From 0d3ea0401c0afb82487a1c2018750350fad790ca Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Tue, 7 Feb 2012 13:22:46 -0500 Subject: [PATCH 01/14] BQSR Parameter cleanup * get rid of 320C argument that nobody uses. * get rid of DEFAULT_READ_GROUP parameter and functionality (later to become an engine argument). --- .../recalibration/CountCovariatesWalker.java | 278 +++++++++--------- .../recalibration/RecalDataManager.java | 26 -- .../RecalibrationArgumentCollection.java | 22 +- .../TableRecalibrationWalker.java | 247 ++++++++-------- 4 files changed, 280 insertions(+), 293 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java index 4e3d4048b..626460be6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java @@ -77,20 +77,20 @@ import java.util.Map; *

Output

*

* A recalibration table file in CSV format that is used by the TableRecalibration walker. - * It is a comma-separated text file relating the desired covariates to the number of such bases and their rate of mismatch in the genome, and its implied empirical quality score. + * It is a comma-separated text file relating the desired covariates to the number of such bases and their rate of mismatch in the genome, and its implied empirical quality score. * - * The first 20 lines of such a file is shown below. + * The first 20 lines of such a file is shown below. * * The file begins with a series of comment lines describing: * ** The number of counted loci * ** The number of counted bases * ** The number of skipped loci and the fraction skipped, due to presence in dbSNP or bad reference bases - * - * * After the comments appears a header line indicating which covariates were used as well as the ordering of elements in the subsequent records. + * + * * After the comments appears a header line indicating which covariates were used as well as the ordering of elements in the subsequent records. * * * After the header, data records occur one per line until the end of the file. The first several items on a line are the values of the individual covariates and will change - * depending on which covariates were specified at runtime. The last three items are the data- that is, number of observations for this combination of covariates, number of + * depending on which covariates were specified at runtime. The last three items are the data- that is, number of observations for this combination of covariates, number of * reference mismatches, and the raw empirical quality score calculated by phred-scaling the mismatch rate. - * + * * 

