Examples of org.broad.igv.sam.Alignment

org.broad.igv.sam.Alignment
@author jrobinso

        String chr = "gi|66043271|ref|NC_007005.1|";
        int start = 800;
        int end = 900;
        CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, false);
        while (iter.hasNext()) {
            Alignment a = iter.next();
            System.out.println(a);
        }
    }

View Full Code Here

            return iteratorQueue.size() > 0;
        }


        public Alignment next() {
            RecordIterWrapper wrapper = iteratorQueue.poll();
            Alignment next = wrapper.advance();
            if (wrapper.hasNext()) {
                iteratorQueue.add(wrapper);
            }
            return next;
        }

View Full Code Here

                this.iterator = iter;
                nextRecord = (iterator.hasNext() ? iterator.next() : null);
            }


            Alignment advance() {
                Alignment tmp = nextRecord;
                nextRecord = (iterator.hasNext() ? iterator.next() : null);
                return tmp;


            }

View Full Code Here

        }


        class AlignmentStartComparator implements Comparator<RecordIterWrapper> {


            public int compare(RecordIterWrapper wrapper1, RecordIterWrapper wrapper2) {
                Alignment a1 = wrapper1.nextRecord;
                Alignment a2 = wrapper2.nextRecord;


                Integer idx1 = chrNameIndex.get(a1.getChr());
                Integer idx2 = chrNameIndex.get(a2.getChr());
                if (idx1 > idx2) {
                    return 1;
                } else if (idx1 < idx2) {
                    return -1;
                } else {
                    return a1.getAlignmentStart() - a2.getAlignmentStart();
                }
            }

View Full Code Here

        //reader.setValidationStringency(ValidationStringency.SILENT);
        //chr1:16,780,602-16,780,774
        //chr1:235675392
        CloseableIterator<Alignment> iter = reader.query("chr1", 50542554, 50542722, true);
        while (iter.hasNext()) {
            Alignment record = iter.next();
            System.out.println(record.getAlignmentStart() + " => " + record.getAlignmentEnd());
        }
    }

View Full Code Here

            reader = new AsciiLineReader(is);
            readNextRecord();
        }


        protected Alignment parseNextRecord() {
            Alignment next;
            try {
                next = parser.readNextRecord(reader);
            } catch (IOException e) {
                log.error("Error reading Gerald record", e);
                return null;

View Full Code Here

            return nextRecord != null;
        }


        @Override
        public Alignment next() {
            Alignment ret = nextRecord;
            readNextRecord();
            return ret;
        }

View Full Code Here

        GobyAlignmentQueryReader.supportsFileType(entriesFile);
        GobyAlignmentQueryReader reader = new GobyAlignmentQueryReader(entriesFile);
        CloseableIterator<Alignment> iter = reader.iterator();


        while (iter.hasNext()) {
            Alignment alignment = iter.next();
            assertNotNull(alignment);
        }
    }

View Full Code Here

        ObjectSet<String> chromosomeSeen = new ObjectArraySet<String>();
        // maximum number of entries to inspect (keep low for faster test).
        int maxEntries = 100000;
        int countVisit = 0;
        while (iter.hasNext()) {
            Alignment a = iter.next();
            final String entryChr = a.getChr();
            //   System.out.println("chr:" + entryChr);


            if (entryChr.equals(previousChr)) {
                assertTrue(a.getAlignmentStart() >= previousAlignmentStart);
            } else {
                assertFalse("Chromosomes should occur in blocks." +
                        " A chromosome that was used in a previous block of entry cannot occur again.",
                        chromosomeSeen.contains(a.getChr()));
                previousChr = a.getChr();
                chromosomeSeen.add(a.getChr());
            }
            countVisit++;
            if (countVisit > maxEntries) break;
        }

View Full Code Here

        String entriesFile = TestUtils.DATA_DIR + "goby/tricky/sorted-tricky-spliced-17.header";
        GobyAlignmentQueryReader reader = new GobyAlignmentQueryReader(entriesFile);
        CloseableIterator<Alignment> iter = reader.iterator();


        assertTrue(iter.hasNext());
        Alignment igvAlignment = iter.next();
        boolean showSoftClipped = PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SAM_SHOW_SOFT_CLIPPED);


        Assert.assertEquals(2 + (showSoftClipped ? 1 : 0), igvAlignment.getAlignmentBlocks().length);
        Assert.assertEquals("==A====G===GA=====T============================================",
                basesToText(igvAlignment.getAlignmentBlocks()[1 + (showSoftClipped ? 1 : 0)].getBases()));
        iter.close();
        reader.close();


    }

View Full Code Here

0 1 2

TOP

Related Classes of org.broad.igv.sam.Alignment

org.broad.igv.cli_plugin.AlignmentIOTest

org.broad.igv.cli_plugin.PluginSource

org.broad.igv.goby.GobyAlignmentQueryReaderTest

org.broad.igv.sam.reader.AlignmentReaderFactoryTest

org.broad.igv.sam.reader.BAMHttpQueryReaderTest

org.broad.igv.sam.reader.CGIAlignmentReader

org.broad.igv.sam.reader.GeraldReader$GeraldIterator

org.broad.igv.sam.reader.MergedAlignmentReader$MergedFileIterator

org.broad.igv.sam.reader.MergedAlignmentReader$MergedFileIterator$AlignmentStartComparator

org.broad.igv.sam.reader.MergedAlignmentReader$MergedFileIterator$RecordIterWrapper

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.