public static String prettyPrintSequenceRecords(SAMSequenceDictionary sequenceDictionary) {
String[] sequenceRecordNames = new String[sequenceDictionary.size()];
int sequenceRecordIndex = 0;
for (SAMSequenceRecord sequenceRecord : sequenceDictionary.getSequences())
sequenceRecordNames[sequenceRecordIndex++] = sequenceRecord.getSequenceName();
return Arrays.deepToString(sequenceRecordNames);
}
private static void setIndexSequenceDictionary(
final Index index, final SAMSequenceDictionary dict) {
for (final SAMSequenceRecord seq : dict.getSequences()) {
final String contig = SequenceDictionaryPropertyPredicate + seq.getSequenceName();
final String length = String.valueOf(seq.getSequenceLength());
index.addProperty(contig, length);
}
}
/**
* create a list of genomic locations, given a reference sequence
*
* @param dict the sequence dictionary to create a collection from
* @return the GenomeLocSet of all references sequences as GenomeLoc's
*/
public static GenomeLocSortedSet createSetFromSequenceDictionary(SAMSequenceDictionary dict) {
GenomeLocParser parser = new GenomeLocParser(dict);
GenomeLocSortedSet returnSortedSet = new GenomeLocSortedSet(parser);
for (SAMSequenceRecord record : dict.getSequences()) {
returnSortedSet.add(
parser.createGenomeLoc(record.getSequenceName(), 1, record.getSequenceLength()));
}
return returnSortedSet;
}
/**
* Throw an exception if all the "to" sequence names in the chains are not found in the given
* sequence dictionary.
*/
public void validateToSequences(final SAMSequenceDictionary sequenceDictionary) {
for (final Chain chain : chains.getAll()) {
if (sequenceDictionary.getSequence(chain.toSequenceName) == null) {
throw new PicardException(
"Sequence "
+ chain.toSequenceName
+ " from chain file is not found in sequence dictionary.");
}
}
}
// copied from LocusViewTemplate
protected GATKSAMRecord buildSAMRecord(
final String readName, final String contig, final int alignmentStart) {
GATKSAMRecord record = new GATKSAMRecord(header);
record.setReadName(readName);
record.setReferenceIndex(dictionary.getSequenceIndex(contig));
record.setAlignmentStart(alignmentStart);
record.setCigarString("1M");
record.setReadString("A");
record.setBaseQualityString("A");
record.setReadGroup(readGroup);
return record;
}
public static Interval parseOne(SAMSequenceDictionary dict, String s) {
int colon = s.indexOf(':');
if (colon < 1 || colon + 1 == s.length()) return null;
int hyphen = s.indexOf('-', colon + 1);
if (hyphen == -1) return null;
int start, end;
try {
SAMSequenceRecord ssr = null;
String chrom = s.substring(0, colon);
if (dict != null) {
ssr = dict.getSequence(chrom);
if (ssr == null) return null;
}
start = Integer.parseInt(s.substring(colon + 1, hyphen));
end = Integer.parseInt(s.substring(hyphen + 1));
if (end < start) return null;
return new Interval(s.substring(0, colon), start, end);
} catch (Exception e) {
return null;
}
}
public Datum map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
GenomeLoc cur = context.getLocation();
if (verbose && showSkipped) {
for (long i = context.getSkippedBases(); i >= 0; i--) {
SAMSequenceDictionary dictionary =
getToolkit().getReferenceDataSource().getReference().getSequenceDictionary();
SAMSequenceRecord contig = dictionary.getSequence(cur.getContig());
if (cur.getStop() < contig.getSequenceLength())
cur = getToolkit().getGenomeLocParser().incPos(cur, 1);
else
cur =
getToolkit()
.getGenomeLocParser()
.createGenomeLoc(
dictionary.getSequence(contig.getSequenceIndex() + 1).getSequenceName(),
1,
1);
out.printf("%s: skipped%n", cur);
}
}
long nRodsHere = 0;
long nTotalBases = 0;
if (ref == null) {
// we're getting the last skipped update
if (verbose)
out.printf(
"Last position was %s: skipping %d bases%n",
context.getLocation(), context.getSkippedBases());
nRodsHere = -1; // don't update this
nTotalBases = context.getSkippedBases();
} else {
Collection<RODRecordList> rods = new LinkedList<RODRecordList>();
for (RODRecordList rod : tracker.getBoundRodTracks()) {
// System.out.printf("Considering rod %s%n", rod);
if (rod.getLocation().getStart() == context.getLocation().getStart()
&& !rod.getName().equals("interval")) {
// only consider the first element
// System.out.printf("adding it%n");
rods.add(rod);
}
}
nRodsHere = rods.size();
if (nRodsHere > 0) {
if (verbose) {
List<String> names = new ArrayList<String>();
for (RODRecordList rod : rods) {
names.add(rod.getName());
}
// System.out.printf("context is %s", context.getSkippedBases());
out.printf(
"At %s: found %d rod(s) [%s] after skipping %d bases%n",
context.getLocation(), nRodsHere, Utils.join(",", names), context.getSkippedBases());
}
}
nTotalBases = context.getSkippedBases() + 1;
}
return new Datum(nRodsHere, context.getSkippedBases(), nTotalBases);
}