369 lines
16 KiB
Java
369 lines
16 KiB
Java
/*
|
|
* 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;
|
|
|
|
import net.sf.samtools.SAMSequenceDictionary;
|
|
import net.sf.samtools.SAMSequenceRecord;
|
|
import org.apache.log4j.Logger;
|
|
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
|
|
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
|
import org.broadinstitute.sting.utils.exceptions.UserException;
|
|
|
|
import java.util.*;
|
|
|
|
/**
|
|
* Created by IntelliJ IDEA.
|
|
* User: depristo
|
|
* Date: Sep 10, 2010
|
|
* Time: 1:56:24 PM
|
|
*
|
|
* A series of utility functions that enable the GATK to compare two sequence dictionaries -- from the reference,
|
|
* from BAMs, or from RODs -- for consistency. The system supports two basic modes: get an enum state that
|
|
* describes at a high level the consistency between two dictionaries, or a validateDictionaries that will
|
|
* blow up with a UserException if the dicts are too incompatible.
|
|
*
|
|
* Dictionaries are tested for contig name overlaps, consistency in ordering in these overlap set, and length,
|
|
* if available. Examines the Engine arguments to decided if the -U option to allow danger seq dict inconsistency
|
|
* is enabled before it blows up.
|
|
*/
|
|
public class SequenceDictionaryUtils {
|
|
//
|
|
// for detecting lexicographically sorted human references
|
|
//
|
|
|
|
private static boolean ENABLE_LEXICOGRAPHIC_REQUIREMENT_FOR_HUMAN = true;
|
|
|
|
// hg18
|
|
private static SAMSequenceRecord CHR1_HG18 = new SAMSequenceRecord("chr1", 247249719);
|
|
private static SAMSequenceRecord CHR2_HG18 = new SAMSequenceRecord("chr2", 242951149);
|
|
private static SAMSequenceRecord CHR10_HG18 = new SAMSequenceRecord("chr10", 135374737);
|
|
|
|
// hg19
|
|
private static SAMSequenceRecord CHR1_HG19 = new SAMSequenceRecord("chr1", 249250621);
|
|
private static SAMSequenceRecord CHR2_HG19 = new SAMSequenceRecord("chr2", 243199373);
|
|
private static SAMSequenceRecord CHR10_HG19 = new SAMSequenceRecord("chr10", 135534747);
|
|
|
|
public enum SequenceDictionaryCompatibility {
|
|
IDENTICAL, // the dictionaries are identical
|
|
COMMON_SUBSET, // there exists a common subset of equivalent contigs
|
|
NO_COMMON_CONTIGS, // no overlap between dictionaries
|
|
UNEQUAL_COMMON_CONTIGS, // common subset has contigs that have the same name but aren't equivalent
|
|
NON_CANONICAL_HUMAN_ORDER, // human reference detected but the order of the contigs is non-standard (lexicographic, for examine)
|
|
OUT_OF_ORDER // the two dictionaries overlap but the contigs occur out of order w.r.t each other
|
|
}
|
|
|
|
/**
|
|
* @param validationExclusion exclusions to validation
|
|
* @return Returns true if the engine is in tolerant mode and we'll let through dangerous but not fatal dictionary inconsistency
|
|
*/
|
|
public static boolean allowNonFatalIncompabilities(ValidationExclusion.TYPE validationExclusion) {
|
|
return ( validationExclusion == ValidationExclusion.TYPE.ALLOW_SEQ_DICT_INCOMPATIBILITY ||
|
|
validationExclusion == ValidationExclusion.TYPE.ALL );
|
|
}
|
|
|
|
/**
|
|
* Testings for compatbility between dict1 and dict2. If the dictionaries are incompatible, then UserExceptions are
|
|
* thrown with detailed error messages. If the engine is in permissive mode, then logger.warnings of generated instead
|
|
*
|
|
* @param logger for warnings
|
|
* @param validationExclusion exclusions to validation
|
|
* @param name1 name associated with dict1
|
|
* @param dict1 the sequence dictionary dict1
|
|
* @param name2 name associated with dict2
|
|
