/** * @return the base quality according to <code>offset</code>. */ public byte getBaseQuality() { return record.getBaseQualities()[offset]; }
/** Calculates a score for the read which is the sum of scores over Q15. */ private static int getSumOfBaseQualities(final SAMRecord rec) { int score = 0; for (final byte b : rec.getBaseQualities()) { if (b >= 15) score += b; } return score; }
/** * @return array of base qualities of inner SAMRecord. */ public byte[] getBaseQualities() { return record.getBaseQualities(); }
/** * @return the base quality according to <code>offset</code>. */ public byte getBaseQuality() { return record.getBaseQualities()[offset]; }
/** Calculates a score for the read which is the sum of scores over Q15. */ private static int getSumOfBaseQualities(final SAMRecord rec) { int score = 0; for (final byte b : rec.getBaseQualities()) { if (b >= 15) score += b; } return score; }
/** * @return Base qualities, encoded as a FASTQ string. */ public String getBaseQualityString() { if (Arrays.equals(NULL_QUALS, getBaseQualities())) { return NULL_QUALS_STRING; } return SAMUtils.phredToFastq(getBaseQualities()); }
/** * @return Base qualities, encoded as a FASTQ string. */ public String getBaseQualityString() { if (Arrays.equals(NULL_QUALS, getBaseQualities())) { return NULL_QUALS_STRING; } return SAMUtils.phredToFastq(getBaseQualities()); }
/** * @return Base qualities, encoded as a FASTQ string. */ public String getBaseQualityString() { if (Arrays.equals(NULL_QUALS, getBaseQualities())) { return NULL_QUALS_STRING; } return SAMUtils.phredToFastq(getBaseQualities()); }
@Override public byte[] getBaseQualities() { if (!initializedFields.contains(LazyField.QUALS)) { setBaseQualities(getBaseQualitiesImpl()); } return super.getBaseQualities(); }
@Override public byte[] getBaseQualities() { if (!initializedFields.contains(LazyField.QUALS)) { setBaseQualities(getBaseQualitiesImpl()); } return super.getBaseQualities(); }
@Override public byte[] getBaseQualities() { byte[] ret = super.getBaseQualities(); if (mRestOfBinaryData != null && ret == null) { ret = decodeBaseQualities(); super.setBaseQualities(ret); } return ret; }
/** * @param position in the reference * @return base quality of a read base, corresponding to a given reference position */ @Override public byte getBaseQuality(int position) { int rOffset = getRelativeOffset(position); byte[] baseQualities = record.getBaseQualities(); validateOffset(rOffset, baseQualities); return baseQualities[rOffset]; }
/** * @param position in the reference * @return base quality of a read base, corresponding to a given reference position */ @Override public byte getBaseQuality(int position) { int rOffset = getRelativeOffset(position); byte[] baseQualities = record.getBaseQualities(); validateOffset(rOffset, baseQualities); return baseQualities[rOffset]; }
@Override public byte[] getBaseQualities() { byte[] ret = super.getBaseQualities(); if (mRestOfBinaryData != null && ret == null) { ret = decodeBaseQualities(); super.setBaseQualities(ret); } return ret; }
@Override public byte[] getBaseQualities() { byte[] ret = super.getBaseQualities(); if (mRestOfBinaryData != null && ret == null) { ret = decodeBaseQualities(); super.setBaseQualities(ret); } return ret; }
/** Get the the number of bases in the given alignment block and record that have base quality greater or equal to the minimum */ public static int getNumBasesPassingMinimumBaseQuality(final SAMRecord record, final AlignmentBlock block, final int minimumBaseQuality) { int basesInBlockAtMinimumQuality = 0; final byte[] baseQualities = record.getBaseQualities(); for (int idx = block.getReadStart(); idx <= CoordMath.getEnd(block.getLength(), block.getReadStart()); idx++) { // idx is one-based if (minimumBaseQuality <= baseQualities[idx-1]) basesInBlockAtMinimumQuality++; } return basesInBlockAtMinimumQuality; }
/** Get the the number of bases in the given alignment block and record that have base quality greater or equal to the minimum */ public static int getNumBasesPassingMinimumBaseQuality(final SAMRecord record, final AlignmentBlock block, final int minimumBaseQuality) { int basesInBlockAtMinimumQuality = 0; final byte[] baseQualities = record.getBaseQualities(); for (int idx = block.getReadStart(); idx <= CoordMath.getEnd(block.getLength(), block.getReadStart()); idx++) { // idx is one-based if (minimumBaseQuality <= baseQualities[idx-1]) basesInBlockAtMinimumQuality++; } return basesInBlockAtMinimumQuality; }
private void testConvertedSAMRecord(final SAMRecord converted, final SAMRecord original) { Assert.assertEquals(converted.getReadName(), original.getReadName()); Assert.assertEquals(converted.getBaseQualities(), original.getBaseQualities()); Assert.assertEquals(converted.getReadBases(), original.getReadBases()); Assert.assertEquals(converted.getStringAttribute(SAMTag.CO.name()), original.getStringAttribute(SAMTag.CO.name())); Assert.assertTrue(converted.getReadUnmappedFlag()); } }
private void assertGoodRead(final SAMRecord read, final ArtificialBAMBuilder bamBuilder) { Assert.assertEquals(read.getReadLength(), bamBuilder.getReadLength()); Assert.assertEquals(read.getReadBases().length, bamBuilder.getReadLength()); Assert.assertEquals(read.getBaseQualities().length, bamBuilder.getReadLength()); Assert.assertTrue(read.getAlignmentStart() >= bamBuilder.getAlignmentStart()); Assert.assertNotNull(read.getReadGroup()); } }
private void testRecord(final String expectedReadName, final FastqRecord fastqRecord, final SAMRecord samRecord) { Assert.assertEquals(fastqRecord.getReadName(), expectedReadName); Assert.assertEquals(fastqRecord.getBaseQualities(), samRecord.getBaseQualities()); Assert.assertEquals(fastqRecord.getReadBases(), samRecord.getReadBases()); Assert.assertEquals(fastqRecord.getBaseQualityHeader(), samRecord.getStringAttribute(SAMTag.CO.name())); }