  * # Counted Sites    19451059
  * # Counted Bases    56582018
@@ -129,13 +129,14 @@ import java.util.Map;
  *   -cov DinucCovariate \
  *   -recalFile my_reads.recal_data.csv
  *
- * */ @BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN) -@By( DataSource.READS ) // Only look at covered loci, not every loci of the reference file -@ReadFilters( {MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class} ) // Filter out all reads with zero or unavailable mapping quality -@Requires( {DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES} ) // This walker requires both -I input.bam and -R reference.fasta +@By(DataSource.READS) // Only look at covered loci, not every loci of the reference file +@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class}) +// Filter out all reads with zero or unavailable mapping quality +@Requires({DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES}) +// This walker requires both -I input.bam and -R reference.fasta @PartitionBy(PartitionType.LOCUS) public class CountCovariatesWalker extends LocusWalker implements TreeReducible { @@ -149,7 +150,8 @@ public class CountCovariatesWalker extends LocusWalker> knownSites = Collections.emptyList(); /** @@ -169,31 +171,31 @@ public class CountCovariatesWalker extends LocusWalker> covariateClasses = new PluginManager( Covariate.class ).getPlugins(); - final List> requiredClasses = new PluginManager( RequiredCovariate.class ).getPlugins(); - final List> standardClasses = new PluginManager( StandardCovariate.class ).getPlugins(); + final List> covariateClasses = new PluginManager(Covariate.class).getPlugins(); + final List> requiredClasses = new PluginManager(RequiredCovariate.class).getPlugins(); + final List> standardClasses = new PluginManager(StandardCovariate.class).getPlugins(); // Print and exit if that's what was requested - if ( LIST_ONLY ) { - logger.info( "Available covariates:" ); - for( Class covClass : covariateClasses ) { - logger.info( covClass.getSimpleName() ); + if (LIST_ONLY) { + logger.info("Available covariates:"); + for (Class covClass : covariateClasses) { + logger.info(covClass.getSimpleName()); } logger.info(""); - System.exit( 0 ); // Early exit here because user requested it + System.exit(0); // Early exit here because user requested it } // Warn the user if no dbSNP file or other variant mask was specified - if( knownSites.isEmpty() && !RUN_WITHOUT_DBSNP ) { + if (knownSites.isEmpty() && !RUN_WITHOUT_DBSNP) { throw new UserException.CommandLineException("This calculation is critically dependent on being able to skip over known variant sites. Please provide a VCF file containing known sites of genetic variation."); } // Initialize the requested covariates by parsing the -cov argument // First add the required covariates - if( requiredClasses.size() == 2) { // readGroup and reported quality score - requestedCovariates.add( new ReadGroupCovariate() ); // Order is important here - requestedCovariates.add( new QualityScoreCovariate() ); - } else { + if (requiredClasses.size() == 2) { // readGroup and reported quality score + requestedCovariates.add(new ReadGroupCovariate()); // Order is important here + requestedCovariates.add(new QualityScoreCovariate()); + } + else { throw new UserException.CommandLineException("There are more required covariates than expected. The instantiation list needs to be updated with the new required covariate and in the correct order."); } // Next add the standard covariates if -standard was specified by the user - if( USE_STANDARD_COVARIATES ) { + if (USE_STANDARD_COVARIATES) { // We want the standard covariates to appear in a consistent order but the packageUtils method gives a random order // A list of Classes can't be sorted, but a list of Class names can be final List standardClassNames = new ArrayList(); - for( Class covClass : standardClasses ) { - standardClassNames.add( covClass.getName() ); + for (Class covClass : standardClasses) { + standardClassNames.add(covClass.getName()); } Collections.sort(standardClassNames); // Sort the list of class names - for( String className : standardClassNames ) { - for( Class covClass : standardClasses ) { // Find the class that matches this class name - if( covClass.getName().equals( className ) ) { + for (String className : standardClassNames) { + for (Class covClass : standardClasses) { // Find the class that matches this class name + if (covClass.getName().equals(className)) { try { - final Covariate covariate = (Covariate)covClass.newInstance(); - requestedCovariates.add( covariate ); + final Covariate covariate = (Covariate) covClass.newInstance(); + requestedCovariates.add(covariate); } catch (Exception e) { throw new DynamicClassResolutionException(covClass, e); } @@ -302,17 +307,17 @@ public class CountCovariatesWalker extends LocusWalker covClass : covariateClasses ) { - if( requestedCovariateString.equalsIgnoreCase( covClass.getSimpleName() ) ) { // -cov argument matches the class name for an implementing class + for (Class covClass : covariateClasses) { + if (requestedCovariateString.equalsIgnoreCase(covClass.getSimpleName())) { // -cov argument matches the class name for an implementing class foundClass = true; - if( !requiredClasses.contains( covClass ) && (!USE_STANDARD_COVARIATES || !standardClasses.contains( covClass )) ) { + if (!requiredClasses.contains(covClass) && (!USE_STANDARD_COVARIATES || !standardClasses.contains(covClass))) { try { // Now that we've found a matching class, try to instantiate it - final Covariate covariate = (Covariate)covClass.newInstance(); - requestedCovariates.add( covariate ); + final Covariate covariate = (Covariate) covClass.newInstance(); + requestedCovariates.add(covariate); } catch (Exception e) { throw new DynamicClassResolutionException(covClass, e); } @@ -320,20 +325,19 @@ public class CountCovariatesWalker extends LocusWalker 0 ) { + if (gatkRead.getBaseQualities()[offset] > 0) { byte[] bases = gatkRead.getReadBases(); byte refBase = ref.getBase(); // Skip if this base is an 'N' or etc. - if( BaseUtils.isRegularBase( bases[offset] ) ) { + if (BaseUtils.isRegularBase(bases[offset])) { // SOLID bams have inserted the reference base into the read if the color space in inconsistent with the read base so skip it - if( !gatkRead.getReadGroup().getPlatform().toUpperCase().contains("SOLID") || RAC.SOLID_RECAL_MODE == RecalDataManager.SOLID_RECAL_MODE.DO_NOTHING || - !RecalDataManager.isInconsistentColorSpace( gatkRead, offset ) ) { + if (!gatkRead.getReadGroup().getPlatform().toUpperCase().contains("SOLID") || RAC.SOLID_RECAL_MODE == RecalDataManager.SOLID_RECAL_MODE.DO_NOTHING || + !RecalDataManager.isInconsistentColorSpace(gatkRead, offset)) { // This base finally passed all the checks for a good base, so add it to the big data hashmap - updateDataFromRead( counter, gatkRead, offset, refBase ); + updateDataFromRead(counter, gatkRead, offset, refBase); - } else { // calculate SOLID reference insertion rate - if( refBase == bases[offset] ) { + } + else { // calculate SOLID reference insertion rate + if (refBase == bases[offset]) { counter.solidInsertedReferenceBases++; - } else { + } + else { counter.otherColorSpaceInconsistency++; } } @@ -405,7 +410,8 @@ public class CountCovariatesWalker extends LocusWalker= DBSNP_VALIDATION_CHECK_FREQUENCY ) { + if (++counter.lociSinceLastDbsnpCheck >= DBSNP_VALIDATION_CHECK_FREQUENCY) { counter.lociSinceLastDbsnpCheck = 0; - if( counter.novelCountsBases != 0L && counter.dbSNPCountsBases != 0L ) { - final double fractionMM_novel = (double)counter.novelCountsMM / (double)counter.novelCountsBases; - final double fractionMM_dbsnp = (double)counter.dbSNPCountsMM / (double)counter.dbSNPCountsBases; + if (counter.novelCountsBases != 0L && counter.dbSNPCountsBases != 0L) { + final double fractionMM_novel = (double) counter.novelCountsMM / (double) counter.novelCountsBases; + final double fractionMM_dbsnp = (double) counter.dbSNPCountsMM / (double) counter.dbSNPCountsBases; - if( fractionMM_dbsnp < DBSNP_VS_NOVEL_MISMATCH_RATE * fractionMM_novel ) { - Utils.warnUser("The variation rate at the supplied list of known variant sites seems suspiciously low. Please double-check that the correct ROD is being used. " + - String.format("[dbSNP variation rate = %.4f, novel variation rate = %.4f]", fractionMM_dbsnp, fractionMM_novel) ); + if (fractionMM_dbsnp < DBSNP_VS_NOVEL_MISMATCH_RATE * fractionMM_novel) { + Utils.warnUser("The variation rate at the supplied list of known variant sites seems suspiciously low. Please double-check that the correct ROD is being used. " + String.format("[dbSNP variation rate = %.4f, novel variation rate = %.4f]", fractionMM_dbsnp, fractionMM_novel)); DBSNP_VALIDATION_CHECK_FREQUENCY *= 2; // Don't annoyingly output the warning message every megabase of a large file } } @@ -518,47 +525,50 @@ public class CountCovariatesWalker extends LocusWalker keyList = new ArrayList(); - for( Object comp : data.keySet() ) { + for (Object comp : data.keySet()) { keyList.add((Comparable) comp); } Collections.sort(keyList); - for( Comparable comp : keyList ) { + for (Comparable comp : keyList) { key[curPos] = comp; final Object val = data.get(comp); - if( val instanceof RecalDatumOptimized ) { // We are at the end of the nested hash maps + if (val instanceof RecalDatumOptimized) { // We are at the end of the nested hash maps // For each Covariate in the key - for( Object compToPrint : key ) { + for (Object compToPrint : key) { // Output the Covariate's value - recalTableStream.print( compToPrint + "," ); + recalTableStream.print(compToPrint + ","); } // Output the RecalDatum entry - recalTableStream.println( ((RecalDatumOptimized)val).outputToCSV() ); - } else { // Another layer in the nested hash map - printMappingsSorted( recalTableStream, curPos + 1, key, (Map) val ); + recalTableStream.println(((RecalDatumOptimized) val).outputToCSV()); + } + else { // Another layer in the nested hash map + printMappingsSorted(recalTableStream, curPos + 1, key, (Map) val); } } } - private void printMappings( final PrintStream recalTableStream, final int curPos, final Object[] key, final Map data) { - for( Object comp : data.keySet() ) { + private void printMappings(final PrintStream recalTableStream, final int curPos, final Object[] key, final Map data) { + for (Object comp : data.keySet()) { key[curPos] = comp; final Object val = data.get(comp); - if( val instanceof RecalDatumOptimized ) { // We are at the end of the nested hash maps + if (val instanceof RecalDatumOptimized) { // We are at the end of the nested hash maps // For each Covariate in the key - for( Object compToPrint : key ) { + for (Object compToPrint : key) { // Output the Covariate's value - recalTableStream.print( compToPrint + "," ); + recalTableStream.print(compToPrint + ","); } // Output the RecalDatum entry - recalTableStream.println( ((RecalDatumOptimized)val).outputToCSV() ); - } else { // Another layer in the nested hash map - printMappings( recalTableStream, curPos + 1, key, (Map) val ); + recalTableStream.println(((RecalDatumOptimized) val).outputToCSV()); + } + else { // Another layer in the nested hash map + printMappings(recalTableStream, curPos + 1, key, (Map) val); } } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java index 18b33c0e8..72c2b2829 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java @@ -256,32 +256,6 @@ public class RecalDataManager { public static void parseSAMRecord(final GATKSAMRecord read, final RecalibrationArgumentCollection RAC) { GATKSAMReadGroupRecord readGroup = ((GATKSAMRecord) read).getReadGroup(); - // If there are no read groups we have to default to something, and that something could be specified by the user using command line arguments - if (readGroup == null) { - if (RAC.DEFAULT_READ_GROUP != null && RAC.DEFAULT_PLATFORM != null) { - if (!warnUserNullReadGroup && RAC.FORCE_READ_GROUP == null) { - Utils.warnUser("The input .bam file contains reads with no read group. " + - "Defaulting to read group ID = " + RAC.DEFAULT_READ_GROUP + " and platform = " + RAC.DEFAULT_PLATFORM + ". " + - "First observed at read with name = " + read.getReadName()); - warnUserNullReadGroup = true; - } - // There is no readGroup so defaulting to these values - readGroup = new GATKSAMReadGroupRecord(RAC.DEFAULT_READ_GROUP); - readGroup.setPlatform(RAC.DEFAULT_PLATFORM); - ((GATKSAMRecord) read).setReadGroup(readGroup); - } - else { - throw new UserException.MalformedBAM(read, "The input .bam file contains reads with no read group. First observed at read with name = " + read.getReadName()); - } - } - - if (RAC.FORCE_READ_GROUP != null && !readGroup.getReadGroupId().equals(RAC.FORCE_READ_GROUP)) { // Collapse all the read groups into a single common String provided by the user - final String oldPlatform = readGroup.getPlatform(); - readGroup = new GATKSAMReadGroupRecord(RAC.FORCE_READ_GROUP); - readGroup.setPlatform(oldPlatform); - ((GATKSAMRecord) read).setReadGroup(readGroup); - } - if (RAC.FORCE_PLATFORM != null && (readGroup.getPlatform() == null || !readGroup.getPlatform().equals(RAC.FORCE_PLATFORM))) { readGroup.setPlatform(RAC.FORCE_PLATFORM); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java index 7f3035f1e..9752b1dee 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java @@ -43,31 +43,15 @@ public class RecalibrationArgumentCollection { // Shared Command Line Arguments ////////////////////////////////// @Hidden - @Argument(fullName = "default_read_group", shortName = "dRG", required = false, doc = "If a read has no read group then default to the provided String.") - public String DEFAULT_READ_GROUP = null; - @Hidden @Argument(fullName = "default_platform", shortName = "dP", required = false, doc = "If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.") public String DEFAULT_PLATFORM = null; @Hidden - @Argument(fullName = "force_read_group", shortName = "fRG", required = false, doc = "If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group.") - public String FORCE_READ_GROUP = null; - @Hidden @Argument(fullName = "force_platform", shortName = "fP", required = false, doc = "If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.") public String FORCE_PLATFORM = null; @Hidden @Argument(fullName = "window_size_nqs", shortName = "nqs", doc = "The window size used by MinimumNQSCovariate for its calculation", required = false) public int WINDOW_SIZE = 5; - /** - * This window size tells the module in how big of a neighborhood around the current base it should look for the minimum base quality score. - */ - @Hidden - @Argument(fullName = "homopolymer_nback", shortName = "nback", doc = "The number of previous bases to look at in HomopolymerCovariate", required = false) - public int HOMOPOLYMER_NBACK = 7; - @Hidden - @Argument(fullName = "exception_if_no_tile", shortName = "throwTileException", doc = "If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1", required = false) - public boolean EXCEPTION_IF_NO_TILE = false; - /** * CountCovariates and TableRecalibration accept a --solid_recal_mode flag which governs how the recalibrator handles the * reads which have had the reference inserted because of color space inconsistencies. @@ -89,4 +73,10 @@ public class RecalibrationArgumentCollection { @Argument(fullName = "context_size", shortName = "cs", doc = "size of the k-mer context to be used", required = false) public int CONTEXT_SIZE = 8; + /** + * This window size tells the module in how big of a neighborhood around the current base it should look for the minimum base quality score. + */ + @Argument(fullName = "homopolymer_nback", shortName = "nback", doc = "The number of previous bases to look at in HomopolymerCovariate", required = false) + public int HOMOPOLYMER_NBACK = 7; + } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java index a8006d506..cd848cd9e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java @@ -86,12 +86,12 @@ import java.util.regex.Pattern; * -o my_reads.recal.bam \ * -recalFile my_reads.recal_data.csv * - * */ @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT) @WalkerName("TableRecalibration") -@Requires({ DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES }) // This walker requires -I input.bam, it also requires -R reference.fasta +@Requires({DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES}) +// This walker requires -I input.bam, it also requires -R reference.fasta public class TableRecalibrationWalker extends ReadWalker { public static final String PROGRAM_RECORD_NAME = "GATK TableRecalibration"; @@ -99,7 +99,8 @@ public class TableRecalibrationWalker extends ReadWalker> classes = new PluginManager(Covariate.class).getPlugins(); @@ -205,31 +206,33 @@ public class TableRecalibrationWalker extends ReadWalker covClass : classes ) { - if( (vals[iii] + "Covariate").equalsIgnoreCase( covClass.getSimpleName() ) ) { + for (Class covClass : classes) { + if ((vals[iii] + "Covariate").equalsIgnoreCase(covClass.getSimpleName())) { foundClass = true; try { - Covariate covariate = (Covariate)covClass.newInstance(); - requestedCovariates.add( covariate ); + Covariate covariate = (Covariate) covClass.newInstance(); + requestedCovariates.add(covariate); } catch (Exception e) { throw new DynamicClassResolutionException(covClass, e); } @@ -237,107 +240,110 @@ public class TableRecalibrationWalker extends ReadWalker oldRecords = header.getProgramRecords(); - List newRecords = new ArrayList(oldRecords.size()+1); - for ( SAMProgramRecord record : oldRecords ) { - if ( !record.getId().startsWith(PROGRAM_RECORD_NAME) ) + List newRecords = new ArrayList(oldRecords.size() + 1); + for (SAMProgramRecord record : oldRecords) { + if (!record.getId().startsWith(PROGRAM_RECORD_NAME)) newRecords.add(record); } newRecords.add(programRecord); header.setProgramRecords(newRecords); // Write out the new header - OUTPUT_BAM.writeHeader( header ); + OUTPUT_BAM.writeHeader(header); } } /** * For each covariate read in a value and parse it. Associate those values with the data itself (num observation and num mismatches) + * * @param line A line of CSV data read from the recalibration table data file */ private void addCSVData(final File file, final String line) { final String[] vals = line.split(","); // Check if the data line is malformed, for example if the read group string contains a comma then it won't be parsed correctly - if( vals.length != requestedCovariates.size() + 3 ) { // +3 because of nObservations, nMismatch, and Qempirical + if (vals.length != requestedCovariates.size() + 3) { // +3 because of nObservations, nMismatch, and Qempirical throw new UserException.MalformedFile(file, "Malformed input recalibration file. Found data line with too many fields: " + line + " --Perhaps the read group string contains a comma and isn't being parsed correctly."); } @@ -345,15 +351,15 @@ public class TableRecalibrationWalker extends ReadWalker Date: Tue, 7 Feb 2012 18:11:53 -0500 Subject: [PATCH 02/14] laying groundwork to have insertions and deletions going through the system. --- .../recalibration/RecalDataManager.java | 17 +- .../broadinstitute/sting/utils/BaseUtils.java | 282 ++++++++++-------- 2 files changed, 163 insertions(+), 136 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java index 72c2b2829..311e33f8a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java @@ -36,6 +36,7 @@ import org.broadinstitute.sting.utils.recalibration.BaseRecalibration; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.sam.ReadUtils; import java.util.ArrayList; import java.util.List; @@ -284,7 +285,7 @@ public class RecalDataManager { public static void parseColorSpace(final GATKSAMRecord read) { // If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base - if (read.getReadGroup().getPlatform().toUpperCase().contains("SOLID")) { + if (ReadUtils.isSOLiDRead(read)) { if (read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) == null) { // Haven't calculated the inconsistency array yet for this read final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG); if (attr != null) { @@ -382,7 +383,7 @@ public class RecalDataManager { } public static boolean checkNoCallColorSpace(final GATKSAMRecord read) { - if (read.getReadGroup().getPlatform().toUpperCase().contains("SOLID")) { + if (ReadUtils.isSOLiDRead(read)) { final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG); if (attr != null) { byte[] colorSpace; @@ -611,21 +612,17 @@ public class RecalDataManager { final Comparable[][] covariateValues_offset_x_covar = new Comparable[readLength][numRequestedCovariates]; final Comparable[] tempCovariateValuesHolder = new Comparable[readLength]; - // Loop through the list of requested covariates and compute the values of each covariate for all positions in this read - for (int i = 0; i < numRequestedCovariates; i++) { + for (int i = 0; i < numRequestedCovariates; i++) { // Loop through the list of requested covariates and compute the values of each covariate for all positions in this read requestedCovariates.get(i).getValues(gatkRead, tempCovariateValuesHolder, modelType); - for (int j = 0; j < readLength; j++) { - //copy values into a 2D array that allows all covar types to be extracted at once for - //an offset j by doing covariateValues_offset_x_covar[j]. This avoids the need to later iterate over covar types. - covariateValues_offset_x_covar[j][i] = tempCovariateValuesHolder[j]; - } + for (int j = 0; j < readLength; j++) + covariateValues_offset_x_covar[j][i] = tempCovariateValuesHolder[j]; // copy values into a 2D array that allows all covar types to be extracted at once for an offset j by doing covariateValues_offset_x_covar[j]. This avoids the need to later iterate over covar types. } return covariateValues_offset_x_covar; } /** - * Perform a ceratin transversion (A <-> C or G <-> T) on the base. + * Perform a certain transversion (A <-> C or G <-> T) on the base. * * @param base the base [AaCcGgTt] * @return the transversion of the base, or the input base if it's not one of the understood ones diff --git a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java index 673b1524d..61812629c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java @@ -2,57 +2,59 @@ package org.broadinstitute.sting.utils; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; - /** * BaseUtils contains some basic utilities for manipulating nucleotides. */ public class BaseUtils { - public final static byte A = (byte)'A'; - public final static byte C = (byte)'C'; - public final static byte G = (byte)'G'; - public final static byte T = (byte)'T'; + public final static byte A = (byte) 'A'; + public final static byte C = (byte) 'C'; + public final static byte G = (byte) 'G'; + public final static byte T = (byte) 'T'; - public final static byte N = (byte)'N'; - public final static byte D = (byte)'D'; + public final static byte N = (byte) 'N'; + public final static byte D = (byte) 'D'; // // todo -- we need a generalized base abstraction using the Base enum. // - public final static byte[] BASES = { 'A', 'C', 'G', 'T' }; - public final static byte[] EXTENDED_BASES = { 'A', 'C', 'G', 'T', 'N', 'D' }; + public final static byte[] BASES = {'A', 'C', 'G', 'T'}; + public final static byte[] EXTENDED_BASES = {'A', 'C', 'G', 'T', 'N', 'D'}; public enum Base { - A ( 'A', 0 ), - C ( 'C', 1 ), - G ( 'G', 2 ), - T ( 'T', 3 ); + A('A', 0), + C('C', 1), + G('G', 2), + T('T', 3); byte b; int index; + private Base(char base, int index) { - this.b = (byte)base; + this.b = (byte) base; this.index = index; } public byte getBase() { return b; } - public char getBaseAsChar() { return (char)b; } + + public char getBaseAsChar() { return (char) b; } + public int getIndex() { return index; } public boolean sameBase(byte o) { return b == o; } - public boolean sameBase(char o) { return b == (byte)o; } - public boolean sameBase(int i) { return index == i; } - } + public boolean sameBase(char o) { return b == (byte) o; } + + public boolean sameBase(int i) { return index == i; } + } // todo -- fix me (enums?) public static final byte DELETION_INDEX = 4; public static final byte NO_CALL_INDEX = 5; // (this is 'N') - public static int gIndex = BaseUtils.simpleBaseToBaseIndex((byte)'G'); - public static int cIndex = BaseUtils.simpleBaseToBaseIndex((byte)'C'); - public static int aIndex = BaseUtils.simpleBaseToBaseIndex((byte)'A'); - public static int tIndex = BaseUtils.simpleBaseToBaseIndex((byte)'T'); - + public static int gIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'G'); + public static int cIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'C'); + public static int aIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'A'); + public static int tIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'T'); /// In genetics, a transition is a mutation changing a purine to another purine nucleotide (A <-> G) or // a pyrimidine to another pyrimidine nucleotide (C <-> T). @@ -64,28 +66,31 @@ public class BaseUtils { /** * Returns the base substitution type of the 2 state SNP + * * @param base1 * @param base2 * @return */ - public static BaseSubstitutionType SNPSubstitutionType( byte base1, byte base2 ) { + public static BaseSubstitutionType SNPSubstitutionType(byte base1, byte base2) { BaseSubstitutionType t = isTransition(base1, base2) ? BaseSubstitutionType.TRANSITION : BaseSubstitutionType.TRANSVERSION; //System.out.printf("SNPSubstitutionType( char %c, char %c ) => %s%n", base1, base2, t); return t; } - public static boolean isTransition( byte base1, byte base2 ) { + public static boolean isTransition(byte base1, byte base2) { int b1 = simpleBaseToBaseIndex(base1); int b2 = simpleBaseToBaseIndex(base2); return b1 == 0 && b2 == 2 || b1 == 2 && b2 == 0 || - b1 == 1 && b2 == 3 || b1 == 3 && b2 == 1; + b1 == 1 && b2 == 3 || b1 == 3 && b2 == 1; } - public static boolean isTransversion( byte base1, byte base2 ) { - return ! isTransition(base1, base2); + public static boolean isTransversion(byte base1, byte base2) { + return !isTransition(base1, base2); } - /** Private constructor. No instantiating this class! */ + /** + * Private constructor. No instantiating this class! + */ private BaseUtils() {} static public boolean basesAreEqual(byte base1, byte base2) { @@ -96,7 +101,6 @@ public class BaseUtils { return extendedBaseToBaseIndex(base1) == extendedBaseToBaseIndex(base2); } - /** * Converts a IUPAC nucleotide code to a pair of bases * @@ -163,33 +167,37 @@ public class BaseUtils { /** * Converts a simple base to a base index * - * @param base [AaCcGgTt] + * @param base [AaCcGgTt] * @return 0, 1, 2, 3, or -1 if the base can't be understood */ static public int simpleBaseToBaseIndex(byte base) { switch (base) { case '*': // the wildcard character counts as an A case 'A': - case 'a': return 0; + case 'a': + return 0; case 'C': - case 'c': return 1; + case 'c': + return 1; case 'G': - case 'g': return 2; + case 'g': + return 2; case 'T': - case 't': return 3; + case 't': + return 3; - default: return -1; + default: + return -1; } } - /** * Converts a simple base to a base index * - * @param base [AaCcGgTt] + * @param base [AaCcGgTt] * @return 0, 1, 2, 3, or -1 if the base can't be understood */ @Deprecated @@ -197,29 +205,37 @@ public class BaseUtils { switch (base) { case '*': // the wildcard character counts as an A case 'A': - case 'a': return 0; + case 'a': + return 0; case 'C': - case 'c': return 1; + case 'c': + return 1; case 'G': - case 'g': return 2; + case 'g': + return 2; case 'T': - case 't': return 3; + case 't': + return 3; - default: return -1; + default: + return -1; } } static public int extendedBaseToBaseIndex(byte base) { switch (base) { case 'd': - case 'D': return DELETION_INDEX; + case 'D': + return DELETION_INDEX; case 'n': - case 'N': return NO_CALL_INDEX; + case 'N': + return NO_CALL_INDEX; - default: return simpleBaseToBaseIndex(base); + default: + return simpleBaseToBaseIndex(base); } } @@ -232,11 +248,6 @@ public class BaseUtils { return simpleBaseToBaseIndex(base) != -1; } - @Deprecated - static public boolean isNBase(char base) { - return isNBase((byte)base); - } - static public boolean isNBase(byte base) { return base == 'N' || base == 'n'; } @@ -244,68 +255,83 @@ public class BaseUtils { /** * Converts a base index to a simple base * - * @param baseIndex 0, 1, 2, 3 + * @param baseIndex 0, 1, 2, 3 * @return A, C, G, T, or '.' if the index can't be understood */ static public byte baseIndexToSimpleBase(int baseIndex) { switch (baseIndex) { - case 0: return 'A'; - case 1: return 'C'; - case 2: return 'G'; - case 3: return 'T'; - default: return '.'; + case 0: + return 'A'; + case 1: + return 'C'; + case 2: + return 'G'; + case 3: + return 'T'; + default: + return '.'; } } @Deprecated static public char baseIndexToSimpleBaseAsChar(int baseIndex) { - return (char)baseIndexToSimpleBase(baseIndex); + return (char) baseIndexToSimpleBase(baseIndex); } /** * Converts a base index to a base index representing its cross-talk partner * - * @param baseIndex 0, 1, 2, 3 + * @param baseIndex 0, 1, 2, 3 * @return 1, 0, 3, 2, or -1 if the index can't be understood */ static public int crossTalkPartnerIndex(int baseIndex) { switch (baseIndex) { - case 0: return 1; // A -> C - case 1: return 0; // C -> A - case 2: return 3; // G -> T - case 3: return 2; // T -> G - default: return -1; + case 0: + return 1; // A -> C + case 1: + return 0; // C -> A + case 2: + return 3; // G -> T + case 3: + return 2; // T -> G + default: + return -1; } } /** * Converts a base to the base representing its cross-talk partner * - * @param base [AaCcGgTt] + * @param base [AaCcGgTt] * @return C, A, T, G, or '.' if the base can't be understood */ @Deprecated static public char crossTalkPartnerBase(char base) { - return (char)baseIndexToSimpleBase(crossTalkPartnerIndex(simpleBaseToBaseIndex(base))); + return (char) baseIndexToSimpleBase(crossTalkPartnerIndex(simpleBaseToBaseIndex(base))); } /** * Return the complement of a base index. * - * @param baseIndex the base index (0:A, 1:C, 2:G, 3:T) + * @param baseIndex the base index (0:A, 1:C, 2:G, 3:T) * @return the complementary base index */ static public byte complementIndex(int baseIndex) { switch (baseIndex) { - case 0: return 3; // a -> t - case 1: return 2; // c -> g - case 2: return 1; // g -> c - case 3: return 0; // t -> a - default: return -1; // wtf? + case 0: + return 3; // a -> t + case 1: + return 2; // c -> g + case 2: + return 1; // g -> c + case 3: + return 0; // t -> a + default: + return -1; // wtf? } } - /** + /** * Return the complement (A <-> T or C <-> G) of a base, or the specified base if it can't be complemented (i.e. an ambiguous base). * * @param base the base [AaCcGgTt] @@ -314,20 +340,25 @@ public class BaseUtils { static public byte simpleComplement(byte base) { switch (base) { case 'A': - case 'a': return 'T'; + case 'a': + return 'T'; case 'C': - case 'c': return 'G'; + case 'c': + return 'G'; case 'G': - case 'g': return 'C'; + case 'g': + return 'C'; case 'T': - case 't': return 'A'; - default: return base; + case 't': + return 'A'; + default: + return base; } } @Deprecated static public char simpleComplement(char base) { - return (char)simpleComplement((byte)base); + return (char) simpleComplement((byte) base); } /** @@ -349,7 +380,7 @@ public class BaseUtils { /** * Complement a byte array of bases (that is, chars casted to bytes, *not* base indices in byte form) * - * @param bases the byte array of bases + * @param bases the byte array of bases * @return the complement of the base byte array */ static public byte[] simpleComplement(byte[] bases) { @@ -382,7 +413,7 @@ public class BaseUtils { /** * Complement a char array of bases * - * @param bases the char array of bases + * @param bases the char array of bases * @return the complement of the base char array */ @Deprecated @@ -399,7 +430,7 @@ public class BaseUtils { /** * Reverse complement a String of bases. Preserves ambiguous bases. * - * @param bases the String of bases + * @param bases the String of bases * @return the reverse complement of the String */ @Deprecated @@ -407,11 +438,10 @@ public class BaseUtils { return new String(simpleReverseComplement(bases.getBytes())); } - /** * Complement a String of bases. Preserves ambiguous bases. * - * @param bases the String of bases + * @param bases the String of bases * @return the complement of the String */ @Deprecated @@ -451,7 +481,7 @@ public class BaseUtils { /** * Returns the most common base in the basecounts array. To be used with pileup.getBaseCounts. * - * @param baseCounts counts of a,c,g,t in order. + * @param baseCounts counts of a,c,g,t in order. * @return the most common base */ static public byte mostFrequentSimpleBase(int[] baseCounts) { @@ -461,13 +491,13 @@ public class BaseUtils { /** * For the most frequent base in the sequence, return the percentage of the read it constitutes. * - * @param sequence the read sequence - * @return the percentage of the read that's made up of the most frequent base + * @param sequence the read sequence + * @return the percentage of the read that's made up of the most frequent base */ static public double mostFrequentBaseFraction(byte[] sequence) { int[] baseCounts = new int[4]; - for ( byte base : sequence ) { + for (byte base : sequence) { int baseIndex = simpleBaseToBaseIndex(base); if (baseIndex >= 0) { @@ -477,7 +507,7 @@ public class BaseUtils { int mostFrequentBaseIndex = mostFrequentBaseIndex(baseCounts); - return ((double) baseCounts[mostFrequentBaseIndex])/((double) sequence.length); + return ((double) baseCounts[mostFrequentBaseIndex]) / ((double) sequence.length); } // -------------------------------------------------------------------------------- @@ -531,50 +561,50 @@ public class BaseUtils { static public byte getRandomBase(char excludeBase) { return BaseUtils.baseIndexToSimpleBase(getRandomBaseIndex(BaseUtils.simpleBaseToBaseIndex(excludeBase))); } - - - /** Computes the smallest period >= minPeriod for the specified string. The period is defined as such p, + + /** + * Computes the smallest period >= minPeriod for the specified string. The period is defined as such p, * that for all i = 0... seq.length-1, seq[ i % p ] = seq[i] (or equivalently seq[i] = seq[i+p] for i=0...seq.length-1-p). - * The sequence does not have to contain whole number of periods. For instance, "ACACACAC" has a period - * of 2 (it has a period of 4 as well), and so does - * "ACACA"; similarly, smallest periods of "CTCCTC", "CTCCT", and "CTCC" are all equal to 3. The "trivial" period is + * The sequence does not have to contain whole number of periods. For instance, "ACACACAC" has a period + * of 2 (it has a period of 4 as well), and so does + * "ACACA"; similarly, smallest periods of "CTCCTC", "CTCCT", and "CTCC" are all equal to 3. The "trivial" period is * the length of the string itself, and it will always be returned if no smaller period can be found in the specified period range * or if specified minPeriod is greater than the sequence length. - * + * * @param seq * @return */ public static int sequencePeriod(byte[] seq, int minPeriod) { - int period = ( minPeriod > seq.length ? seq.length : minPeriod ); - // we assume that bases [0,period-1] repeat themselves and check this assumption - // until we find correct period - - for ( int pos = period ; pos < seq.length ; pos++ ) { - - int offset = pos % period; // we are currenlty 'offset' bases into the putative repeat of period 'period' - // if our current hypothesis holds, base[pos] must be the same as base[offset] - - if ( Character.toUpperCase( seq[pos] ) != - Character.toUpperCase( seq[offset] ) - ) { - - // period we have been trying so far does not work. - // two possibilities: - // A) offset = 0, i.e. current position pos must be start of the next repeat, but it is not; - // in this case only bases from start up to the current one, inclusive, may form a repeat, if at all; - // so period is at least pos+1 (remember, pos is 0-based), then on the next loop re-entrance - // pos will be autoincremented and we will be checking next base - // B) offset != 0, i.e. the current base breaks the repeat, but maybe it starts a new one? - // hence we should first check if it matches the first base of the sequence, and to do that - // we set period to pos (thus trying the hypothesis that bases from start up to the current one, - // non-inclusive are repeated hereafter), and decrement pos (this will re-test current base against the first base - // on the next loop re-entrance after pos is autoincremented) - if ( offset == 0 ) period = pos+1; - else period = pos-- ; - - } - } - return period; + int period = (minPeriod > seq.length ? seq.length : minPeriod); + // we assume that bases [0,period-1] repeat themselves and check this assumption + // until we find correct period + + for (int pos = period; pos < seq.length; pos++) { + + int offset = pos % period; // we are currenlty 'offset' bases into the putative repeat of period 'period' + // if our current hypothesis holds, base[pos] must be the same as base[offset] + + if (Character.toUpperCase(seq[pos]) != Character.toUpperCase(seq[offset])) { + + // period we have been trying so far does not work. + // two possibilities: + // A) offset = 0, i.e. current position pos must be start of the next repeat, but it is not; + // in this case only bases from start up to the current one, inclusive, may form a repeat, if at all; + // so period is at least pos+1 (remember, pos is 0-based), then on the next loop re-entrance + // pos will be autoincremented and we will be checking next base + // B) offset != 0, i.e. the current base breaks the repeat, but maybe it starts a new one? + // hence we should first check if it matches the first base of the sequence, and to do that + // we set period to pos (thus trying the hypothesis that bases from start up to the current one, + // non-inclusive are repeated hereafter), and decrement pos (this will re-test current base against the first base + // on the next loop re-entrance after pos is autoincremented) + if (offset == 0) + period = pos + 1; + else + period = pos--; + + } + } + return period; } } From c0c676590b49d3d384aebc716a0ac2388f9c850f Mon Sep 17 00:00:00 2001 From: Roger Zurawicki Date: Mon, 9 Jan 2012 23:46:48 -0500 Subject: [PATCH 03/14] First implementation of GATKReportGatherer - Added the GATKReportGatherer - Added private methods in GATKReport to combine Tables and Reports - It is very conservative and it will only gather if the table columns, match. - At the column level it uses the (redundant) row ids to add new rows. It will throw an exception if it is overwriting data. Added the gatherer functions to CoverageByRG Also added the scatterCount parameter in the Interval Coverage script Made some more GATKReport methods public The UnitTest included shows that the merging methods work Added a getter for the PrimaryKeyName Fixed bugs that prevented the gatherer form working Working GATKReportGatherer Has only the functional to addLines The input file parser assumes that the first column is the primary key Signed-off-by: Mauricio Carneiro --- .../sting/gatk/report/GATKReport.java | 65 +++-- .../sting/gatk/report/GATKReportGatherer.java | 46 ++++ .../sting/gatk/report/GATKReportTable.java | 252 +++++++++++------- .../sting/gatk/report/GATKReportUnitTest.java | 128 +++++++-- 4 files changed, 357 insertions(+), 134 deletions(-) create mode 100644 public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java index 608b5d1d0..c0abe7450 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java @@ -24,7 +24,8 @@ public class GATKReport { /** * Create a new GATKReport with the contents of a GATKReport on disk. - * @param filename the path to the file to load + * + * @param filename the path to the file to load */ public GATKReport(String filename) { this(new File(filename)); @@ -32,7 +33,8 @@ public class GATKReport { /** * Create a new GATKReport with the contents of a GATKReport on disk. - * @param file the file to load + * + * @param file the file to load */ public GATKReport(File file) { loadReport(file); @@ -40,7 +42,8 @@ public class GATKReport { /** * Load a GATKReport file from disk - * @param file the file to load + * + * @param file the file to load */ private void loadReport(File file) { try { @@ -48,12 +51,11 @@ public class GATKReport { GATKReportTable table = null; String[] header = null; - int id = 0; GATKReportVersion version = null; List columnStarts = null; String line; - while ( (line = reader.readLine()) != null ) { + while ((line = reader.readLine()) != null) { if (line.startsWith(GATKREPORT_HEADER_PREFIX)) { @@ -71,7 +73,7 @@ public class GATKReport { header = null; columnStarts = null; - } else if ( line.trim().isEmpty() ) { + } else if (line.trim().isEmpty()) { // do nothing } else { if (table != null) { @@ -97,19 +99,22 @@ public class GATKReport { if (header == null) { header = splitLine; - table.addPrimaryKey("id", false); - - for ( String columnName : header ) { - table.addColumn(columnName, ""); + // Set the first column as the primary key + table.addPrimaryKey(header[0]); + // Set every other column as column + for (int i = 1; i < header.length; i++) { + table.addColumn(header[i], ""); } - id = 0; } else { - for (int columnIndex = 0; columnIndex < header.length; columnIndex++) { - table.set(id, header[columnIndex], splitLine[columnIndex]); + //Get primary key Value from the current line array + String primaryKey = splitLine[0]; + //Input all the remaining values + for (int columnIndex = 1; columnIndex < header.length; columnIndex++) { + table.set(primaryKey, header[columnIndex], splitLine[columnIndex]); } - id++; + } } } @@ -124,8 +129,8 @@ public class GATKReport { /** * Add a new table to the collection * - * @param tableName the name of the table - * @param tableDescription the description of the table + * @param tableName the name of the table + * @param tableDescription the description of the table */ public void addTable(String tableName, String tableDescription) { addTable(tableName, tableDescription, true); @@ -139,7 +144,7 @@ public class GATKReport { /** * Return true if table with a given name exists * - * @param tableName the name of the table + * @param tableName the name of the table * @return true if the table exists, false otherwise */ public boolean hasTable(String tableName) { @@ -149,8 +154,8 @@ public class GATKReport { /** * Return a table with a given name * - * @param tableName the name of the table - * @return the table object + * @param tableName the name of the table + * @return the table object */ public GATKReportTable getTable(String tableName) { GATKReportTable table = tables.get(tableName); @@ -162,7 +167,7 @@ public class GATKReport { /** * Print all tables contained within this container to a PrintStream * - * @param out the PrintStream to which the tables should be written + * @param out the PrintStream to which the tables should be written */ public void print(PrintStream out) { for (GATKReportTable table : tables.values()) { @@ -175,4 +180,24 @@ public class GATKReport { public Collection getTables() { return tables.values(); } + + public void combineWith(GATKReport input) { + + // For every input table, add values + System.out.println("This.tables: keySet"); + for (String s : tables.keySet()) + System.out.println(s); + + // todo test tables exist + + + for (String tableName : input.tables.keySet()) { + System.out.println("Input table key: " + tableName); + if (tables.containsKey(tableName)) + tables.get(tableName).mergeRows(input.getTable(tableName)); + else + throw new ReviewedStingException("Failed to combine GATKReport, tables don't match!"); + } + + } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java new file mode 100644 index 000000000..0d15971ae --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java @@ -0,0 +1,46 @@ +package org.broadinstitute.sting.gatk.report; + +import org.broadinstitute.sting.commandline.Gatherer; +import org.broadinstitute.sting.utils.exceptions.UserException; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.PrintStream; +import java.util.List; + +/** + * Created by IntelliJ IDEA. + * User: roger + * Date: 1/9/12 + * Time: 11:17 PM + * To change this template use File | Settings | File Templates. + */ +public class GATKReportGatherer extends Gatherer { + @Override + public void gather(List inputs, File output) { + //Combines inputs GATKReport to one output + + PrintStream o; + try { + o = new PrintStream(output); + } catch (FileNotFoundException e) { + throw new UserException("File to be output by CoverageByRG Gather function was not found"); + } + + GATKReport current = new GATKReport(); + boolean isFirst = true; + for (File input : inputs) { + + // If the table is empty + if (isFirst) { + current = new GATKReport(input); + isFirst = false; + } else { + GATKReport toAdd = new GATKReport(input); + current.combineWith(toAdd); + } + } + + current.print(o); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java index b72b20e0b..ac18891d7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java @@ -4,7 +4,10 @@ import org.apache.commons.lang.ObjectUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.PrintStream; -import java.util.*; +import java.util.Collection; +import java.util.HashMap; +import java.util.LinkedList; +import java.util.TreeSet; import java.util.regex.Matcher; import java.util.regex.Pattern; @@ -12,12 +15,12 @@ import java.util.regex.Pattern; * A data structure that allows data to be collected over the course of a walker's computation, then have that data * written to a PrintStream such that it's human-readable, AWK-able, and R-friendly (given that you load it using the * GATKReport loader module). - * + *

* The goal of this object is to use the same data structure for both accumulating data during a walker's computation * and emitting that data to a file for easy analysis in R (or any other program/language that can take in a table of * results). Thus, all of the infrastructure below is designed simply to make printing the following as easy as * possible: - * + *

* ##:GATKReport.v0.1 ErrorRatePerCycle : The error rate per sequenced position in the reads * cycle errorrate.61PA8.7 qualavg.61PA8.7 * 0 0.007451835696110506 25.474613284804366 @@ -29,60 +32,60 @@ import java.util.regex.Pattern; * 6 5.452562704471102E-4 36.1217248908297 * 7 5.452562704471102E-4 36.1910480349345 * 8 5.452562704471102E-4 36.00345705967977 - * + *

* Here, we have a GATKReport table - a well-formatted, easy to read representation of some tabular data. Every single * table has this same GATKReport.v0.1 header, which permits multiple files from different sources to be cat-ed * together, which makes it very easy to pull tables from different programs into R via a single file. - * + *

* ------------ * Definitions: - * + *

* Table info: - * The first line, structured as - * ##: :
- * + * The first line, structured as + * ##:
:
+ *

* Table header: - * The second line, specifying a unique name for each column in the table. - * - * The first column mentioned in the table header is the "primary key" column - a column that provides the unique - * identifier for each row in the table. Once this column is created, any element in the table can be referenced by - * the row-column coordinate, i.e. "primary key"-"column name" coordinate. - * - * When a column is added to a table, a default value must be specified (usually 0). This is the initial value for - * an element in a column. This permits operations like increment() and decrement() to work properly on columns that - * are effectively counters for a particular event. - * - * Finally, the display property for each column can be set during column creation. This is useful when a given - * column stores an intermediate result that will be used later on, perhaps to calculate the value of another column. - * In these cases, it's obviously necessary to store the value required for further computation, but it's not - * necessary to actually print the intermediate column. - * + * The second line, specifying a unique name for each column in the table. + *

