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com.google.cloud.genomics.dataflow.utils.BAMDiff Maven / Gradle / Ivy
/*
* Copyright (C) 2014 Google Inc.
*
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except
* in compliance with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software distributed under the License
* is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
* or implied. See the License for the specific language governing permissions and limitations under
* the License.
*/
package com.google.cloud.genomics.dataflow.utils;
import com.google.cloud.genomics.utils.Contig;
import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMProgramRecord;
import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordIterator;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.ValidationStringency;
import htsjdk.samtools.util.PeekIterator;
import java.io.File;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.logging.Logger;
/**
* Diffs 2 BAM files and checks that they are identical.
* This is useful when comparing outputs of various BAM exporting mechanisms.
* Callers can specify which differences are tolerable (e.g. unmapped reads).
* Dumps the unexpected differences found.
* You can run this tool from the command line like so:
* java -cp target/google-genomics-dataflow*runnable.jar \
* com.google.cloud.genomics.dataflow.utils.BAMDiff \
* file1 file2
* The default options for what to ignore are currently not passed via command line
* but are just set in the main().
* A lot of header comparison code has been borrowed from Picrd's CompareSAMs tool.
*/
public class BAMDiff {
private static final Logger LOG = Logger.getLogger(BAMDiff.class.getName());
public static class Options {
public Options(String contigsToProcess,boolean ignoreUnmappedReads, boolean ignoreSequenceOrder,
boolean ignoreSequenceProperties, boolean ignoreFileFormatVersion,
boolean ignoreNullVsZeroPI, boolean throwOnError) {
this.contigsToProcess = contigsToProcess;
this.ignoreUnmappedReads = ignoreUnmappedReads;
this.ignoreSequenceOrder = ignoreSequenceOrder;
this.ignoreSequenceProperties = ignoreSequenceProperties;
this.ignoreFileFormatVersion = ignoreFileFormatVersion;
this.ignoreNullVsZeroPI = ignoreNullVsZeroPI;
this.throwOnError = throwOnError;
}
String contigsToProcess;
public boolean ignoreUnmappedReads;
public boolean throwOnError;
public boolean ignoreSequenceOrder;
public boolean ignoreSequenceProperties;
public boolean ignoreFileFormatVersion;
public boolean ignoreNullVsZeroPI;
}
public static void main(String[] args) {
BAMDiff diff = new BAMDiff(args[0], args[1], new BAMDiff.Options(
args.length >= 3 ? args[2] : null, true, true, true, true, true, false ));
try {
diff.runDiff();
} catch (Exception e) {
e.printStackTrace();
LOG.severe(e.getMessage());
}
}
String BAMFile1;
String BAMFile2;
Options options;
Set referencesToProcess = null;
int processedContigs = 0;
int processedLoci = 0;
int processedReads = 0;
public BAMDiff(String bAMFile1, String bAMFile2, Options options) {
BAMFile1=bAMFile1;
BAMFile2=bAMFile2;
this.options=options;
}
public void runDiff() throws Exception {
SamReaderFactory readerFactory = SamReaderFactory
.makeDefault()
.validationStringency(ValidationStringency.SILENT)
.enable(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES);
LOG.info("Opening file 1 for diff: " + BAMFile1);
SamReader reader1 = readerFactory.open(new File(BAMFile1));
LOG.info("Opening file 2 for diff: " + BAMFile2);
SamReader reader2 = readerFactory.open(new File(BAMFile2));
try {
Iterator contigsToProcess = null;
if (options.contigsToProcess != null && !options.contigsToProcess.isEmpty()) {
Iterable parsedContigs = Contig.parseContigsFromCommandLine(options.contigsToProcess);
referencesToProcess = Sets.newHashSet();
for (Contig c : parsedContigs) {
referencesToProcess.add(c.referenceName);
}
contigsToProcess = parsedContigs.iterator();
if (!contigsToProcess.hasNext()) {
return;
}
}
LOG.info("Comparing headers");
