Phase 3: constrained movement is now the only option available in the realigner (so I guess technically it's not really an option). Several command-line options are deprecated. Code cleaned up. Wiki updated. Release coming. One phase left...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5299 348d0f76-0448-11de-a6fe-93d51630548a
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@ -44,7 +44,6 @@ 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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import org.broadinstitute.sting.gatk.walkers.BAQMode;
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import org.broadinstitute.sting.gatk.filters.BadMateFilter;
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import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
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import org.broadinstitute.sting.utils.*;
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import org.broadinstitute.sting.utils.baq.BAQ;
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@ -96,12 +95,12 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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@Argument(fullName="doNotUseSW", shortName="doNotUseSW", required=false, doc="Don't run 'Smith-Waterman' to generate alternate consenses; use only known indels provided as RODs or indels in the reads for constructing the alternate references.")
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protected boolean NO_SW = false;
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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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@Argument(fullName="maxIsizeForMovement", shortName="maxIsize", doc="maximum insert size of read pairs that we attempt to realign", required=false)
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protected int MAX_ISIZE_FOR_MOVEMENT = 3000;
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@Argument(fullName="maxConsensuses", shortName="maxConsensuses", doc="max alternate consensuses to try (necessary to improve performance in deep coverage)", required=false)
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protected int MAX_CONSENSUSES = 30;
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@ -112,20 +111,6 @@ 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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@Hidden
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@Argument(fullName="doNotSortEvenThoughItIsHighlyUnsafe", required=false,
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doc="Should we not sort the final bam at all?")
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protected boolean DO_NOT_SORT = false;
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@Argument(fullName="sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", required=false,
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doc="Should we sort the final bam in coordinate order even though it will be malformed because "+
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"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="realignReadsWithBadMates", required=false,
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doc="Should we try to realign paired-end reads whose mates map to other chromosomes?")
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protected boolean REALIGN_BADLY_MATED_READS = false;
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@Argument(fullName="noPGTag", shortName="noPG", required=false,
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doc="Don't output the usual PG tag in the realigned bam file header. FOR DEBUGGING PURPOSES ONLY. "+
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"This option is required in order to pass integration tests.")
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@ -159,6 +144,21 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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protected boolean CHECKEARLY = false;
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// DEPRECATED
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@Deprecated
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@Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="This argument is no longer used.", required=false)
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protected int DEPRECATED_MAX_IN_RAM = 0;
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@Deprecated
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@Argument(fullName="sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", doc="This argument is no longer used.", required=false)
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protected boolean DEPRECATED_SORT_IN_COORDINATE_ORDER = false;
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@Deprecated
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@Argument(fullName="realignReadsWithBadMates", doc="This argument is no longer used.", required=false)
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protected boolean DEPRECATED_REALIGN_MATES = false;
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// DEBUGGING OPTIONS FOLLOW
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@Hidden
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@ -173,16 +173,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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@Output(fullName="SNPsFileForDebugging", shortName="snps", doc="print out whether mismatching columns do or don't get cleaned out; FOR DEBUGGING PURPOSES ONLY", required=false)
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protected String OUT_SNPS = null;
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//
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// Experimental output constraints
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//
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// TODO -- eric promised me he'll validate this further and release to the world as the only option to do cleaning
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//
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@Hidden
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@Argument(fullName="constrainMovement", shortName="CM", required=false, doc="If provided, we'll try the experimental constraining output system")
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protected boolean CONSTRAIN_MOVEMENT = false;
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protected int MAX_ISIZE_FOR_MOVEMENT = 3000;
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// fasta reference reader to supplement the edges of the reference sequence
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private IndexedFastaSequenceFile referenceReader;
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@ -297,8 +287,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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}
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}
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SAMFileWriterImpl.setDefaultMaxRecordsInRam(MAX_RECORDS_IN_RAM);
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for ( SAMReaderID rid : getToolkit().getReadsDataSource().getReaderIDs() ) {
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String fName = getToolkit().getReadsDataSource().getSAMFile(rid).getName();
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@ -323,7 +311,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered");
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File f = new File(outName);
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SAMFileWriter sw = new SAMFileWriterFactory().makeSAMOrBAMWriter(setupHeader(getToolkit().getSAMFileHeader(rid)), false, f);
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SAMFileHeader header = getToolkit().getSAMFileHeader(rid);
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header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
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SAMFileWriter sw = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, false, f);
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nwayWriters.put(rid,sw);
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}