+ * The first column mentioned in the table header is the "primary key" column - a column that provides the unique + * identifier for each row in the table. Once this column is created, any element in the table can be referenced by + * the row-column coordinate, i.e. "primary key"-"column name" coordinate. + *

+ * When a column is added to a table, a default value must be specified (usually 0). This is the initial value for + * an element in a column. This permits operations like increment() and decrement() to work properly on columns that + * are effectively counters for a particular event. + *

+ * Finally, the display property for each column can be set during column creation. This is useful when a given + * column stores an intermediate result that will be used later on, perhaps to calculate the value of another column. + * In these cases, it's obviously necessary to store the value required for further computation, but it's not + * necessary to actually print the intermediate column. + *

* Table body: - * The values of the table itself. - * + * The values of the table itself. + *

* --------------- * Implementation: - * + *

* The implementation of this table has two components: - * 1. A TreeSet that stores all the values ever specified for the primary key. Any get() operation that - * refers to an element where the primary key object does not exist will result in its implicit creation. I - * haven't yet decided if this is a good idea... - * - * 2. A HashMap that stores a mapping from column name to column contents. Each - * GATKReportColumn is effectively a map (in fact, GATKReportColumn extends TreeMap) between - * primary key and the column value. This means that, given N columns, the primary key information is stored - * N+1 times. This is obviously wasteful and can likely be handled much more elegantly in future implementations. - * + * 1. A TreeSet that stores all the values ever specified for the primary key. Any get() operation that + * refers to an element where the primary key object does not exist will result in its implicit creation. I + * haven't yet decided if this is a good idea... + *

+ * 2. A HashMap that stores a mapping from column name to column contents. Each + * GATKReportColumn is effectively a map (in fact, GATKReportColumn extends TreeMap) between + * primary key and the column value. This means that, given N columns, the primary key information is stored + * N+1 times. This is obviously wasteful and can likely be handled much more elegantly in future implementations. + *

* ------------------------------ * Element and column operations: - * + *

* In addition to simply getting and setting values, this object also permits some simple operations to be applied to * individual elements or to whole columns. For instance, an element can be easily incremented without the hassle of * calling get(), incrementing the obtained value by 1, and then calling set() with the new value. Also, some vector * operations are supported. For instance, two whole columns can be divided and have the result be set to a third * column. This is especially useful when aggregating counts in two intermediate columns that will eventually need to * be manipulated row-by-row to compute the final column. - * + *