* @param dict2 the sequence dictionary dict2
|
|
*/
|
|
public static void validateDictionaries(Logger logger, ValidationExclusion.TYPE validationExclusion, String name1, SAMSequenceDictionary dict1, String name2, SAMSequenceDictionary dict2) {
|
|
SequenceDictionaryCompatibility type = compareDictionaries(dict1, dict2);
|
|
switch ( type ) {
|
|
case IDENTICAL:
|
|
return;
|
|
case COMMON_SUBSET:
|
|
return;
|
|
case NO_COMMON_CONTIGS:
|
|
throw new UserException.IncompatibleSequenceDictionaries("No overlapping contigs found", name1, dict1, name2, dict2);
|
|
|
|
case UNEQUAL_COMMON_CONTIGS: {
|
|
List<SAMSequenceRecord> x = findDisequalCommonContigs(getCommonContigsByName(dict1, dict2), dict1, dict2);
|
|
SAMSequenceRecord elt1 = x.get(0);
|
|
SAMSequenceRecord elt2 = x.get(1);
|
|
|
|
// todo -- replace with toString when SAMSequenceRecord has a nice toString routine
|
|
UserException ex = new UserException.IncompatibleSequenceDictionaries(String.format("Found contigs with the same name but different lengths:\n contig %s = %s / %d\n contig %s = %s / %d",
|
|
name1, elt1.getSequenceName(), elt1.getSequenceLength(),
|
|
name2, elt2.getSequenceName(), elt2.getSequenceLength()),
|
|
name1, dict1, name2, dict2);
|
|
|
|
if ( allowNonFatalIncompabilities(validationExclusion) )
|
|
logger.warn(ex.getMessage());
|
|
else
|
|
throw ex;
|
|
break;
|
|
}
|
|
|
|
case NON_CANONICAL_HUMAN_ORDER: {
|
|
UserException ex;
|
|
if ( nonCanonicalHumanContigOrder(dict1) )
|
|
ex = new UserException.LexicographicallySortedSequenceDictionary(name1, dict1);
|
|
else
|
|
ex = new UserException.LexicographicallySortedSequenceDictionary(name2, dict2);
|
|
|
|
if ( allowNonFatalIncompabilities(validationExclusion) )
|
|
logger.warn(ex.getMessage());
|
|
else
|
|
throw ex;
|
|
}
|
|
|
|
case OUT_OF_ORDER: {
|
|
UserException ex = new UserException.IncompatibleSequenceDictionaries("Order of contigs differences, which is unsafe", name1, dict1, name2, dict2);
|
|
if ( allowNonFatalIncompabilities(validationExclusion) )
|
|
logger.warn(ex.getMessage());
|
|
else
|
|
throw ex;
|
|
} break;
|
|
default:
|
|
throw new ReviewedStingException("Unexpected SequenceDictionaryComparison type: " + type);
|
|
}
|
|
}
|
|
|
|
/**
|
|
* Workhorse routine that takes two dictionaries and returns their compatibility.
|
|
*
|
|
* @param dict1
|
|
* @param dict2
|
|
* @return
|
|
*/
|
|
public static SequenceDictionaryCompatibility compareDictionaries(SAMSequenceDictionary dict1, SAMSequenceDictionary dict2) {
|
|
// If there's no overlap between reads and reference, data will be bogus. Throw an exception.
|
|
if ( nonCanonicalHumanContigOrder( dict1 ) || nonCanonicalHumanContigOrder(dict2) )
|
|
return SequenceDictionaryCompatibility.NON_CANONICAL_HUMAN_ORDER;
|
|
|
|
Set<String> commonContigs = getCommonContigsByName(dict1, dict2);
|
|
|
|
if (commonContigs.size() == 0)
|
|
return SequenceDictionaryCompatibility.NO_COMMON_CONTIGS;
|
|
else if ( ! commonContigsAreEquivalent( commonContigs, dict1, dict2 ) )
|
|
return SequenceDictionaryCompatibility.UNEQUAL_COMMON_CONTIGS;
|
|
else if ( ! commonContigsAreInOrder( commonContigs, dict1, dict2 ) )
|
|
return SequenceDictionaryCompatibility.OUT_OF_ORDER;
|
|
else if ( commonContigs.size() == dict1.size() && commonContigs.size() == dict2.size() )
|
|
return SequenceDictionaryCompatibility.IDENTICAL;
|
|
else {
|
|
return SequenceDictionaryCompatibility.COMMON_SUBSET;
|
|
}
|
|
}
|
|
|
|
/**
|
|
* Utility function that tests whether the commonContigs in both dicts are equivalent. Equivalece means
|
|
* that the seq records have the same length, if both are non-zero.
