-Remove Nway output option
-Remove in-memory sorting -Default to name-sorting (although we allow coordinate sorting with the --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe flag). Cleaner, faster code. Wiki has been updated (including how to use FixMateInformation.jar from Picard). More changes coming soon. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3612 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks
parent
30cf78fdc0
commit
b5df2705c9
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@ -31,7 +31,6 @@ import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
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import org.broadinstitute.sting.utils.interval.IntervalUtils;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
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import org.broadinstitute.sting.gatk.refdata.*;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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@ -67,26 +66,15 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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@Argument(fullName="entropyThreshold", shortName="entropy", doc="percentage of mismatches at a locus to be considered having high entropy", required=false)
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protected double MISMATCH_THRESHOLD = 0.15;
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@Argument(fullName="output", shortName="O", required=false, doc="Output bam (or directory if using --NwayOutput)")
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protected String baseWriterFilename = null;
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@Argument(fullName="NWayOutput", shortName="nway", required=false, doc="Should the reads be emitted in a separate bam file for each one of the input bams? [default:no]")
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protected boolean NWAY_OUTPUT = false;
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@Argument(fullName="outputSuffix", shortName="suffix", required=false, doc="Suffix to append to output bams (when using --NwayOutput) [default:'.cleaned']")
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protected String outputSuffix = "cleaned";
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@Argument(fullName="output", shortName="O", required=false, doc="Output bam")
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protected String writerFilename = null;
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@Argument(fullName="bam_compression", shortName="compress", required=false, doc="Compression level to use for output bams [default:5]")
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protected Integer compressionLevel = 5;
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public enum RealignerSortingStrategy {
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NO_SORT,
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ON_DISK,
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IN_MEMORY
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}
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@Argument(fullName="sortStrategy", shortName="sort", required=false, doc="What type of sorting strategy should we use? Options include NO_SORT, ON_DISK, and IN_MEMORY. Sorting in memory is much faster than on disk but should be used with care - with too much coverage or with long reads it might generate failures [default:ON_DISK]")
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protected RealignerSortingStrategy SORTING_STRATEGY = RealignerSortingStrategy.ON_DISK;
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@Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="max reads allowed to be kept in memory at a time by the SAMFileWriter. "+
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"If too low, the tool may run out of system file descriptors needed to perform sorting; if too high, the tool may run out of memory.", required=false)
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protected int MAX_RECORDS_IN_RAM = 500000;
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// ADVANCED OPTIONS FOLLOW
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@ -109,14 +97,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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"if this value is exceeded, realignment is not attempted and the reads are passed to the output file(s) as-is", required=false)
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protected int MAX_READS = 20000;
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@Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="max reads allowed to be kept in memory at a time "+
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"when using ON_DISK sorting option. If too low, the tool may run out of system file descriptors needed to perform sorting; "+
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"if too high, the tool may run out of memory in the regions of unusually deep coverage (consider also increasing VM heap size if this happens)",
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required=false)
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protected int MAX_RECORDS_IN_RAM = 500000;
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@Argument(fullName="writerWindowSize", shortName="writerWindowSize", doc="the window over which the writer will store reads when --sortInMemory is enabled", required=false)
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protected int SORTING_WRITER_WINDOW = 300;
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@Argument(fullName="sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", required=false, doc="Should we sort the final bam in coordinate order even though it will be malformed because mate pairs of realigned reads will contain inaccurate information?")
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protected boolean SORT_IN_COORDINATE_ORDER = false;
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@Argument(fullName="no_pg_tag", shortName="noPG", required=false, doc="Don't output the usual PG tag in the realigned bam file header. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.")
