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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
/*
* The MIT License
*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.illumina.parser;
import htsjdk.samtools.util.CloseableIterator;
import picard.illumina.parser.readers.BclQualityEvaluationStrategy;
import picard.illumina.parser.readers.BclReader;
import java.io.File;
import java.util.Collections;
import java.util.List;
import java.util.NoSuchElementException;
import java.util.Set;
import static htsjdk.samtools.util.CollectionUtil.makeSet;
/**
* BclParser parses a number of BclFiles equal to the total of all the values in outputLengths and returns a BclData object
* segmented based on these lengths. The only client of this class should be IlluminaDataProvider and an test classes. See BclReader for
* more information on BclFiles. BclParser provides support for reading BaseCalls and QualityScores.
*/
class BclParser extends PerTileCycleParser {
private static final int EAMSS_M2_GE_THRESHOLD = 30;
private static final int EAMSS_S1_LT_THRESHOLD = 15; //was 15
public static final byte MASKING_QUALITY = (byte) 0x02;
private static final Set SUPPORTED_TYPES = Collections.unmodifiableSet(makeSet(IlluminaDataType.BaseCalls, IlluminaDataType.QualityScores));
protected final BclQualityEvaluationStrategy bclQualityEvaluationStrategy;
private final boolean applyEamssFilter;
public BclParser(final File directory, final int lane, final CycleIlluminaFileMap tilesToCycleFiles, final OutputMapping outputMapping, final BclQualityEvaluationStrategy bclQualityEvaluationStrategy) {
this(directory, lane, tilesToCycleFiles, outputMapping, true, bclQualityEvaluationStrategy);
this.initialize();
}
public BclParser(final File directory, final int lane, final CycleIlluminaFileMap tilesToCycleFiles, final OutputMapping outputMapping, final boolean applyEamssFilter, final BclQualityEvaluationStrategy bclQualityEvaluationStrategy) {
super(directory, lane, tilesToCycleFiles, outputMapping);
this.bclQualityEvaluationStrategy = bclQualityEvaluationStrategy;
this.applyEamssFilter = applyEamssFilter;
this.initialize();
}
/**
* Create a Bcl parser for an individual cycle and wrap it with the CycleFilesParser interface which populates
* the correct cycle in BclData.
*
* @param files The files to parse.
* @return A CycleFilesParser that populates a BclData object with data for a single cycle
*/
@Override
protected CycleFilesParser makeCycleFileParser(final List files) {
return new BclDataCycleFileParser(files);
}
@Override
public void initialize() {
seekToTile(currentTile);
}
@Override
public Set supportedTypes() {
return SUPPORTED_TYPES;
}
@Override
public BclData next() {
final BclData bclData = super.next();
final byte[][] bases = bclData.getBases();
final byte[][] qualities = bclData.getQualities();
//first run EAMSS
if (this.applyEamssFilter) {
for (int i = 0; i < bases.length; i++) {
runEamssForReadInPlace(bases[i], qualities[i]);
}
}
return bclData;
}
/**
* EAMSS is an Illumina Developed Algorithm for detecting reads whose quality has deteriorated towards
* their end and revising the quality to the masking quality (2) if this is the case. This algorithm
* works as follows (with one exception):
*
* Start at the end (high indices, at the right below) of the read and calculate an EAMSS tally at each
* location as follow:
* if(quality[i] < 15) tally += 1
* if(quality[i] >= 15 and < 30) tally = tally
* if(quality[i] >= 30) tally -= 2
*
*
* For each location, keep track of this tally (e.g.)
* Read Starts at <- this end
* Cycle: 1 2 3 4 5 6 7 8 9
* Bases: A C T G G G T C A
* Qualities: 32 32 16 15 8 10 32 2 2
* Cycle Score: -2 -2 0 0 1 1 -2 1 1 //The EAMSS Score determined for this cycle alone
* EAMSS TALLY: 0 0 2 2 2 1 0 2 1
* X - Earliest instance of Max-Score
*
* You must keep track of the maximum EAMSS tally (in this case 2) and the earliest(lowest) cycle at which
* it occurs. If and only if, the max EAMSS tally >= 1 then from there until the end(highest cycle) of the
* read reassign these qualities as 2 (the masking quality). The output qualities would therefore be
* transformed from:
*
* Original Qualities: 32 32 16 15 8 10 32 2 2 to
* Final Qualities: 32 32 2 2 2 2 2 2 2
* X - Earliest instance of max-tally/end of masking
*
* IMPORTANT:
* The one exception is: If the max EAMSS Tally is preceded by a long string of G basecalls (10 or more, with a single basecall exception per10 bases)
* then the masking continues to the beginning of that string of G's. E.g.:
*
* Cycle: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
* Bases: C T A C A G A G G G G G G G G C A T
* Qualities: 30 22 26 27 28 30 7 34 20 19 38 15 32 32 10 4 2 5
* Cycle Score: -2 0 0 0 0 -2 1 -2 0 0 -2 0 -2 -2 1 1 1 1
* EAMSS TALLY: -2 -5 -5 -5 -5 -5 -3 -4 -2 -2 -2 0 0 2 4 3 2 1
* X- Earliest instance of Max-Tally
*
* Resulting Transformation:
