Package htsjdk.tribble

Examples of htsjdk.tribble.Feature

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            if (expChr.equalsIgnoreCase(".")) {
                continue;
            }

            Feature actFeature = actFeatures.get(ind);
            assertEquals(expChr, actFeature.getChr());
            assertEquals(expStart, actFeature.getStart());
            assertEquals(expEnd, actFeature.getEnd());

            ind++;

        }
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        Iterator<Feature> features = tstOperationBED(bedfiles, "multiinter", 3).iterator();
        int ind = 0;
        int[] expStarts = new int[]{100, 200, 300};
        int[] expEnds = new int[]{101, 201, 301};
        while (features.hasNext()) {
            Feature feat = features.next();
            assertEquals(expStarts[ind], feat.getStart());
            assertEquals(expEnds[ind], feat.getEnd());
            ind++;
        }
    }
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        FeatureSearcher searcher = new FeatureSearcher(getTestBedSource(), genome, "chr1", 0);

        runSearch(searcher, sepThread);

        Feature feat = searcher.getResult().next();

        assertEquals("chr1", feat.getChr());
        assertEquals(100, feat.getStart());
        assertEquals(101, feat.getEnd());
    }
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        FeatureSearcher searcher = new FeatureSearcher(getTestBedSource(), genome, "chr1", 500);
        searcher.setSearchIncrement(10000);

        runSearch(searcher, sepThread);

        Feature feat = searcher.getResult().next();

        assertEquals("chr1", feat.getChr());
        assertEquals(100000, feat.getStart());
        assertEquals(100010, feat.getEnd());
    }
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        FeatureSearcher searcher = new FeatureSearcher(getTestBedSource(), genome, "chr1", 500000);
        searcher.setSearchIncrement(-10000);

        runSearch(searcher, sepThread);

        Feature feat = searcher.getResult().next();

        assertEquals("chr1", feat.getChr());
        assertEquals(100000, feat.getStart());
        assertEquals(100010, feat.getEnd());
    }
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        FeatureSearcher searcher = new FeatureSearcher(getTestBedSource(), genome, "chr1", 500000);
        searcher.setSearchIncrement(10000);

        runSearch(searcher, sepThread);

        Feature feat = searcher.getResult().next();

        assertEquals("chr2", feat.getChr());
        assertEquals(1, feat.getStart());
        assertEquals(10, feat.getEnd());
    }
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    }

    private int countNonNullFeatures(Iterator<Feature> featureIterator){
        int count = 0;
        while(featureIterator.hasNext()){
            Feature feat = featureIterator.next();
            assertNotNull(feat);
            count++;
        }
        return count;
    }
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        assertTrue("No matches found for motif " + motif, matchIter.hasNext());

        int count = 0;
        int lastStart = -1;
        while(matchIter.hasNext()){
            Feature feat = matchIter.next();
            count++;
            assertTrue("Features out of order", feat.getStart() >= lastStart);
            checkPatternMatches(motif, feat, shortSeq.getBytes());
            lastStart = feat.getStart();
        }
        assertEquals("Unexpected number of features", expFeatures, count);
    }
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        List<String> fullCmd = Arrays.asList(toolPath);
        PluginFeatureSource source = new PluginFeatureSource(fullCmd, arguments, outputAttr, pluginPath);
        List<Feature> feats = new ArrayList<Feature>();
        Iterator<Feature> featIter = source.getFeatures("chr2", 0, Integer.MAX_VALUE);
        Feature feat;
        while (featIter.hasNext()) {
            feat = featIter.next();
            int length = feat.getEnd() - feat.getStart();
            assertTrue(length >= min);
            assertTrue(length <= max);
            feats.add(feat);
        }
        assertEquals(expectedNum, feats.size());
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        String motif = "CTGATC";
        Strand strand = Strand.NEGATIVE;

        Iterator<Feature> matchIter = MotifFinderSource.searchSingleStrand(motif, strand, null, posStart, shortSeq.getBytes());
        assertTrue("No matches found for motif " + motif, matchIter.hasNext());
        Feature feat = matchIter.next();

        int expStart = posStart + shortSeq.length() - motif.length();
        int expEnd = expStart + motif.length();
        assertEquals(expStart, feat.getStart());
        assertEquals(expEnd, feat.getEnd());
        checkPatternMatches(motif, feat, shortSeq.getBytes());

        assertFalse(matchIter.hasNext());
    }
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