Examples with Probe uk.ac.babraham.SeqMonk.DataTypes.Probes.Probe used on opensource projects

Example 21 with Probe

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.Probe in project SeqMonk by s-andrews.

the class EvenCoverageProbeGenerator method run.

/* (non-Javadoc)
	 * @see java.lang.Runnable#run()
	 */
public void run() {
    Chromosome[] chromosomes = collection.genome().getAllChromosomes();
    Vector<Probe> newProbes = new Vector<Probe>();
    for (int c = 0; c < chromosomes.length; c++) {
        // Time for an update
        updateGenerationProgress("Processed " + c + " chromosomes", c, chromosomes.length);
        // We'll merge together the reads for all of the selected DataStores and
        // compute a single set of probes which covers all of them.
        ReadsWithCounts[] v = new ReadsWithCounts[selectedStores.length];
        for (int s = 0; s < selectedStores.length; s++) {
            v[s] = selectedStores[s].getReadsForChromosome(chromosomes[c]);
        }
        ReadsWithCounts reads = new ReadsWithCounts(v);
        v = null;
        if (reads.totalCount() == 0) {
            // System.err.println("Skipping strand "+strandsToTry[strand]+" on chr "+chromosomes[c]);
            continue;
        }
        int strandForNewProbes = Location.UNKNOWN;
        int start = SequenceRead.start(reads.reads[0]);
        int end = SequenceRead.end(reads.reads[0]);
        int count = reads.counts[0];
        for (int r = 1; r < reads.reads.length; r++) {
            // See if we need to quit
            if (cancel) {
                generationCancelled();
                return;
            }
            if (count > 0 && ((maxSize > 0 && (SequenceRead.end(reads.reads[r]) - start) + 1 > maxSize)) || (count + reads.counts[r] > targetReadCount)) {
                // Make a probe out of what we have and start a new one with the
                // read we're currently looking at
                Probe p = new Probe(chromosomes[c], start, end, strandForNewProbes);
                newProbes.add(p);
                start = end + 1;
                end = Math.max(end + 2, SequenceRead.end(reads.reads[r]));
                count = SequenceRead.end(reads.counts[r]);
            } else {
                count += reads.counts[r];
                if (SequenceRead.end(reads.reads[r]) > end) {
                    end = SequenceRead.end(reads.reads[r]);
                }
            }
        }
        if (count > 0) {
            Probe p = new Probe(chromosomes[c], start, end, strandForNewProbes);
            newProbes.add(p);
        }
    }
    Probe[] finalList = newProbes.toArray(new Probe[0]);
    newProbes.clear();
    ProbeSet finalSet = new ProbeSet(getDescription(), finalList);
    generationComplete(finalSet);
}

Example 22 with Probe

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.Probe in project SeqMonk by s-andrews.

the class FeatureProbeGenerator method removeDuplicates.

/**
 * Removes the duplicates.
 *
 * @param original the original
 * @return the probe[]
 */
private Probe[] removeDuplicates(Probe[] original) {
    if (original == null || original.length == 0)
        return original;
    Arrays.sort(original);
    Vector<Probe> keepers = new Vector<Probe>();
    Probe lastProbe = original[0];
    keepers.add(original[0]);
    for (int i = 1; i < original.length; i++) {
        if (original[i].start() == lastProbe.start() && original[i].end() == lastProbe.end() && original[i].chromosome().equals(lastProbe.chromosome())) {
            // This is a duplicate
            continue;
        }
        keepers.add(original[i]);
        lastProbe = original[i];
    }
    return keepers.toArray(new Probe[0]);
}

Example 23 with Probe

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.Probe in project SeqMonk by s-andrews.

the class MacsPeakCaller method getReadsFromDataStoreCollection.