* Note: I've made no attempt whatsoever to make these operations efficient. Right now, some of the methods check the * type of the stored object using an instanceof call and attempt to do the right thing. Others cast the contents of * the cell to a Number, call the Number.toDouble() method and compute a result. This is clearly not the ideal design, @@ -92,7 +95,9 @@ import java.util.regex.Pattern; * @author Khalid Shakir */ public class GATKReportTable { - /** REGEX that matches any table with an invalid name */ + /** + * REGEX that matches any table with an invalid name + */ public final static String INVALID_TABLE_NAME_REGEX = "[^a-zA-Z0-9_\\-\\.]"; private static final GATKReportVersion LATEST_REPORT_VERSION = GATKReportVersion.V0_2; private String tableName; @@ -109,8 +114,8 @@ public class GATKReportTable { /** * Verifies that a table or column name has only alphanumeric characters - no spaces or special characters allowed * - * @param name the name of the table or column - * @return true if the name is valid, false if otherwise + * @param name the name of the table or column + * @return true if the name is valid, false if otherwise */ private boolean isValidName(String name) { Pattern p = Pattern.compile(INVALID_TABLE_NAME_REGEX); @@ -122,8 +127,8 @@ public class GATKReportTable { /** * Verifies that a table or column name has only alphanumeric characters - no spaces or special characters allowed * - * @param description the name of the table or column - * @return true if the name is valid, false if otherwise + * @param description the name of the table or column + * @return true if the name is valid, false if otherwise */ private boolean isValidDescription(String description) { Pattern p = Pattern.compile("\\r|\\n"); @@ -135,15 +140,15 @@ public class GATKReportTable { /** * Construct a new GATK report table with the specified name and description * - * @param tableName the name of the table - * @param tableDescription the description of the table + * @param tableName the name of the table + * @param tableDescription the description of the table */ public GATKReportTable(String tableName, String tableDescription) { this(tableName, tableDescription, true); } public GATKReportTable(String tableName, String tableDescription, boolean sortByPrimaryKey) { - if (!isValidName(tableName)) { + if (!isValidName(tableName)) { throw new ReviewedStingException("Attempted to set a GATKReportTable name of '" + tableName + "'. GATKReportTable names must be purely alphanumeric - no spaces or special characters are allowed."); } @@ -169,7 +174,7 @@ public class GATKReportTable { /** * Add a primary key column. This becomes the unique identifier for every column in the table. * - * @param primaryKeyName the name of the primary key column + * @param primaryKeyName the name of the primary key column */ public void addPrimaryKey(String primaryKeyName) { addPrimaryKey(primaryKeyName, true); @@ -178,8 +183,8 @@ public class GATKReportTable { /** * Add an optionally visible primary key column. This becomes the unique identifier for every column in the table, and will always be printed as the first column. * - * @param primaryKeyName the name of the primary key column - * @param display should this primary key be displayed? + * @param primaryKeyName the name of the primary key column + * @param display should this primary key be displayed? */ public void addPrimaryKey(String primaryKeyName, boolean display) { if (!isValidName(primaryKeyName)) { @@ -195,6 +200,7 @@ public class GATKReportTable { /** * Returns the first primary key matching the dotted column values. * Ex: dbsnp.eval.called.all.novel.all + * * @param dottedColumnValues Period concatenated values. * @return The first primary key matching the column values or throws an exception. */ @@ -208,6 +214,7 @@ public class GATKReportTable { /** * Returns true if there is at least on row with the dotted column values. * Ex: dbsnp.eval.called.all.novel.all + * * @param dottedColumnValues Period concatenated values. * @return true if there is at least one row matching the columns. */ @@ -218,6 +225,7 @@ public class GATKReportTable { /** * Returns the first primary key matching the dotted column values. * Ex: dbsnp.eval.called.all.novel.all + * * @param dottedColumnValues Period concatenated values. * @return The first primary key matching the column values or null. */ @@ -228,6 +236,7 @@ public class GATKReportTable { /** * Returns the first primary key matching the column values. * Ex: new String[] { "dbsnp", "eval", "called", "all", "novel", "all" } + * * @param columnValues column values. * @return The first primary key matching the column values. */ @@ -235,7 +244,7 @@ public class GATKReportTable { for (Object primaryKey : primaryKeyColumn) { boolean matching = true; for (int i = 0; matching && i < columnValues.length; i++) { - matching = ObjectUtils.equals(columnValues[i], get(primaryKey, i+1)); + matching = ObjectUtils.equals(columnValues[i], get(primaryKey, i + 1)); } if (matching) return primaryKey; @@ -246,8 +255,8 @@ public class GATKReportTable { /** * Add a column to the report and specify the default value that should be supplied if a given position in the table is never explicitly set. * - * @param columnName the name of the column - * @param defaultValue the default value for the column + * @param columnName the name of the column + * @param defaultValue the default value for the column */ public void addColumn(String columnName, Object defaultValue) { addColumn(columnName, defaultValue, null); @@ -256,12 +265,13 @@ public class GATKReportTable { public void addColumn(String columnName, Object defaultValue, String format) { addColumn(columnName, defaultValue, true, format); } + /** * Add a column to the report, specify the default column value, and specify whether the column should be displayed in the final output (useful when intermediate columns are necessary for later calculations, but are not required to be in the output file. * - * @param columnName the name of the column - * @param defaultValue the default value of the column - * @param display if true - the column will be displayed; if false - the column will be hidden + * @param columnName the name of the column + * @param defaultValue the default value of the column + * @param display if true - the column will be displayed; if false - the column will be hidden */ public void addColumn(String columnName, Object defaultValue, boolean display) { addColumn(columnName, defaultValue, display, null); @@ -277,8 +287,8 @@ public class GATKReportTable { /** * Check if the requested element exists, and if not, create it. * - * @param primaryKey the primary key value - * @param columnName the name of the column + * @param primaryKey the primary key value + * @param columnName the name of the column */ private void verifyEntry(Object primaryKey, String columnName) { if (!columns.containsKey(columnName)) { @@ -299,9 +309,9 @@ public class GATKReportTable { /** * Set the value for a given position in the table * - * @param primaryKey the primary key value - * @param columnName the name of the column - * @param value the value to set + * @param primaryKey the primary key value + * @param columnName the name of the column + * @param value the value to set */ public void set(Object primaryKey, String columnName, Object value) { verifyEntry(primaryKey, columnName); @@ -312,13 +322,13 @@ public class GATKReportTable { /** * Get a value from the given position in the table * - * @param primaryKey the primary key value - * @param columnName the name of the column - * @return the value stored at the specified position in the table + * @param primaryKey the primary key value + * @param columnName the name of the column + * @return the value stored at the specified position in the table */ public Object get(Object primaryKey, String columnName) { verifyEntry(primaryKey, columnName); - + return columns.get(columnName).get(primaryKey); } @@ -327,7 +337,7 @@ public class GATKReportTable { * * @param primaryKey the primary key value * @param columnIndex the index of the column - * @return the value stored at the specified position in the table + * @return the value stored at the specified position in the table */ private Object get(Object primaryKey, int columnIndex) { return columns.getByIndex(columnIndex).get(primaryKey); @@ -336,8 +346,8 @@ public class GATKReportTable { /** * Increment an element in the table. This implementation is awful - a functor would probably be better. * - * @param primaryKey the primary key value - * @param columnName the name of the column + * @param primaryKey the primary key value + * @param columnName the name of the column */ public void increment(Object primaryKey, String columnName) { Object oldValue = get(primaryKey, columnName); @@ -365,8 +375,8 @@ public class GATKReportTable { /** * Decrement an element in the table. This implementation is awful - a functor would probably be better. * - * @param primaryKey the primary key value - * @param columnName the name of the column + * @param primaryKey the primary key value + * @param columnName the name of the column */ public void decrement(Object primaryKey, String columnName) { Object oldValue = get(primaryKey, columnName); @@ -394,9 +404,9 @@ public class GATKReportTable { /** * Add the specified value to an element in the table * - * @param primaryKey the primary key value - * @param columnName the name of the column - * @param valueToAdd the value to add + * @param primaryKey the primary key value + * @param columnName the name of the column + * @param valueToAdd the value to add */ public void add(Object primaryKey, String columnName, Object valueToAdd) { Object oldValue = get(primaryKey, columnName); @@ -424,8 +434,8 @@ public class GATKReportTable { /** * Subtract the specified value from an element in the table * - * @param primaryKey the primary key value - * @param columnName the name of the column + * @param primaryKey the primary key value + * @param columnName the name of the column * @param valueToSubtract the value to subtract */ public void subtract(Object primaryKey, String columnName, Object valueToSubtract) { @@ -454,9 +464,9 @@ public class GATKReportTable { /** * Multiply the specified value to an element in the table * - * @param primaryKey the primary key value - * @param columnName the name of the column - * @param valueToMultiply the value to multiply by + * @param primaryKey the primary key value + * @param columnName the name of the column + * @param valueToMultiply the value to multiply by */ public void multiply(Object primaryKey, String columnName, Object valueToMultiply) { Object oldValue = get(primaryKey, columnName); @@ -484,9 +494,9 @@ public class GATKReportTable { /** * Divide the specified value from an element in the table * - * @param primaryKey the primary key value - * @param columnName the name of the column - * @param valueToDivide the value to divide by + * @param primaryKey the primary key value + * @param columnName the name of the column + * @param valueToDivide the value to divide by */ public void divide(Object primaryKey, String columnName, Object valueToDivide) { Object oldValue = get(primaryKey, columnName); @@ -514,9 +524,9 @@ public class GATKReportTable { /** * Add two columns to each other and set the results to a third column * - * @param columnToSet the column that should hold the results - * @param augend the column that shall be the augend - * @param addend the column that shall be the addend + * @param columnToSet the column that should hold the results + * @param augend the column that shall be the augend + * @param addend the column that shall be the addend */ public void addColumns(String columnToSet, String augend, String addend) { for (Object primaryKey : primaryKeyColumn) { @@ -532,8 +542,8 @@ public class GATKReportTable { /** * Subtract one column from another and set the results to a third column * - * @param columnToSet the column that should hold the results - * @param minuend the column that shall be the minuend (the a in a - b) + * @param columnToSet the column that should hold the results + * @param minuend the column that shall be the minuend (the a in a - b) * @param subtrahend the column that shall be the subtrahend (the b in a - b) */ public void subtractColumns(String columnToSet, String minuend, String subtrahend) { @@ -551,8 +561,8 @@ public class GATKReportTable { * Multiply two columns by each other and set the results to a third column * * @param columnToSet the column that should hold the results - * @param multiplier the column that shall be the multiplier - * @param multiplicand the column that shall be the multiplicand + * @param multiplier the column that shall be the multiplier + * @param multiplicand the column that shall be the multiplicand */ public void multiplyColumns(String columnToSet, String multiplier, String multiplicand) { for (Object primaryKey : primaryKeyColumn) { @@ -568,9 +578,9 @@ public class GATKReportTable { /** * Divide two columns by each other and set the results to a third column * - * @param columnToSet the column that should hold the results - * @param numeratorColumn the column that shall be the numerator - * @param denominatorColumn the column that shall be the denominator + * @param columnToSet the column that should hold the results + * @param numeratorColumn the column that shall be the numerator + * @param denominatorColumn the column that shall be the denominator */ public void divideColumns(String columnToSet, String numeratorColumn, String denominatorColumn) { for (Object primaryKey : primaryKeyColumn) { @@ -585,10 +595,11 @@ public class GATKReportTable { /** * Return the print width of the primary key column - * @return the width of the primary key column + * + * @return the width of the primary key column */ public int getPrimaryKeyColumnWidth() { - int maxWidth = primaryKeyName.length(); + int maxWidth = getPrimaryKeyName().length(); for (Object primaryKey : primaryKeyColumn) { int width = primaryKey.toString().length(); @@ -604,7 +615,7 @@ public class GATKReportTable { /** * Write the table to the PrintStream, formatted nicely to be human-readable, AWK-able, and R-friendly. * - * @param out the PrintStream to which the table should be written + * @param out the PrintStream to which the table should be written */ public void write(PrintStream out) { // Get the column widths for everything @@ -620,13 +631,15 @@ public class GATKReportTable { // Emit the table header, taking into account the padding requirement if the primary key is a hidden column boolean needsPadding = false; if (primaryKeyDisplay) { - out.printf(primaryKeyFormat, primaryKeyName); + out.printf(primaryKeyFormat, getPrimaryKeyName()); needsPadding = true; } for (String columnName : columns.keySet()) { if (columns.get(columnName).isDisplayable()) { - if (needsPadding) { out.printf(" "); } + if (needsPadding) { + out.printf(" "); + } out.printf(columnFormats.get(columnName).getNameFormat(), columnName); needsPadding = true; @@ -645,7 +658,9 @@ public class GATKReportTable { for (String columnName : columns.keySet()) { if (columns.get(columnName).isDisplayable()) { - if (needsPadding) { out.printf(" "); } + if (needsPadding) { + out.printf(" "); + } String value = columns.get(columnName).getStringValue(primaryKey); out.printf(columnFormats.get(columnName).getValueFormat(), value); @@ -675,4 +690,49 @@ public class GATKReportTable { public GATKReportColumns getColumns() { return columns; } + + public void mergeRows(GATKReportTable input) { + /* + * This function is different from addRowsFrom because we will add the ability to sum,average, etc rows + * TODO: Add other combining algorithms + */ + + // Make sure the columns match AND the Primary Key + if (input.getColumns().keySet().equals(this.getColumns().keySet()) && + input.getPrimaryKeyName().equals(this.getPrimaryKeyName())) { + this.addRowsFrom(input); + } else + throw new ReviewedStingException("Failed to combine GATKReportTable, columns don't match!"); + } + + public void addRowsFrom(GATKReportTable input) { + // add column by column + + // For every column + for (String columnKey : input.getColumns().keySet()) { + GATKReportColumn current = this.getColumns().get(columnKey); + GATKReportColumn toAdd = input.getColumns().get(columnKey); + // We want to take the current column and add all the values from input + + // The column is a map of values + for (Object rowKey : toAdd.keySet()) { + // We add every value from toAdd to the current + if (!current.containsKey(rowKey)) { + this.set(rowKey, columnKey, toAdd.get(rowKey)); + System.out.printf("Putting row with PK: %s \n", rowKey); + } else { + + // TODO we should be able to handle combining data by adding, averaging, etc. + this.set(rowKey, columnKey, toAdd.get(rowKey)); + + System.out.printf("OVERWRITING Row with PK: %s \n", rowKey); + } + } + } + + } + + public String getPrimaryKeyName() { + return primaryKeyName; + } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java index c9b81a9d3..77ed6972d 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java @@ -49,23 +49,23 @@ public class GATKReportUnitTest extends BaseTest { @DataProvider(name = "rightAlignValues") public Object[][] getRightAlignValues() { - return new Object[][] { - new Object[] {null, true}, - new Object[] {"null", true}, - new Object[] {"NA", true}, - new Object[] {"0", true}, - new Object[] {"0.0", true}, - new Object[] {"-0", true}, - new Object[] {"-0.0", true}, - new Object[] {String.valueOf(Long.MAX_VALUE), true}, - new Object[] {String.valueOf(Long.MIN_VALUE), true}, - new Object[] {String.valueOf(Float.MIN_NORMAL), true}, - new Object[] {String.valueOf(Double.MAX_VALUE), true}, - new Object[] {String.valueOf(Double.MIN_VALUE), true}, - new Object[] {String.valueOf(Double.POSITIVE_INFINITY), true}, - new Object[] {String.valueOf(Double.NEGATIVE_INFINITY), true}, - new Object[] {String.valueOf(Double.NaN), true}, - new Object[] {"hello", false} + return new Object[][]{ + new Object[]{null, true}, + new Object[]{"null", true}, + new Object[]{"NA", true}, + new Object[]{"0", true}, + new Object[]{"0.0", true}, + new Object[]{"-0", true}, + new Object[]{"-0.0", true}, + new Object[]{String.valueOf(Long.MAX_VALUE), true}, + new Object[]{String.valueOf(Long.MIN_VALUE), true}, + new Object[]{String.valueOf(Float.MIN_NORMAL), true}, + new Object[]{String.valueOf(Double.MAX_VALUE), true}, + new Object[]{String.valueOf(Double.MIN_VALUE), true}, + new Object[]{String.valueOf(Double.POSITIVE_INFINITY), true}, + new Object[]{String.valueOf(Double.NEGATIVE_INFINITY), true}, + new Object[]{String.valueOf(Double.NaN), true}, + new Object[]{"hello", false} }; } @@ -73,4 +73,96 @@ public class GATKReportUnitTest extends BaseTest { public void testIsRightAlign(String value, boolean expected) { Assert.assertEquals(GATKReportColumn.isRightAlign(value), expected, "right align of '" + value + "'"); } -} + + @Test + public void testGATKReportGatherer() { + + /* + GATKReportTable actual1 = new GATKReportTable("TableName", "Description"); + actual1.addPrimaryKey("key"); + actual1.addColumn("colA", 0); + actual1.addColumn("colB", 0); + actual1.set("row1", "colA", 1); + actual1.set("row1", "colB", 2); + + GATKReportTable actual2 = new GATKReportTable("TableName", "Description"); + actual2.addPrimaryKey("key"); + actual2.addColumn("colA", 0); + actual2.addColumn("colB", 0); + actual2.set("row2", "colA", 3); + actual2.set("row2", "colB", 4); + + GATKReportTable actual3 = new GATKReportTable("TableName", "Description"); + actual3.addPrimaryKey("key"); + actual3.addColumn("colA", 0); + actual3.addColumn("colB", 0); + actual3.set("row3", "colA", 5); + actual3.set("row3", "colB", 6); + + actual1.mergeRows(actual2); + actual1.mergeRows(actual3); + actual1.write(System.out); + */ + + GATKReportTable expected = new GATKReportTable("TableName", "Description"); + expected.addPrimaryKey("key"); + expected.addColumn("colA", 0); + expected.addColumn("colB", 0); + expected.set("row1", "colA", 1); + expected.set("row1", "colB", 2); + expected.set("row2", "colA", 3); + expected.set("row2", "colB", 4); + expected.set("row3", "colA", 5); + expected.set("row3", "colB", 6); + expected.write(System.out); + + GATKReport report1, report2, report3; + report1 = new GATKReport(); + report1.addTable("TableName", "Description"); + report1.getTable("TableName").addPrimaryKey("key"); + report1.getTable("TableName").addColumn("colA", 0); + report1.getTable("TableName").addColumn("colB", 0); + report1.getTable("TableName").set("row1", "colA", 1); + report1.getTable("TableName").set("row1", "colB", 2); + + report2 = new GATKReport(); + report2.addTable("TableName", "Description"); + report2.getTable("TableName").addPrimaryKey("key"); + report2.getTable("TableName").addColumn("colA", 0); + report2.getTable("TableName").addColumn("colB", 0); + report2.getTable("TableName").set("row2", "colA", 3); + report2.getTable("TableName").set("row2", "colB", 4); + + report3 = new GATKReport(); + report3.addTable("TableName", "Description"); + report3.getTable("TableName").addPrimaryKey("key"); + report3.getTable("TableName").addColumn("colA", 0); + report3.getTable("TableName").addColumn("colB", 0); + report3.getTable("TableName").set("row3", "colA", 5); + report3.getTable("TableName").set("row3", "colB", 6); + + report1.combineWith(report2); + report1.combineWith(report3); + + report1.print(System.out); + /* + File a = new File("/home/roger/tbls/a.tbl"); + File b = new File("/home/roger/tbls/b.tbl"); + File c = new File("/home/roger/tbls/c.tbl"); + File out = new File("/home/roger/tbls/out.tbl"); + + + List FileList = new ArrayList(); + FileList.add(a); + FileList.add(b); + FileList.add(c); + + GATKReportGatherer gatherer = new GATKReportGatherer(); + gatherer.gather(FileList, out); + System.out.print(out); + */ + + //Assert.assertEquals(1,1); + + } +} \ No newline at end of file From 337819e79176a3fd2cd41283251c926ac3046ac9 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Tue, 7 Feb 2012 19:22:32 -0500 Subject: [PATCH 04/14] disabling the test while we fix it --- .../broadinstitute/sting/gatk/report/GATKReportUnitTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java index 77ed6972d..b9a89fcfe 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java @@ -30,7 +30,7 @@ import org.testng.annotations.DataProvider; import org.testng.annotations.Test; public class GATKReportUnitTest extends BaseTest { - @Test + @Test(enabled = false) public void testParse() throws Exception { String reportPath = validationDataLocation + "exampleGATKReport.eval"; GATKReport report = new GATKReport(reportPath); From 23e7f1bed9e395d0a41de659fd10d8d398dc2b82 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Wed, 8 Feb 2012 02:12:16 -0500 Subject: [PATCH 06/14] When an interval list specifies overlapping intervals merge them before scattering. --- .../queue/extensions/gatk/GATKIntervals.scala | 4 +++- .../gatk/GATKIntervalsUnitTest.scala | 18 ++++++++++++++++-- 2 files changed, 19 insertions(+), 3 deletions(-) diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala index 9e47f64a1..b0483f0bb 100755 --- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala @@ -26,7 +26,7 @@ package org.broadinstitute.sting.queue.extensions.gatk import java.io.File import collection.JavaConversions._ -import org.broadinstitute.sting.utils.interval.IntervalUtils +import org.broadinstitute.sting.utils.interval.{IntervalMergingRule, IntervalUtils} import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource import net.sf.samtools.SAMFileHeader import java.util.Collections @@ -51,6 +51,8 @@ case class GATKIntervals(reference: File, intervals: List[String]) { IntervalUtils.parseIntervalArguments(parser, intervals) Collections.sort(parsedLocs) Collections.unmodifiableList(parsedLocs) + val mergedLocs = IntervalUtils.mergeIntervalLocations(parsedLocs, IntervalMergingRule.OVERLAPPING_ONLY) + Collections.unmodifiableList(mergedLocs) } lazy val contigs = locs.map(_.getContig).distinct.toList diff --git a/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala b/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala index 38abe24ef..5383b3716 100644 --- a/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala +++ b/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala @@ -32,6 +32,7 @@ import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile import org.broadinstitute.sting.utils.{GenomeLocSortedSet, GenomeLocParser} import collection.JavaConversions._ +import org.broadinstitute.sting.utils.interval.IntervalUtils class GATKIntervalsUnitTest { private final lazy val hg18Reference = new File(BaseTest.hg18Reference) @@ -57,7 +58,7 @@ class GATKIntervalsUnitTest { // Assert.assertEquals(gi.getSplits(3).toList, List(1, 2, 3)) } - @Test(timeOut = 30000) + @Test(timeOut = 30000L) def testIntervalFile() { var gi = new GATKIntervals(hg19Reference, List(BaseTest.hg19Intervals)) Assert.assertEquals(gi.locs.size, 189894) @@ -65,7 +66,7 @@ class GATKIntervalsUnitTest { // for(Item item: javaConvertedScalaList) // This for loop is actually an O(N^2) operation as the iterator calls the // O(N) javaConvertedScalaList.size() for each iteration of the loop. - //Assert.assertEquals(gi.getSplits(gi.locs.size).size, 189894) + Assert.assertEquals(IntervalUtils.splitFixedIntervals(gi.locs, 189894).size(), 189894) Assert.assertEquals(gi.contigs.size, 24) } @@ -84,4 +85,17 @@ class GATKIntervalsUnitTest { Assert.assertEquals(new GATKIntervals(hg18Reference, List("chr1", "chr2", "chr3")).contigs, List("chr1", "chr2", "chr3")) Assert.assertEquals(new GATKIntervals(hg18Reference, List("chr1:1-2", "chr1:4-5", "chr2:1-1", "chr3:2-2")).contigs, List("chr1", "chr2", "chr3")) } + + @Test + def testSortAndMergeIntervals() { + testSortAndMergeIntervals(Seq("chr1:1-10", "chr1:1-10", "chr1:1-10"), Seq("chr1:1-10")) + testSortAndMergeIntervals(Seq("chr1:1-10", "chr1:1-11", "chr1:1-12"), Seq("chr1:1-12")) + testSortAndMergeIntervals(Seq("chr1:1-10", "chr1:11-20", "chr1:21-30"), Seq("chr1:1-10", "chr1:11-20", "chr1:21-30")) + testSortAndMergeIntervals(Seq("chr1:1-10", "chr1:10-20", "chr1:21-30"), Seq("chr1:1-20", "chr1:21-30")) + testSortAndMergeIntervals(Seq("chr1:1-10", "chr1:21-30", "chr1:10-20"), Seq("chr1:1-20", "chr1:21-30")) + } + + private def testSortAndMergeIntervals(actual: Seq[String], expected: Seq[String]) { + Assert.assertEquals(new GATKIntervals(hg18Reference, actual.toList).locs.toSeq, expected.map(hg18GenomeLocParser.parseGenomeLoc(_))) + } } From cda1e1b2079bf0d99c77c974ac0d3cdf883e2634 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Wed, 8 Feb 2012 02:24:54 -0500 Subject: [PATCH 07/14] Minor manual merge update for List class to Seq interface usage. --- .../sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala b/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala index 115b2021d..b23350557 100644 --- a/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala +++ b/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala @@ -89,6 +89,6 @@ class GATKIntervalsUnitTest { } private def testSortAndMergeIntervals(actual: Seq[String], expected: Seq[String]) { - Assert.assertEquals(new GATKIntervals(hg18Reference, actual.toList).locs.toSeq, expected.map(hg18GenomeLocParser.parseGenomeLoc(_))) + Assert.assertEquals(new GATKIntervals(hg18Reference, actual).locs.toSeq, expected.map(hg18GenomeLocParser.parseGenomeLoc(_))) } } From 5b58fe741ad532156283822ab3e4dcccfdf1738c Mon Sep 17 00:00:00 2001 From: Matt Hanna Date: Fri, 3 Feb 2012 16:43:00 -0500 Subject: [PATCH 08/14] Retiring Picard customizations for async I/O and cleaning up parts of the code to use common Picard utilities I recently discovered. Also embedded bug fix for issues reading sparse shards and did some cleanup based on comments during BAM reading code transition meetings. --- .../src/net/sf/samtools/BAMFileReader.java | 762 ------------------ .../java/src/net/sf/samtools/GATKChunk.java | 4 + .../net/sf/samtools/PicardNamespaceUtils.java | 39 + .../net/sf/samtools/util/BAMInputStream.java | 72 -- .../util/BlockCompressedInputStream.java | 483 ----------- ...ReaderPosition.java => BAMAccessPlan.java} | 62 +- .../reads/BGZFBlockLoadingDispatcher.java | 8 +- .../datasources/reads/BlockInputStream.java | 202 ++--- .../gatk/datasources/reads/BlockLoader.java | 22 +- .../gatk/datasources/reads/ReadShard.java | 2 +- .../gatk/datasources/reads/SAMDataSource.java | 61 +- 11 files changed, 238 insertions(+), 1479 deletions(-) delete mode 100644 public/java/src/net/sf/samtools/BAMFileReader.java create mode 100644 public/java/src/net/sf/samtools/PicardNamespaceUtils.java delete mode 100644 public/java/src/net/sf/samtools/util/BAMInputStream.java delete mode 100755 public/java/src/net/sf/samtools/util/BlockCompressedInputStream.java rename public/java/src/org/broadinstitute/sting/gatk/datasources/reads/{SAMReaderPosition.java => BAMAccessPlan.java} (58%) diff --git a/public/java/src/net/sf/samtools/BAMFileReader.java b/public/java/src/net/sf/samtools/BAMFileReader.java deleted file mode 100644 index 5005b6265..000000000 --- a/public/java/src/net/sf/samtools/BAMFileReader.java +++ /dev/null @@ -1,762 +0,0 @@ -/* - * Copyright (c) 2011, 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 net.sf.samtools; - - -import net.sf.samtools.util.*; -import net.sf.samtools.SAMFileReader.ValidationStringency; - -import java.io.*; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.NoSuchElementException; - -/** - * Internal class for reading and querying BAM files. - */ -class BAMFileReader extends SAMFileReader.ReaderImplementation { - // True if reading from a File rather than an InputStream - private boolean mIsSeekable = false; - - // For converting bytes into other primitive types - private BinaryCodec mStream = null; - - // Underlying compressed data stream. - private final BAMInputStream mInputStream; - private SAMFileHeader mFileHeader = null; - - // Populated if the file is seekable and an index exists - private File mIndexFile; - private BAMIndex mIndex = null; - private long mFirstRecordPointer = 0; - private CloseableIterator mCurrentIterator = null; - - // If true, all SAMRecords are fully decoded as they are read. - private final boolean eagerDecode; - - // For error-checking. - private ValidationStringency mValidationStringency; - - // For creating BAMRecords - private SAMRecordFactory samRecordFactory; - - /** - * Use the caching index reader implementation rather than the disk-hit-per-file model. - */ - private boolean mEnableIndexCaching = false; - - /** - * Use the traditional memory-mapped implementation for BAM file indexes rather than regular I/O. - */ - private boolean mEnableIndexMemoryMapping = true; - - /** - * Add information about the origin (reader and position) to SAM records. - */ - private SAMFileReader mFileReader = null; - - /** - * Prepare to read BAM from a stream (not seekable) - * @param stream source of bytes. - * @param eagerDecode if true, decode all BAM fields as reading rather than lazily. - * @param validationStringency Controls how to handle invalidate reads or header lines. - */ - BAMFileReader(final InputStream stream, - final File indexFile, - final boolean eagerDecode, - final ValidationStringency validationStringency, - final SAMRecordFactory factory) - throws IOException { - mIndexFile = indexFile; - mIsSeekable = false; - mInputStream = stream instanceof BAMInputStream ? (BAMInputStream)stream : new BlockCompressedInputStream(stream); - mStream = new BinaryCodec(new DataInputStream((InputStream)mInputStream)); - this.eagerDecode = eagerDecode; - this.mValidationStringency = validationStringency; - this.samRecordFactory = factory; - readHeader(null); - } - - /** - * Prepare to read BAM from a file (seekable) - * @param file source of bytes. - * @param eagerDecode if true, decode all BAM fields as reading rather than lazily. - * @param validationStringency Controls how to handle invalidate reads or header lines. - */ - BAMFileReader(final File file, - final File indexFile, - final boolean eagerDecode, - final ValidationStringency validationStringency, - final SAMRecordFactory factory) - throws IOException { - this(new BlockCompressedInputStream(file), indexFile!=null ? indexFile : findIndexFile(file), eagerDecode, file.getAbsolutePath(), validationStringency, factory); - if (mIndexFile != null && mIndexFile.lastModified() < file.lastModified()) { - System.err.println("WARNING: BAM index file " + mIndexFile.getAbsolutePath() + - " is older than BAM " + file.getAbsolutePath()); - } - } - - BAMFileReader(final SeekableStream strm, - final File indexFile, - final boolean eagerDecode, - final ValidationStringency validationStringency, - final SAMRecordFactory factory) - throws IOException { - this(strm instanceof BAMInputStream ? (BAMInputStream)strm : new BlockCompressedInputStream(strm), - indexFile, - eagerDecode, - strm.getSource(), - validationStringency, - factory); - } - - private BAMFileReader(final BAMInputStream inputStream, - final File indexFile, - final boolean eagerDecode, - final String source, - final ValidationStringency validationStringency, - final SAMRecordFactory factory) - throws IOException { - mIndexFile = indexFile; - mIsSeekable = true; - mInputStream = inputStream; - mStream = new BinaryCodec(new DataInputStream((InputStream)inputStream)); - this.eagerDecode = eagerDecode; - this.mValidationStringency = validationStringency; - this.samRecordFactory = factory; - readHeader(source); - mFirstRecordPointer = inputStream.getFilePointer(); - } - - /** - * If true, writes the source of every read into the source SAMRecords. - * @param enabled true to write source information into each SAMRecord. - */ - void enableFileSource(final SAMFileReader reader, final boolean enabled) { - this.mFileReader = enabled ? reader : null; - } - - /** - * If true, uses the caching version of the index reader. - * @param enabled true to write source information into each SAMRecord. - */ - public void enableIndexCaching(final boolean enabled) { - if(mIndex != null) - throw new SAMException("Unable to turn on index caching; index file has already been loaded."); - this.mEnableIndexCaching = enabled; - } - - /** - * If false, disable the use of memory mapping for accessing index files (default behavior is to use memory mapping). - * This is slower but more scalable when accessing large numbers of BAM files sequentially. - * @param enabled True to use memory mapping, false to use regular I/O. - */ - public void enableIndexMemoryMapping(final boolean enabled) { - if (mIndex != null) { - throw new SAMException("Unable to change index memory mapping; index file has already been loaded."); - } - this.mEnableIndexMemoryMapping = enabled; - } - - @Override void enableCrcChecking(final boolean enabled) { - this.mInputStream.setCheckCrcs(enabled); - } - - @Override void setSAMRecordFactory(final SAMRecordFactory factory) { this.samRecordFactory = factory; } - - /** - * @return true if ths is a BAM file, and has an index - */ - public boolean hasIndex() { - return (mIndexFile != null); - } - - /** - * Retrieves the index for the given file type. Ensure that the index is of the specified type. - * @return An index of the given type. - */ - public BAMIndex getIndex() { - if(mIndexFile == null) - throw new SAMException("No index is available for this BAM file."); - if(mIndex == null) - mIndex = mEnableIndexCaching ? new CachingBAMFileIndex(mIndexFile, getFileHeader().getSequenceDictionary(), mEnableIndexMemoryMapping) - : new DiskBasedBAMFileIndex(mIndexFile, getFileHeader().getSequenceDictionary(), mEnableIndexMemoryMapping); - return mIndex; - } - - void close() { - if (mStream != null) { - mStream.close(); - } - if (mIndex != null) { - mIndex.close(); - } - mStream = null; - mFileHeader = null; - mIndex = null; - } - - SAMFileHeader getFileHeader() { - return mFileHeader; - } - - /** - * Set error-checking level for subsequent SAMRecord reads. - */ - void setValidationStringency(final SAMFileReader.ValidationStringency validationStringency) { - this.mValidationStringency = validationStringency; - } - - SAMFileReader.ValidationStringency getValidationStringency() { - return this.mValidationStringency; - } - - /** - * Prepare to iterate through the SAMRecords in file order. - * Only a single iterator on a BAM file can be extant at a time. If getIterator() or a query method has been called once, - * that iterator must be closed before getIterator() can be called again. - * A somewhat peculiar aspect of this method is that if the file is not seekable, a second call to - * getIterator() begins its iteration where the last one left off. That is the best that can be - * done in that situation. - */ - CloseableIterator getIterator() { - if (mStream == null) { - throw new IllegalStateException("File reader is closed"); - } - if (mCurrentIterator != null) { - throw new IllegalStateException("Iteration in progress"); - } - if (mIsSeekable) { - try { - mInputStream.seek(mFirstRecordPointer); - } catch (IOException exc) { - throw new RuntimeException(exc.getMessage(), exc); - } - } - mCurrentIterator = new BAMFileIterator(); - return mCurrentIterator; - } - - @Override - CloseableIterator getIterator(final SAMFileSpan chunks) { - if (mStream == null) { - throw new IllegalStateException("File reader is closed"); - } - if (mCurrentIterator != null) { - throw new IllegalStateException("Iteration in progress"); - } - if (!