本文整理汇总了Java中htsjdk.tribble.index.tabix.TabixFormat类的典型用法代码示例。如果您正苦于以下问题：Java TabixFormat类的具体用法？Java TabixFormat怎么用？Java TabixFormat使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
TabixFormat类属于htsjdk.tribble.index.tabix包，在下文中一共展示了TabixFormat类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: makeTabixCompressedIndex
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
private void makeTabixCompressedIndex(final File sourceFile, final File indexFile, final AsciiFeatureCodec codec,
final TabixFormat format) throws IOException {
TabixIndexCreator indexCreator = new TabixIndexCreator(format);
try (
BlockCompressedInputStream inputStream = new BlockCompressedInputStream(
new FileInputStream(sourceFile));
LittleEndianOutputStream outputStream = new LittleEndianOutputStream(
new BlockCompressedOutputStream(indexFile))
) {
long p = 0;
String line = inputStream.readLine();
while (line != null) {
//add the feature to the index
Feature decode = codec.decode(line);
if (decode != null) {
indexCreator.addFeature(decode, p);
}
// read the next line if available
p = inputStream.getFilePointer();
line = inputStream.readLine();
}
// write the index to a file
Index index = indexCreator.finalizeIndex(p);
// VERY important! either use write based on input file or pass the little endian a BGZF stream
index.write(outputStream);
}
}
示例2: readFormat
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
public void readFormat(BlockCompressedInputStream is) throws IOException {
mChr2tid = new HashMap<String, Integer>();
mTid2chr = new HashMap<Integer, String>();
mPreset = readInt(is);
mSc = readInt(is);
mBc = readInt(is);
mEc = readInt(is);
mMeta = readInt(is);
mSkip = readInt(is); //read skip
format = new TabixFormat(this.mPreset, this.mSc, this.mBc, this.mEc, (char)this.mMeta, this.mSkip);
// if((mPreset & 0xffff) == 2) {
// this.formatWithRef = FormatWithRef.VCF;
// } else {
// if(mBc == mEc) {
// formatWithRef = new FormatWithRef(this.format, readInt(is), readInt(is), readInt(is), readInt(is));
// } else {
//
// }
// }
formatWithRef = new FormatWithRef(this.format, readInt(is), readInt(is), readInt(is), readInt(is));
mSeq = new String[readInt(is)]; // # sequences
}
示例3: makeBedIndex
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
/**
* Creates an index for a specified BedFile
* @param bedFile BedFile to create index for
*/
public void makeBedIndex(final BedFile bedFile) {
final Map<String, Object> params = new HashMap<>();
params.put(DIR_ID.name(), bedFile.getId());
params.put(USER_ID.name(), bedFile.getCreatedBy());
File file = new File(bedFile.getPath());
File indexFile = new File(toRealPath(substitute(BED_INDEX, params)));
NggbBedCodec bedCodec = new NggbBedCodec();
TabixIndex index = IndexUtils.createTabixIndex(file, bedCodec, TabixFormat.BED);
index.write(indexFile);
BiologicalDataItem indexItem = new BiologicalDataItem();
indexItem.setCreatedDate(new Date());
indexItem.setPath(indexFile.getAbsolutePath());
indexItem.setFormat(BiologicalDataItemFormat.BED_INDEX);
indexItem.setType(BiologicalDataItemResourceType.FILE);
indexItem.setName("");
indexItem.setCreatedBy(AuthUtils.getCurrentUserId());
bedFile.setIndex(indexItem);
}
示例4: makeMafIndex
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
private void makeMafIndex(final MafFile mafFile, final TabixFormat tabixFormat) throws IOException {
final Map<String, Object> params = new HashMap<>();
params.put(DIR_ID.name(), mafFile.getId());
params.put(USER_ID.name(), mafFile.getCreatedBy());
File file = new File(mafFile.getPath());
File indexFile = new File(toRealPath(substitute(MAF_INDEX, params)));
LOGGER.debug("Writing MAF index at {}", indexFile.getAbsolutePath());
if (mafFile.getCompressed()) {
makeTabixCompressedIndex(file, indexFile, new MafCodec(mafFile.getPath()), tabixFormat);
} else {
makeTabixIndex(file, indexFile, new MafCodec(mafFile.getPath()), tabixFormat);
}
BiologicalDataItem indexItem = new BiologicalDataItem();
indexItem.setCreatedDate(new Date());
indexItem.setPath(indexFile.getAbsolutePath());
indexItem.setFormat(BiologicalDataItemFormat.MAF_INDEX);
indexItem.setType(BiologicalDataItemResourceType.FILE);
indexItem.setName("");
indexItem.setCreatedBy(AuthUtils.getCurrentUserId());
mafFile.setIndex(indexItem);
}
示例5: addLineToIndex
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
/** Set vcfHeader and vcfCodec to null if reading non-vcf line.
