@Test
public void testWigAndBigWig() throws Exception {
String wigPath = TestUtils.DATA_DIR + "wig/test_fixedStep.wig";
String bigWigPath = TestUtils.DATA_DIR + "wig/test_fixedStep.bigwig";
List<Track> wigtracks = tstLoadFi(wigPath, 1, false);
List<Track> bigWigtracks = tstLoadFi(bigWigPath, 1, false);
String chr = "chr19";
int start = 5930725;
int end = 5930764;
int zoom = 21;
DataSourceTrack wigTrack = (DataSourceTrack) wigtracks.get(0);
DataSourceTrack bigWigTrack = (DataSourceTrack) bigWigtracks.get(0);
int trials = 10;
for (int ii = 0; ii < trials; ii++) {
int strt = start + ii;
List<LocusScore> wigScores = wigTrack.getSummaryScores(chr, strt, end, zoom);
List<LocusScore> bigWigScores = bigWigTrack.getSummaryScores(chr, strt, end, zoom);
assertEquals(wigScores.size(), bigWigScores.size());
int ind = 0;
for (LocusScore ws : wigScores) {
LocusScore bws = bigWigScores.get(ind);
assertEquals(ws.getScore(), bws.getScore());
ind++;
}
}
}
@Test
public void testLoadDataSourceTrack() throws Exception {
String path = TestUtils.DATA_DIR + "sessions/tdf_session.xml";
rewriteRestoreSession(path);
DataSourceTrack track = (DataSourceTrack) IGV.getInstance().getAllTracks().get(0);
assertEquals(true, TestUtils.runMethod(track, "getNormalize"));
assertEquals("NA12878.SLX.egfr.sam.tdf", track.getName());
}
@Test
public void testLoadCombinedDataSourceSession() throws Exception {
String sessionpath = TestUtils.DATA_DIR + "sessions/subtypes_wdiff.xml";
rewriteRestoreSession(sessionpath);
String combPart0 = "TRIBE_p_TCGAaffx_B1_2_GBM_Nsp_GenomeWideSNP_6_E11_155884";
String combPart1 = "TRIGS_p_TCGAaffxB5_sty_GenomeWideSNP_6_D05_223156";
DataTrack track0 =
Iterables.find(IGV.getInstance().getDataTracks(), new ContIdPredicate(combPart0));
DataTrack track1 =
Iterables.find(IGV.getInstance().getDataTracks(), new ContIdPredicate(combPart1));
DataSourceTrack combTrack =
(DataSourceTrack)
Iterables.find(
IGV.getInstance().getDataTracks(),
new ContIdPredicate(new String[] {combPart0, combPart1}));
assertTrue(combTrack.getRenderer() instanceof BarChartRenderer);
assertEquals("Difference", combTrack.getName());
String chr = "chr1";
int start = 0;
int end = 1000;
LocusScore sumScore0 = track0.getSummaryScores(chr, start, end, 0).get(0);
LocusScore sumScore1 = track1.getSummaryScores(chr, start, end, 0).get(0);
LocusScore sumScoreComb = combTrack.getSummaryScores(chr, start, end, 0).get(0);
assertEquals(sumScore0.getStart(), sumScore1.getStart());
assertEquals(sumScore0.getStart(), sumScoreComb.getStart());
assertEquals(sumScore1.getEnd(), sumScoreComb.getEnd());
assertEquals(sumScore0.getScore() - sumScore1.getScore(), sumScoreComb.getScore(), 1e-10);
}
