Package net.sf.cram.encoding.read_features

Examples of net.sf.cram.encoding.read_features.BaseQualityScore

29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
    BitCodec<BaseQualityScore> codec = new BitCodec<BaseQualityScore>() {

      @Override
      public BaseQualityScore read(BitInputStream bis) throws IOException {
        BaseQualityScore bqs = new BaseQualityScore(-1,
            qualityScoreCodec.read(bis));
        return bqs;
      }

      @Override
      public long write(BitOutputStream bos, BaseQualityScore bqs)
          throws IOException {
        return qualityScoreCodec.write(bos, bqs.getQualityScore());
      }

      @Override
      public long numberOfBits(BaseQualityScore bqs) {
        return qualityScoreCodec.numberOfBits(bqs.getQualityScore());
      }
    };

    DefaultMutableTreeNode node = buildNode(codec, "Base QS codec");
    parent.add(node);
View Full Code Here
335
336
337
338
339
340
341
342
343
344
345
      boolean qualityMasked = (scores[i] < uncategorisedQualityScoreCutoff);
      if (captureInsertScores || qualityMasked) {
        byte score = (byte) (QS_asciiOffset + scores[zeroBasedPositionInRead
            + i]);
        // if (score >= QS_asciiOffset) {
        features.add(new BaseQualityScore(zeroBasedPositionInRead + 1
            + i, score));
        landedTotalScores++;
        // }
      }
    }
View Full Code Here
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
          continue;

        if (captureSubtitutionScores) {
          byte score = (byte) (QS_asciiOffset + qualityScore[i
              + fromPosInRead]);
          features.add(new BaseQualityScore(oneBasedPositionInRead,
              score));
          qualityAdded = true;
        }
      }

      if (noQS)
        continue;

      if (!qualityAdded && refSNPs != null) {
        byte snpOrNot = refSNPs[refCoord];
        if (snpOrNot != 0) {
          byte score = (byte) (QS_asciiOffset + qualityScore[i
              + fromPosInRead]);
          features.add(new BaseQualityScore(oneBasedPositionInRead,
              score));
          qualityAdded = true;
          landedRefMaskScores++;
        }
      }

      if (!qualityAdded && refPile != null) {
        if (refPile.shouldStore(refCoord, refBase)) {
          byte score = (byte) (QS_asciiOffset + qualityScore[i
              + fromPosInRead]);
          features.add(new BaseQualityScore(oneBasedPositionInRead,
              score));
          qualityAdded = true;
          landedPiledScores++;
        }
      }

      qualityMasked = (qualityScore[i + fromPosInRead] < uncategorisedQualityScoreCutoff);
      if (!qualityAdded && qualityMasked) {
        byte score = (byte) (QS_asciiOffset + qualityScore[i
            + fromPosInRead]);
        features.add(new BaseQualityScore(oneBasedPositionInRead, score));
        qualityAdded = true;
      }

      if (qualityAdded)
        landedTotalScores++;
View Full Code Here
180
181
182
183
184
185
186
187
188
189
190
    if (!r.forcePreserveQualityScores) {
      for (int i = 0; i < scores.length; i++) {
        if (scores[i] > -1) {
          if (r.getReadFeatures() == null) r.setReadFeatures(new LinkedList<ReadFeature>()) ;
          r.getReadFeatures().add(
              new BaseQualityScore(i + 1, scores[i]));
        }
      }
      if (r.getReadFeatures() != null)
        Collections.sort(r.getReadFeatures(),
            readFeaturePositionComparator);
View Full Code Here
225
226
227
228
229
230
231
232
233
234
235
          case InsertBase.operator:
            InsertBase ib = new InsertBase(pos, bc.readData());
            rf.add(ib);
            break;
          case BaseQualityScore.operator:
            BaseQualityScore bqs = new BaseQualityScore(pos,
                qc.readData());
            rf.add(bqs);
            break;
          default:
            throw new RuntimeException(
View Full Code Here
214
215
216
217
218
219
220
221
222
223
224
225
        case InsertBase.operator:
          InsertBase ib = (InsertBase) f;
          bc.writeData(ib.getBase());
          break;
        case BaseQualityScore.operator:
          BaseQualityScore bqs = (BaseQualityScore) f;
          qc.writeData(bqs.getQualityScore());
          break;
        default:
          throw new RuntimeException(
              "Unknown read feature operator: "
                  + (char) f.getOperator());
View Full Code Here
418
419
420
421
422
423
424
425
426
427
428
                "ACGT".getBytes()[random.nextInt(4)],
                (byte) (33 + random.nextInt(40)));
            record.getReadFeatures().add(rb);
            break;
          case BaseQualityScore.operator:
            BaseQualityScore qs = new BaseQualityScore(newPos,
                (byte) (33 + random.nextInt(40)));
            record.getReadFeatures().add(qs);
            break;
          case InsertBase.operator:
            InsertBase ib = new InsertBase();
View Full Code Here
TOP

Related Classes of net.sf.cram.encoding.read_features.BaseQualityScore

  • net.sf.cram.BLOCK_PROTO
  • net.sf.cram.encoding.factory.BaseQualityCodecFactory
  • net.sf.cram.encoding.Reader
  • net.sf.cram.encoding.Writer
  • net.sf.cram.lossy.QualityScorePreservation
  • net.sf.cram.Sam2CramRecordFactory
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.