Examples of htsjdk.samtools.SAMSequenceRecord

htsjdk.samtools.SAMSequenceRecord

    }


    private GenomeLocParser createGenomeLocParser() {
        SAMSequenceDictionary dict = new SAMSequenceDictionary();
        for (Chromosome chr : GenomeManager.getInstance().getCurrentGenome().getChromosomes()) {
            dict.addSequence(new SAMSequenceRecord(chromoNameToStandard(chr.getName()), chr.getLength()));
        }
        return new GenomeLocParser(dict);
    }

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        return haplotypeList;
    }




    protected SAMSequenceDictionary artificialSAMSequenceDictionary() {
        return new SAMSequenceDictionary(Collections.singletonList(new SAMSequenceRecord("00",reference.length())));
    }

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            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

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     * @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;

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     */
    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;
        }
    }

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    private static boolean commonContigsAreInSameRelativeOrder(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;
    }

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     * @return true if the contigs common to dict1 and dict2 occur at the same indices in both dictionaries,
     *         otherwise false
     */
    private static boolean commonContigsAreAtSameIndices( final Set<String> commonContigs, final SAMSequenceDictionary dict1, final SAMSequenceDictionary dict2 ) {
        for ( String commonContig : commonContigs ) {
            SAMSequenceRecord dict1Record = dict1.getSequence(commonContig);
            SAMSequenceRecord dict2Record = dict2.getSequence(commonContig);


            // Each common contig must have the same index in both dictionaries
            if ( dict1Record.getSequenceIndex() != dict2Record.getSequenceIndex() ) {
                return false;
            }
        }


        return true;

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    private BAMScheduleEntry getNextOverlappingBAMScheduleEntry(final GenomeLoc currentLocus) {
        // Make sure that we consult the BAM header to ensure that we're using the correct contig index for this contig name.
        // This will ensure that if the two sets of contigs don't quite match (b36 male vs female ref, hg19 Epstein-Barr), then
        // we'll be using the correct contig index for the BAMs.
        // TODO: Warning: assumes all BAMs use the same sequence dictionary!  Get around this with contig aliasing.
        SAMSequenceRecord currentContigSequenceRecord = dataSource.getHeader().getSequence(currentLocus.getContig());
        if ( currentContigSequenceRecord == null ) {
            throw new UserException(String.format("Contig %s not present in sequence dictionary for merged BAM header: %s",
                                                  currentLocus.getContig(),
                                                  ReadUtils.prettyPrintSequenceRecords(dataSource.getHeader().getSequenceDictionary())));
        }


        final int currentContigIndex = currentContigSequenceRecord.getSequenceIndex();


        // Stale reference sequence or first invocation.  (Re)create the binTreeIterator.
        if(lastReferenceSequenceLoaded == null || lastReferenceSequenceLoaded != currentContigIndex) {
            if(bamScheduleIterator != null)
                bamScheduleIterator.close();

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     */
    public static SAMSequenceDictionary getSequenceDictionaryFromProperties(Index index) {
        SAMSequenceDictionary dict = new SAMSequenceDictionary();
        for (Map.Entry<String,String> entry : index.getProperties().entrySet()) {
            if (entry.getKey().startsWith(SequenceDictionaryPropertyPredicate))
                dict.addSequence(new SAMSequenceRecord(entry.getKey().substring(SequenceDictionaryPropertyPredicate.length() , entry.getKey().length()),
                        Integer.valueOf(entry.getValue())));
        }
        return dict;
    }

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        final List<String> seqNames = index.getSequenceNames();
        if (seqNames == null) {
            return dict;
        }
        for (final String name : seqNames) {
            SAMSequenceRecord seq = new SAMSequenceRecord(name, 0);
            dict.addSequence(seq);
        }
        return dict;
    }

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