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protected boolean NO_PG_TAG = false;
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@ -133,7 +115,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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private final IdentityHashMap<Object, VariantContext> knownIndelsToTry = new IdentityHashMap<Object, VariantContext>();
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// the wrapper around the SAM writer
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private Map<String, SAMFileWriter> writers = null;
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private SAMFileWriter writer = null;
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// random number generator
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private static final long RANDOM_SEED = 1252863495;
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@ -173,32 +155,13 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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currentInterval = intervals.hasNext() ? intervals.next() : null;
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// set up the output writer(s)
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if ( baseWriterFilename != null ) {
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writers = new HashMap<String, SAMFileWriter>();
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Map<File, Set<String>> readGroupMap = getToolkit().getFileToReadGroupIdMapping();
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if ( writerFilename != null ) {
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SAMFileWriterFactory factory = new SAMFileWriterFactory();
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factory.setMaxRecordsInRam(MAX_RECORDS_IN_RAM);
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if ( NWAY_OUTPUT ) {
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List<SAMReaderID> ids = getToolkit().getDataSource().getReaderIDs();
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for ( SAMReaderID id: ids ) {
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File file = getToolkit().getDataSource().getSAMFile(id);
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SAMFileHeader header = getToolkit().getSAMFileHeader();
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String newFileName = file.getName().substring(0, file.getName().length()-3) + outputSuffix + ".bam";
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File newFile = new File(baseWriterFilename, newFileName);
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SAMFileWriter writer = makeWriter(factory, header, newFile);
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for ( String rg : readGroupMap.get(file) )
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writers.put(rg, writer);
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}
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} else {
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SAMFileHeader header = getToolkit().getSAMFileHeader();
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File file = new File(baseWriterFilename);
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SAMFileWriter writer = makeWriter(factory, header, file);
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for ( Set<String> set : readGroupMap.values() ) {
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for ( String rg : set )
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writers.put(rg, writer);
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}
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}
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SAMFileHeader header = getToolkit().getSAMFileHeader();
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File file = new File(writerFilename);
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writer = makeWriter(factory, header, file);
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}
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if ( OUT_INDELS != null ) {
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@ -231,8 +194,10 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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}
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private SAMFileWriter makeWriter(SAMFileWriterFactory factory, SAMFileHeader header, File file) {
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if ( SORTING_STRATEGY == RealignerSortingStrategy.NO_SORT )
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header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
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if ( SORT_IN_COORDINATE_ORDER )
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header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
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else
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header.setSortOrder(SAMFileHeader.SortOrder.queryname);
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if ( !NO_PG_TAG ) {
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final SAMProgramRecord programRecord = new SAMProgramRecord("GATK IndelRealigner");
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@ -241,61 +206,23 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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header.addProgramRecord( programRecord );
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}
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SAMFileWriter writer = factory.makeBAMWriter(header, SORTING_STRATEGY == RealignerSortingStrategy.IN_MEMORY, file, compressionLevel);
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if ( SORTING_STRATEGY == RealignerSortingStrategy.IN_MEMORY )
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writer = new SortingSAMFileWriter(writer, SORTING_WRITER_WINDOW);
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SAMFileWriter writer = factory.makeBAMWriter(header, false, file, compressionLevel);
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return writer;
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}
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private void emit(final SAMRecord read) {
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if ( writers != null ) {
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SAMReadGroupRecord readGroup = read.getReadGroup();
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if ( readGroup == null || readGroup.getReadGroupId() == null ) {
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if ( writers.size() > 1 )
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throw new StingException("There are multiple output writers but read " + read.toString() + " has no read group");
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writers.values().iterator().next().addAlignment(read);
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} else {
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writers.get(readGroup.getReadGroupId()).addAlignment(read);
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}
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}
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if ( writer != null )
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writer.addAlignment(read);
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}
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private void emit(final List<SAMRecord> reads) {
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if ( writers == null )
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return;
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// break out the reads into sets for their respective writers
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Map<SAMFileWriter, Set<SAMRecord>> bins = new HashMap<SAMFileWriter, Set<SAMRecord>>();
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for ( SAMFileWriter writer : writers.values() )
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bins.put(writer, new HashSet<SAMRecord>());
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for ( SAMRecord read : reads ) {
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SAMReadGroupRecord readGroup = read.getReadGroup();
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if ( readGroup == null || readGroup.getReadGroupId() == null ) {
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if ( writers.size() > 1 )
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throw new StingException("There are multiple output writers but read " + read.toString() + " has no read group");
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bins.get(writers.values().iterator().next()).add(read);
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} else {
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bins.get(writers.get(readGroup.getReadGroupId())).add(read);
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}
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}
