new BAMSplitGuesser(ss, hs, conf).guessNextBAMRecordStart(beg, end);
fillBuffer(beg, end); final PosSize psz = guessNextBGZFPos(cp, firstBGZFEnd); if (psz == null) return end; long nextBAMPos = findNextBAMPos(cp0, 0); if (nextBAMPos < 0) { return end;
final PosSize psz = guessNextBGZFPos(cp, firstBGZFEnd); if (psz == null) return end; final int up0 = up = guessNextBAMPos(cp0Virt, up, psz.size);
final PosSize psz = guessNextBGZFPos(cp, firstBGZFEnd); if (psz == null) return end; final int up0 = up = guessNextBAMPos(cp0Virt, up, psz.size);
new BAMSplitGuesser(ss, hs, conf).guessNextBAMRecordStart(beg, end);
new BAMSplitGuesser(ss, hs, conf).guessNextBAMRecordStart(beg, end);
@Test public void test() throws Exception { Configuration conf = new Configuration(); String bam = getClass().getClassLoader().getResource("test.bam").getFile(); SeekableStream ss = WrapSeekable.openPath(conf, new Path(bam)); BAMSplitGuesser bamSplitGuesser = new BAMSplitGuesser(ss, conf); long startGuess = bamSplitGuesser.guessNextBAMRecordStart(0, 3 * 0xffff + 0xfffe); assertEquals(SAMUtils.findVirtualOffsetOfFirstRecordInBam(new File(bam)), startGuess); } }
try (final SeekableStream sin = WrapSeekable.openPath(path.getFileSystem(cfg), path)) { final BAMSplitGuesser guesser = new BAMSplitGuesser(sin, cfg); long end = beg + fspl.getLength(); long alignedBeg = guesser.guessNextBAMRecordStart(beg, end);
try (final SeekableStream sin = WrapSeekable.openPath(path.getFileSystem(cfg), path)) { final BAMSplitGuesser guesser = new BAMSplitGuesser(sin, cfg); long end = beg + fspl.getLength(); long alignedBeg = guesser.guessNextBAMRecordStart(beg, end);
WrapSeekable.openPath(path.getFileSystem(cfg), path); final BAMSplitGuesser guesser = new BAMSplitGuesser(sin, cfg); long end = beg + fspl.getLength(); long alignedBeg = guesser.guessNextBAMRecordStart(beg, end);
SAMSequenceDictionary dict = header.getSequenceDictionary(); final BAMSplitGuesser guesser = new BAMSplitGuesser(guesserSin, conf); } else { long alignedBeg = guesser.guessNextBAMRecordStart(fSplit.getStart(), fSplit.getStart() + fSplit.getLength()); newSplit.setEndVirtualOffset(alignedBeg - 1);
SAMSequenceDictionary dict = header.getSequenceDictionary(); final BAMSplitGuesser guesser = new BAMSplitGuesser(guesserSin, conf); } else { long alignedBeg = guesser.guessNextBAMRecordStart(fSplit.getStart(), fSplit.getStart() + fSplit.getLength()); newSplit.setEndVirtualOffset(alignedBeg - 1);