public static String prettyPrintSequenceRecords(final SAMSequenceDictionary sequenceDictionary) {
final String[] sequenceRecordNames = new String[sequenceDictionary.size()];
int sequenceRecordIndex = 0;
for (final SAMSequenceRecord sequenceRecord : sequenceDictionary.getSequences()) {
sequenceRecordNames[sequenceRecordIndex++] = sequenceRecord.getSequenceName();
}
return Arrays.deepToString(sequenceRecordNames);
}
private SAMFileHeader makeHeader() {
final SAMFileHeader header = new SAMFileHeader();
final SAMSequenceDictionary dict = header.getSequenceDictionary();
dict.addSequence(new SAMSequenceRecord("chr20", 62435964));
return header;
}
private boolean isSequenceRecognized(final String sequence) {
return (sequenceDictionary.getSequence(sequence) != null);
}
@Override
public int doWork(String[] args) {
com.github.lindenb.jvarkit.util.cli.GetOpt opt =
new com.github.lindenb.jvarkit.util.cli.GetOpt();
int c;
while ((c = opt.getopt(args, getGetOptDefault() + "k:")) != -1) {
switch (c) {
case 'k':
this.ucscKnownGene = opt.getOptArg();
break;
default:
{
switch (handleOtherOptions(c, opt, null)) {
case EXIT_FAILURE:
return -1;
case EXIT_SUCCESS:
return 0;
default:
break;
}
}
}
}
VcfIterator iter = null;
BufferedReader r = null;
try {
if (opt.getOptInd() == args.length) {
info("Reading from stdin");
iter = new VcfIterator(System.in);
} else if (opt.getOptInd() + 1 == args.length) {
String uri = args[opt.getOptInd()];
info("Reading from " + uri);
iter = new VcfIterator(IOUtils.openURIForReading(uri));
} else {
error("Illegal number of arguments.");
return -1;
}
info("Reading " + this.ucscKnownGene);
SAMSequenceDictionary dict = iter.getHeader().getSequenceDictionary();
int nKG = 0;
r = IOUtils.openURIForBufferedReading(ucscKnownGene);
Pattern tab = Pattern.compile("[\t]");
String line;
while ((line = r.readLine()) != null) {
String tokens[] = tab.split(line);
KnownGene g = new KnownGene(tokens);
if (dict != null && dict.getSequence(g.getChr()) == null) continue;
List<KnownGene> kg = this.chrom2knownGenes.get(g.getChr());
if (kg == null) {
kg = new ArrayList<KnownGene>();
this.chrom2knownGenes.put(g.getChr(), kg);
}
kg.add(g);
++nKG;
}
r.close();
info("Done Reading knownGenes. N=" + nKG);
final double ticksH = (fHeight / 2.0f) * 0.6f;
final double ticksx = 20;
System.out.print(
"%!PS\n"
+ "%%Creator: Pierre Lindenbaum PhD [email protected] http://plindenbaum.blogspot.com\n"
+ "%%Title: "
+ getClass().getSimpleName()
+ "\n"
+ "%%CreationDate: "
+ new Date()
+ "\n"
+ "%%EndComments\n"
+ "%%BoundingBox: 0 0 "
+ (this.pageDef.width + margin.left + margin.right)
+ " "
+ (this.pageDef.height + margin.top + margin.bottom)
+ "\n"
+ "/Courier findfont 9 scalefont setfont\n"
+ "/circle { 10 0 360 arc} bind def\n"
+ "/ticksF {\n"
+ (-ticksH)
+ " "
+ (ticksH)
+ " rmoveto\n"
+ ticksH
+ " "
+ (-ticksH)
+ " rlineto\n"
+ (-ticksH)
+ " "
+ (-ticksH)
+ " rlineto\n"
+ ticksH
+ " "
+ ticksH
+ " rmoveto\n"
+ "} bind def\n"
+ "/ticksR {\n"
+ (ticksH)
+ " "
+ (ticksH)
+ " rmoveto\n"
+ (-ticksH)
+ " "
+ (-ticksH)
+ " rlineto\n"
+ (ticksH)
+ " "
+ (-ticksH)
+ " rlineto\n"
+ (-ticksH)
+ " "
+ (ticksH)
+ " rmoveto\n"
+ "} bind def\n"
+ "/forticksF {2 dict begin\n"
+ "/x2 exch def\n"
+ "/x1 exch def\n"
+ "0 1 x2 x1 sub "
+ ticksx
+ " div {\n"
+ "ticksF "
+ ticksx
+ " 0 rmoveto\n"
+ "}for\n"
+ "} bind def\n"
+ "/forticksR {2 dict begin\n"
+ "/x2 exch def\n"
+ "/x1 exch def\n"
+ "0 1 x2 x1 sub "
+ ticksx
+ " div {\n"
+ " ticksR "
+ ticksx
+ " 0 rmoveto\n"
+ "}for\n"
+ "} bind def\n"
+ "/box\n"
+ "{\n"
+ "4 dict begin\n"
+ "/height exch def\n"
+ "/width exch def\n"
+ "/y exch def\n"
+ "/x exch def\n"
+ "x y moveto\n"
+ "width 0 rlineto\n"
+ "0 height rlineto\n"
+ "width -1 mul 0 rlineto\n"
+ "0 height -1 mul rlineto\n"
+ "end\n"
+ "} bind def\n"
+ "/gradient\n"
+ "{\n"
+ "4 dict begin\n"
+ "/height exch def\n"
+ "/width exch def\n"
+ "/y exch def\n"
+ "/x exch def\n"
+ "/i 0 def\n"
+ "height 2 div /i exch def\n"
+ "\n"
+ "0 1 height 2 div {\n"
+ " 1 i height 2.0 div div sub setgray\n"
+ " newpath\n"
+ " x \n"
+ " y height 2 div i sub add\n"
+ " width\n"
+ " i 2 mul\n"
+ " box\n"
+ " closepath\n"
+ " fill\n"
+ " i 1 sub /i exch def\n"
+ " }for\n"
+ "newpath\n"
+ "0 setgray\n"
+ "0.4 setlinewidth\n"
+ "x y width height box\n"
+ "closepath\n"
+ "stroke\n"
+ "end\n"
+ "} bind def\n");