if (!compareHeaders(reader1.getFileHeader(), reader2.getFileHeader())) {
error("Headers are not equal");
return;
}
LOG.info("Headers are equal");
do {
SAMRecordIterator it1;
SAMRecordIterator it2;
if (contigsToProcess == null) {
LOG.info("Checking all the reads");
it1 = reader1.iterator();
it2 = reader2.iterator();
} else {
Contig contig = contigsToProcess.next();
LOG.info("Checking contig " + contig.toString());
processedContigs++;
it1 = reader1.queryOverlapping(contig.referenceName, (int)contig.start, (int)contig.end);
it2 = reader2.queryOverlapping(contig.referenceName, (int)contig.start, (int)contig.end);
}
if (!compareRecords(it1, it2)) {
break;
}
it1.close();
it2.close();
} while (contigsToProcess != null && contigsToProcess.hasNext());
} catch (Exception ex) {
throw ex;
} finally {
reader1.close();
reader2.close();
}
LOG.info("Processed " + processedContigs + " contigs, " +
processedLoci + " loci, " + processedReads + " reads.");
}
class SameCoordReadSet {
public Map map;
public int coord;
public String reference;
}
boolean compareRecords(SAMRecordIterator it1, SAMRecordIterator it2) throws Exception {
PeekIterator pit1 = new PeekIterator(it1);
PeekIterator pit2 = new PeekIterator(it2);
do {
SameCoordReadSet reads1 = getSameCoordReads(pit1, BAMFile1);
SameCoordReadSet reads2 = getSameCoordReads(pit2, BAMFile2);
if (reads1 == null) {
if (reads2 == null) {
return true;
} else {
error(BAMFile1 + " reads exhausted but there are still reads at " +
reads2.reference + ":" + reads2.coord + " in " + BAMFile2);
return false;
}
} else {
if (reads2 == null) {
error(BAMFile2 + " reads exhausted but there are still reads at " +
reads1.reference + ":" + reads1.coord + " in " + BAMFile1);
return false;
} else {
processedLoci++;
if (!compareSameCoordReads(reads1, reads2)) {
return false;
}
LOG.fine("Same reads at " + reads1.reference + ":" + reads1.coord);
}
}
if (processedLoci % 100000000 == 0) {
LOG.info("Working..., processed " +
processedLoci + " loci, " + processedReads + " reads.");
}
} while(true);
}
SameCoordReadSet getSameCoordReads(PeekIterator it, String fileName) throws Exception {
SameCoordReadSet ret = null;
try {
SAMRecord record;
while (it.hasNext()) {
record = it.peek();
if (record.isSecondaryOrSupplementary() ||
(options.ignoreUnmappedReads && record.getReadUnmappedFlag())) {
it.next();
continue;
}
if (ret != null) {
if (record.getAlignmentStart() != ret.coord || !record.getReferenceName().equals(ret.reference)) {
break;
}
} else {
ret = new SameCoordReadSet();
ret.map = Maps.newHashMap();
ret.coord = record.getAlignmentStart();
ret.reference = record.getReferenceName();
}
ret.map.put(record.getReadName(), record);
it.next();
}
} catch (Exception ex) {
throw new Exception("Error reading from " + fileName + "\n" + ex.getMessage());
}
return ret;
}
boolean compareSameCoordReads(SameCoordReadSet reads1, SameCoordReadSet reads2) throws Exception {
if (!reads1.reference.equals(reads2.reference)) {
error("Different references " + reads1.reference + "!=" + reads2.reference + " at " + reads1.coord);
return false;
}
if (reads1.coord != reads2.coord) {
error("Different coordinates " + reads1.coord + "!=" + reads2.coord + " at " + reads1.reference);
return false;
}
for (String readName : reads1.map.keySet()) {
processedReads++;
SAMRecord sr1 = reads1.map.get(readName);
SAMRecord sr2 = reads2.map.get(readName);
if (sr2 == null) {
error("Read " + readName + " not found at " + reads1.reference + ":" + reads1.coord +
" in " + BAMFile2);
return false;
}
String str1 = sr1.getSAMString();
String str2 = sr2.getSAMString();
if (!str1.equals(str2)) {
error("Records are not equal for read " + readName +
" at " + reads1.reference + ":" + reads1.coord + "\n" + str1 + "\n" + str2);
}
}
for (String readName : reads2.map.keySet()) {
if (reads1.map.get(readName) == null) {
error("Read " + readName + " not found at " + reads2.reference + ":" + reads2.coord +
" in " + BAMFile1);
return false;
}
}
return true;
}
void error(String msg) throws Exception {
LOG.severe(msg);
