.disable(SamReaderFactory.Option.EAGERLY_DECODE) .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS) .open(SamInputResource.of(inputUrl));
.disable(SamReaderFactory.Option.EAGERLY_DECODE) .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS) .open(SamInputResource.of(inputUrl));
private void runLocalRemoteTest(final URL bamURL, final File bamFile, final String sequence, final int startPos, final int endPos, final boolean contained) { verbose("Testing query " + sequence + ":" + startPos + "-" + endPos + " ..."); final SamReader reader1 = SamReaderFactory.makeDefault() .disable(SamReaderFactory.Option.EAGERLY_DECODE) .open(SamInputResource.of(bamFile).index(BAM_INDEX_FILE)); final SamReader reader2 = SamReaderFactory.makeDefault() .disable(SamReaderFactory.Option.EAGERLY_DECODE) .open(SamInputResource.of(bamURL).index(BAM_INDEX_FILE)); final Iterator<SAMRecord> iter1 = reader1.query(sequence, startPos, endPos, contained); final Iterator<SAMRecord> iter2 = reader2.query(sequence, startPos, endPos, contained); final List<SAMRecord> records1 = new ArrayList<SAMRecord>(); final List<SAMRecord> records2 = new ArrayList<SAMRecord>(); while (iter1.hasNext()) { records1.add(iter1.next()); } while (iter2.hasNext()) { records2.add(iter2.next()); } assertTrue(records1.size() > 0); assertEquals(records1.size(), records2.size()); for (int i = 0; i < records1.size(); i++) { //System.out.println(records1.get(i).format()); assertEquals(records1.get(i).getSAMString(), records2.get(i).getSAMString()); } }
/** Runnable implementation that reads the entire stream and writes the index. */ @Override public void run() { final SamReader in = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT) .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS).disable(SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS) .open(SamInputResource.of(this.stream)); final BAMIndexer indexer = new BAMIndexer(this.index, in.getFileHeader()); for (final SAMRecord rec : in) { indexer.processAlignment(rec); } indexer.finish(); CloserUtil.close(in); } }
/** Runnable implementation that reads the entire stream and writes the index. */ @Override public void run() { final SamReader in = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT) .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS).disable(SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS) .open(SamInputResource.of(this.stream)); final BAMIndexer indexer = new BAMIndexer(this.index, in.getFileHeader()); for (final SAMRecord rec : in) { indexer.processAlignment(rec); } indexer.finish(); CloserUtil.close(in); } }
private int runQueryTest(final URL bamURL, final String sequence, final int startPos, final int endPos, final boolean contained) { verbose("Testing query " + sequence + ":" + startPos + "-" + endPos + " ..."); final SamReader reader1 = SamReaderFactory.makeDefault() .disable(SamReaderFactory.Option.EAGERLY_DECODE) .open(SamInputResource.of(bamURL).index(BAM_INDEX_FILE)); final SamReader reader2 = SamReaderFactory.makeDefault() .disable(SamReaderFactory.Option.EAGERLY_DECODE) .open(SamInputResource.of(bamURL).index(BAM_INDEX_FILE)); final Iterator<SAMRecord> iter1 = reader1.query(sequence, startPos, endPos, contained);