private long[] getReadsFromDataStoreCollection(Probe probe, DataStore[] stores, int strandOffset) {
    Probe p = probe;
    if (strandOffset > 0) {
        p = new Probe(probe.chromosome(), Math.max(probe.start() - strandOffset, 1), Math.min(probe.end() + strandOffset, probe.chromosome().length()));
    }
    long[][] allProbeReads = new long[stores.length][];
    for (int d = 0; d < stores.length; d++) {
        allProbeReads[d] = stores[d].getReadsForProbe(p);
    }
    int totalProbeReadCount = 0;
    for (int i = 0; i < allProbeReads.length; i++) {
        totalProbeReadCount += allProbeReads[i].length;
    }
    long[] mergedChrReads = new long[totalProbeReadCount];
    int index = 0;
    for (int i = 0; i < allProbeReads.length; i++) {
        for (int j = 0; j < allProbeReads[i].length; j++) {
            if (strandOffset == 0 || SequenceRead.strand(allProbeReads[i][j]) == Location.UNKNOWN) {
                mergedChrReads[index] = allProbeReads[i][j];
            } else if (SequenceRead.strand(allProbeReads[i][j]) == Location.FORWARD) {
                mergedChrReads[index] = SequenceRead.packPosition(Math.min(SequenceRead.start(allProbeReads[i][j]) + strandOffset, p.chromosome().length()), Math.min(SequenceRead.end(allProbeReads[i][j]) + strandOffset, p.chromosome().length()), SequenceRead.strand(allProbeReads[i][j]));
            } else if (SequenceRead.strand(allProbeReads[i][j]) == Location.REVERSE) {
                mergedChrReads[index] = SequenceRead.packPosition(Math.max(SequenceRead.start(allProbeReads[i][j]) - strandOffset, 1), Math.max(SequenceRead.end(allProbeReads[i][j]) - strandOffset, 1), SequenceRead.strand(allProbeReads[i][j]));
            }
            index++;
        }
        allProbeReads[i] = null;
    }
    return mergedChrReads;
}

Example 24 with Probe

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.Probe in project SeqMonk by s-andrews.

the class RandomProbeGenerator method designPerChromosome.

private ProbeSet designPerChromosome() {
    Chromosome[] chromosomes = collection.genome().getAllChromosomes();
    long[] offsets = new long[chromosomes.length];
    offsets[0] = chromosomes[0].length();
    for (int i = 1; i < chromosomes.length; i++) {
        offsets[i] = offsets[i - 1] + chromosomes[i].length();
    }
    // Now make up the probes
    Vector<Probe> newProbes = new Vector<Probe>();
    Random rand = new Random();
    while (newProbes.size() < numberToGenerate) {
        if (cancel) {
            return null;
        }
        if (newProbes.size() % 1000 == 0) {
            updateGenerationProgress("Designed " + newProbes.size() + " probes", newProbes.size(), numberToGenerate);
        }
        // Select a random position in the genome
        long random = (long) (collection.genome().getTotalGenomeLength() * rand.nextDouble());
        Chromosome chromosome = null;
        int start = 0;
        int end = 0;
        // Find out which chromosome this comes from
        for (int o = 0; o < offsets.length; o++) {
            if (random < offsets[o]) {
                chromosome = chromosomes[o];
                if (o > 0) {
                    start = (int) (random - offsets[o - 1]) + 1;
                } else {
                    start = (int) random + 1;
                }
                end = start + (windowSize - 1);
                break;
            }
        }
        if (end > chromosome.length()) {
            // Try again
            continue;
        }
        // Make a probe
        newProbes.add(new Probe(chromosome, start, end));
    }
    Probe[] finalList = newProbes.toArray(new Probe[0]);
    ProbeSet finalSet = new ProbeSet(getDescription(), finalList);
    return finalSet;
}

Example 25 with Probe

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.Probe in project SeqMonk by s-andrews.

the class RandomProbeGenerator method designPerProbe.

private ProbeSet designPerProbe() {
    Probe[] probes = collection.probeSet().getActiveList().getAllProbes();
    // TODO: We could remove all probes which are smaller than the windows we're going to
    // generate?
    long[] offsets = new long[probes.length];
    offsets[0] = probes[0].length();
    for (int i = 1; i < probes.length; i++) {
        offsets[i] = offsets[i - 1] + probes[i].length();
    }
    long totalLength = offsets[offsets.length - 1];
    // Now make up the probes
    Vector<Probe> newProbes = new Vector<Probe>();
    Random rand = new Random();
    RANDLOOP: while (newProbes.size() < numberToGenerate) {
        if (cancel) {
            return null;
        }
        if (newProbes.size() % 1000 == 0) {
            updateGenerationProgress("Designed " + newProbes.size() + " probes", newProbes.size(), numberToGenerate);
        }
        // Select a random position in the genome
        long random = (long) (totalLength * rand.nextDouble());
        Chromosome chromosome = null;
        int start = 0;
        int end = 0;
        // Find out which chromosome this comes from
        for (int o = 0; o < offsets.length; o++) {
            if (random < offsets[o]) {
                chromosome = probes[o].chromosome();
                if (o > 0) {
                    start = (int) (random - offsets[o - 1]) + probes[o].start();
                } else {
                    start = (int) random + probes[o].start();
                }
                end = start + (windowSize - 1);
                // Check that this is valid
                if (end > probes[o].end()) {
                    // Try again
                    continue RANDLOOP;
                }
                break;
            }
        }
        // Make a probe
        newProbes.add(new Probe(chromosome, start, end));
    }
    Probe[] finalList = newProbes.toArray(new Probe[0]);
    ProbeSet finalSet = new ProbeSet(getDescription(), finalList);
    return finalSet;
}