* */
private void addLineToIndex(String line, TabixIndexCreator indexCreator, long filePosition, TabixFormat fmt, VCFHeader vcfHeader, VCFCodec vcfCodec) throws InvalidRecordException {
if(fmt.equals(TabixFormat.BED)){
BedLineCodec bedCodec= new BedLineCodec();
BedLine bed = bedCodec.decode(line);
indexCreator.addFeature(bed, filePosition);
} else if(fmt.equals(TabixFormat.GFF)){
GtfLine gtf= new GtfLine(line.split("\t"));
indexCreator.addFeature(gtf, filePosition);
} else if(fmt.equals(TabixFormat.VCF)) {
VariantContext vcf = vcfCodec.decode(line);
indexCreator.addFeature(vcf, filePosition);
} else {
System.err.println("Unexpected TabixFormat: " + fmt.sequenceColumn + " " + fmt.startPositionColumn);
throw new InvalidRecordException();
}
}
示例6: trackFormatToTabixFormat
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
public static TabixFormat trackFormatToTabixFormat(TrackFormat fmt){
TabixFormat tbx= null;
if(fmt.equals(TrackFormat.BAM)){
tbx= TabixFormat.SAM;
} else if (fmt.equals(TrackFormat.BED) || fmt.equals(TrackFormat.BEDGRAPH)){
tbx= TabixFormat.BED;
} else if (fmt.equals(TrackFormat.GFF) || fmt.equals(TrackFormat.GTF)){
tbx= TabixFormat.GFF;
} else if (fmt.equals(TrackFormat.VCF)){
tbx= TabixFormat.VCF;
} else {
throw new RuntimeException();
}
return tbx;
}
示例7: canCompressAndIndexHeaderlessVCF
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
@Test
public void canCompressAndIndexHeaderlessVCF() throws ClassNotFoundException, IOException, InvalidRecordException, SQLException{
String infile= "test_data/noheader.vcf";
File outfile= new File("test_data/noheader.vcf.gz");
outfile.deleteOnExit();
File expectedTbi= new File(outfile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
expectedTbi.deleteOnExit();
new MakeTabixIndex(infile, outfile, TabixFormat.VCF);
assertTrue(outfile.exists());
assertTrue(outfile.length() > 200);
assertTrue(expectedTbi.exists());
assertTrue(expectedTbi.length() > 100);
TabixReader tbx = new TabixReader(outfile.getAbsolutePath());
Iterator x = tbx.query("1", 1, 10000000);
assertTrue(x.next().startsWith("1"));
}
示例8: testRealFileSizeVCF
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
@Test
public void testRealFileSizeVCF() throws ClassNotFoundException, IOException, InvalidRecordException, SQLException{
// See test_data/README.md for this file. This is fairly large and we want to check it is processed
// in a reasonable amount of time.
String infile= "test_data/ALL.wex.union_illumina_wcmc_bcm_bc_bi.20110521.snps.exome.sites.vcf";
File outfile= new File("deleteme.vcf.gz");
outfile.deleteOnExit();
File expectedTbi= new File(outfile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
expectedTbi.deleteOnExit();
long t0= System.currentTimeMillis();
new MakeTabixIndex(infile, outfile, TabixFormat.VCF);
long t1= System.currentTimeMillis();
assertTrue(outfile.exists());
assertTrue(outfile.length() > 1000);
assertTrue((t1 - t0) < 20000); // Should be << than 20 sec, ~2 sec
// Check you can read ok
this.vcfTester(outfile.getAbsolutePath());
}
示例9: canCompressAndIndexVCF_CEU
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
@Test
public void canCompressAndIndexVCF_CEU() throws ClassNotFoundException, IOException, InvalidRecordException, SQLException{
String infile= "test_data/CEU.exon.2010_06.genotypes.vcf";
File outfile= new File("deleteme.vcf.gz");
outfile.deleteOnExit();
File expectedTbi= new File(outfile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
expectedTbi.deleteOnExit();
new MakeTabixIndex(infile, outfile, TabixFormat.VCF);
assertTrue(outfile.exists());
assertTrue(outfile.length() > 1000);
// Check you can read ok
this.vcfTester(outfile.getAbsolutePath());
}
示例10: canHandleEmptyFile
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
@Test
public void canHandleEmptyFile() throws ClassNotFoundException, IOException, InvalidRecordException, SQLException, InvalidGenomicCoordsException{
String infile= "test_data/empty.bed";
File outfile= new File("test_data/empty.tmp.bed.gz");
outfile.deleteOnExit();