* Bases: C T A C A G A G G G G G G G G C A T
* Original Qualities: 30 22 26 27 28 30 7 34 20 19 38 15 32 32 10 4 2 5
* Final Qualities: 30 22 26 27 28 2 2 2 2 2 2 2 2 2 2 2 2 2
* X- Earliest instance of Max-Tally
* X - Start of EAMSS masking due to G-Run
*
* To further clarify the exception rule here are a few examples:
* A C G A C G G G G G G G G G G G G G G G G G G G G A C T
* X - Earliest instance of Max-Tally
* X - Start of EAMSS masking (with a two base call jump because we have 20 bases in the run already)
*
* T T G G A G G G G G G G G G G G G G G G G G G A G A C T
* X - Earliest instance of Max-Tally
* X - We can skip this A as well as the earlier A because we have 20 or more bases in the run already
* X - Start of EAMSS masking (with a two base call jump because we have 20 bases in the run)
*
* T T G G G A A G G G G G G G G G G G G G G G G G G T T A T
* X - Earliest instance of Max-Tally
* X X - WE can skip these bases because the first A counts as the first skip and as far as the length of the string of G's is
* concerned, these are both counted like G's
* X - This A is the 20th base in the string of G's and therefore can be skipped
* X - Note that the A's previous to the G's are only included because there are G's further on that are within the number
* of allowable exceptions away (i.e. 2 in this instance), if there were NO G's after the A's you CANNOT count the A's
* as part of the G strings (even if no exceptions have previously occured) In other words, the end of the string of G's
* MUST end in a G not an "exception"
*
* However, if the max-tally occurs to the right of the run of Gs then this is still part of the string of G's but does count towards
* the number of exceptions allowable
* (e.g.)
* T T G G G G G G G G G G A C G
* X - Earliest instance of Max-tally
* The first index CAN be considered as an exception, the above would be masked to
* the following point:
* T T G G G G G G G G G G A C G
* X - End of EAMSS masking due to G-Run
*
* To sum up the final points, a string of G's CAN START with an exception but CANNOT END in an exception.
*
* @param bases Bases for a single read in the cluster ( not the entire cluster )
* @param qualities Qualities for a single read in the cluster ( not the entire cluster )
*/
protected static void runEamssForReadInPlace(final byte[] bases, final byte[] qualities) {
int eamssTally = 0;
int maxTally = Integer.MIN_VALUE;
int indexOfMax = -1;
for (int i = bases.length - 1; i >= 0; i--) {
final int quality = (0xff & qualities[i]);
if (quality >= EAMSS_M2_GE_THRESHOLD) {
eamssTally -= 2;
} else if (quality < EAMSS_S1_LT_THRESHOLD) {
eamssTally += 1;
}
if (eamssTally >= maxTally) {
indexOfMax = i;
maxTally = eamssTally;
}
}
if (maxTally >= 1) {
int numGs = 0;
int exceptions = 0;
for (int i = indexOfMax; i >= 0; i--) {
if (bases[i] == 'G') {
++numGs;
} else {
final Integer skip = skipBy(i, numGs, exceptions, bases);
if (skip != null) {
exceptions += skip;
numGs += skip;
i -= (skip - 1);
} else {
break;
}
}
}
if (numGs >= 10) {
indexOfMax = (indexOfMax + 1) - numGs;
}
for (int i = indexOfMax; i < qualities.length; i++) {
qualities[i] = MASKING_QUALITY;
}
}
}
/**
* Determine whether or not the base at index is part of a skippable section in a run of G's, if so
* return the number of bases that the section is composed of.
*
* @param index Current index, which should be the index of a non-'G' base
* @param numGs The number of bases in the current string of G's for this read
* @param prevExceptions The number of exceptions previously detected in this string by this method
* @param bases The bases of this read
* @return If we have not reached our exception limit (1/every 10bases) and a G is within exceptionLimit(numGs/10)
* indices before the current index then return index - (index of next g), else return null Null indicates this is
* NOT a skippable region, if we run into index 0 without finding a g then NULL is also returned
*/
private static Integer skipBy(final int index, final int numGs, final int prevExceptions, final byte[] bases) {
Integer skip = null;
for (int backup = 1; backup <= index; backup++) {
final int exceptionLimit = Math.max((numGs + backup) / 10, 1);
if (prevExceptions + backup > exceptionLimit) {
break;
}
if (bases[index - backup] == 'G') {
skip = backup;
break;
}
}
return skip;
}
private class BclDataCycleFileParser implements CycleFilesParser {
final CloseableIterator reader;
public BclDataCycleFileParser(final List files) {
reader = new BclReader(files, outputMapping.getOutputReadLengths(),
bclQualityEvaluationStrategy, false);
}
@Override
public void close() {
reader.close();
}
@Override
public BclData next() {
if (!hasNext()) {
throw new NoSuchElementException();
}
return reader.next();
}
@Override
public boolean hasNext() {
try {
return reader.hasNext();
} catch (final NullPointerException npe) {
return false;
}
}
}
}