Examples of AlignmentContext

org.apache.fop.layoutmgr.inline.AlignmentContext
The alignment context is carried within a LayoutContext and as part of the Knuth Inline elements to facilitate proper line building. All measurements are in mpt.
org.broadinstitute.gatk.engine.contexts.AlignmentContext
Useful class for forwarding on locusContext data from this iterator Created by IntelliJ IDEA. User: mdepristo Date: Feb 22, 2009 Time: 3:01:34 PM To change this template use File | Settings | File Templates.

Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

                createTestReadProperties(downsampler, false),
                genomeLocParser,
                samples);


        while ( li.hasNext() ) {
            final AlignmentContext next = li.next();
            Assert.assertTrue(next.getBasePileup().getNumberOfElements() <= downsampleTo, "Too many elements in pileup " + next);
            // TODO -- assert that there are <= X reads in memory after GC for some X
        }
    }

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

                LocusIteratorByState.sampleListForSAMWithoutReadGroups());


        int expectedPos = read.getAlignmentStart() + nClipsOnLeft;
        int nPileups = 0;
        while ( li.hasNext() ) {
            final AlignmentContext next = li.next();
            Assert.assertEquals(next.getLocation().getStart(), expectedPos);
            nPileups++;
            expectedPos++;
        }


        final int nExpectedPileups = nReadContainingPileups;

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

                            LocusIteratorByStateBaseTest.createTestReadProperties(),
                            genomeLocParser,
                            LocusIteratorByState.sampleListForSAMWithoutReadGroups());


            while ( libs.hasNext() ) {
                AlignmentContext context = libs.next();
            }
        }
    }

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

            if( expectedReadsAtSite < 1 )
                continue;


            Assert.assertTrue(coveredLocusView.hasNext(),"Incorrect number of loci in view");


            AlignmentContext locusContext = coveredLocusView.next();
            Assert.assertEquals(locusContext.getLocation(), site, "Target locus context location is incorrect");
            Assert.assertEquals(locusContext.getReads().size(), expectedReadsAtSite, "Found wrong number of reads at site");


            for( GATKSAMRecord read: reads ) {
                if(genomeLocParser.createGenomeLoc(read).containsP(locusContext.getLocation()))
                    Assert.assertTrue(locusContext.getReads().contains(read),"Target locus context does not contain reads");
            }
        }


        Assert.assertFalse(coveredLocusView.hasNext(),"Iterator is not bounded at boundaries of shard");
    }

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

        GenomeLoc lastLoc = range.get(range.size()-1);
        GenomeLoc bounds = genomeLocParser.createGenomeLoc(firstLoc.getContig(),firstLoc.getStart(),lastLoc.getStop());


        for( int i = bounds.getStart(); i <= bounds.getStop(); i++ ) {
            GenomeLoc site = genomeLocParser.createGenomeLoc("chr1",i);
            AlignmentContext locusContext = allLocusView.next();
            Assert.assertEquals(locusContext.getLocation(), site, "Locus context location is incorrect");
            int expectedReadsAtSite = 0;


            for( GATKSAMRecord read: reads ) {
                if(genomeLocParser.createGenomeLoc(read).containsP(locusContext.getLocation())) {
                    Assert.assertTrue(locusContext.getReads().contains(read),"Target locus context does not contain reads");
                    expectedReadsAtSite++;
                }
            }


            Assert.assertEquals(locusContext.getReads().size(), expectedReadsAtSite, "Found wrong number of reads at site");
        }


    }

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext


        final SimpleTimer timer = new SimpleTimer().start();
        int bp = 0;
        double lastElapsed = 0;
        while ( libs.hasNext() ) {
            AlignmentContext context = libs.next();
            bp++;
            if ( timer.getElapsedTime() - lastElapsed > 10 ) {
                logger.info(bp + " iterations at " + context.getLocation());
                lastElapsed = timer.getElapsedTime();
            }
        }
        logger.info(String.format("runtime in seconds: %.2f", timer.getElapsedTime()));

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

    @Override
    public AlignmentContext next() {
        lazyLoadNextAlignmentContext();
        if (!hasNext())
            throw new NoSuchElementException("LocusIteratorByState: out of elements.");
        AlignmentContext currentAlignmentContext = nextAlignmentContext;
        nextAlignmentContext = null;
        return currentAlignmentContext;
    }

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

     *                                             for subsequent use
     * @return a AlignmentContext at position, or null if this isn't possible
     */
    public AlignmentContext advanceToLocus(final int position, final boolean stopAtFirstNonEmptySiteAfterPosition) {
        while ( hasNext() ) {
            final AlignmentContext context = next();


            if ( context == null )
                // we ran out of data
                return null;


            if ( context.getPosition() == position )
                return context;


            if ( context.getPosition() > position)
                return stopAtFirstNonEmptySiteAfterPosition ? context : null;
        }


        return null;
    }

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

                    fullPileup.put(sample, new ReadBackedPileupImpl(location, pile));
            }


            readStates.updateReadStates(); // critical - must be called after we get the current state offsets and location
            if (!fullPileup.isEmpty()) // if we got reads with non-D/N over the current position, we are done
                nextAlignmentContext = new AlignmentContext(location, new ReadBackedPileupImpl(location, fullPileup), false);
        }
    }

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