if (options.throwOnError) {
throw new Exception(msg);
}
}
private boolean compareHeaders(SAMFileHeader h1, SAMFileHeader h2) throws Exception {
boolean ret = true;
if (!options.ignoreFileFormatVersion) {
ret = compareValues(h1.getVersion(), h2.getVersion(), "File format version") && ret;
}
ret = compareValues(h1.getCreator(), h2.getCreator(), "File creator") && ret;
ret = compareValues(h1.getAttribute("SO"), h2.getAttribute("SO"), "Sort order") && ret;
if (!compareSequenceDictionaries(h1, h2)) {
return false;
}
ret = compareReadGroups(h1, h2) && ret;
ret = compareProgramRecords(h1, h2) && ret;
return ret;
}
private boolean compareProgramRecords(final SAMFileHeader h1, final SAMFileHeader h2) throws Exception {
final List l1 = h1.getProgramRecords();
final List l2 = h2.getProgramRecords();
if (!compareValues(l1.size(), l2.size(), "Number of program records")) {
return false;
}
boolean ret = true;
for (SAMProgramRecord pr1 : l1) {
for (SAMProgramRecord pr2 : l2) {
if (pr1.getId().equals(pr2.getId())) {
ret = compareProgramRecord(pr1, pr2) && ret;
}
}
}
return ret;
}
private boolean compareProgramRecord(final SAMProgramRecord programRecord1, final SAMProgramRecord programRecord2) throws Exception {
if (programRecord1 == null && programRecord2 == null) {
return true;
}
if (programRecord1 == null) {
reportDifference("null", programRecord2.getProgramGroupId(), "Program Record");
return false;
}
if (programRecord2 == null) {
reportDifference(programRecord1.getProgramGroupId(), "null", "Program Record");
return false;
}
boolean ret = compareValues(programRecord1.getProgramGroupId(), programRecord2.getProgramGroupId(),
"Program Name");
final String[] attributes = {"VN", "CL"};
for (final String attribute : attributes) {
ret = compareValues(programRecord1.getAttribute(attribute), programRecord2.getAttribute(attribute),
attribute + " Program Record attribute") && ret;
}
return ret;
}
private boolean compareReadGroups(final SAMFileHeader h1, final SAMFileHeader h2) throws Exception {
final List l1 = h1.getReadGroups();
final List l2 = h2.getReadGroups();
if (!compareValues(l1.size(), l2.size(), "Number of read groups")) {
return false;
}
boolean ret = true;
for (int i = 0; i < l1.size(); ++i) {
ret = compareReadGroup(l1.get(i), l2.get(i)) && ret;
}
return ret;
}
private boolean compareReadGroup(final SAMReadGroupRecord samReadGroupRecord1, final SAMReadGroupRecord samReadGroupRecord2) throws Exception {
boolean ret = compareValues(samReadGroupRecord1.getReadGroupId(), samReadGroupRecord2.getReadGroupId(),
"Read Group ID");
ret = compareValues(samReadGroupRecord1.getSample(), samReadGroupRecord2.getSample(),
"Sample for read group " + samReadGroupRecord1.getReadGroupId()) && ret;
ret = compareValues(samReadGroupRecord1.getLibrary(), samReadGroupRecord2.getLibrary(),
"Library for read group " + samReadGroupRecord1.getReadGroupId()) && ret;
final String[] attributes = {"DS", "PU", "PI", "CN", "DT", "PL"};
for (final String attribute : attributes) {
String a1 = samReadGroupRecord1.getAttribute(attribute);
String a2 = samReadGroupRecord2.getAttribute(attribute);
if (options.ignoreNullVsZeroPI && attribute.equals("PI")) {
if (a1 == null) {
a1 = "0";
}
if (a2 == null) {
a2 = "0";
}
}
ret = compareValues(a1, a2,
attribute + " for read group " + samReadGroupRecord1.getReadGroupId()) && ret;
}
return ret;
}
private boolean compareSequenceDictionaries(final SAMFileHeader h1, final SAMFileHeader h2) throws Exception {
final List s1 = h1.getSequenceDictionary().getSequences();
final List s2 = h2.getSequenceDictionary().getSequences();
if (referencesToProcess == null && s1.size() != s2.size()) {
reportDifference(s1.size(), s2.size(), "Length of sequence dictionaries");
return false;
}
boolean ret = true;
if (referencesToProcess == null) {
LOG.info("Comparing all sequences in the headers");
for (int i = 0; i < s1.size(); ++i) {
LOG.info("Comparing reference at index " + i);
SAMSequenceRecord sr1 = s1.get(i);
SAMSequenceRecord sr2 = options.ignoreSequenceOrder ?