run(iter);
System.out.print("\n%%Trailer\n%%EOF\n");
return 0;
} catch (Exception err) {
error(err);
return -1;
} finally {
CloserUtil.close(r);
CloserUtil.close(iter);
}
}
/** Combines multiple SAM/BAM files into one. */
@Override
protected int doWork() {
boolean matchedSortOrders = true;
// read interval list if it is defined
final List<Interval> intervalList =
(INTERVALS == null ? null : IntervalList.fromFile(INTERVALS).uniqued().getIntervals());
// map reader->iterator used if INTERVALS is defined
final Map<SamReader, CloseableIterator<SAMRecord>> samReaderToIterator =
new HashMap<SamReader, CloseableIterator<SAMRecord>>(INPUT.size());
// Open the files for reading and writing
final List<SamReader> readers = new ArrayList<SamReader>();
final List<SAMFileHeader> headers = new ArrayList<SAMFileHeader>();
{
SAMSequenceDictionary dict = null; // Used to try and reduce redundant SDs in memory
for (final File inFile : INPUT) {
IOUtil.assertFileIsReadable(inFile);
final SamReader in =
SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(inFile);
if (INTERVALS != null) {
if (!in.hasIndex())
throw new PicardException(
"Merging with interval but Bam file is not indexed " + inFile);
final CloseableIterator<SAMRecord> samIterator =
new SamRecordIntervalIteratorFactory()
.makeSamRecordIntervalIterator(in, intervalList, true);
samReaderToIterator.put(in, samIterator);
}
readers.add(in);
headers.add(in.getFileHeader());
// A slightly hackish attempt to keep memory consumption down when merging multiple files
// with
// large sequence dictionaries (10,000s of sequences). If the dictionaries are identical,
// then
// replace the duplicate copies with a single dictionary to reduce the memory footprint.
if (dict == null) {
dict = in.getFileHeader().getSequenceDictionary();
} else if (dict.equals(in.getFileHeader().getSequenceDictionary())) {
in.getFileHeader().setSequenceDictionary(dict);
}
matchedSortOrders = matchedSortOrders && in.getFileHeader().getSortOrder() == SORT_ORDER;
}
}
// If all the input sort orders match the output sort order then just merge them and
// write on the fly, otherwise setup to merge and sort before writing out the final file
IOUtil.assertFileIsWritable(OUTPUT);
final boolean presorted;
final SAMFileHeader.SortOrder headerMergerSortOrder;
final boolean mergingSamRecordIteratorAssumeSorted;
if (matchedSortOrders
|| SORT_ORDER == SAMFileHeader.SortOrder.unsorted
|| ASSUME_SORTED
|| INTERVALS != null) {
log.info(
"Input files are in same order as output so sorting to temp directory is not needed.");
headerMergerSortOrder = SORT_ORDER;
mergingSamRecordIteratorAssumeSorted = ASSUME_SORTED;
presorted = true;
} else {
log.info("Sorting input files using temp directory " + TMP_DIR);
headerMergerSortOrder = SAMFileHeader.SortOrder.unsorted;
mergingSamRecordIteratorAssumeSorted = false;
presorted = false;
}
final SamFileHeaderMerger headerMerger =
new SamFileHeaderMerger(headerMergerSortOrder, headers, MERGE_SEQUENCE_DICTIONARIES);
final MergingSamRecordIterator iterator;
// no interval defined, get an iterator for the whole bam
if (intervalList == null) {
iterator =
new MergingSamRecordIterator(headerMerger, readers, mergingSamRecordIteratorAssumeSorted);
} else {
// show warning related to https://github.com/broadinstitute/picard/pull/314/files
log.info(
"Warning: merged bams from different interval lists may contain the same read in both files");
iterator = new MergingSamRecordIterator(headerMerger, samReaderToIterator, true);
}
final SAMFileHeader header = headerMerger.getMergedHeader();
for (final String comment : COMMENT) {
header.addComment(comment);
}
header.setSortOrder(SORT_ORDER);
final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
if (USE_THREADING) {
samFileWriterFactory.setUseAsyncIo(true);
}
final SAMFileWriter out = samFileWriterFactory.makeSAMOrBAMWriter(header, presorted, OUTPUT);
// Lastly loop through and write out the records
final ProgressLogger progress = new ProgressLogger(log, PROGRESS_INTERVAL);
while (iterator.hasNext()) {
final SAMRecord record = iterator.next();
out.addAlignment(record);
progress.record(record);
}
log.info("Finished reading inputs.");
for (final CloseableIterator<SAMRecord> iter : samReaderToIterator.values())
CloserUtil.close(iter);
CloserUtil.close(readers);
out.close();
return 0;
}