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for ( Map.Entry<SAMFileWriter, Set<SAMRecord>> entry : bins.entrySet() ) {
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if ( SORTING_STRATEGY == RealignerSortingStrategy.IN_MEMORY ) {
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// we can be efficient in this case by batching the reads all together
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((SortingSAMFileWriter)entry.getKey()).addAlignments(entry.getValue());
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} else {
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for ( SAMRecord read : entry.getValue() )
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entry.getKey().addAlignment(read);
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}
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if ( writer != null ) {
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for ( SAMRecord read : reads )
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writer.addAlignment(read);
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}
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}
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long nPerfectMatches = 0;
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long nReadsToClean = 0;
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public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
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if ( currentInterval == null ) {
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emit(read);
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@ -328,7 +255,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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readsNotToClean.add(read);
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}
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else {
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nReadsToClean++;
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readsToClean.add(read, ref.getBases());
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// add the rods to the list of known variants
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populateKnownIndels(metaDataTracker, null);
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@ -386,14 +312,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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emit(readsNotToClean);
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}
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if ( writers != null ) {
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HashSet<SAMFileWriter> uniqueWriters = new HashSet<SAMFileWriter>(writers.values());
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for ( SAMFileWriter writer : uniqueWriters ) {
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writer.close();
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if ( SORTING_STRATEGY == RealignerSortingStrategy.IN_MEMORY )
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((SortingSAMFileWriter)writer).getBaseWriter().close();
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}
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}
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if ( writer != null )
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writer.close();
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if ( OUT_INDELS != null ) {
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try {
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@ -536,11 +456,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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}
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// otherwise, we can emit it as is
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else {
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// nPerfectMatches++;
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// if ( nPerfectMatches % 1000 == 0 ) {
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// logger.info(String.format("Perfect matching fraction: %d %d => %.2f", nPerfectMatches, nReadsToClean, 100.0 * nPerfectMatches / ( nReadsToClean + 1)));
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// }
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// if ( debugOn ) System.out.println("Emitting as is...");
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//logger.debug("Adding " + aRead.getRead().getReadName() + " with raw mismatch score " + rawMismatchScore + " to ref reads");
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refReads.add(read);
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@ -1,125 +0,0 @@
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package org.broadinstitute.sting.gatk.walkers.indels;
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import net.sf.samtools.*;
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import java.util.TreeSet;
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import java.util.Iterator;
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import java.util.Collection;
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/**
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* @author ebanks
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* SortingSAMFileWriter
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*
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* this class extends the samtools SAMFileWriter class and caches reads for N loci so that reads
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* can be emitted out of order (provided they are within the N-locus window)
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*
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*/
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public class SortingSAMFileWriter implements SAMFileWriter {
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// the base writer from Picard
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private SAMFileWriter baseWriter;
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// the window over which we agree to accumulate reads
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private int window;
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// the reads we are accumulating
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private TreeSet<SAMRecord> cachedReads = new TreeSet<SAMRecord>(new SAMRecordCoordinateComparatorWithUnmappedReads());
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/**
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* Constructor
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*
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* @param baseWriter the real SAMFileWriter
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* @param window the window over which we agree to store reads
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*/
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public SortingSAMFileWriter(SAMFileWriter baseWriter, int window) {
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this.baseWriter = baseWriter;
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this.window = window;
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}
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/**
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* Add a read to the writer for emission
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*
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* @param read the read to emit
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*/
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public void addAlignment(SAMRecord read) {
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// at a new contig, clear the cache
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if ( cachedReads.size() > 0 && cachedReads.first().getReferenceIndex() < read.getReferenceIndex() )
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clearCache();
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long currentPos = read.getAlignmentStart();
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Iterator<SAMRecord> iter = cachedReads.iterator();
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while ( iter.hasNext() ) {
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SAMRecord cachedRead = iter.next();
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if ( currentPos - cachedRead.getAlignmentStart() >= window ) {
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baseWriter.addAlignment(cachedRead);
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iter.remove();
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} else {
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break;
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}
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}
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cachedReads.add(read);
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}
