/* * 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 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 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 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 findDisequalCommonContigs(Set 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 commonContigs, SAMSequenceDictionary dict1, SAMSequenceDictionary dict2) { List list1 = sortSequenceListByIndex(getSequencesOfName(commonContigs, dict1)); List 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 getSequencesOfName(Set commonContigs, SAMSequenceDictionary dict) { List l = new ArrayList(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 { 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 sortSequenceListByIndex(List 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 getCommonContigsByName(SAMSequenceDictionary dict1, SAMSequenceDictionary dict2) { Set intersectingSequenceNames = getContigNames(dict1); intersectingSequenceNames.retainAll(getContigNames(dict2)); return intersectingSequenceNames; } public static Set getContigNames(SAMSequenceDictionary dict) { Set contigNames = new HashSet((int)(dict.size() / 0.75f) + 1, 0.75f); for (SAMSequenceRecord dictionaryEntry : dict.getSequences()) contigNames.add(dictionaryEntry.getSequenceName()); return contigNames; } }