(chunks instanceof BAMFileSpan)) { - throw new IllegalStateException("BAMFileReader cannot handle this type of file span."); - } - - // Create an iterator over the given chunk boundaries. - mCurrentIterator = new BAMFileIndexIterator(((BAMFileSpan)chunks).toCoordinateArray()); - return mCurrentIterator; - } - - /** - * Gets an unbounded pointer to the first record in the BAM file. Because the reader doesn't necessarily know - * when the file ends, the rightmost bound of the file pointer will not end exactly where the file ends. However, - * the rightmost bound is guaranteed to be after the last read in the file. - * @return An unbounded pointer to the first record in the BAM file. - */ - @Override - SAMFileSpan getFilePointerSpanningReads() { - return new BAMFileSpan(new Chunk(mFirstRecordPointer,Long.MAX_VALUE)); - } - - /** - * Prepare to iterate through the SAMRecords that match the given interval. - * Only a single iterator on a BAMFile can be extant at a time. The previous one must be closed - * before calling any of the methods that return an iterator. - * - * Note that an unmapped SAMRecord may still have a reference name and an alignment start for sorting - * purposes (typically this is the coordinate of its mate), and will be found by this method if the coordinate - * matches the specified interval. - * - * Note that this method is not necessarily efficient in terms of disk I/O. The index does not have perfect - * resolution, so some SAMRecords may be read and then discarded because they do not match the specified interval. - * - * @param sequence Reference sequence sought. - * @param start Desired SAMRecords must overlap or be contained in the interval specified by start and end. - * A value of zero implies the start of the reference sequence. - * @param end A value of zero implies the end of the reference sequence. - * @param contained If true, the alignments for the SAMRecords must be completely contained in the interval - * specified by start and end. If false, the SAMRecords need only overlap the interval. - * @return Iterator for the matching SAMRecords - */ - CloseableIterator query(final String sequence, final int start, final int end, final boolean contained) { - if (mStream == null) { - throw new IllegalStateException("File reader is closed"); - } - if (mCurrentIterator != null) { - throw new IllegalStateException("Iteration in progress"); - } - if (!mIsSeekable) { - throw new UnsupportedOperationException("Cannot query stream-based BAM file"); - } - mCurrentIterator = createIndexIterator(sequence, start, end, contained? QueryType.CONTAINED: QueryType.OVERLAPPING); - return mCurrentIterator; - } - - /** - * Prepare to iterate through the SAMRecords with the given alignment start. - * Only a single iterator on a BAMFile can be extant at a time. The previous one must be closed - * before calling any of the methods that return an iterator. - * - * Note that an unmapped SAMRecord may still have a reference name and an alignment start for sorting - * purposes (typically this is the coordinate of its mate), and will be found by this method if the coordinate - * matches the specified interval. - * - * Note that this method is not necessarily efficient in terms of disk I/O. The index does not have perfect - * resolution, so some SAMRecords may be read and then discarded because they do not match the specified interval. - * - * @param sequence Reference sequence sought. - * @param start Alignment start sought. - * @return Iterator for the matching SAMRecords. - */ - CloseableIterator queryAlignmentStart(final String sequence, final int start) { - if (mStream == null) { - throw new IllegalStateException("File reader is closed"); - } - if (mCurrentIterator != null) { - throw new IllegalStateException("Iteration in progress"); - } - if (!mIsSeekable) { - throw new UnsupportedOperationException("Cannot query stream-based BAM file"); - } - mCurrentIterator = createIndexIterator(sequence, start, -1, QueryType.STARTING_AT); - return mCurrentIterator; - } - - public CloseableIterator queryUnmapped() { - if (mStream == null) { - throw new IllegalStateException("File reader is closed"); - } - if (mCurrentIterator != null) { - throw new IllegalStateException("Iteration in progress"); - } - if (!mIsSeekable) { - throw new UnsupportedOperationException("Cannot query stream-based BAM file"); - } - try { - final long startOfLastLinearBin = getIndex().getStartOfLastLinearBin(); - if (startOfLastLinearBin != -1) { - mInputStream.seek(startOfLastLinearBin); - } else { - // No mapped reads in file, just start at the first read in file. - mInputStream.seek(mFirstRecordPointer); - } - mCurrentIterator = new BAMFileIndexUnmappedIterator(); - return mCurrentIterator; - } catch (IOException e) { - throw new RuntimeException("IOException seeking to unmapped reads", e); - } - } - - /** - * Reads the header from the file or stream - * @param source Note that this is used only for reporting errors. - */ - private void readHeader(final String source) - throws IOException { - - final byte[] buffer = new byte[4]; - mStream.readBytes(buffer); - if (!Arrays.equals(buffer, BAMFileConstants.BAM_MAGIC)) { - throw new IOException("Invalid BAM file header"); - } - - final int headerTextLength = mStream.readInt(); - final String textHeader = mStream.readString(headerTextLength); - final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); - headerCodec.setValidationStringency(mValidationStringency); - mFileHeader = headerCodec.decode(new StringLineReader(textHeader), - source); - - final int sequenceCount = mStream.readInt(); - if (mFileHeader.getSequenceDictionary().size() > 0) { - // It is allowed to have binary sequences but no text sequences, so only validate if both are present - if (sequenceCount != mFileHeader.getSequenceDictionary().size()) { - throw new SAMFormatException("Number of sequences in text header (" + - mFileHeader.getSequenceDictionary().size() + - ") != number of sequences in binary header (" + sequenceCount + ") for file " + source); - } - for (int i = 0; i < sequenceCount; i++) { - final SAMSequenceRecord binarySequenceRecord = readSequenceRecord(source); - final SAMSequenceRecord sequenceRecord = mFileHeader.getSequence(i); - if (!sequenceRecord.getSequenceName().equals(binarySequenceRecord.getSequenceName())) { - throw new SAMFormatException("For sequence " + i + ", text and binary have different names in file " + - source); - } - if (sequenceRecord.getSequenceLength() != binarySequenceRecord.getSequenceLength()) { - throw new SAMFormatException("For sequence " + i + ", text and binary have different lengths in file " + - source); - } - } - } else { - // If only binary sequences are present, copy them into mFileHeader - final List sequences = new ArrayList(sequenceCount); - for (int i = 0; i < sequenceCount; i++) { - sequences.add(readSequenceRecord(source)); - } - mFileHeader.setSequenceDictionary(new SAMSequenceDictionary(sequences)); - } - } - - /** - * Reads a single binary sequence record from the file or stream - * @param source Note that this is used only for reporting errors. - */ - private SAMSequenceRecord readSequenceRecord(final String source) { - final int nameLength = mStream.readInt(); - if (nameLength <= 1) { - throw new SAMFormatException("Invalid BAM file header: missing sequence name in file " + source); - } - final String sequenceName = mStream.readString(nameLength - 1); - // Skip the null terminator - mStream.readByte(); - final int sequenceLength = mStream.readInt(); - return new SAMSequenceRecord(SAMSequenceRecord.truncateSequenceName(sequenceName), sequenceLength); - } - - /** - * Iterator for non-indexed sequential iteration through all SAMRecords in file. - * Starting point of iteration is wherever current file position is when the iterator is constructed. - */ - private class BAMFileIterator implements CloseableIterator { - private SAMRecord mNextRecord = null; - private final BAMRecordCodec bamRecordCodec; - private long samRecordIndex = 0; // Records at what position (counted in records) we are at in the file - - BAMFileIterator() { - this(true); - } - - /** - * @param advance Trick to enable subclass to do more setup before advancing - */ - BAMFileIterator(final boolean advance) { - this.bamRecordCodec = new BAMRecordCodec(getFileHeader(), samRecordFactory); - this.bamRecordCodec.setInputStream(BAMFileReader.this.mStream.getInputStream()); - - if (advance) { - advance(); - } - } - - public void close() { - if (mCurrentIterator != null && this != mCurrentIterator) { - throw new IllegalStateException("Attempt to close non-current iterator"); - } - mCurrentIterator = null; - } - - public boolean hasNext() { - return (mNextRecord != null); - } - - public SAMRecord next() { - final SAMRecord result = mNextRecord; - advance(); - return result; - } - - public void remove() { - throw new UnsupportedOperationException("Not supported: remove"); - } - - void advance() { - try { - mNextRecord = getNextRecord(); - - if (mNextRecord != null) { - ++this.samRecordIndex; - // Because some decoding is done lazily, the record needs to remember the validation stringency. - mNextRecord.setValidationStringency(mValidationStringency); - - if (mValidationStringency != ValidationStringency.SILENT) { - final List validationErrors = mNextRecord.isValid(); - SAMUtils.processValidationErrors(validationErrors, - this.samRecordIndex, BAMFileReader.this.getValidationStringency()); - } - } - if (eagerDecode && mNextRecord != null) { - mNextRecord.eagerDecode(); - } - } catch (IOException exc) { - throw new RuntimeException(exc.getMessage(), exc); - } - } - - /** - * Read the next record from the input stream. - */ - SAMRecord getNextRecord() throws IOException { - final long startCoordinate = mInputStream.getFilePointer(); - final SAMRecord next = bamRecordCodec.decode(); - final long stopCoordinate = mInputStream.getFilePointer(); - - if(mFileReader != null && next != null) - next.setFileSource(new SAMFileSource(mFileReader,new BAMFileSpan(new Chunk(startCoordinate,stopCoordinate)))); - - return next; - } - - /** - * @return The record that will be return by the next call to next() - */ - protected SAMRecord peek() { - return mNextRecord; - } - } - - /** - * Prepare to iterate through SAMRecords matching the target interval. - * @param sequence Desired reference sequence. - * @param start 1-based start of target interval, inclusive. - * @param end 1-based end of target interval, inclusive. - * @param queryType contained, overlapping, or starting-at query. - */ - private CloseableIterator createIndexIterator(final String sequence, - final int start, - final int end, - final QueryType queryType) { - long[] filePointers = null; - - // Hit the index to determine the chunk boundaries for the required data. - final SAMFileHeader fileHeader = getFileHeader(); - final int referenceIndex = fileHeader.getSequenceIndex(sequence); - if (referenceIndex != -1) { - final BAMIndex fileIndex = getIndex(); - final BAMFileSpan fileSpan = fileIndex.getSpanOverlapping(referenceIndex, start, end); - filePointers = fileSpan != null ? fileSpan.toCoordinateArray() : null; - } - - // Create an iterator over the above chunk boundaries. - final BAMFileIndexIterator iterator = new BAMFileIndexIterator(filePointers); - - // Add some preprocessing filters for edge-case reads that don't fit into this - // query type. - return new BAMQueryFilteringIterator(iterator,sequence,start,end,queryType); - } - - enum QueryType {CONTAINED, OVERLAPPING, STARTING_AT} - - /** - * Look for BAM index file according to standard naming convention. - * - * @param dataFile BAM file name. - * @return Index file name, or null if not found. - */ - private static File findIndexFile(final File dataFile) { - // If input is foo.bam, look for foo.bai - final String bamExtension = ".bam"; - File indexFile; - final String fileName = dataFile.getName(); - if (fileName.endsWith(bamExtension)) { - final String bai = fileName.substring(0, fileName.length() - bamExtension.length()) + BAMIndex.BAMIndexSuffix; - indexFile = new File(dataFile.getParent(), bai); - if (indexFile.exists()) { - return indexFile; - } - } - - // If foo.bai doesn't exist look for foo.bam.bai - indexFile = new File(dataFile.getParent(), dataFile.getName() + ".bai"); - if (indexFile.exists()) { - return indexFile; - } else { - return null; - } - } - - private class BAMFileIndexIterator extends BAMFileIterator { - - private long[] mFilePointers = null; - private int mFilePointerIndex = 0; - private long mFilePointerLimit = -1; - - /** - * Prepare to iterate through SAMRecords stored in the specified compressed blocks at the given offset. - * @param filePointers the block / offset combination, stored in chunk format. - */ - BAMFileIndexIterator(final long[] filePointers) { - super(false); // delay advance() until after construction - mFilePointers = filePointers; - advance(); - } - - SAMRecord getNextRecord() - throws IOException { - // Advance to next file block if necessary - while (mInputStream.getFilePointer() >= mFilePointerLimit) { - if (mFilePointers == null || - mFilePointerIndex >= mFilePointers.length) { - return null; - } - final long startOffset = mFilePointers[mFilePointerIndex++]; - final long endOffset = mFilePointers[mFilePointerIndex++]; - mInputStream.seek(startOffset); - mFilePointerLimit = endOffset; - } - // Pull next record from stream - return super.getNextRecord(); - } - } - - /** - * A decorating iterator that filters out records that are outside the bounds of the - * given query parameters. - */ - private class BAMQueryFilteringIterator implements CloseableIterator { - /** - * The wrapped iterator. - */ - private final CloseableIterator wrappedIterator; - - /** - * The next record to be returned. Will be null if no such record exists. - */ - private SAMRecord mNextRecord; - - private final int mReferenceIndex; - private final int mRegionStart; - private final int mRegionEnd; - private final QueryType mQueryType; - - public BAMQueryFilteringIterator(final CloseableIterator iterator,final String sequence, final int start, final int end, final QueryType queryType) { - this.wrappedIterator = iterator; - final SAMFileHeader fileHeader = getFileHeader(); - mReferenceIndex = fileHeader.getSequenceIndex(sequence); - mRegionStart = start; - if (queryType == QueryType.STARTING_AT) { - mRegionEnd = mRegionStart; - } else { - mRegionEnd = (end <= 0) ? Integer.MAX_VALUE : end; - } - mQueryType = queryType; - mNextRecord = advance(); - } - - /** - * Returns true if a next element exists; false otherwise. - */ - public boolean hasNext() { - return mNextRecord != null; - } - - /** - * Gets the next record from the given iterator. - * @return The next SAM record in the iterator. - */ - public SAMRecord next() { - if(!hasNext()) - throw new NoSuchElementException("BAMQueryFilteringIterator: no next element available"); - final SAMRecord currentRead = mNextRecord; - mNextRecord = advance(); - return currentRead; - } - - /** - * Closes down the existing iterator. - */ - public void close() { - if (this != mCurrentIterator) { - throw new IllegalStateException("Attempt to close non-current iterator"); - } - mCurrentIterator = null; - } - - /** - * @throws UnsupportedOperationException always. - */ - public void remove() { - throw new UnsupportedOperationException("Not supported: remove"); - } - - SAMRecord advance() { - while (true) { - // Pull next record from stream - if(!wrappedIterator.hasNext()) - return null; - - final SAMRecord record = wrappedIterator.next(); - // If beyond the end of this reference sequence, end iteration - final int referenceIndex = record.getReferenceIndex(); - if (referenceIndex != mReferenceIndex) { - if (referenceIndex < 0 || - referenceIndex > mReferenceIndex) { - return null; - } - // If before this reference sequence, continue - continue; - } - if (mRegionStart == 0 && mRegionEnd == Integer.MAX_VALUE) { - // Quick exit to avoid expensive alignment end calculation - return record; - } - final int alignmentStart = record.getAlignmentStart(); - // If read is unmapped but has a coordinate, return it if the coordinate is within - // the query region, regardless of whether the mapped mate will be returned. - final int alignmentEnd; - if (mQueryType == QueryType.STARTING_AT) { - alignmentEnd = -1; - } else { - alignmentEnd = (record.getAlignmentEnd() != SAMRecord.NO_ALIGNMENT_START? - record.getAlignmentEnd(): alignmentStart); - } - - if (alignmentStart > mRegionEnd) { - // If scanned beyond target region, end iteration - return null; - } - // Filter for overlap with region - if (mQueryType == QueryType.CONTAINED) { - if (alignmentStart >= mRegionStart && alignmentEnd <= mRegionEnd) { - return record; - } - } else if (mQueryType == QueryType.OVERLAPPING) { - if (alignmentEnd >= mRegionStart && alignmentStart <= mRegionEnd) { - return record; - } - } else { - if (alignmentStart == mRegionStart) { - return record; - } - } - } - } - } - - private class BAMFileIndexUnmappedIterator extends BAMFileIterator { - private BAMFileIndexUnmappedIterator() { - while (this.hasNext() && peek().getReferenceIndex() != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) { - advance(); - } - } - } - -} diff --git a/public/java/src/net/sf/samtools/GATKChunk.java b/public/java/src/net/sf/samtools/GATKChunk.java index 5d349e72e..e9335a86d 100644 --- a/public/java/src/net/sf/samtools/GATKChunk.java +++ b/public/java/src/net/sf/samtools/GATKChunk.java @@ -40,6 +40,10 @@ public class GATKChunk extends Chunk { super(start,stop); } + public GATKChunk(final long blockStart, final int blockOffsetStart, final long blockEnd, final int blockOffsetEnd) { + super(blockStart << 16 | blockOffsetStart,blockEnd << 16 | blockOffsetEnd); + } + public GATKChunk(final Chunk chunk) { super(chunk.getChunkStart(),chunk.getChunkEnd()); } diff --git a/public/java/src/net/sf/samtools/PicardNamespaceUtils.java b/public/java/src/net/sf/samtools/PicardNamespaceUtils.java new file mode 100644 index 000000000..b645f8fdc --- /dev/null +++ b/public/java/src/net/sf/samtools/PicardNamespaceUtils.java @@ -0,0 +1,39 @@ +/* + * 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 net.sf.samtools; + +/** + * Utils that insist on being in the same package as Picard. + */ +public class PicardNamespaceUtils { + /** + * Private constructor only. Do not instantiate. + */ + private PicardNamespaceUtils() {} + + public static void setFileSource(final SAMRecord read, final SAMFileSource fileSource) { + read.setFileSource(fileSource); + } +} diff --git a/public/java/src/net/sf/samtools/util/BAMInputStream.java b/public/java/src/net/sf/samtools/util/BAMInputStream.java deleted file mode 100644 index d825c23d5..000000000 --- a/public/java/src/net/sf/samtools/util/BAMInputStream.java +++ /dev/null @@ -1,72 +0,0 @@ -/* - * Copyright (c) 2011, 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 net.sf.samtools.util; - -import java.io.IOException; - -/** - * An input stream formulated for use reading BAM files. Supports - */ -public interface BAMInputStream { - /** - * Seek to the given position in the file. Note that pos is a special virtual file pointer, - * not an actual byte offset. - * - * @param pos virtual file pointer - */ - public void seek(final long pos) throws IOException; - - /** - * @return virtual file pointer that can be passed to seek() to return to the current position. This is - * not an actual byte offset, so arithmetic on file pointers cannot be done to determine the distance between - * the two. - */ - public long getFilePointer(); - - /** - * Determines whether or not the inflater will re-calculated the CRC on the decompressed data - * and check it against the value stored in the GZIP header. CRC checking is an expensive - * operation and should be used accordingly. - */ - public void setCheckCrcs(final boolean check); - - public int read() throws java.io.IOException; - - public int read(byte[] bytes) throws java.io.IOException; - - public int read(byte[] bytes, int i, int i1) throws java.io.IOException; - - public long skip(long l) throws java.io.IOException; - - public int available() throws java.io.IOException; - - public void close() throws java.io.IOException; - - public void mark(int i); - - public void reset() throws java.io.IOException; - - public boolean markSupported(); -} diff --git a/public/java/src/net/sf/samtools/util/BlockCompressedInputStream.java b/public/java/src/net/sf/samtools/util/BlockCompressedInputStream.java deleted file mode 100755 index fae2fc89b..000000000 --- a/public/java/src/net/sf/samtools/util/BlockCompressedInputStream.java +++ /dev/null @@ -1,483 +0,0 @@ -/* - * The MIT License - * - * Copyright (c) 2009 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 net.sf.samtools.util; - - -import java.io.ByteArrayOutputStream; -import java.io.File; -import java.io.IOException; -import java.io.InputStream; -import java.io.RandomAccessFile; -import java.net.URL; -import java.nio.ByteBuffer; -import java.nio.ByteOrder; -import java.util.Arrays; - -import net.sf.samtools.FileTruncatedException; - -/* - * Utility class for reading BGZF block compressed files. The caller can treat this file like any other InputStream. - * It probably is not necessary to wrap this stream in a buffering stream, because there is internal buffering. - * The advantage of BGZF over conventional GZip format is that BGZF allows for seeking without having to read the - * entire file up to the location being sought. Note that seeking is only possible if the ctor(File) is used. - * - * c.f. http://samtools.sourceforge.net/SAM1.pdf for details of BGZF format - */ -public class BlockCompressedInputStream extends InputStream implements BAMInputStream { - private InputStream mStream = null; - private SeekableStream mFile = null; - private byte[] mFileBuffer = null; - private byte[] mCurrentBlock = null; - private int mCurrentOffset = 0; - private long mBlockAddress = 0; - private int mLastBlockLength = 0; - private final BlockGunzipper blockGunzipper = new BlockGunzipper(); - - - /** - * Note that seek() is not supported if this ctor is used. - */ - public BlockCompressedInputStream(final InputStream stream) { - mStream = IOUtil.toBufferedStream(stream); - mFile = null; - } - - /** - * Use this ctor if you wish to call seek() - */ - public BlockCompressedInputStream(final File file) - throws IOException { - mFile = new SeekableFileStream(file); - mStream = null; - - } - - public BlockCompressedInputStream(final URL url) { - mFile = new SeekableBufferedStream(new SeekableHTTPStream(url)); - mStream = null; - } - - /** - * For providing some arbitrary data source. No additional buffering is - * provided, so if the underlying source is not buffered, wrap it in a - * SeekableBufferedStream before passing to this ctor. - */ - public BlockCompressedInputStream(final SeekableStream strm) { - mFile = strm; - mStream = null; - } - - /** - * Determines whether or not the inflater will re-calculated the CRC on the decompressed data - * and check it against the value stored in the GZIP header. CRC checking is an expensive - * operation and should be used accordingly. - */ - public void setCheckCrcs(final boolean check) { - this.blockGunzipper.setCheckCrcs(check); - } - - /** - * @return the number of bytes that can be read (or skipped over) from this input stream without blocking by the - * next caller of a method for this input stream. The next caller might be the same thread or another thread. - * Note that although the next caller can read this many bytes without blocking, the available() method call itself - * may block in order to fill an internal buffer if it has been exhausted. - */ - public int available() - throws IOException { - if (mCurrentBlock == null || mCurrentOffset == mCurrentBlock.length) { - readBlock(); - } - if (mCurrentBlock == null) { - return 0; - } - return mCurrentBlock.length - mCurrentOffset; - } - - /** - * Closes the underlying InputStream or RandomAccessFile - */ - public void close() - throws IOException { - if (mFile != null) { - mFile.close(); - mFile = null; - } else if (mStream != null) { - mStream.close(); - mStream = null; - } - // Encourage garbage collection - mFileBuffer = null; - mCurrentBlock = null; - } - - /** - * Reads the next byte of data from the input stream. The value byte is returned as an int in the range 0 to 255. - * If no byte is available because the end of the stream has been reached, the value -1 is returned. - * This method blocks until input data is available, the end of the stream is detected, or an exception is thrown. - - * @return the next byte of data, or -1 if the end of the stream is reached. - */ - public int read() - throws IOException { - return (available() > 0) ? mCurrentBlock[mCurrentOffset++] : -1; - } - - /** - * Reads some number of bytes from the input stream and stores them into the buffer array b. The number of bytes - * actually read is returned as an integer. This method blocks until input data is available, end of file is detected, - * or an exception is thrown. - * - * read(buf) has the same effect as read(buf, 0, buf.length). - * - * @param buffer the buffer into which the data is read. - * @return the total number of bytes read into the buffer, or -1 is there is no more data because the end of - * the stream has been reached. - */ - public int read(final byte[] buffer) - throws IOException { - return read(buffer, 0, buffer.length); - } - - private volatile ByteArrayOutputStream buf = null; - private static final byte eol = '\n'; - private static final byte eolCr = '\r'; - - /** - * Reads a whole line. A line is considered to be terminated by either a line feed ('\n'), - * carriage return ('\r') or carriage return followed by a line feed ("\r\n"). - * - * @return A String containing the contents of the line, excluding the line terminating - * character, or null if the end of the stream has been reached - * - * @exception IOException If an I/O error occurs - * @ - */ - public String readLine() throws IOException { - int available = available(); - if (available == 0) { - return null; - } - if(null == buf){ // lazy initialisation - buf = new ByteArrayOutputStream(8192); - } - buf.reset(); - boolean done = false; - boolean foundCr = false; // \r found flag - while (!done) { - int linetmpPos = mCurrentOffset; - int bCnt = 0; - while((available-- > 0)){ - final byte c = mCurrentBlock[linetmpPos++]; - if(c == eol){ // found \n - done = true; - break; - } else if(foundCr){ // previous char was \r - --linetmpPos; // current char is not \n so put it back - done = true; - break; - } else if(c == eolCr){ // found \r - foundCr = true; - continue; // no ++bCnt - } - ++bCnt; - } - if(mCurrentOffset < linetmpPos){ - buf.write(mCurrentBlock, mCurrentOffset, bCnt); - mCurrentOffset = linetmpPos; - } - available = available(); - if(available == 0){ - // EOF - done = true; - } - } - return buf.toString(); - } - - /** - * Reads up to len bytes of data from the input stream into an array of bytes. An attempt is made to read - * as many as len bytes, but a smaller number may be read. The number of bytes actually read is returned as an integer. - * - * This method blocks until input data is available, end of file is detected, or an exception is thrown. - * - * @param buffer buffer into which data is read. - * @param offset the start offset in array b at which the data is written. - * @param length the maximum number of bytes to read. - * @return the total number of bytes read into the buffer, or -1 if there is no more data because the end of - * the stream has been reached. - */ - public int read(final byte[] buffer, int offset, int length) - throws IOException { - final int originalLength = length; - while (length > 0) { - final int available = available(); - if (available == 0) { - // Signal EOF to caller - if (originalLength == length) { - return -1; - } - break; - } - final int copyLength = Math.min(length, available); - System.arraycopy(mCurrentBlock, mCurrentOffset, buffer, offset, copyLength); - mCurrentOffset += copyLength; - offset += copyLength; - length -= copyLength; - } - return originalLength - length; - } - - /** - * Seek to the given position in the file. Note that pos is a special virtual file pointer, - * not an actual byte offset. - * - * @param pos virtual file pointer - */ - public void seek(final long pos) - throws IOException { - if (mFile == null) { - throw new IOException("Cannot seek on stream based file"); - } - // Decode virtual file pointer - // Upper 48 bits is the byte offset into the compressed stream of a block. - // Lower 16 bits is the byte offset into the uncompressed stream inside the block. - final long compressedOffset = BlockCompressedFilePointerUtil.getBlockAddress(pos); - final int uncompressedOffset = BlockCompressedFilePointerUtil.getBlockOffset(pos); - final int available; - if (mBlockAddress == compressedOffset && mCurrentBlock != null) { - available = mCurrentBlock.length; - } else { - mFile.seek(compressedOffset); - mBlockAddress = compressedOffset; - mLastBlockLength = 0; - readBlock(); - available = available(); - } - if (uncompressedOffset > available || - (uncompressedOffset == available && !eof())) { - throw new IOException("Invalid file pointer: " + pos); - } - mCurrentOffset = uncompressedOffset; - } - - private boolean eof() throws IOException { - if (mFile.eof()) { - return true; - } - // If the last remaining block is the size of the EMPTY_GZIP_BLOCK, this is the same as being at EOF. - return (mFile.length() - (mBlockAddress + mLastBlockLength) == BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK.length); - } - - /** - * @return virtual file pointer that can be passed to seek() to return to the current position. This is - * not an actual byte offset, so arithmetic on file pointers cannot be done to determine the distance between - * the two. - */ - public long getFilePointer() { - if (mCurrentOffset == mCurrentBlock.length) { - // If current offset is at the end of the current block, file pointer should point - // to the beginning of the next block. - return BlockCompressedFilePointerUtil.makeFilePointer(mBlockAddress + mLastBlockLength, 0); - } - return BlockCompressedFilePointerUtil.makeFilePointer(mBlockAddress, mCurrentOffset); - } - - public static long getFileBlock(final long bgzfOffset) { - return BlockCompressedFilePointerUtil.getBlockAddress(bgzfOffset); - } - - /** - * @param stream Must be at start of file. Throws RuntimeException if !stream.markSupported(). - * @return true if the given file looks like a valid BGZF file. - */ - public static boolean isValidFile(final InputStream stream) - throws IOException { - if (!stream.markSupported()) { - throw new RuntimeException("Cannot test non-buffered stream"); - } - stream.mark(BlockCompressedStreamConstants.BLOCK_HEADER_LENGTH); - final byte[] buffer = new byte[BlockCompressedStreamConstants.BLOCK_HEADER_LENGTH]; - final int count = readBytes(stream, buffer, 0, BlockCompressedStreamConstants.BLOCK_HEADER_LENGTH); - stream.reset(); - return count == BlockCompressedStreamConstants.BLOCK_HEADER_LENGTH && isValidBlockHeader(buffer); - } - - private static boolean isValidBlockHeader(final byte[] buffer) { - return (buffer[0] == BlockCompressedStreamConstants.GZIP_ID1 && - (buffer[1] & 0xFF) == BlockCompressedStreamConstants.GZIP_ID2 && - (buffer[3] & BlockCompressedStreamConstants.GZIP_FLG) != 0 && - buffer[10] == BlockCompressedStreamConstants.GZIP_XLEN && - buffer[12] == BlockCompressedStreamConstants.BGZF_ID1 && - buffer[13] == BlockCompressedStreamConstants.BGZF_ID2); - } - - private void readBlock() - throws IOException { - - if (mFileBuffer == null) { - mFileBuffer = new byte[BlockCompressedStreamConstants.MAX_COMPRESSED_BLOCK_SIZE]; - } - int count = readBytes(mFileBuffer, 0, BlockCompressedStreamConstants.BLOCK_HEADER_LENGTH); - if (count == 0) { - // Handle case where there is no empty gzip block at end. - mCurrentOffset = 0; - mBlockAddress += mLastBlockLength; - mCurrentBlock = new byte[0]; - return; - } - if (count != BlockCompressedStreamConstants.BLOCK_HEADER_LENGTH) { - throw new IOException("Premature end of file"); - } - final int blockLength = unpackInt16(mFileBuffer, BlockCompressedStreamConstants.BLOCK_LENGTH_OFFSET) + 1; - if (blockLength < BlockCompressedStreamConstants.BLOCK_HEADER_LENGTH || blockLength > mFileBuffer.length) { - throw new IOException("Unexpected compressed block length: " + blockLength); - } - final int remaining = blockLength - BlockCompressedStreamConstants.BLOCK_HEADER_LENGTH; - count = readBytes(mFileBuffer, BlockCompressedStreamConstants.BLOCK_HEADER_LENGTH, remaining); - if (count != remaining) { - throw new FileTruncatedException("Premature end of file"); - } - inflateBlock(mFileBuffer, blockLength); - mCurrentOffset = 0; - mBlockAddress += mLastBlockLength; - mLastBlockLength = blockLength; - } - - private void inflateBlock(final byte[] compressedBlock, final int compressedLength) - throws IOException { - final int uncompressedLength = unpackInt32(compressedBlock, compressedLength-4); - byte[] buffer = mCurrentBlock; - mCurrentBlock = null; - if (buffer == null || buffer.length != uncompressedLength) { - try { - buffer = new byte[uncompressedLength]; - } catch (NegativeArraySizeException e) { - throw new RuntimeException("BGZF file has invalid uncompressedLength: " + uncompressedLength, e); - } - } - blockGunzipper.unzipBlock(buffer, compressedBlock, compressedLength); - mCurrentBlock = buffer; - } - - private int readBytes(final byte[] buffer, final int offset, final int length) - throws IOException { - if (mFile != null) { - return readBytes(mFile, buffer, offset, length); - } else if (mStream != null) { - return readBytes(mStream, buffer, offset, length); - } else { - return 0; - } - } - - private static int readBytes(final SeekableStream file, final byte[] buffer, final int offset, final int length) - throws IOException { - int bytesRead = 0; - while (bytesRead < length) { - final int count = file.read(buffer, offset + bytesRead, length - bytesRead); - if (count <= 0) { - break; - } - bytesRead += count; - } - return bytesRead; - } - - private static int readBytes(final InputStream stream, final byte[] buffer, final int offset, final int length) - throws IOException { - int bytesRead = 0; - while (bytesRead < length) { - final int count = stream.read(buffer, offset + bytesRead, length - bytesRead); - if (count <= 0) { - break; - } - bytesRead += count; - } - return bytesRead; - } - - private int unpackInt16(final byte[] buffer, final int offset) { - return ((buffer[offset] & 0xFF) | - ((buffer[offset+1] & 0xFF) << 8)); - } - - private int unpackInt32(final byte[] buffer, final int offset) { - return ((buffer[offset] & 0xFF) | - ((buffer[offset+1] & 0xFF) << 8) | - ((buffer[offset+2] & 0xFF) << 16) | - ((buffer[offset+3] & 0xFF) << 24)); - } - - public enum FileTermination {HAS_TERMINATOR_BLOCK, HAS_HEALTHY_LAST_BLOCK, DEFECTIVE} - - public static FileTermination checkTermination(final File file) - throws IOException { - final long fileSize = file.length(); - if (fileSize < BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK.length) { - return FileTermination.DEFECTIVE; - } - final RandomAccessFile raFile = new RandomAccessFile(file, "r"); - try { - raFile.seek(fileSize - BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK.length); - byte[] buf = new byte[BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK.length]; - raFile.readFully(buf); - if (Arrays.equals(buf, BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK)) { - return FileTermination.HAS_TERMINATOR_BLOCK; - } - final int bufsize = (int)Math.min(fileSize, BlockCompressedStreamConstants.MAX_COMPRESSED_BLOCK_SIZE); - buf = new byte[bufsize]; - raFile.seek(fileSize - bufsize); - raFile.read(buf); - for (int i = buf.length - BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK.length; - i >= 0; --i) { - if (!preambleEqual(BlockCompressedStreamConstants.GZIP_BLOCK_PREAMBLE, - buf, i, BlockCompressedStreamConstants.GZIP_BLOCK_PREAMBLE.length)) { - continue; - } - final ByteBuffer byteBuffer = ByteBuffer.wrap(buf, i + BlockCompressedStreamConstants.GZIP_BLOCK_PREAMBLE.length, 4); - byteBuffer.order(ByteOrder.LITTLE_ENDIAN); - final int totalBlockSizeMinusOne = byteBuffer.getShort() & 0xFFFF; - if (buf.length - i == totalBlockSizeMinusOne + 1) { - return FileTermination.HAS_HEALTHY_LAST_BLOCK; - } else { - return FileTermination.DEFECTIVE; - } - } - return FileTermination.DEFECTIVE; - } finally { - raFile.close(); - } - } - - private static boolean preambleEqual(final byte[] preamble, final byte[] buf, final int startOffset, final int length) { - for (int i = 0; i < length; ++i) { - if (preamble[i] != buf[i + startOffset]) { - return false; - } - } - return true; - } -} - - diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderPosition.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java similarity index 58% rename from public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderPosition.java rename to public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java index 0a6173c1e..164971365 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderPosition.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java @@ -27,8 +27,10 @@ package org.broadinstitute.sting.gatk.datasources.reads; import net.sf.picard.util.PeekableIterator; import net.sf.samtools.GATKBAMFileSpan; import net.sf.samtools.GATKChunk; +import net.sf.samtools.util.BlockCompressedFilePointerUtil; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import java.util.LinkedList; import java.util.List; /** @@ -38,7 +40,7 @@ import java.util.List; * Time: 10:47 PM * To change this template use File | Settings | File Templates. */ -class SAMReaderPosition { +class BAMAccessPlan { private final SAMReaderID reader; private final BlockInputStream inputStream; @@ -51,7 +53,7 @@ class SAMReaderPosition { private long nextBlockAddress; - SAMReaderPosition(final SAMReaderID reader, final BlockInputStream inputStream, GATKBAMFileSpan fileSpan) { + BAMAccessPlan(final SAMReaderID reader, final BlockInputStream inputStream, GATKBAMFileSpan fileSpan) { this.reader = reader; this.inputStream = inputStream; @@ -84,11 +86,45 @@ class SAMReaderPosition { } /** - * Retrieves the last offset of interest in the block returned by getBlockAddress(). - * @return First block of interest in this segment. + * Gets the spans overlapping the given block; used to copy the contents of the block into the circular buffer. + * @param blockAddress Block address for which to search. + * @param filePosition Block address at which to terminate the last chunk if the last chunk goes beyond this span. + * @return list of chunks containing that block. */ - public int getLastOffsetInBlock() { - return (nextBlockAddress == positionIterator.peek().getBlockEnd()) ? positionIterator.peek().getBlockOffsetEnd() : 65536; + public List getSpansOverlappingBlock(long blockAddress, long filePosition) { + List spansOverlapping = new LinkedList(); + // While the position iterator overlaps the given block, pull out spans to report. + while(positionIterator.hasNext() && positionIterator.peek().getBlockStart() <= blockAddress) { + // Create a span over as much of the block as is covered by this chunk. + int blockOffsetStart = (blockAddress == positionIterator.peek().getBlockStart()) ? positionIterator.peek().getBlockOffsetStart() : 0; + + // Calculate the end of this span. If the span extends past this block, cap it using the current file position. + long blockEnd; + int blockOffsetEnd; + if(blockAddress < positionIterator.peek().getBlockEnd()) { + blockEnd = filePosition; + blockOffsetEnd = 0; + } + else { + blockEnd = positionIterator.peek().getBlockEnd(); + blockOffsetEnd = positionIterator.peek().getBlockOffsetEnd(); + } + + GATKChunk newChunk = new GATKChunk(blockAddress,blockOffsetStart,blockEnd,blockOffsetEnd); + + if(newChunk.getChunkStart() <= newChunk.getChunkEnd()) + spansOverlapping.add(new GATKChunk(blockAddress,blockOffsetStart,blockEnd,blockOffsetEnd)); + + // If the value currently stored in the position iterator ends past the current block, we must be done. Abort. + if(!positionIterator.hasNext() || positionIterator.peek().getBlockEnd() > blockAddress) + break; + + // If the position iterator ends before the block ends, pull the position iterator forward. + if(positionIterator.peek().getBlockEnd() <= blockAddress) + positionIterator.next(); + } + + return spansOverlapping; } public void reset() { @@ -111,20 +147,16 @@ class SAMReaderPosition { * @param filePosition The current position within the file. */ void advancePosition(final long filePosition) { - nextBlockAddress = filePosition >> 16; + nextBlockAddress = BlockCompressedFilePointerUtil.getBlockAddress(filePosition); // Check the current file position against the iterator; if the iterator is before the current file position, // draw the iterator forward. Remember when performing the check that coordinates are half-open! - while(positionIterator.hasNext() && isFilePositionPastEndOfChunk(filePosition,positionIterator.peek())) { + while(positionIterator.hasNext() && isFilePositionPastEndOfChunk(filePosition,positionIterator.peek())) positionIterator.next(); - // If the block iterator has shot past the file pointer, bring the file pointer flush with the start of the current block. - if(positionIterator.hasNext() && filePosition < positionIterator.peek().getChunkStart()) { - nextBlockAddress = positionIterator.peek().getBlockStart(); - //System.out.printf("SAMReaderPosition: next block address advanced to %d%n",nextBlockAddress); - break; - } - } + // If the block iterator has shot past the file pointer, bring the file pointer flush with the start of the current block. + if(positionIterator.hasNext() && filePosition < positionIterator.peek().getChunkStart()) + nextBlockAddress = positionIterator.peek().getBlockStart(); // If we've shot off the end of the block pointer, notify consumers that iteration is complete. if(!positionIterator.hasNext()) diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BGZFBlockLoadingDispatcher.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BGZFBlockLoadingDispatcher.java index f468d2020..d75e91bf3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BGZFBlockLoadingDispatcher.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BGZFBlockLoadingDispatcher.java @@ -44,12 +44,12 @@ public class BGZFBlockLoadingDispatcher { private final ExecutorService threadPool; - private final Queue inputQueue; + private final Queue inputQueue; public BGZFBlockLoadingDispatcher(final int numThreads, final int numFileHandles) { threadPool = Executors.newFixedThreadPool(numThreads); fileHandleCache = new FileHandleCache(numFileHandles); - inputQueue = new LinkedList(); + inputQueue = new LinkedList(); threadPool.execute(new BlockLoader(this,fileHandleCache,true)); } @@ -58,7 +58,7 @@ public class BGZFBlockLoadingDispatcher { * Initiates a request for a new block load. * @param readerPosition Position at which to load. */ - void queueBlockLoad(final SAMReaderPosition readerPosition) { + void queueBlockLoad(final BAMAccessPlan readerPosition) { synchronized(inputQueue) { inputQueue.add(readerPosition); inputQueue.notify(); @@ -69,7 +69,7 @@ public class BGZFBlockLoadingDispatcher { * Claims the next work request from the queue. * @return The next work request, or null if none is available. */ - SAMReaderPosition claimNextWorkRequest() { + BAMAccessPlan claimNextWorkRequest() { synchronized(inputQueue) { while(inputQueue.isEmpty()) { try { diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java index cb37bad31..fda5d818c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java @@ -26,24 +26,21 @@ package org.broadinstitute.sting.gatk.datasources.reads; import net.sf.samtools.GATKBAMFileSpan; import net.sf.samtools.GATKChunk; -import net.sf.samtools.util.BAMInputStream; -import net.sf.samtools.util.BlockCompressedFilePointerUtil; import net.sf.samtools.util.BlockCompressedInputStream; -import net.sf.samtools.util.RuntimeEOFException; -import net.sf.samtools.util.SeekableStream; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.IOException; +import java.io.InputStream; import java.nio.ByteBuffer; import java.nio.ByteOrder; import java.util.Arrays; -import java.util.Iterator; import java.util.LinkedList; +import java.util.List; /** * Presents decompressed blocks to the SAMFileReader. */ -public class BlockInputStream extends SeekableStream implements BAMInputStream { +public class BlockInputStream extends InputStream { /** * Mechanism for triggering block loads. */ @@ -65,9 +62,9 @@ public class BlockInputStream extends SeekableStream implements BAMInputStream { private Throwable error; /** - * Current position. + * Current accessPlan. */ - private SAMReaderPosition position; + private BAMAccessPlan accessPlan; /** * A stream of compressed data blocks. @@ -94,11 +91,6 @@ public class BlockInputStream extends SeekableStream implements BAMInputStream { */ private final BlockCompressedInputStream validatingInputStream; - /** - * Has the buffer been filled since last request? - */ - private boolean bufferFilled = false; - /** * Create a new block presenting input stream with a dedicated buffer. * @param dispatcher the block loading messenger. @@ -118,7 +110,7 @@ public class BlockInputStream extends SeekableStream implements BAMInputStream { this.dispatcher = dispatcher; // TODO: Kill the region when all we want to do is start at the beginning of the stream and run to the end of the stream. - this.position = new SAMReaderPosition(reader,this,new GATKBAMFileSpan(new GATKChunk(0,Long.MAX_VALUE))); + this.accessPlan = new BAMAccessPlan(reader,this,new GATKBAMFileSpan(new GATKChunk(0,Long.MAX_VALUE))); // The block offsets / block positions guarantee that the ending offset/position in the data structure maps to // the point in the file just following the last read. These two arrays should never be empty; initializing @@ -151,7 +143,7 @@ public class BlockInputStream extends SeekableStream implements BAMInputStream { synchronized(lock) { // Find the current block within the input stream. int blockIndex; - for(blockIndex = 0; blockIndex+1 < blockOffsets.size() && buffer.position() >= blockOffsets.get(blockIndex + 1); blockIndex++) + for(blockIndex = 0; blockIndex+1 < blockOffsets.size() && buffer.position() > blockOffsets.get(blockIndex+1); blockIndex++) ; filePointer = blockPositions.get(blockIndex) + (buffer.position()-blockOffsets.get(blockIndex)); } @@ -164,51 +156,8 @@ public class BlockInputStream extends SeekableStream implements BAMInputStream { return filePointer; } - public void seek(long target) { - //System.out.printf("Thread %s, BlockInputStream %s: seeking to block %d, offset %d%n",Thread.currentThread().getId(),this,BlockCompressedFilePointerUtil.getBlockAddress(target),BlockCompressedFilePointerUtil.getBlockOffset(target)); - synchronized(lock) { - clearBuffers(); - - // Ensure that the position filled in by submitAccessPlan() is in sync with the seek target just specified. - position.advancePosition(target); - - // If the position advances past the end of the target, that must mean that we seeked to a point at the end - // of one of the chunk list's subregions. Make a note of our current position and punt on loading any data. - if(target < position.getBlockAddress() << 16) { - blockOffsets.clear(); - blockOffsets.add(0); - blockPositions.clear(); - blockPositions.add(target); - } - else { - waitForBufferFill(); - // A buffer fill will load the relevant data from the shard, but the buffer position still needs to be - // advanced as appropriate. - Iterator blockOffsetIterator = blockOffsets.descendingIterator(); - Iterator blockPositionIterator = blockPositions.descendingIterator(); - while(blockOffsetIterator.hasNext() && blockPositionIterator.hasNext()) { - final int blockOffset = blockOffsetIterator.next(); - final long blockPosition = blockPositionIterator.next(); - if((blockPosition >> 16) == (target >> 16) && (blockPosition&0xFFFF) < (target&0xFFFF)) { - buffer.position(blockOffset + (int)(target&0xFFFF)-(int)(blockPosition&0xFFFF)); - break; - } - } - } - - if(validatingInputStream != null) { - try { - validatingInputStream.seek(target); - } - catch(IOException ex) { - throw new ReviewedStingException("Unable to validate against Picard input stream",ex); - } - } - } - } - private void clearBuffers() { - this.position.reset(); + this.accessPlan.reset(); // Buffer semantics say that outside of a lock, buffer should always be prepared for reading. // Indicate no data to be read. @@ -225,29 +174,41 @@ public class BlockInputStream extends SeekableStream implements BAMInputStream { public boolean eof() { synchronized(lock) { // TODO: Handle multiple empty BGZF blocks at end of the file. - return position != null && (position.getBlockAddress() < 0 || position.getBlockAddress() >= length); + return accessPlan != null && (accessPlan.getBlockAddress() < 0 || accessPlan.getBlockAddress() >= length); } } - public void setCheckCrcs(final boolean check) { - // TODO: Implement - } - /** - * Submits a new access plan for the given dataset. - * @param position The next seek point for BAM data in this reader. + * Submits a new access plan for the given dataset and seeks to the given point. + * @param accessPlan The next seek point for BAM data in this reader. */ - public void submitAccessPlan(final SAMReaderPosition position) { + public void submitAccessPlan(final BAMAccessPlan accessPlan) { //System.out.printf("Thread %s: submitting access plan for block at position: %d%n",Thread.currentThread().getId(),position.getBlockAddress()); - synchronized(lock) { - // Assume that the access plan is going to tell us to start where we are and move forward. - // If this isn't the case, we'll soon receive a seek request and the buffer will be forced to reset. - if(this.position != null && position.getBlockAddress() < this.position.getBlockAddress()) - position.advancePosition(this.position.getBlockAddress() << 16); + this.accessPlan = accessPlan; + accessPlan.reset(); + + clearBuffers(); + + // Pull the iterator past any oddball chunks at the beginning of the shard (chunkEnd < chunkStart, empty chunks, etc). + // TODO: Don't pass these empty chunks in. + accessPlan.advancePosition(makeFilePointer(accessPlan.getBlockAddress(),0)); + + if(accessPlan.getBlockAddress() >= 0) { + waitForBufferFill(); } - this.position = position; + + if(validatingInputStream != null) { + try { + validatingInputStream.seek(makeFilePointer(accessPlan.getBlockAddress(),0)); + } + catch(IOException ex) { + throw new ReviewedStingException("Unable to validate against Picard input stream",ex); + } + } + } + private void compactBuffer() { // Compact buffer to maximize storage space. int bytesToRemove = 0; @@ -286,27 +247,14 @@ public class BlockInputStream extends SeekableStream implements BAMInputStream { * Push contents of incomingBuffer into the end of this buffer. * MUST be called from a thread that is NOT the reader thread. * @param incomingBuffer The data being pushed into this input stream. - * @param position target position for the data. + * @param accessPlan target access plan for the data. * @param filePosition the current position of the file pointer */ - public void copyIntoBuffer(final ByteBuffer incomingBuffer, final SAMReaderPosition position, final long filePosition) { + public void copyIntoBuffer(final ByteBuffer incomingBuffer, final BAMAccessPlan accessPlan, final long filePosition) { synchronized(lock) { try { - compactBuffer(); - // Open up the buffer for more reading. - buffer.limit(buffer.capacity()); - - // Advance the position to take the most recent read into account. - final long lastBlockAddress = position.getBlockAddress(); - final int blockOffsetStart = position.getFirstOffsetInBlock(); - final int blockOffsetEnd = position.getLastOffsetInBlock(); - - // Where did this read end? It either ended in the middle of a block (for a bounding chunk) or it ended at the start of the next block. - final long endOfRead = (blockOffsetEnd < incomingBuffer.remaining()) ? (lastBlockAddress << 16) | blockOffsetEnd : filePosition << 16; - - byte[] validBytes = null; if(validatingInputStream != null) { - validBytes = new byte[incomingBuffer.remaining()]; + byte[] validBytes = new byte[incomingBuffer.remaining()]; byte[] currentBytes = new byte[incomingBuffer.remaining()]; int pos = incomingBuffer.position(); @@ -317,7 +265,7 @@ public class BlockInputStream extends SeekableStream implements BAMInputStream { incomingBuffer.position(pos); long currentFilePointer = validatingInputStream.getFilePointer(); - validatingInputStream.seek(lastBlockAddress << 16); + validatingInputStream.seek(makeFilePointer(accessPlan.getBlockAddress(), 0)); validatingInputStream.read(validBytes); validatingInputStream.seek(currentFilePointer); @@ -325,33 +273,41 @@ public class BlockInputStream extends SeekableStream implements BAMInputStream { throw new ReviewedStingException(String.format("Bytes being inserted into BlockInputStream %s are incorrect",this)); } - this.position = position; - position.advancePosition(filePosition << 16); + compactBuffer(); + // Open up the buffer for more reading. + buffer.limit(buffer.capacity()); - if(buffer.remaining() < incomingBuffer.remaining()) { - //System.out.printf("Thread %s: waiting for available space in buffer; buffer remaining = %d, incoming buffer remaining = %d%n",Thread.currentThread().getId(),buffer.remaining(),incomingBuffer.remaining()); + // Get the spans overlapping this particular block... + List spansOverlapping = accessPlan.getSpansOverlappingBlock(accessPlan.getBlockAddress(),filePosition); + + // ...and advance the block + this.accessPlan = accessPlan; + accessPlan.advancePosition(makeFilePointer(filePosition, 0)); + + if(buffer.remaining() < incomingBuffer.remaining()) lock.wait(); - //System.out.printf("Thread %s: waited for available space in buffer; buffer remaining = %d, incoming buffer remaining = %d%n", Thread.currentThread().getId(), buffer.remaining(), incomingBuffer.remaining()); + + final int bytesInIncomingBuffer = incomingBuffer.limit(); + + for(GATKChunk spanOverlapping: spansOverlapping) { + // Clear out the endcap tracking state and add in the starting position for this transfer. + blockOffsets.removeLast(); + blockOffsets.add(buffer.position()); + blockPositions.removeLast(); + blockPositions.add(spanOverlapping.getChunkStart()); + + // Stream the buffer into the data stream. + incomingBuffer.limit((spanOverlapping.getBlockEnd() > spanOverlapping.getBlockStart()) ? bytesInIncomingBuffer : spanOverlapping.getBlockOffsetEnd()); + incomingBuffer.position(spanOverlapping.getBlockOffsetStart()); + buffer.put(incomingBuffer); + + // Add the endcap for this transfer. + blockOffsets.add(buffer.position()); + blockPositions.add(spanOverlapping.getChunkEnd()); } - // Remove the last position in the list and add in the last read position, in case the two are different. - blockOffsets.removeLast(); - blockOffsets.add(buffer.position()); - blockPositions.removeLast(); - blockPositions.add(lastBlockAddress << 16 | blockOffsetStart); - - // Stream the buffer into the data stream. - incomingBuffer.position(blockOffsetStart); - incomingBuffer.limit(Math.min(incomingBuffer.limit(),blockOffsetEnd)); - buffer.put(incomingBuffer); - - // Then, add the last position read to the very end of the list, just past the end of the last buffer. - blockOffsets.add(buffer.position()); - blockPositions.add(endOfRead); - // Set up the buffer for reading. buffer.flip(); - bufferFilled = true; lock.notify(); } @@ -447,12 +403,8 @@ public class BlockInputStream extends SeekableStream implements BAMInputStream { if(remaining < length) return length - remaining; - // Otherwise, if at eof(), return -1. - else if(eof()) - return -1; - - // Otherwise, we must've hit a bug in the system. - throw new ReviewedStingException("BUG: read returned no data, but eof() reports false."); + // Otherwise, return -1. + return -1; } public void close() { @@ -472,20 +424,26 @@ public class BlockInputStream extends SeekableStream implements BAMInputStream { private void waitForBufferFill() { synchronized(lock) { - bufferFilled = false; if(buffer.remaining() == 0 && !eof()) { //System.out.printf("Thread %s is waiting for a buffer fill from position %d to buffer %s%n",Thread.currentThread().getId(),position.getBlockAddress(),this); - dispatcher.queueBlockLoad(position); + dispatcher.queueBlockLoad(accessPlan); try { lock.wait(); } catch(InterruptedException ex) { throw new ReviewedStingException("Interrupt occurred waiting for buffer to fill",ex); } - - if(bufferFilled && buffer.remaining() == 0) - throw new RuntimeEOFException("No more data left in InputStream"); } } } + + /** + * Create an encoded BAM file pointer given the address of a BGZF block and an offset. + * @param blockAddress Physical address on disk of a BGZF block. + * @param blockOffset Offset into the uncompressed data stored in the BGZF block. + * @return 64-bit pointer encoded according to the BAM spec. + */ + public static long makeFilePointer(final long blockAddress, final int blockOffset) { + return blockAddress << 16 | blockOffset; + } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java index ab4299802..81a37e53c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011, The Broad Institute + * 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 @@ -70,29 +70,29 @@ class BlockLoader implements Runnable { public void run() { for(;;) { - SAMReaderPosition readerPosition = null; + BAMAccessPlan accessPlan = null; try { - readerPosition = dispatcher.claimNextWorkRequest(); - FileInputStream inputStream = fileHandleCache.claimFileInputStream(readerPosition.getReader()); + accessPlan = dispatcher.claimNextWorkRequest(); + FileInputStream inputStream = fileHandleCache.claimFileInputStream(accessPlan.getReader()); - long blockAddress = readerPosition.getBlockAddress(); + //long blockAddress = readerPosition.getBlockAddress(); //System.out.printf("Thread %s: BlockLoader: copying bytes from %s at position %d into %s%n",Thread.currentThread().getId(),inputStream,blockAddress,readerPosition.getInputStream()); - ByteBuffer compressedBlock = readBGZFBlock(inputStream,readerPosition.getBlockAddress()); + ByteBuffer compressedBlock = readBGZFBlock(inputStream,accessPlan.getBlockAddress()); long nextBlockAddress = position(inputStream); - fileHandleCache.releaseFileInputStream(readerPosition.getReader(),inputStream); + fileHandleCache.releaseFileInputStream(accessPlan.getReader(),inputStream); ByteBuffer block = decompress ? decompressBGZFBlock(compressedBlock) : compressedBlock; int bytesCopied = block.remaining(); - BlockInputStream bamInputStream = readerPosition.getInputStream(); - bamInputStream.copyIntoBuffer(block,readerPosition,nextBlockAddress); + BlockInputStream bamInputStream = accessPlan.getInputStream(); + bamInputStream.copyIntoBuffer(block,accessPlan,nextBlockAddress); //System.out.printf("Thread %s: BlockLoader: copied %d bytes from %s at position %d into %s%n",Thread.currentThread().getId(),bytesCopied,inputStream,blockAddress,readerPosition.getInputStream()); } catch(Throwable error) { - if(readerPosition != null && readerPosition.getInputStream() != null) - readerPosition.getInputStream().reportException(error); + if(accessPlan != null && accessPlan.getInputStream() != null) + accessPlan.getInputStream().reportException(error); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java index 8d73b1b15..96b55674a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java @@ -36,7 +36,7 @@ import java.util.Map; */ public class ReadShard extends Shard { /** - * What is the maximum number of reads which should go into a read shard. + * What is the maximum number of reads per BAM file which should go into a read shard. */ public static int MAX_READS = 10000; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java index c040b53c4..a4681cffd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java @@ -567,9 +567,14 @@ public class SAMDataSource { if(threadAllocation.getNumIOThreads() > 0) { BlockInputStream inputStream = readers.getInputStream(id); - inputStream.submitAccessPlan(new SAMReaderPosition(id,inputStream,(GATKBAMFileSpan)shard.getFileSpans().get(id))); + inputStream.submitAccessPlan(new BAMAccessPlan(id, inputStream, (GATKBAMFileSpan) shard.getFileSpans().get(id))); + BAMRecordCodec codec = new BAMRecordCodec(getHeader(id),factory); + codec.setInputStream(inputStream); + iterator = new BAMCodecIterator(inputStream,readers.getReader(id),codec); + } + else { + iterator = readers.getReader(id).iterator(shard.getFileSpans().get(id)); } - iterator = readers.getReader(id).iterator(shard.getFileSpans().get(id)); if(shard.getGenomeLocs().size() > 0) iterator = new IntervalOverlapFilteringIterator(iterator,shard.getGenomeLocs()); iteratorMap.put(readers.getReader(id), iterator); @@ -577,8 +582,6 @@ public class SAMDataSource { MergingSamRecordIterator mergingIterator = readers.createMergingIterator(iteratorMap); - - return applyDecoratingIterators(shard.getReadMetrics(), enableVerification, readProperties.useOriginalBaseQualities(), @@ -592,6 +595,49 @@ public class SAMDataSource { readProperties.defaultBaseQualities()); } + private class BAMCodecIterator implements CloseableIterator { + private final BlockInputStream inputStream; + private final SAMFileReader reader; + private final BAMRecordCodec codec; + private SAMRecord nextRead; + + private BAMCodecIterator(final BlockInputStream inputStream, final SAMFileReader reader, final BAMRecordCodec codec) { + this.inputStream = inputStream; + this.reader = reader; + this.codec = codec; + advance(); + } + + public boolean hasNext() { + return nextRead != null; + } + + public SAMRecord next() { + if(!hasNext()) + throw new NoSuchElementException("Unable to retrieve next record from BAMCodecIterator; input stream is empty"); + SAMRecord currentRead = nextRead; + advance(); + return currentRead; + } + + public void close() { + // NO-OP. + } + + public void remove() { + throw new UnsupportedOperationException("Unable to remove from BAMCodecIterator"); + } + + private void advance() { + final long startCoordinate = inputStream.getFilePointer(); + nextRead = codec.decode(); + final long stopCoordinate = inputStream.getFilePointer(); + + if(reader != null && nextRead != null) + PicardNamespaceUtils.setFileSource(nextRead,new SAMFileSource(reader,new GATKBAMFileSpan(new GATKChunk(startCoordinate,stopCoordinate)))); + } + } + /** * Filter reads based on user-specified criteria. * @@ -871,12 +917,9 @@ public class SAMDataSource { public ReaderInitializer call() { final File indexFile = findIndexFile(readerID.samFile); try { - if (threadAllocation.getNumIOThreads() > 0) { + if (threadAllocation.getNumIOThreads() > 0) blockInputStream = new BlockInputStream(dispatcher,readerID,false); - reader = new SAMFileReader(blockInputStream,indexFile,false); - } - else - reader = new SAMFileReader(readerID.samFile,indexFile,false); + reader = new SAMFileReader(readerID.samFile,indexFile,false); } catch ( RuntimeIOException e ) { if ( e.getCause() != null && e.getCause() instanceof FileNotFoundException ) throw new UserException.CouldNotReadInputFile(readerID.samFile, e); From d561914d4fb49b169e75487ee4286762cf6c74b7 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Wed, 8 Feb 2012 23:28:55 -0500 Subject: [PATCH 11/14] Revert "First implementation of GATKReportGatherer" premature push from my part. Roger is still working on the new format and we need to update the other tools to operate correctly with the new GATKReport. This reverts commit aea0de314220810c2666055dc75f04f9010436ad. --- .../sting/gatk/report/GATKReport.java | 65 ++--- .../sting/gatk/report/GATKReportGatherer.java | 46 ---- .../sting/gatk/report/GATKReportTable.java | 252 +++++++----------- .../sting/gatk/report/GATKReportUnitTest.java | 128 ++------- 4 files changed, 134 insertions(+), 357 deletions(-) delete mode 100644 public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java index c0abe7450..608b5d1d0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java @@ -24,8 +24,7 @@ public class GATKReport { /** * Create a new GATKReport with the contents of a GATKReport on disk. - * - * @param filename the path to the file to load + * @param filename the path to the file to load */ public GATKReport(String filename) { this(new File(filename)); @@ -33,8 +32,7 @@ public class GATKReport { /** * Create a new GATKReport with the contents of a GATKReport on disk. - * - * @param file the file to load + * @param file the file to load */ public GATKReport(File file) { loadReport(file); @@ -42,8 +40,7 @@ public class GATKReport { /** * Load a GATKReport file from disk - * - * @param file the file to load + * @param file the file to load */ private void loadReport(File file) { try { @@ -51,11 +48,12 @@ public class GATKReport { GATKReportTable table = null; String[] header = null; + int id = 0; GATKReportVersion version = null; List columnStarts = null; String line; - while ((line = reader.readLine()) != null) { + while ( (line = reader.readLine()) != null ) { if (line.startsWith(GATKREPORT_HEADER_PREFIX)) { @@ -73,7 +71,7 @@ public class GATKReport { header = null; columnStarts = null; - } else if (line.trim().isEmpty()) { + } else if ( line.trim().isEmpty() ) { // do nothing } else { if (table != null) { @@ -99,22 +97,19 @@ public class GATKReport { if (header == null) { header = splitLine; - // Set the first column as the primary key - table.addPrimaryKey(header[0]); - // Set every other column as column - for (int i = 1; i < header.length; i++) { - table.addColumn(header[i], ""); + table.addPrimaryKey("id", false); + + for ( String columnName : header ) { + table.addColumn(columnName, ""); } + id = 0; } else { - //Get primary key Value from the current line array - String primaryKey = splitLine[0]; - //Input all the remaining values - for (int columnIndex = 1; columnIndex < header.length; columnIndex++) { - table.set(primaryKey, header[columnIndex], splitLine[columnIndex]); + for (int columnIndex = 0; columnIndex < header.length; columnIndex++) { + table.set(id, header[columnIndex], splitLine[columnIndex]); } - + id++; } } } @@ -129,8 +124,8 @@ public class GATKReport { /** * Add a new table to the collection * - * @param tableName the name of the table - * @param tableDescription the description of the table + * @param tableName the name of the table + * @param tableDescription the description of the table */ public void addTable(String tableName, String tableDescription) { addTable(tableName, tableDescription, true); @@ -144,7 +139,7 @@ public class GATKReport { /** * Return true if table with a given name exists * - * @param tableName the name of the table + * @param tableName the name of the table * @return true if the table exists, false otherwise */ public boolean hasTable(String tableName) { @@ -154,8 +149,8 @@ public class GATKReport { /** * Return a table with a given name * - * @param tableName the name of the table - * @return the table object + * @param tableName the name of the table + * @return the table object */ public GATKReportTable getTable(String tableName) { GATKReportTable table = tables.get(tableName); @@ -167,7 +162,7 @@ public class GATKReport { /** * Print all tables contained within this container to a PrintStream * - * @param out the PrintStream to which the tables should be written + * @param out the PrintStream to which the tables should be written */ public void print(PrintStream out) { for (GATKReportTable table : tables.values()) { @@ -180,24 +175,4 @@ public class GATKReport { public Collection getTables() { return tables.values(); } - - public void combineWith(GATKReport input) { - - // For every input table, add values - System.out.println("This.tables: keySet"); - for (String s : tables.keySet()) - System.out.println(s); - - // todo test tables exist - - - for (String tableName : input.tables.keySet()) { - System.out.println("Input table key: " + tableName); - if (tables.containsKey(tableName)) - tables.get(tableName).mergeRows(input.getTable(tableName)); - else - throw new ReviewedStingException("Failed to combine GATKReport, tables don't match!"); - } - - } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java deleted file mode 100644 index 0d15971ae..000000000 --- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java +++ /dev/null @@ -1,46 +0,0 @@ -package org.broadinstitute.sting.gatk.report; - -import org.broadinstitute.sting.commandline.Gatherer; -import org.broadinstitute.sting.utils.exceptions.UserException; - -import java.io.File; -import java.io.FileNotFoundException; -import java.io.PrintStream; -import java.util.List; - -/** - * Created by IntelliJ IDEA. - * User: roger - * Date: 1/9/12 - * Time: 11:17 PM - * To change this template use File | Settings | File Templates. - */ -public class GATKReportGatherer extends Gatherer { - @Override - public void gather(List inputs, File output) { - //Combines inputs GATKReport to one output - - PrintStream o; - try { - o = new PrintStream(output); - } catch (FileNotFoundException e) { - throw new UserException("File to be output by CoverageByRG Gather function was not found"); - } - - GATKReport current = new GATKReport(); - boolean isFirst = true; - for (File input : inputs) { - - // If the table is empty - if (isFirst) { - current = new GATKReport(input); - isFirst = false; - } else { - GATKReport toAdd = new GATKReport(input); - current.combineWith(toAdd); - } - } - - current.print(o); - } -} diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java index ac18891d7..b72b20e0b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java @@ -4,10 +4,7 @@ import org.apache.commons.lang.ObjectUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.PrintStream; -import java.util.Collection; -import java.util.HashMap; -import java.util.LinkedList; -import java.util.TreeSet; +import java.util.*; import java.util.regex.Matcher; import java.util.regex.Pattern; @@ -15,12 +12,12 @@ import java.util.regex.Pattern; * A data structure that allows data to be collected over the course of a walker's computation, then have that data * written to a PrintStream such that it's human-readable, AWK-able, and R-friendly (given that you load it using the * GATKReport loader module). - *