File expectedTbi= new File(outfile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
expectedTbi.deleteOnExit();
new MakeTabixIndex(infile, outfile, TabixFormat.BED);
assertTrue(outfile.exists());
assertTrue(expectedTbi.exists());
assertEquals(28, outfile.length()); // Checked with `bgzip empty.bed && ls -l empty.bed.gz`
assertTrue(expectedTbi.length() > 0);
}
示例11: canCompressAndIndexSortedFile
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
@Test
public void canCompressAndIndexSortedFile() throws IOException, InvalidRecordException, ClassNotFoundException, SQLException {
String infile= "test_data/overlapped.bed";
File outfile= new File("test_data/tmp.bed.gz");
outfile.deleteOnExit();
File expectedTbi= new File(outfile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
expectedTbi.deleteOnExit();
new MakeTabixIndex(infile, outfile, TabixFormat.BED);
assertTrue(outfile.exists());
assertTrue(outfile.length() > 80);
assertTrue(expectedTbi.exists());
assertTrue(expectedTbi.length() > 80);
TabixReader tbx = new TabixReader(outfile.getAbsolutePath());
Iterator x = tbx.query("chr1", 1, 1000000);
assertTrue(x.next().startsWith("chr1"));
}
示例12: canCompressAndIndexSortedGzipFile
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
@Test
public void canCompressAndIndexSortedGzipFile() throws IOException, InvalidRecordException, ClassNotFoundException, SQLException {
String infile= "test_data/hg19_genes.gtf.gz";
File outfile= new File("test_data/tmp2.bed.gz");
outfile.deleteOnExit();
File expectedTbi= new File(outfile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
expectedTbi.deleteOnExit();
new MakeTabixIndex(infile, outfile, TabixFormat.GFF);
assertTrue(outfile.exists());
assertTrue(outfile.length() > 7000000);
assertTrue(expectedTbi.exists());
assertTrue(expectedTbi.length() > 500000);
TabixReader tbx = new TabixReader(outfile.getAbsolutePath());
Iterator x = tbx.query("chr1", 1, 1000000);
assertTrue(x.next().startsWith("chr1"));
}
示例13: canCompressAndIndexUnsortedFile
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
@Test
public void canCompressAndIndexUnsortedFile() throws IOException, InvalidRecordException, ClassNotFoundException, SQLException {
String infile= "test_data/refSeq.hg19.bed.gz";
File outfile= new File("test_data/tmp3.bed.gz");
outfile.deleteOnExit();
File expectedTbi= new File(outfile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
expectedTbi.deleteOnExit();
new MakeTabixIndex(infile, outfile, TabixFormat.BED);
assertTrue(outfile.exists());
assertTrue(outfile.length() > 200000);
assertTrue(expectedTbi.exists());
assertTrue(expectedTbi.length() > 100000);
}
示例14: canCompressAndIndexSortedURL
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
@Test
public void canCompressAndIndexSortedURL() throws IOException, InvalidRecordException, ClassNotFoundException, SQLException {
String infile= "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz";
File outfile= new File("test_data/tmp4.bed.gz");
outfile.deleteOnExit();
File expectedTbi= new File(outfile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
expectedTbi.deleteOnExit();
new MakeTabixIndex(infile, outfile, TabixFormat.BED);
assertTrue(outfile.exists());
assertTrue(outfile.length() > 1000);
assertTrue(expectedTbi.exists());
assertTrue(expectedTbi.length() > 1000);
}
示例15: canCompressAndIndexUnsortedURL
import htsjdk.tribble.index.tabix.TabixFormat; //导入依赖的package包/类
@Test
public void canCompressAndIndexUnsortedURL() throws IOException, InvalidRecordException, ClassNotFoundException, SQLException {
String infile= "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878P300bStdPk.narrowPeak.gz";
File outfile= new File("test_data/tmp5.bed.gz");
outfile.deleteOnExit();
File expectedTbi= new File(outfile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
expectedTbi.deleteOnExit();
new MakeTabixIndex(infile, outfile, TabixFormat.BED);
assertTrue(outfile.exists());
assertTrue(outfile.length() > 1000);
assertTrue(expectedTbi.exists());
assertTrue(expectedTbi.length() > 1000);
}