/** * Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error */ public static BufferedWriter openFileForBufferedWriting(final File file) { return openFileForBufferedWriting(file, false); }
/** * Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error */ public static BufferedWriter openFileForBufferedWriting(final File file) { return openFileForBufferedWriting(file, false); }
/** * Preferred over PrintStream and PrintWriter because an exception is thrown on I/O error */ public static BufferedWriter openFileForBufferedWriting(final File file) { return openFileForBufferedWriting(file, false); }
/** Method that writes out all the parameter values that were used in the design using reflection. */ void writeParametersFile(final File file) { try { final BufferedWriter out = IOUtil.openFileForBufferedWriting(file); for (final Field field : getClass().getDeclaredFields()) { if (Modifier.isPrivate(field.getModifiers())) continue; final String name = field.getName(); if (name.toUpperCase().equals(name) && !name.equals("USAGE")) { final Object value = field.get(this); if (value != null) { out.append(name); out.append("="); out.append(value.toString()); out.newLine(); } } } out.close(); } catch (Exception e) { throw new PicardException("Error writing out parameters file.", e); } }
/** Method that writes out all the parameter values that were used in the design using reflection. */ void writeParametersFile(final File file) { try { final BufferedWriter out = IOUtil.openFileForBufferedWriting(file); for (final Field field : getClass().getDeclaredFields()) { if (Modifier.isPrivate(field.getModifiers())) continue; final String name = field.getName(); if (name.toUpperCase().equals(name) && !name.equals("USAGE")) { final Object value = field.get(this); if (value != null) { out.append(name); out.append("="); out.append(value.toString()); out.newLine(); } } } out.close(); } catch (Exception e) { throw new PicardException("Error writing out parameters file.", e); } }
void writeDesignFastaFile(final File file, final IntervalList baits) { final BufferedWriter out = IOUtil.openFileForBufferedWriting(file); for (final Interval i : baits) { writeBaitFasta(out, i, false); } CloserUtil.close(out); }
void writeDesignFastaFile(final File file, final IntervalList baits) { final BufferedWriter out = IOUtil.openFileForBufferedWriting(file); for (final Interval i : baits) { writeBaitFasta(out, i, false); } CloserUtil.close(out); }
/** * Writes a set of pedigrees out to disk. */ public void write(final File file) { IOUtil.assertFileIsWritable(file); final BufferedWriter out = IOUtil.openFileForBufferedWriting(file); try { for (final PedTrio trio : values()) { out.write(trio.getFamilyId()); out.write("\t"); out.write(trio.getIndividualId()); out.write("\t"); out.write(trio.getPaternalId()); out.write("\t"); out.write(trio.getMaternalId()); out.write("\t"); out.write(String.valueOf(trio.getSex().toCode())); out.write("\t"); out.write(trio.getPhenotype().toString()); out.newLine(); } out.close(); } catch (final IOException ioe) { throw new RuntimeIOException("IOException while writing to file " + file.getAbsolutePath(), ioe); } }
/** * Writes a set of pedigrees out to disk. */ public void write(final File file) { IOUtil.assertFileIsWritable(file); final BufferedWriter out = IOUtil.openFileForBufferedWriting(file); try { for (final PedTrio trio : values()) { out.write(trio.getFamilyId()); out.write("\t"); out.write(trio.getIndividualId()); out.write("\t"); out.write(trio.getPaternalId()); out.write("\t"); out.write(trio.getMaternalId()); out.write("\t"); out.write(String.valueOf(trio.getSex().toCode())); out.write("\t"); out.write(trio.getPhenotype().toString()); out.newLine(); } out.close(); } catch (final IOException ioe) { throw new RuntimeIOException("IOException while writing to file " + file.getAbsolutePath(), ioe); } }
final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT);