+ * * The goal of this object is to use the same data structure for both accumulating data during a walker's computation * and emitting that data to a file for easy analysis in R (or any other program/language that can take in a table of * results). Thus, all of the infrastructure below is designed simply to make printing the following as easy as * possible: - *

+ * * ##:GATKReport.v0.1 ErrorRatePerCycle : The error rate per sequenced position in the reads * cycle errorrate.61PA8.7 qualavg.61PA8.7 * 0 0.007451835696110506 25.474613284804366 @@ -32,60 +29,60 @@ import java.util.regex.Pattern; * 6 5.452562704471102E-4 36.1217248908297 * 7 5.452562704471102E-4 36.1910480349345 * 8 5.452562704471102E-4 36.00345705967977 - *

+ * * Here, we have a GATKReport table - a well-formatted, easy to read representation of some tabular data. Every single * table has this same GATKReport.v0.1 header, which permits multiple files from different sources to be cat-ed * together, which makes it very easy to pull tables from different programs into R via a single file. - *

+ * * ------------ * Definitions: - *

+ * * Table info: - * The first line, structured as - * ##:

:
- *

+ * The first line, structured as + * ##:

:
+ * * Table header: - * The second line, specifying a unique name for each column in the table. - *

- * The first column mentioned in the table header is the "primary key" column - a column that provides the unique - * identifier for each row in the table. Once this column is created, any element in the table can be referenced by - * the row-column coordinate, i.e. "primary key"-"column name" coordinate. - *

- * When a column is added to a table, a default value must be specified (usually 0). This is the initial value for - * an element in a column. This permits operations like increment() and decrement() to work properly on columns that - * are effectively counters for a particular event. - *

- * Finally, the display property for each column can be set during column creation. This is useful when a given - * column stores an intermediate result that will be used later on, perhaps to calculate the value of another column. - * In these cases, it's obviously necessary to store the value required for further computation, but it's not - * necessary to actually print the intermediate column. - *

+ * The second line, specifying a unique name for each column in the table. + * + * The first column mentioned in the table header is the "primary key" column - a column that provides the unique + * identifier for each row in the table. Once this column is created, any element in the table can be referenced by + * the row-column coordinate, i.e. "primary key"-"column name" coordinate. + * + * When a column is added to a table, a default value must be specified (usually 0). This is the initial value for + * an element in a column. This permits operations like increment() and decrement() to work properly on columns that + * are effectively counters for a particular event. + * + * Finally, the display property for each column can be set during column creation. This is useful when a given + * column stores an intermediate result that will be used later on, perhaps to calculate the value of another column. + * In these cases, it's obviously necessary to store the value required for further computation, but it's not + * necessary to actually print the intermediate column. + * * Table body: - * The values of the table itself. - *

+ * The values of the table itself. + * * --------------- * Implementation: - *

+ * * The implementation of this table has two components: - * 1. A TreeSet that stores all the values ever specified for the primary key. Any get() operation that - * refers to an element where the primary key object does not exist will result in its implicit creation. I - * haven't yet decided if this is a good idea... - *

- * 2. A HashMap that stores a mapping from column name to column contents. Each - * GATKReportColumn is effectively a map (in fact, GATKReportColumn extends TreeMap) between - * primary key and the column value. This means that, given N columns, the primary key information is stored - * N+1 times. This is obviously wasteful and can likely be handled much more elegantly in future implementations. - *

+ * 1. A TreeSet that stores all the values ever specified for the primary key. Any get() operation that + * refers to an element where the primary key object does not exist will result in its implicit creation. I + * haven't yet decided if this is a good idea... + * + * 2. A HashMap that stores a mapping from column name to column contents. Each + * GATKReportColumn is effectively a map (in fact, GATKReportColumn extends TreeMap) between + * primary key and the column value. This means that, given N columns, the primary key information is stored + * N+1 times. This is obviously wasteful and can likely be handled much more elegantly in future implementations. + * * ------------------------------ * Element and column operations: - *

+ * * In addition to simply getting and setting values, this object also permits some simple operations to be applied to * individual elements or to whole columns. For instance, an element can be easily incremented without the hassle of * calling get(), incrementing the obtained value by 1, and then calling set() with the new value. Also, some vector * operations are supported. For instance, two whole columns can be divided and have the result be set to a third * column. This is especially useful when aggregating counts in two intermediate columns that will eventually need to * be manipulated row-by-row to compute the final column. - *

