From 45ee380541f8512665f0452a96fb3cb5b83868a0 Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Thu, 22 Sep 2016 10:42:56 -0400 Subject: [PATCH] - responding to review comments --- .../htsjdk/samtools/SAMSequenceDictionary.java | 100 +++++++++------------ .../htsjdk/samtools/SAMSequenceDictionaryTest.java | 8 +- 2 files changed, 49 insertions(+), 59 deletions(-) diff --git a/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java b/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java index 14cc52321..b7744d796 100644 --- a/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java +++ b/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java @@ -29,13 +29,15 @@ import java.math.BigInteger; import java.security.MessageDigest; 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.UNKNOWN_SEQUENCE_LENGTH; +import static htsjdk.samtools.SAMSequenceRecord.*; +import static java.util.stream.Collectors.toList; /** * Collection of SAMSequenceRecords. @@ -279,87 +281,73 @@ public String toString() { * 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.) + * 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. Typical values will be MD, and LN + * @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) { - if(dict1.getSequences().size()!=dict2.getSequences().size()) { + // 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 number of sequences in them. Found %d and %d sequences", - dict1.getSequences().size(), dict2.getSequences().size())); + "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 (final SAMSequenceRecord sequence : dict1.getSequences()) { - final SAMSequenceRecord mergedSequence = new SAMSequenceRecord(sequence.getSequenceName(), - UNKNOWN_SEQUENCE_LENGTH); - finalDict.addSequence(mergedSequence); - final int sequenceIndex = sequence.getSequenceIndex(); - if (!dict2.getSequence(sequenceIndex).getSequenceName().equals(sequence.getSequenceName())) { - throw new IllegalArgumentException(String.format("Non-equal sequence names (%s and %s) at index %d in " + - "the dictionaries.", - sequence.getSequenceName(), dict2.getSequence(sequenceIndex).getSequenceName(), sequenceIndex)); - } + for (int sequenceIndex = 0; sequenceIndex < dict1.getSequences().size(); sequenceIndex++) { + final SAMSequenceRecord s1 = dict1.getSequence(sequenceIndex); + final SAMSequenceRecord s2 = dict2.getSequence(sequenceIndex); - final Set allTags = new HashSet<>(dict1.getSequence(sequenceIndex).getAttributes() - .stream().map(Map.Entry::getKey).collect(Collectors.toSet())); - allTags.addAll(dict2.getSequence(sequenceIndex).getAttributes() - .stream().map(Map.Entry::getKey).collect(Collectors.toSet())); + 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 = dict1.getSequence(sequenceIndex).getAttribute(tag); - final String value2 = dict2.getSequence(sequenceIndex).getAttribute(tag); + 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)) { - final String error = String.format("Cannot merge the two dictionaries. Found sequence entry for which " + - "tag values differ: Sequence %s at tag %s has the values: %s and %s", - dict1.getSequence(sequenceIndex).getSequenceName(), - tag, - value1, - value2); - - log.error(error); - throw new IllegalArgumentException(error); + log.error("Cannot merge dictionaries. ", baseMessage); + throw new IllegalArgumentException("Cannot merge dictionaries. " + baseMessage); } else { - log.warn("Found sequence entry for which " + - "tags differ: %s and tag %s has the two values: %s and %s. Using Value %s", - dict1.getSequence(sequenceIndex).getSequenceName(), - tag, - value1, - value2, value1); + log.warn(baseMessage, " Using ", value1); } } - mergedSequence.setAttribute(tag, value1 == null ? value2 : value1); + sMerged.setAttribute(tag, value1 == null ? value2 : value1); } - final int length1 = dict1.getSequence(sequenceIndex).getSequenceLength(); - final int length2 = dict2.getSequence(sequenceIndex).getSequenceLength(); + final int length1 = s1.getSequenceLength(); + final int length2 = s2.getSequenceLength(); if (length1 != UNKNOWN_SEQUENCE_LENGTH && length2 != UNKNOWN_SEQUENCE_LENGTH && length1 != length2) { - if (tagsToMatch.contains(SAMSequenceRecord.SEQUENCE_LENGTH_TAG)) { - final String error = String.format("Cannot merge the two dictionaries. Found sequence entry for which " + - "lengths differ: %s has lengths %s and %s", - dict1.getSequence(sequenceIndex).getSequenceName(), - length1, length2); - - log.error(error); - throw new IllegalArgumentException(error); - } else { - log.warn("Found sequence entry for which " + - "lengths differ: Sequence %s has lengths %s and %s. Using Value %s", - dict1.getSequence(sequenceIndex).getSequenceName(), - length1, length2, length1); - } + 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)); } - mergedSequence.setSequenceLength(length1 == UNKNOWN_SEQUENCE_LENGTH ? length2 : length1); + 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 a7d369d48..0b1a50780 100644 --- a/src/test/java/htsjdk/samtools/SAMSequenceDictionaryTest.java +++ b/src/test/java/htsjdk/samtools/SAMSequenceDictionaryTest.java @@ -32,8 +32,10 @@ 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; @@ -130,10 +132,10 @@ public void testMergeDictionaries(final SAMSequenceRecord rec1, final SAMSequenc try { SAMSequenceDictionary.mergeDictionaries(dict1, dict2, SAMSequenceDictionary.DEFAULT_DICTIONARY_EQUAL_TAG); } catch (final IllegalArgumentException e) { - if (!canMerge){ + if (canMerge) { + throw new Exception("Expected to be able to merge dictionaries, but wasn't:" , e); + } else { throw e; - } else{ - throw new Exception("Expected to be able to merge dictionaries, but wasn't"); } } if (canMerge){