final Iterator thatSequences = that.mSequences.iterator(); for (final SAMSequenceRecord thisSequence : mSequences) { if (!thatSequences.hasNext()) @@ -189,7 +193,7 @@ public boolean equals(Object o) { * alternate names fo a given contig. e.g: * 1,chr1,chr01,01,CM000663,NC_000001.10 e.g: * MT,chrM - * + * * @param originalName * existing contig name * @param altName @@ -219,11 +223,11 @@ public SAMSequenceRecord addSequenceAlias(final String originalName, /** * return a MD5 sum for ths dictionary, the checksum is re-computed each * time this method is called. - * + * * 
      * md5( (seq1.md5_if_available) + ' '+(seq2.name+seq2.length) + ' '+...)
      *
- * + * * @return a MD5 checksum for this dictionary or the empty string if it is * empty */ @@ -266,5 +270,86 @@ public String toString() { " length:"+ getReferenceLength()+" "+ " md5:"+md5()+")"; } + + public static final List DEFAULT_DICTIONARY_EQUAL_TAG = Arrays.asList( + SAMSequenceRecord.MD5_TAG, + SAMSequenceRecord.SEQUENCE_LENGTH_TAG); + + /** + * Will merge dictionaryTags from two dictionaries into one focusing on merging the tags rather than the sequences. + * + * Requires that dictionaries have the same SAMSequence records in the same order. + * For each sequenceIndex, the union of the tags from both sequences will be added to the new sequence, mismatching + * values (for tags that are in both) will generate a warning, and the value from dict1 will be used. + * For tags that are in tagsToEquate an unequal value will generate an error (an IllegalArgumentException will + * be thrown.) tagsToEquate must include LN and MD. + * + * @param dict1 first dictionary + * @param dict2 first dictionary + * @param tagsToMatch list of tags that must be equal if present in both sequence. Must contain MD, and LN + * @return dictionary consisting of the same sequences as the two inputs with the merged values of tags. + */ + static public SAMSequenceDictionary mergeDictionaries(final SAMSequenceDictionary dict1, + final SAMSequenceDictionary dict2, + final List tagsToMatch) { + + // We require MD and LN to match. + if (!tagsToMatch.contains(MD5_TAG) || !tagsToMatch.contains(SEQUENCE_LENGTH_TAG)) { + throw new IllegalArgumentException("Both " + MD5_TAG + " and " + SEQUENCE_LENGTH_TAG + " must be matched " + + "when merging dictionaries. Found: " + String.join(",", tagsToMatch)); + } + + if (!dict1.getSequences().stream().map(SAMSequenceRecord::getSequenceName).collect(Collectors.toList()).equals( + dict2.getSequences().stream().map(SAMSequenceRecord::getSequenceName).collect(Collectors.toList()))) { + + throw new IllegalArgumentException(String.format("Do not use this function to merge dictionaries with " + + "different sequences in them. Sequences must be in the same order as well. Found [%s] and [%s].", + String.join(", ", dict1.getSequences().stream().map(SAMSequenceRecord::getSequenceName).collect(toList())), + String.join(", ", dict2.getSequences().stream().map(SAMSequenceRecord::getSequenceName).collect(toList())))); + } + + final SAMSequenceDictionary finalDict = new SAMSequenceDictionary(); + for (int sequenceIndex = 0; sequenceIndex < dict1.getSequences().size(); sequenceIndex++) { + final SAMSequenceRecord s1 = dict1.getSequence(sequenceIndex); + final SAMSequenceRecord s2 = dict2.getSequence(sequenceIndex); + + final String sName = s1.getSequenceName(); + final SAMSequenceRecord sMerged = new SAMSequenceRecord(sName, UNKNOWN_SEQUENCE_LENGTH); + finalDict.addSequence(sMerged); + + final Set allTags = new HashSet<>(); + s1.getAttributes().stream().forEach(a -> allTags.add(a.getKey())); + s2.getAttributes().stream().forEach(a -> allTags.add(a.getKey())); + + for (final String tag : allTags) { + final String value1 = s1.getAttribute(tag); + final String value2 = s2.getAttribute(tag); + + if (value1 != null && value2 != null && !value1.equals(value2)) { + String baseMessage = String.format("Found sequence entry for which " + + "tags differ: %s and tag %s has the two values: %s and %s.", + sName, tag, value1, value2); + + if (tagsToMatch.contains(tag)) { + log.error("Cannot merge dictionaries. ", baseMessage); + throw new IllegalArgumentException("Cannot merge dictionaries. " + baseMessage); + } else { + log.warn(baseMessage, " Using ", value1); + } + } + sMerged.setAttribute(tag, value1 == null ? value2 : value1); + } + + final int length1 = s1.getSequenceLength(); + final int length2 = s2.getSequenceLength(); + + if (length1 != UNKNOWN_SEQUENCE_LENGTH && length2 != UNKNOWN_SEQUENCE_LENGTH && length1 != length2) { + throw new IllegalArgumentException(String.format("Cannot merge the two dictionaries. " + + "Found sequence entry for which " + "lengths differ: %s has lengths %s and %s", sName, length1, length2)); + } + sMerged.setSequenceLength(length1 == UNKNOWN_SEQUENCE_LENGTH ? length2 : length1); + } + return finalDict; + } } diff --git a/src/test/java/htsjdk/samtools/SAMSequenceDictionaryTest.java b/src/test/java/htsjdk/samtools/SAMSequenceDictionaryTest.java index 89e1b35fb..0b1a50780 100644 --- a/src/test/java/htsjdk/samtools/SAMSequenceDictionaryTest.java +++ b/src/test/java/htsjdk/samtools/SAMSequenceDictionaryTest.java @@ -27,11 +27,15 @@ package htsjdk.samtools; import org.testng.Assert; +import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.io.StringReader; import java.io.StringWriter; +import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; +import java.util.List; import javax.xml.bind.JAXBContext; import javax.xml.bind.JAXBException; @@ -89,4 +93,55 @@ public void testXmlSeralization() throws JAXBException { Assert.assertEquals(dict1, dict2); } + @DataProvider(name="testMergeDictionariesData") + public Object[][] testMergeDictionariesData(){ + + final SAMSequenceRecord rec1, rec2, rec3, rec4, rec5; + rec1 = new SAMSequenceRecord("chr1", 100); + rec2 = new SAMSequenceRecord("chr1", 101); + rec2.setMd5("dummy"); + rec3 = new SAMSequenceRecord("chr1", SAMSequenceRecord.UNKNOWN_SEQUENCE_LENGTH); + rec3.setMd5("dummy2"); + + rec4 = new SAMSequenceRecord("chr1", 100); + rec4.setAttribute(SAMSequenceRecord.URI_TAG,"file://some/file/name.ok"); + + rec5 = new SAMSequenceRecord("chr2", 200); + rec4.setAttribute(SAMSequenceRecord.URI_TAG,"file://some/file/name.ok"); + + return new Object[][]{ + new Object[]{rec1, rec1, true}, + new Object[]{rec2, rec2, true}, + new Object[]{rec3, rec3, true}, + new Object[]{rec4, rec4, true}, + new Object[]{rec1, rec2, false},//since 100 != 101 in Length + new Object[]{rec1, rec3, true}, + new Object[]{rec1, rec4, true}, + new Object[]{rec2, rec3, false}, // since MD5 is not equal + new Object[]{rec2, rec4, false}, //length differs + new Object[]{rec3, rec4, true}, + new Object[]{rec4, rec5, false}, // different name + }; + } + + @Test(dataProvider = "testMergeDictionariesData", expectedExceptions = IllegalArgumentException.class) + public void testMergeDictionaries(final SAMSequenceRecord rec1, final SAMSequenceRecord rec2, boolean canMerge) throws Exception { + final SAMSequenceDictionary dict1 = new SAMSequenceDictionary(Collections.singletonList(rec1)); + final SAMSequenceDictionary dict2 = new SAMSequenceDictionary(Collections.singletonList(rec2)); + + try { + SAMSequenceDictionary.mergeDictionaries(dict1, dict2, SAMSequenceDictionary.DEFAULT_DICTIONARY_EQUAL_TAG); + } catch (final IllegalArgumentException e) { + if (canMerge) { + throw new Exception("Expected to be able to merge dictionaries, but wasn't:" , e); + } else { + throw e; + } + } + if (canMerge){ + throw new IllegalArgumentException("Expected to be able to merge dictionaries, and was indeed able to do so."); + } else { + throw new Exception("Expected to not be able to merge dictionaries, but was able"); + } + } }