h2.getSequenceDictionary().getSequence(sr1.getSequenceName()) :
s2.get(i);
if (sr2 == null) {
error("Failed to find sequence " + sr1.getSequenceName() + " in " + BAMFile2);
}
ret = compareSequenceRecord(sr1, sr2, i + 1) && ret;
}
} else {
LOG.info("Comparing specified sequences in the headers");
for (String r : referencesToProcess) {
LOG.info("Comparing reference " + r);
ret = compareSequenceRecord(h1.getSequenceDictionary().getSequence(r),
h2.getSequenceDictionary().getSequence(r), -1) && ret;
}
}
return ret;
}
private boolean compareSequenceRecord(final SAMSequenceRecord sequenceRecord1, final SAMSequenceRecord sequenceRecord2, final int which) throws Exception {
if (!sequenceRecord1.getSequenceName().equals(sequenceRecord2.getSequenceName())) {
reportDifference(sequenceRecord1.getSequenceName(), sequenceRecord2.getSequenceName(),
"Name of sequence record " + which);
return false;
}
boolean ret = compareValues(sequenceRecord1.getSequenceLength(), sequenceRecord2.getSequenceLength(), "Length of sequence " +
sequenceRecord1.getSequenceName());
if (!options.ignoreSequenceProperties) {
ret = compareValues(sequenceRecord1.getSpecies(), sequenceRecord2.getSpecies(), "Species of sequence " +
sequenceRecord1.getSequenceName()) && ret;
ret = compareValues(sequenceRecord1.getAssembly(), sequenceRecord2.getAssembly(), "Assembly of sequence " +
sequenceRecord1.getSequenceName()) && ret;
ret = compareValues(sequenceRecord1.getAttribute("M5"), sequenceRecord2.getAttribute("M5"), "MD5 of sequence " +
sequenceRecord1.getSequenceName()) && ret;
ret = compareValues(sequenceRecord1.getAttribute("UR"), sequenceRecord2.getAttribute("UR"), "URI of sequence " +
sequenceRecord1.getSequenceName()) && ret;
}
return ret;
}
private boolean compareValues(final T v1, final T v2, final String label) throws Exception {
if (v1 == null) {
if (v2 == null) {
return true;
}
reportDifference(v1, v2, label);
return false;
}
if (v2 == null) {
reportDifference(v1, v2, label);
return false;
}
if (!v1.equals(v2)) {
reportDifference(v1, v2, label);
return false;
}
return true;
}
private void reportDifference(final String s1, final String s2, final String label) throws Exception {
error(label + " differs.\n" +
BAMFile1 + ": " + s1 + "\n" +
BAMFile2 + ": " + s2);
}
private void reportDifference(Object o1, Object o2, final String label) throws Exception {
if (o1 == null) {
o1 = "null";
}
if (o2 == null) {
o2 = "null";
}
reportDifference(o1.toString(), o2.toString(), label);
}
}