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@ -362,19 +352,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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}
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}
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private SAMFileHeader setupHeader(SAMFileHeader header) {
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if ( DO_NOT_SORT )
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header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
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else if ( SORT_IN_COORDINATE_ORDER || CONSTRAIN_MOVEMENT )
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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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return header;
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}
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private void setupWriter(SAMFileHeader header) {
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header = setupHeader(header);
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if ( !NO_PG_TAG ) {
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final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME);
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final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText");
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@ -395,13 +374,10 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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}
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writer.writeHeader(header);
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writer.setPresorted(CONSTRAIN_MOVEMENT);
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writer.setMaxRecordsInRam(MAX_RECORDS_IN_RAM);
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writer.setPresorted(true);
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if ( CONSTRAIN_MOVEMENT ) {
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writer.setUseConstrainedFileWriter(true);
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writer.setMaxInsertSizeForMovingReadPairs(MAX_ISIZE_FOR_MOVEMENT);
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}
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writer.setUseConstrainedFileWriter(true);
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writer.setMaxInsertSizeForMovingReadPairs(MAX_ISIZE_FOR_MOVEMENT);
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}
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private void emit(final SAMRecord read) {
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@ -489,19 +465,12 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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}
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private boolean doNotTryToClean(SAMRecord read) {
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boolean immobileReadForWriting = CONSTRAIN_MOVEMENT && ConstrainedMateFixingSAMFileWriter.iSizeTooBigToMove(read, MAX_ISIZE_FOR_MOVEMENT);
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boolean old = read.getReadUnmappedFlag() ||
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return read.getReadUnmappedFlag() ||
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read.getNotPrimaryAlignmentFlag() ||
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read.getReadFailsVendorQualityCheckFlag() ||
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read.getMappingQuality() == 0 ||
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read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ||
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(!REALIGN_BADLY_MATED_READS && BadMateFilter.hasBadMate(read));
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// if ( immobileReadForWriting && ! old)
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// logger.warn("Newly skipping read: " + read + " isize = " + read.getInferredInsertSize());
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return old || immobileReadForWriting;
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ConstrainedMateFixingSAMFileWriter.iSizeTooBigToMove(read, MAX_ISIZE_FOR_MOVEMENT);
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}
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private void cleanAndCallMap(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
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@ -73,8 +73,9 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
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@Argument(fullName="maxIntervalSize", shortName="maxInterval", doc="maximum interval size", required=false)
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protected int maxIntervalSize = 500;
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@Argument(fullName="realignReadsWithBadMates", required=false, doc="Should we try to realign paired-end reads whose mates map to other chromosomes?")
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protected boolean REALIGN_BADLY_MATED_READS = false;
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@Deprecated
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@Argument(fullName="realignReadsWithBadMates", doc="This argument is no longer used.", required=false)
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protected boolean DEPRECATED_REALIGN_MATES = false;
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@Override
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public boolean generateExtendedEvents() { return true; }
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@ -140,7 +141,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
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int mismatchQualities = 0, totalQualities = 0;
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byte refBase = ref.getBase();
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for (PileupElement p : pileup ) {
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if ( !REALIGN_BADLY_MATED_READS && BadMateFilter.hasBadMate(p.getRead()) )
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if ( BadMateFilter.hasBadMate(p.getRead()) )
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continue;
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// check the ends of the reads to see how far they extend
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@ -12,7 +12,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
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private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.bam";
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private static final String mainTestIntervals = validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals";
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private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf";
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private static final String baseCommandPrefix = "--constrainMovement -T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe ";
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private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 ";
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private static final String baseCommand = baseCommandPrefix + "-o %s ";
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@Test
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@ -91,7 +91,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
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@Test
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public void testLongRun() {
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WalkerTestSpec spec = new WalkerTestSpec(
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"--constrainMovement -T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -o %s",
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"-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s",
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1,
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Arrays.asList("be859f9a98d738becee0526887cae42e"));
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executeTest("realigner long run", spec);
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