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/**
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* Add a list of reads to the writer for emission; the reads do NOT need to be sorted
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*
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* @param reads the reads to emit
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*/
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public void addAlignments(Collection<SAMRecord> reads) {
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if ( reads.size() == 0 )
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return;
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// at a new contig, clear the cache
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if ( cachedReads.size() > 0 && cachedReads.first().getReferenceIndex() < reads.iterator().next().getReferenceIndex() )
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clearCache();
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cachedReads.addAll(reads);
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// get the last read in the cache
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SAMRecord last = cachedReads.last();
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long currentPos = last.getAlignmentStart();
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Iterator<SAMRecord> iter = cachedReads.iterator();
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while ( iter.hasNext() ) {
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SAMRecord cachedRead = iter.next();
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if ( currentPos - cachedRead.getAlignmentStart() >= window ) {
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baseWriter.addAlignment(cachedRead);
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iter.remove();
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} else {
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break;
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}
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}
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}
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/**
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* @return the SAM file header
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*/
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public SAMFileHeader getFileHeader() {
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return baseWriter.getFileHeader();
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}
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/**
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* close this writer by clearing the cache (but DO NOT close the underlying SAMFileWriter)
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*/
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public void close() {
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clearCache();
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}
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/**
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* @return the underlying SAMFileWriter
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*/
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public SAMFileWriter getBaseWriter() {
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return baseWriter;
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}
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private void clearCache() {
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Iterator<SAMRecord> iter = cachedReads.iterator();
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while ( iter.hasNext() )
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baseWriter.addAlignment(iter.next());
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cachedReads.clear();
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}
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}
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@ -4,38 +4,23 @@ import org.broadinstitute.sting.WalkerTest;
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import org.junit.Test;
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import java.util.Arrays;
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import java.io.File;
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public class IndelRealignerIntegrationTest extends WalkerTest {
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@Test
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public void testRealigner() {
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String[] md5lod5 = {"96edef86cea95f312ee8295b38227eb8", "d4d8ff567b614729ab8c52bd7d6bef48"};
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String[] md5lod5 = {"d9cbff4832fc3ee7a7ad1c58cc891bdd", "d4d8ff567b614729ab8c52bd7d6bef48"};
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WalkerTestSpec spec1 = new WalkerTestSpec(
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"-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023800-10332350 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -snps %s",
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"-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023800-10332350 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -snps %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
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2,
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Arrays.asList(md5lod5));
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executeTest("test Lod5", spec1);
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String[] md5lod200 = {"96edef86cea95f312ee8295b38227eb8", "d4d8ff567b614729ab8c52bd7d6bef48"};
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String[] md5lod200 = {"d9cbff4832fc3ee7a7ad1c58cc891bdd", "d4d8ff567b614729ab8c52bd7d6bef48"};
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WalkerTestSpec spec2 = new WalkerTestSpec(
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"-T IndelRealigner -noPG -LOD 200 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023800-10332350 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -snps %s",
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"-T IndelRealigner -noPG -LOD 200 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023800-10332350 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -snps %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
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2,
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Arrays.asList(md5lod200));
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executeTest("test Lod200", spec2);
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String filename1 = "NA12878.chrom1.SLX.SRP000032.2009_06";
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String filename2 = "low_coverage_CEU.chr1.10k-11k";
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WalkerTestSpec spec3 = new WalkerTestSpec(
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"-T IndelRealigner -nway -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + filename1 + ".bam -I " + validationDataLocation + filename2 + ".bam -L 1:10023900-10024000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O /tmp -snps %s",
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1,
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Arrays.asList("bd42a4fa66d7ec7a480c2b94313a78d3"));
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File file1 = new File("/tmp/" + filename1 + ".cleaned.bam");
|
||||
file1.deleteOnExit();
|
||||
spec3.addAuxFile("1ceae553c8aa20681ed0736d4d2b4541", file1);
|
||||
File file2 = new File("/tmp/" + filename2 + ".cleaned.bam");
|
||||
file2.deleteOnExit();
|
||||
spec3.addAuxFile("ce8ddeae5a5aab836ac1dde9448ccb66", file2);
|
||||
executeTest("test NWay", spec3);
|
||||
}
|
||||
}
|
||||
|
|
@ -18,10 +18,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
|
|||
" -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
|
||||
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
|
||||
" -L chr1:1-5,650,000" +
|
||||
" -compress 1" +
|
||||
" -sort NO_SORT" +
|
||||
" -targetIntervals " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.realigner.intervals" +
|
||||
" -O /dev/null",
|
||||
" -targetIntervals " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.realigner.intervals",
|
||||
0,
|
||||
new ArrayList<String>(0));
|
||||
try {
|
||||
|
|
@ -38,10 +35,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
|
|||
" -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
|
||||
" -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
|
||||
" -L chr1:1-150,000,000" +
|
||||
" -compress 1" +
|
||||
" -sort NO_SORT" +
|
||||
" -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals" +
|
||||
" -O /dev/null",
|
||||
" -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals",
|
||||
0,
|
||||
new ArrayList<String>(0));
|
||||
try {
|
||||
|
|
|
|||
Loading…
Reference in New Issue