|
|
*
|
|
* @param commonContigs
|
|
* @param dict1
|
|
* @param dict2
|
|
* @return true if all of the common contigs are equivalent
|
|
*/
|
|
private static boolean commonContigsAreEquivalent(Set<String> commonContigs, SAMSequenceDictionary dict1, SAMSequenceDictionary dict2) {
|
|
return findDisequalCommonContigs(commonContigs, dict1, dict2) == null;
|
|
}
|
|
|
|
/**
|
|
* Returns a List(x,y) that contains two disequal sequence records among the common contigs in both dicts. Returns
|
|
* null if all common contigs are equivalent
|
|
*
|
|
* @param commonContigs
|
|
* @param dict1
|
|
* @param dict2
|
|
* @return
|
|
*/
|
|
private static List<SAMSequenceRecord> findDisequalCommonContigs(Set<String> commonContigs, SAMSequenceDictionary dict1, SAMSequenceDictionary dict2) {
|
|
for ( String name : commonContigs ) {
|
|
SAMSequenceRecord elt1 = dict1.getSequence(name);
|
|
SAMSequenceRecord elt2 = dict2.getSequence(name);
|
|
if ( ! SequenceRecordsAreEquivalent(elt1, elt2) )
|
|
return Arrays.asList(elt1,elt2);
|
|
}
|
|
|
|
return null;
|
|
}
|
|
|
|
/**
|
|
* Helper routine that returns two sequence records are equivalent, defined as having the same name and
|
|
* lengths, if both are non-zero
|
|
*
|
|
* @param me
|
|
* @param that
|
|
* @return
|
|
*/
|
|
private static boolean SequenceRecordsAreEquivalent(final SAMSequenceRecord me, final SAMSequenceRecord that) {
|
|
if (me == that) return true;
|
|
if (that == null) return false;
|
|
|
|
// I don't care if the indices are difference
|
|
//if (me.getSequenceIndex() != that.getSequenceIndex()) return false;
|
|
if (me.getSequenceLength() != 0 && that.getSequenceLength() != 0 && me.getSequenceLength() != that.getSequenceLength())
|
|
return false;
|
|
|
|
// todo -- reenable if we want to be really strict here
|
|
// if (me.getExtendedAttribute(SAMSequenceRecord.MD5_TAG) != null && that.getExtendedAttribute(SAMSequenceRecord.MD5_TAG) != null) {
|
|
// final BigInteger thisMd5 = new BigInteger((String)me.getExtendedAttribute(SAMSequenceRecord.MD5_TAG), 16);
|
|
// final BigInteger thatMd5 = new BigInteger((String)that.getExtendedAttribute(SAMSequenceRecord.MD5_TAG), 16);
|
|
// if (!thisMd5.equals(thatMd5)) {
|
|
// return false;
|
|
// }
|
|
// }
|
|
// else {
|
|
if (me.getSequenceName() != that.getSequenceName())
|
|
return false; // Compare using == since we intern() the Strings
|
|
// }
|
|
|
|
return true;
|
|
}
|
|
|
|
/**
|
|
* A very simple (and naive) algorithm to determine (1) if the dict is a human reference (hg18/hg19) and if it's
|
|
* lexicographically sorted. Works by matching lengths of the static chr1, chr10, and chr2, and then if these
|
|
* are all matched, requiring that the order be chr1, chr2, chr10.
|
|
*
|
|
* @param dict
|
|
* @return
|
|
*/
|
|
private static boolean nonCanonicalHumanContigOrder(SAMSequenceDictionary dict) {
|
|
if ( ! ENABLE_LEXICOGRAPHIC_REQUIREMENT_FOR_HUMAN ) // if we don't want to enable this test, just return false
|
|
return false;
|
|
|
|
SAMSequenceRecord chr1 = null, chr2 = null, chr10 = null;
|
|
|
|
for ( SAMSequenceRecord elt : dict.getSequences() ) {
|
|
if ( isHumanSeqRecord(elt, CHR1_HG18, CHR1_HG19 ) ) chr1 = elt;
|
|
if ( isHumanSeqRecord(elt, CHR2_HG18, CHR2_HG19 ) ) chr2 = elt;
|
|
if ( isHumanSeqRecord(elt, CHR10_HG18, CHR10_HG19 ) ) chr10 = elt;
|
|
}
|
|
|
|
if ( chr1 != null && chr2 != null && chr10 != null) {
|
|
// we found them all
|
|
return ! ( chr1.getSequenceIndex() < chr2.getSequenceIndex() && chr2.getSequenceIndex() < chr10.getSequenceIndex() );
|
|
} else {
|
|
return false;
|
|
}
|
|
}
|
|
|
|
/**
|
|
* Trivial helper that returns true if elt has the same length as rec1 or rec2
|
|
* @param elt record to test
|
|