/** * Write out a file of read names for debugging purposes. * * @param samOrBamFile The SAM or BAM file for which we are going to write out a file of its * containing read names */ private void writeReadsFile(final File samOrBamFile) throws IOException { final File readsFile = new File(OUTPUT.getParentFile(), IOUtil.basename(samOrBamFile) + ".reads"); IOUtil.assertFileIsWritable(readsFile); try (final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(samOrBamFile); final BufferedWriter bw = IOUtil.openFileForBufferedWriting(readsFile, false)) { for (final SAMRecord rec : reader) { bw.write(rec.toString() + "\n"); } } IOUtil.assertFileIsReadable(readsFile); }
@Override protected int doWork() { IOUtil.assertFileIsReadable(INPUT); IOUtil.assertFileIsWritable(OUTPUT); IntervalList intervals = IntervalList.fromFile(INPUT); if (SORT) intervals = intervals.sorted(); try { final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT); for (final Interval i : intervals) { final String strand = i.isNegativeStrand() ? "-" : "+"; final List<?> fields = CollectionUtil.makeList(i.getContig(), i.getStart()-1, i.getEnd(), i.getName(), SCORE, strand); out.append(fields.stream().map(String::valueOf).collect(Collectors.joining("\t"))); out.newLine(); } out.close(); } catch (IOException ioe) { throw new RuntimeIOException(ioe); } return 0; } }
try (final BufferedWriter out = IOUtil.openFileForBufferedWriting(file)) { final FormatUtil format = new FormatUtil();
/** * Write out a file of read names for debugging purposes. * * @param samOrBamFile The SAM or BAM file for which we are going to write out a file of its * containing read names */ private void writeReadsFile(final File samOrBamFile) throws IOException { final File readsFile = new File(OUTPUT.getParentFile(), IOUtil.basename(samOrBamFile) + ".reads"); IOUtil.assertFileIsWritable(readsFile); try (final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(samOrBamFile); final BufferedWriter bw = IOUtil.openFileForBufferedWriting(readsFile, false)) { for (final SAMRecord rec : reader) { bw.write(rec.toString() + "\n"); } } IOUtil.assertFileIsReadable(readsFile); }
try (final BufferedWriter out = IOUtil.openFileForBufferedWriting(file)) { final FormatUtil format = new FormatUtil();
@Override protected int doWork() { IOUtil.assertFileIsReadable(INPUT); IOUtil.assertFileIsWritable(OUTPUT); IntervalList intervals = IntervalList.fromFile(INPUT); if (SORT) intervals = intervals.sorted(); try { final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT); for (final Interval i : intervals) { final String strand = i.isNegativeStrand() ? "-" : "+"; final List<?> fields = CollectionUtil.makeList(i.getContig(), i.getStart()-1, i.getEnd(), i.getName(), SCORE, strand); out.append(fields.stream().map(String::valueOf).collect(Collectors.joining("\t"))); out.newLine(); } out.close(); } catch (IOException ioe) { throw new RuntimeIOException(ioe); } return 0; } }
public void onTraversalDone(EventPair sum) { if ( sum.left != null && sum.left.isReportableEvent() ) sum.intervals.add(sum.left.getLoc()); if ( sum.right != null && sum.right.isReportableEvent() ) sum.intervals.add(sum.right.getLoc()); if ( FilenameUtils.getExtension(out.getName()).equals("interval_list") ) { final SAMFileHeader masterSequenceDictionaryHeader = new SAMFileHeader(); masterSequenceDictionaryHeader.setSequenceDictionary(getToolkit().getMasterSequenceDictionary()); final IntervalList intervalList = new IntervalList(masterSequenceDictionaryHeader); for ( GenomeLoc loc : sum.intervals ) { intervalList.add(new Interval(loc.getContig(), loc.getStart(), loc.getStop())); } intervalList.write(out); } else { try ( BufferedWriter bufferedWriter = IOUtil.openFileForBufferedWriting(out) ) { for ( GenomeLoc loc : sum.intervals ) { bufferedWriter.write(loc.toString()); bufferedWriter.newLine(); } } catch (final IOException e) { throw new GATKException("Error writing out intervals to file: " + out.getAbsolutePath(), e); } } }
SequenceUtil.assertSequenceDictionariesEqual(intervals.getHeader().getSequenceDictionary(), ref.getSequenceDictionary()); final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT);
SequenceUtil.assertSequenceDictionariesEqual(intervals.getHeader().getSequenceDictionary(), ref.getSequenceDictionary()); final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT);
final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT); out.write(nonNbases + "\n"); out.close();