* @param rec1 first record to test for length equivalence
|
|
* @param rec2 first record to test for length equivalence
|
|
* @return true if elt has the same length as either rec1 or rec2
|
|
*/
|
|
private static boolean isHumanSeqRecord(SAMSequenceRecord elt, SAMSequenceRecord rec1, SAMSequenceRecord rec2 ) {
|
|
return elt.getSequenceLength() == rec1.getSequenceLength() || elt.getSequenceLength() == rec2.getSequenceLength();
|
|
}
|
|
|
|
|
|
/**
|
|
* Returns true if the common contigs in dict1 and dict2 are in the same order. This is accomplished by getting the
|
|
* common contigs in both dictionaries, sorting these according to their indices, and the walking through
|
|
* the sorted list to ensure that each ordered contig is equivalent
|
|
*
|
|
* @param commonContigs
|
|
* @param dict1
|
|
* @param dict2
|
|
* @return
|
|
*/
|
|
public static boolean commonContigsAreInOrder(Set<String> commonContigs, SAMSequenceDictionary dict1, SAMSequenceDictionary dict2) {
|
|
List<SAMSequenceRecord> list1 = sortSequenceListByIndex(getSequencesOfName(commonContigs, dict1));
|
|
List<SAMSequenceRecord> list2 = sortSequenceListByIndex(getSequencesOfName(commonContigs, dict2));
|
|
|
|
for ( int i = 0; i < list1.size(); i++ ) {
|
|
SAMSequenceRecord elt1 = list1.get(i);
|
|
SAMSequenceRecord elt2 = list2.get(i);
|
|
if ( ! elt1.getSequenceName().equals(elt2.getSequenceName()) )
|
|
return false;
|
|
}
|
|
|
|
return true;
|
|
}
|
|
|
|
/**
|
|
* Gets the subset of SAMSequenceRecords in commonContigs in dict
|
|
*
|
|
* @param commonContigs
|
|
* @param dict
|
|
* @return
|
|
*/
|
|
private static List<SAMSequenceRecord> getSequencesOfName(Set<String> commonContigs, SAMSequenceDictionary dict) {
|
|
List<SAMSequenceRecord> l = new ArrayList<SAMSequenceRecord>(commonContigs.size());
|
|
for ( String name : commonContigs ) {
|
|
l.add(dict.getSequence(name) );
|
|
}
|
|
|
|
return l;
|
|
}
|
|
|
|
// --------------------------------------------------------------------------------------------------------------
|
|
// Utilities for comparing the order of sequence records
|
|
// --------------------------------------------------------------------------------------------------------------
|
|
|
|
/**
|
|
* Compares sequence records by their order
|
|
*/
|
|
private static class CompareSequenceRecordsByIndex implements Comparator<SAMSequenceRecord> {
|
|
public int compare(SAMSequenceRecord x, SAMSequenceRecord y) {
|
|
return Integer.valueOf(x.getSequenceIndex()).compareTo(y.getSequenceIndex());
|
|
}
|
|
}
|
|
|
|
/**
|
|
* Returns a sorted list of SAMSequenceRecords sorted by their indices. Note that the
|
|
* list is modified in place, so the returned list is == to the unsorted list.
|
|
*
|
|
* @param unsorted
|
|
* @return
|
|
*/
|
|
private static List<SAMSequenceRecord> sortSequenceListByIndex(List<SAMSequenceRecord> unsorted) {
|
|
Collections.sort(unsorted, new CompareSequenceRecordsByIndex());
|
|
return unsorted;
|
|
}
|
|
|
|
|
|
/**
|
|
* Returns the set of contig names found in both dicts.
|
|
* @param dict1
|
|
* @param dict2
|
|
* @return
|
|
*/
|
|
public static Set<String> getCommonContigsByName(SAMSequenceDictionary dict1, SAMSequenceDictionary dict2) {
|
|
Set<String> intersectingSequenceNames = getContigNames(dict1);
|
|
intersectingSequenceNames.retainAll(getContigNames(dict2));
|
|
return intersectingSequenceNames;
|
|
}
|
|
|
|
public static Set<String> getContigNames(SAMSequenceDictionary dict) {
|
|
Set<String> contigNames = new HashSet<String>((int)(dict.size() / 0.75f) + 1, 0.75f);
|
|
for (SAMSequenceRecord dictionaryEntry : dict.getSequences())
|
|
contigNames.add(dictionaryEntry.getSequenceName());
|
|
return contigNames;
|
|
}
|
|
}
|