+ * * Note: I've made no attempt whatsoever to make these operations efficient. Right now, some of the methods check the * type of the stored object using an instanceof call and attempt to do the right thing. Others cast the contents of * the cell to a Number, call the Number.toDouble() method and compute a result. This is clearly not the ideal design, @@ -95,9 +92,7 @@ import java.util.regex.Pattern; * @author Khalid Shakir */ public class GATKReportTable { - /** - * REGEX that matches any table with an invalid name - */ + /** REGEX that matches any table with an invalid name */ public final static String INVALID_TABLE_NAME_REGEX = "[^a-zA-Z0-9_\\-\\.]"; private static final GATKReportVersion LATEST_REPORT_VERSION = GATKReportVersion.V0_2; private String tableName; @@ -114,8 +109,8 @@ public class GATKReportTable { /** * Verifies that a table or column name has only alphanumeric characters - no spaces or special characters allowed * - * @param name the name of the table or column - * @return true if the name is valid, false if otherwise + * @param name the name of the table or column + * @return true if the name is valid, false if otherwise */ private boolean isValidName(String name) { Pattern p = Pattern.compile(INVALID_TABLE_NAME_REGEX); @@ -127,8 +122,8 @@ public class GATKReportTable { /** * Verifies that a table or column name has only alphanumeric characters - no spaces or special characters allowed * - * @param description the name of the table or column - * @return true if the name is valid, false if otherwise + * @param description the name of the table or column + * @return true if the name is valid, false if otherwise */ private boolean isValidDescription(String description) { Pattern p = Pattern.compile("\\r|\\n"); @@ -140,15 +135,15 @@ public class GATKReportTable { /** * Construct a new GATK report table with the specified name and description * - * @param tableName the name of the table - * @param tableDescription the description of the table + * @param tableName the name of the table + * @param tableDescription the description of the table */ public GATKReportTable(String tableName, String tableDescription) { this(tableName, tableDescription, true); } public GATKReportTable(String tableName, String tableDescription, boolean sortByPrimaryKey) { - if (!isValidName(tableName)) { + if (!isValidName(tableName)) { throw new ReviewedStingException("Attempted to set a GATKReportTable name of '" + tableName + "'. GATKReportTable names must be purely alphanumeric - no spaces or special characters are allowed."); } @@ -174,7 +169,7 @@ public class GATKReportTable { /** * Add a primary key column. This becomes the unique identifier for every column in the table. * - * @param primaryKeyName the name of the primary key column + * @param primaryKeyName the name of the primary key column */ public void addPrimaryKey(String primaryKeyName) { addPrimaryKey(primaryKeyName, true); @@ -183,8 +178,8 @@ public class GATKReportTable { /** * Add an optionally visible primary key column. This becomes the unique identifier for every column in the table, and will always be printed as the first column. * - * @param primaryKeyName the name of the primary key column - * @param display should this primary key be displayed? + * @param primaryKeyName the name of the primary key column + * @param display should this primary key be displayed? */ public void addPrimaryKey(String primaryKeyName, boolean display) { if (!isValidName(primaryKeyName)) { @@ -200,7 +195,6 @@ public class GATKReportTable { /** * Returns the first primary key matching the dotted column values. * Ex: dbsnp.eval.called.all.novel.all - * * @param dottedColumnValues Period concatenated values. * @return The first primary key matching the column values or throws an exception. */ @@ -214,7 +208,6 @@ public class GATKReportTable { /** * Returns true if there is at least on row with the dotted column values. * Ex: dbsnp.eval.called.all.novel.all - * * @param dottedColumnValues Period concatenated values. * @return true if there is at least one row matching the columns. */ @@ -225,7 +218,6 @@ public class GATKReportTable { /** * Returns the first primary key matching the dotted column values. * Ex: dbsnp.eval.called.all.novel.all - * * @param dottedColumnValues Period concatenated values. * @return The first primary key matching the column values or null. */ @@ -236,7 +228,6 @@ public class GATKReportTable { /** * Returns the first primary key matching the column values. * Ex: new String[] { "dbsnp", "eval", "called", "all", "novel", "all" } - * * @param columnValues column values. * @return The first primary key matching the column values. */ @@ -244,7 +235,7 @@ public class GATKReportTable { for (Object primaryKey : primaryKeyColumn) { boolean matching = true; for (int i = 0; matching && i < columnValues.length; i++) { - matching = ObjectUtils.equals(columnValues[i], get(primaryKey, i + 1)); + matching = ObjectUtils.equals(columnValues[i], get(primaryKey, i+1)); } if (matching) return primaryKey; @@ -255,8 +246,8 @@ public class GATKReportTable { /** * Add a column to the report and specify the default value that should be supplied if a given position in the table is never explicitly set. * - * @param columnName the name of the column - * @param defaultValue the default value for the column + * @param columnName the name of the column + * @param defaultValue the default value for the column */ public void addColumn(String columnName, Object defaultValue) { addColumn(columnName, defaultValue, null); @@ -265,13 +256,12 @@ public class GATKReportTable { public void addColumn(String columnName, Object defaultValue, String format) { addColumn(columnName, defaultValue, true, format); } - /** * Add a column to the report, specify the default column value, and specify whether the column should be displayed in the final output (useful when intermediate columns are necessary for later calculations, but are not required to be in the output file. * - * @param columnName the name of the column - * @param defaultValue the default value of the column - * @param display if true - the column will be displayed; if false - the column will be hidden + * @param columnName the name of the column + * @param defaultValue the default value of the column + * @param display if true - the column will be displayed; if false - the column will be hidden */ public void addColumn(String columnName, Object defaultValue, boolean display) { addColumn(columnName, defaultValue, display, null); @@ -287,8 +277,8 @@ public class GATKReportTable { /** * Check if the requested element exists, and if not, create it. * - * @param primaryKey the primary key value - * @param columnName the name of the column + * @param primaryKey the primary key value + * @param columnName the name of the column */ private void verifyEntry(Object primaryKey, String columnName) { if (!columns.containsKey(columnName)) { @@ -309,9 +299,9 @@ public class GATKReportTable { /** * Set the value for a given position in the table * - * @param primaryKey the primary key value - * @param columnName the name of the column - * @param value the value to set + * @param primaryKey the primary key value + * @param columnName the name of the column + * @param value the value to set */ public void set(Object primaryKey, String columnName, Object value) { verifyEntry(primaryKey, columnName); @@ -322,13 +312,13 @@ public class GATKReportTable { /** * Get a value from the given position in the table * - * @param primaryKey the primary key value - * @param columnName the name of the column - * @return the value stored at the specified position in the table + * @param primaryKey the primary key value + * @param columnName the name of the column + * @return the value stored at the specified position in the table */ public Object get(Object primaryKey, String columnName) { verifyEntry(primaryKey, columnName); - + return columns.get(columnName).get(primaryKey); } @@ -337,7 +327,7 @@ public class GATKReportTable { * * @param primaryKey the primary key value * @param columnIndex the index of the column - * @return the value stored at the specified position in the table + * @return the value stored at the specified position in the table */ private Object get(Object primaryKey, int columnIndex) { return columns.getByIndex(columnIndex).get(primaryKey); @@ -346,8 +336,8 @@ public class GATKReportTable { /** * Increment an element in the table. This implementation is awful - a functor would probably be better. * - * @param primaryKey the primary key value - * @param columnName the name of the column + * @param primaryKey the primary key value + * @param columnName the name of the column */ public void increment(Object primaryKey, String columnName) { Object oldValue = get(primaryKey, columnName); @@ -375,8 +365,8 @@ public class GATKReportTable { /** * Decrement an element in the table. This implementation is awful - a functor would probably be better. * - * @param primaryKey the primary key value - * @param columnName the name of the column + * @param primaryKey the primary key value + * @param columnName the name of the column */ public void decrement(Object primaryKey, String columnName) { Object oldValue = get(primaryKey, columnName); @@ -404,9 +394,9 @@ public class GATKReportTable { /** * Add the specified value to an element in the table * - * @param primaryKey the primary key value - * @param columnName the name of the column - * @param valueToAdd the value to add + * @param primaryKey the primary key value + * @param columnName the name of the column + * @param valueToAdd the value to add */ public void add(Object primaryKey, String columnName, Object valueToAdd) { Object oldValue = get(primaryKey, columnName); @@ -434,8 +424,8 @@ public class GATKReportTable { /** * Subtract the specified value from an element in the table * - * @param primaryKey the primary key value - * @param columnName the name of the column + * @param primaryKey the primary key value + * @param columnName the name of the column * @param valueToSubtract the value to subtract */ public void subtract(Object primaryKey, String columnName, Object valueToSubtract) { @@ -464,9 +454,9 @@ public class GATKReportTable { /** * Multiply the specified value to an element in the table * - * @param primaryKey the primary key value - * @param columnName the name of the column - * @param valueToMultiply the value to multiply by + * @param primaryKey the primary key value + * @param columnName the name of the column + * @param valueToMultiply the value to multiply by */ public void multiply(Object primaryKey, String columnName, Object valueToMultiply) { Object oldValue = get(primaryKey, columnName); @@ -494,9 +484,9 @@ public class GATKReportTable { /** * Divide the specified value from an element in the table * - * @param primaryKey the primary key value - * @param columnName the name of the column - * @param valueToDivide the value to divide by + * @param primaryKey the primary key value + * @param columnName the name of the column + * @param valueToDivide the value to divide by */ public void divide(Object primaryKey, String columnName, Object valueToDivide) { Object oldValue = get(primaryKey, columnName); @@ -524,9 +514,9 @@ public class GATKReportTable { /** * Add two columns to each other and set the results to a third column * - * @param columnToSet the column that should hold the results - * @param augend the column that shall be the augend - * @param addend the column that shall be the addend + * @param columnToSet the column that should hold the results + * @param augend the column that shall be the augend + * @param addend the column that shall be the addend */ public void addColumns(String columnToSet, String augend, String addend) { for (Object primaryKey : primaryKeyColumn) { @@ -542,8 +532,8 @@ public class GATKReportTable { /** * Subtract one column from another and set the results to a third column * - * @param columnToSet the column that should hold the results - * @param minuend the column that shall be the minuend (the a in a - b) + * @param columnToSet the column that should hold the results + * @param minuend the column that shall be the minuend (the a in a - b) * @param subtrahend the column that shall be the subtrahend (the b in a - b) */ public void subtractColumns(String columnToSet, String minuend, String subtrahend) { @@ -561,8 +551,8 @@ public class GATKReportTable { * Multiply two columns by each other and set the results to a third column * * @param columnToSet the column that should hold the results - * @param multiplier the column that shall be the multiplier - * @param multiplicand the column that shall be the multiplicand + * @param multiplier the column that shall be the multiplier + * @param multiplicand the column that shall be the multiplicand */ public void multiplyColumns(String columnToSet, String multiplier, String multiplicand) { for (Object primaryKey : primaryKeyColumn) { @@ -578,9 +568,9 @@ public class GATKReportTable { /** * Divide two columns by each other and set the results to a third column * - * @param columnToSet the column that should hold the results - * @param numeratorColumn the column that shall be the numerator - * @param denominatorColumn the column that shall be the denominator + * @param columnToSet the column that should hold the results + * @param numeratorColumn the column that shall be the numerator + * @param denominatorColumn the column that shall be the denominator */ public void divideColumns(String columnToSet, String numeratorColumn, String denominatorColumn) { for (Object primaryKey : primaryKeyColumn) { @@ -595,11 +585,10 @@ public class GATKReportTable { /** * Return the print width of the primary key column - * - * @return the width of the primary key column + * @return the width of the primary key column */ public int getPrimaryKeyColumnWidth() { - int maxWidth = getPrimaryKeyName().length(); + int maxWidth = primaryKeyName.length(); for (Object primaryKey : primaryKeyColumn) { int width = primaryKey.toString().length(); @@ -615,7 +604,7 @@ public class GATKReportTable { /** * Write the table to the PrintStream, formatted nicely to be human-readable, AWK-able, and R-friendly. * - * @param out the PrintStream to which the table should be written + * @param out the PrintStream to which the table should be written */ public void write(PrintStream out) { // Get the column widths for everything @@ -631,15 +620,13 @@ public class GATKReportTable { // Emit the table header, taking into account the padding requirement if the primary key is a hidden column boolean needsPadding = false; if (primaryKeyDisplay) { - out.printf(primaryKeyFormat, getPrimaryKeyName()); + out.printf(primaryKeyFormat, primaryKeyName); needsPadding = true; } for (String columnName : columns.keySet()) { if (columns.get(columnName).isDisplayable()) { - if (needsPadding) { - out.printf(" "); - } + if (needsPadding) { out.printf(" "); } out.printf(columnFormats.get(columnName).getNameFormat(), columnName); needsPadding = true; @@ -658,9 +645,7 @@ public class GATKReportTable { for (String columnName : columns.keySet()) { if (columns.get(columnName).isDisplayable()) { - if (needsPadding) { - out.printf(" "); - } + if (needsPadding) { out.printf(" "); } String value = columns.get(columnName).getStringValue(primaryKey); out.printf(columnFormats.get(columnName).getValueFormat(), value); @@ -690,49 +675,4 @@ public class GATKReportTable { public GATKReportColumns getColumns() { return columns; } - - public void mergeRows(GATKReportTable input) { - /* - * This function is different from addRowsFrom because we will add the ability to sum,average, etc rows - * TODO: Add other combining algorithms - */ - - // Make sure the columns match AND the Primary Key - if (input.getColumns().keySet().equals(this.getColumns().keySet()) && - input.getPrimaryKeyName().equals(this.getPrimaryKeyName())) { - this.addRowsFrom(input); - } else - throw new ReviewedStingException("Failed to combine GATKReportTable, columns don't match!"); - } - - public void addRowsFrom(GATKReportTable input) { - // add column by column - - // For every column - for (String columnKey : input.getColumns().keySet()) { - GATKReportColumn current = this.getColumns().get(columnKey); - GATKReportColumn toAdd = input.getColumns().get(columnKey); - // We want to take the current column and add all the values from input - - // The column is a map of values - for (Object rowKey : toAdd.keySet()) { - // We add every value from toAdd to the current - if (!current.containsKey(rowKey)) { - this.set(rowKey, columnKey, toAdd.get(rowKey)); - System.out.printf("Putting row with PK: %s \n", rowKey); - } else { - - // TODO we should be able to handle combining data by adding, averaging, etc. - this.set(rowKey, columnKey, toAdd.get(rowKey)); - - System.out.printf("OVERWRITING Row with PK: %s \n", rowKey); - } - } - } - - } - - public String getPrimaryKeyName() { - return primaryKeyName; - } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java index b9a89fcfe..b3b9ab555 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java @@ -49,23 +49,23 @@ public class GATKReportUnitTest extends BaseTest { @DataProvider(name = "rightAlignValues") public Object[][] getRightAlignValues() { - return new Object[][]{ - new Object[]{null, true}, - new Object[]{"null", true}, - new Object[]{"NA", true}, - new Object[]{"0", true}, - new Object[]{"0.0", true}, - new Object[]{"-0", true}, - new Object[]{"-0.0", true}, - new Object[]{String.valueOf(Long.MAX_VALUE), true}, - new Object[]{String.valueOf(Long.MIN_VALUE), true}, - new Object[]{String.valueOf(Float.MIN_NORMAL), true}, - new Object[]{String.valueOf(Double.MAX_VALUE), true}, - new Object[]{String.valueOf(Double.MIN_VALUE), true}, - new Object[]{String.valueOf(Double.POSITIVE_INFINITY), true}, - new Object[]{String.valueOf(Double.NEGATIVE_INFINITY), true}, - new Object[]{String.valueOf(Double.NaN), true}, - new Object[]{"hello", false} + return new Object[][] { + new Object[] {null, true}, + new Object[] {"null", true}, + new Object[] {"NA", true}, + new Object[] {"0", true}, + new Object[] {"0.0", true}, + new Object[] {"-0", true}, + new Object[] {"-0.0", true}, + new Object[] {String.valueOf(Long.MAX_VALUE), true}, + new Object[] {String.valueOf(Long.MIN_VALUE), true}, + new Object[] {String.valueOf(Float.MIN_NORMAL), true}, + new Object[] {String.valueOf(Double.MAX_VALUE), true}, + new Object[] {String.valueOf(Double.MIN_VALUE), true}, + new Object[] {String.valueOf(Double.POSITIVE_INFINITY), true}, + new Object[] {String.valueOf(Double.NEGATIVE_INFINITY), true}, + new Object[] {String.valueOf(Double.NaN), true}, + new Object[] {"hello", false} }; } @@ -73,96 +73,4 @@ public class GATKReportUnitTest extends BaseTest { public void testIsRightAlign(String value, boolean expected) { Assert.assertEquals(GATKReportColumn.isRightAlign(value), expected, "right align of '" + value + "'"); } - - @Test - public void testGATKReportGatherer() { - - /* - GATKReportTable actual1 = new GATKReportTable("TableName", "Description"); - actual1.addPrimaryKey("key"); - actual1.addColumn("colA", 0); - actual1.addColumn("colB", 0); - actual1.set("row1", "colA", 1); - actual1.set("row1", "colB", 2); - - GATKReportTable actual2 = new GATKReportTable("TableName", "Description"); - actual2.addPrimaryKey("key"); - actual2.addColumn("colA", 0); - actual2.addColumn("colB", 0); - actual2.set("row2", "colA", 3); - actual2.set("row2", "colB", 4); - - GATKReportTable actual3 = new GATKReportTable("TableName", "Description"); - actual3.addPrimaryKey("key"); - actual3.addColumn("colA", 0); - actual3.addColumn("colB", 0); - actual3.set("row3", "colA", 5); - actual3.set("row3", "colB", 6); - - actual1.mergeRows(actual2); - actual1.mergeRows(actual3); - actual1.write(System.out); - */ - - GATKReportTable expected = new GATKReportTable("TableName", "Description"); - expected.addPrimaryKey("key"); - expected.addColumn("colA", 0); - expected.addColumn("colB", 0); - expected.set("row1", "colA", 1); - expected.set("row1", "colB", 2); - expected.set("row2", "colA", 3); - expected.set("row2", "colB", 4); - expected.set("row3", "colA", 5); - expected.set("row3", "colB", 6); - expected.write(System.out); - - GATKReport report1, report2, report3; - report1 = new GATKReport(); - report1.addTable("TableName", "Description"); - report1.getTable("TableName").addPrimaryKey("key"); - report1.getTable("TableName").addColumn("colA", 0); - report1.getTable("TableName").addColumn("colB", 0); - report1.getTable("TableName").set("row1", "colA", 1); - report1.getTable("TableName").set("row1", "colB", 2); - - report2 = new GATKReport(); - report2.addTable("TableName", "Description"); - report2.getTable("TableName").addPrimaryKey("key"); - report2.getTable("TableName").addColumn("colA", 0); - report2.getTable("TableName").addColumn("colB", 0); - report2.getTable("TableName").set("row2", "colA", 3); - report2.getTable("TableName").set("row2", "colB", 4); - - report3 = new GATKReport(); - report3.addTable("TableName", "Description"); - report3.getTable("TableName").addPrimaryKey("key"); - report3.getTable("TableName").addColumn("colA", 0); - report3.getTable("TableName").addColumn("colB", 0); - report3.getTable("TableName").set("row3", "colA", 5); - report3.getTable("TableName").set("row3", "colB", 6); - - report1.combineWith(report2); - report1.combineWith(report3); - - report1.print(System.out); - /* - File a = new File("/home/roger/tbls/a.tbl"); - File b = new File("/home/roger/tbls/b.tbl"); - File c = new File("/home/roger/tbls/c.tbl"); - File out = new File("/home/roger/tbls/out.tbl"); - - - List FileList = new ArrayList(); - FileList.add(a); - FileList.add(b); - FileList.add(c); - - GATKReportGatherer gatherer = new GATKReportGatherer(); - gatherer.gather(FileList, out); - System.out.print(out); - */ - - //Assert.assertEquals(1,1); - - } -} \ No newline at end of file +} From b57d4250bfae1ea8c6cdb5da8fca83e5affa01ea Mon Sep 17 00:00:00 2001 From: Matt Hanna Date: Thu, 9 Feb 2012 11:24:52 -0500 Subject: [PATCH 13/14] Documentation request by Eric. At each stage of the GATK where filtering occurs, added documentation suggesting the goal of the filtering along with examples of suggested inputs and outputs. --- .../gatk/datasources/providers/LocusView.java | 9 +- .../IntervalOverlapFilteringIterator.java | 203 ++++++++++++++++++ .../gatk/datasources/reads/SAMDataSource.java | 162 -------------- .../sting/gatk/executive/WindowMaker.java | 18 +- .../sting/gatk/traversals/TraverseLoci.java | 4 +- 5 files changed, 228 insertions(+), 168 deletions(-) create mode 100644 public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java index f9ed0cb74..a3ce6dd27 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java @@ -25,9 +25,14 @@ import java.util.NoSuchElementException; */ /** - * A queue of locus context entries. + * The two goals of the LocusView are as follows: + * 1) To provide a 'trigger track' iteration interface so that TraverseLoci can easily switch + * between iterating over all bases in a region, only covered bases in a region covered by + * reads, only bases in a region covered by RODs, or any other sort of trigger track + * implementation one can think of. + * 2) To manage the copious number of iterators that have to be jointly pulled through the + * genome to make a locus traversal function. */ - public abstract class LocusView extends LocusIterator implements View { /** * The locus bounding this view. diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java new file mode 100644 index 000000000..4005f1c32 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java @@ -0,0 +1,203 @@ +/* + * 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 org.broadinstitute.sting.gatk.datasources.reads; + +import net.sf.samtools.SAMRecord; +import net.sf.samtools.util.CloseableIterator; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; + +import java.util.List; +import java.util.NoSuchElementException; + +/** + * High efficiency filtering iterator designed to filter out reads only included + * in the query results due to the granularity of the BAM index. + * + * Built into the BAM index is a notion of 16kbase granularity -- an index query for + * two regions contained within a 16kbase chunk (say, chr1:5-10 and chr1:11-20) will + * return exactly the same regions within the BAM file. This iterator is optimized + * to subtract out reads which do not at all overlap the interval list passed to the + * constructor. + * + * Example: + * interval list: chr20:6-10 + * Reads that would pass through the filter: chr20:6-10, chr20:1-15, chr20:1-7, chr20:8-15. + * Reads that would be discarded by the filter: chr20:1-5, chr20:11-15. + */ +class IntervalOverlapFilteringIterator implements CloseableIterator { + /** + * The wrapped iterator. + */ + private CloseableIterator iterator; + + /** + * The next read, queued up and ready to go. + */ + private SAMRecord nextRead; + + /** + * Rather than using the straight genomic bounds, use filter out only mapped reads. + */ + private boolean keepOnlyUnmappedReads; + + /** + * Custom representation of interval bounds. + * Makes it simpler to track current position. + */ + private int[] intervalContigIndices; + private int[] intervalStarts; + private int[] intervalEnds; + + /** + * Position within the interval list. + */ + private int currentBound = 0; + + public IntervalOverlapFilteringIterator(CloseableIterator iterator, List intervals) { + this.iterator = iterator; + + // Look at the interval list to detect whether we should worry about unmapped reads. + // If we find a mix of mapped/unmapped intervals, throw an exception. + boolean foundMappedIntervals = false; + for(GenomeLoc location: intervals) { + if(! GenomeLoc.isUnmapped(location)) + foundMappedIntervals = true; + keepOnlyUnmappedReads |= GenomeLoc.isUnmapped(location); + } + + + if(foundMappedIntervals) { + if(keepOnlyUnmappedReads) + throw new ReviewedStingException("Tried to apply IntervalOverlapFilteringIterator to a mixed of mapped and unmapped intervals. Please apply this filter to only mapped or only unmapped reads"); + this.intervalContigIndices = new int[intervals.size()]; + this.intervalStarts = new int[intervals.size()]; + this.intervalEnds = new int[intervals.size()]; + int i = 0; + for(GenomeLoc interval: intervals) { + intervalContigIndices[i] = interval.getContigIndex(); + intervalStarts[i] = interval.getStart(); + intervalEnds[i] = interval.getStop(); + i++; + } + } + + advance(); + } + + public boolean hasNext() { + return nextRead != null; + } + + public SAMRecord next() { + if(nextRead == null) + throw new NoSuchElementException("No more reads left in this iterator."); + SAMRecord currentRead = nextRead; + advance(); + return currentRead; + } + + public void remove() { + throw new UnsupportedOperationException("Cannot remove from an IntervalOverlapFilteringIterator"); + } + + + public void close() { + iterator.close(); + } + + private void advance() { + nextRead = null; + + if(!iterator.hasNext()) + return; + + SAMRecord candidateRead = iterator.next(); + while(nextRead == null && (keepOnlyUnmappedReads || currentBound < intervalStarts.length)) { + if(!keepOnlyUnmappedReads) { + // Mapped read filter; check against GenomeLoc-derived bounds. + if(readEndsOnOrAfterStartingBound(candidateRead)) { + // This read ends after the current interval begins. + // Promising, but this read must be checked against the ending bound. + if(readStartsOnOrBeforeEndingBound(candidateRead)) { + // Yes, this read is within both bounds. This must be our next read. + nextRead = candidateRead; + break; + } + else { + // Oops, we're past the end bound. Increment the current bound and try again. + currentBound++; + continue; + } + } + } + else { + // Found an unmapped read. We're done. + if(candidateRead.getReadUnmappedFlag()) { + nextRead = candidateRead; + break; + } + } + + // No more reads available. Stop the search. + if(!iterator.hasNext()) + break; + + // No reasonable read found; advance the iterator. + candidateRead = iterator.next(); + } + } + + /** + * Check whether the read lies after the start of the current bound. If the read is unmapped but placed, its + * end will be distorted, so rely only on the alignment start. + * @param read The read to position-check. + * @return True if the read starts after the current bounds. False otherwise. + */ + private boolean readEndsOnOrAfterStartingBound(final SAMRecord read) { + return + // Read ends on a later contig, or... + read.getReferenceIndex() > intervalContigIndices[currentBound] || + // Read ends of this contig... + (read.getReferenceIndex() == intervalContigIndices[currentBound] && + // either after this location, or... + (read.getAlignmentEnd() >= intervalStarts[currentBound] || + // read is unmapped but positioned and alignment start is on or after this start point. + (read.getReadUnmappedFlag() && read.getAlignmentStart() >= intervalStarts[currentBound]))); + } + + /** + * Check whether the read lies before the end of the current bound. + * @param read The read to position-check. + * @return True if the read starts after the current bounds. False otherwise. + */ + private boolean readStartsOnOrBeforeEndingBound(final SAMRecord read) { + return + // Read starts on a prior contig, or... + read.getReferenceIndex() < intervalContigIndices[currentBound] || + // Read starts on this contig and the alignment start is registered before this end point. + (read.getReferenceIndex() == intervalContigIndices[currentBound] && read.getAlignmentStart() <= intervalEnds[currentBound]); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java index a4681cffd..27b9e7f77 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java @@ -39,7 +39,6 @@ import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator; import org.broadinstitute.sting.gatk.filters.ReadFilter; import org.broadinstitute.sting.gatk.iterators.*; import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; -import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.SimpleTimer; @@ -976,167 +975,6 @@ public class SAMDataSource { */ private class ReadGroupMapping extends HashMap {} - /** - * Filters out reads that do not overlap the current GenomeLoc. - * Note the custom implementation: BAM index querying returns all reads that could - * possibly overlap the given region (and quite a few extras). In order not to drag - * down performance, this implementation is highly customized to its task. - */ - private class IntervalOverlapFilteringIterator implements CloseableIterator { - /** - * The wrapped iterator. - */ - private CloseableIterator iterator; - - /** - * The next read, queued up and ready to go. - */ - private SAMRecord nextRead; - - /** - * Rather than using the straight genomic bounds, use filter out only mapped reads. - */ - private boolean keepOnlyUnmappedReads; - - /** - * Custom representation of interval bounds. - * Makes it simpler to track current position. - */ - private int[] intervalContigIndices; - private int[] intervalStarts; - private int[] intervalEnds; - - /** - * Position within the interval list. - */ - private int currentBound = 0; - - public IntervalOverlapFilteringIterator(CloseableIterator iterator, List intervals) { - this.iterator = iterator; - - // Look at the interval list to detect whether we should worry about unmapped reads. - // If we find a mix of mapped/unmapped intervals, throw an exception. - boolean foundMappedIntervals = false; - for(GenomeLoc location: intervals) { - if(! GenomeLoc.isUnmapped(location)) - foundMappedIntervals = true; - keepOnlyUnmappedReads |= GenomeLoc.isUnmapped(location); - } - - - if(foundMappedIntervals) { - if(keepOnlyUnmappedReads) - throw new ReviewedStingException("Tried to apply IntervalOverlapFilteringIterator to a mixed of mapped and unmapped intervals. Please apply this filter to only mapped or only unmapped reads"); - this.intervalContigIndices = new int[intervals.size()]; - this.intervalStarts = new int[intervals.size()]; - this.intervalEnds = new int[intervals.size()]; - int i = 0; - for(GenomeLoc interval: intervals) { - intervalContigIndices[i] = interval.getContigIndex(); - intervalStarts[i] = interval.getStart(); - intervalEnds[i] = interval.getStop(); - i++; - } - } - - advance(); - } - - public boolean hasNext() { - return nextRead != null; - } - - public SAMRecord next() { - if(nextRead == null) - throw new NoSuchElementException("No more reads left in this iterator."); - SAMRecord currentRead = nextRead; - advance(); - return currentRead; - } - - public void remove() { - throw new UnsupportedOperationException("Cannot remove from an IntervalOverlapFilteringIterator"); - } - - - public void close() { - iterator.close(); - } - - private void advance() { - nextRead = null; - - if(!iterator.hasNext()) - return; - - SAMRecord candidateRead = iterator.next(); - while(nextRead == null && (keepOnlyUnmappedReads || currentBound < intervalStarts.length)) { - if(!keepOnlyUnmappedReads) { - // Mapped read filter; check against GenomeLoc-derived bounds. - if(readEndsOnOrAfterStartingBound(candidateRead)) { - // This read ends after the current interval begins. - // Promising, but this read must be checked against the ending bound. - if(readStartsOnOrBeforeEndingBound(candidateRead)) { - // Yes, this read is within both bounds. This must be our next read. - nextRead = candidateRead; - break; - } - else { - // Oops, we're past the end bound. Increment the current bound and try again. - currentBound++; - continue; - } - } - } - else { - // Found an unmapped read. We're done. - if(candidateRead.getReadUnmappedFlag()) { - nextRead = candidateRead; - break; - } - } - - // No more reads available. Stop the search. - if(!iterator.hasNext()) - break; - - // No reasonable read found; advance the iterator. - candidateRead = iterator.next(); - } - } - - /** - * Check whether the read lies after the start of the current bound. If the read is unmapped but placed, its - * end will be distorted, so rely only on the alignment start. - * @param read The read to position-check. - * @return True if the read starts after the current bounds. False otherwise. - */ - private boolean readEndsOnOrAfterStartingBound(final SAMRecord read) { - return - // Read ends on a later contig, or... - read.getReferenceIndex() > intervalContigIndices[currentBound] || - // Read ends of this contig... - (read.getReferenceIndex() == intervalContigIndices[currentBound] && - // either after this location, or... - (read.getAlignmentEnd() >= intervalStarts[currentBound] || - // read is unmapped but positioned and alignment start is on or after this start point. - (read.getReadUnmappedFlag() && read.getAlignmentStart() >= intervalStarts[currentBound]))); - } - - /** - * Check whether the read lies before the end of the current bound. - * @param read The read to position-check. - * @return True if the read starts after the current bounds. False otherwise. - */ - private boolean readStartsOnOrBeforeEndingBound(final SAMRecord read) { - return - // Read starts on a prior contig, or... - read.getReferenceIndex() < intervalContigIndices[currentBound] || - // Read starts on this contig and the alignment start is registered before this end point. - (read.getReferenceIndex() == intervalContigIndices[currentBound] && read.getAlignmentStart() <= intervalEnds[currentBound]); - } - } - /** * Locates the index file alongside the given BAM, if present. * TODO: This is currently a hachetjob that reaches into Picard and pulls out its index file locator. Replace with something more permanent. diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java b/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java index d1f5d80da..da11d36dd 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java @@ -17,9 +17,21 @@ import java.util.List; import java.util.NoSuchElementException; /** - * Buffer shards of data which may or may not contain multiple loci into - * iterators of all data which cover an interval. Its existence is an homage - * to Mark's stillborn WindowMaker, RIP 2009. + * Transforms an iterator of reads which overlap the given interval list into an iterator of covered single-base loci + * completely contained within the interval list. To do this, it creates a LocusIteratorByState which will emit a single-bp + * locus for every base covered by the read iterator, then uses the WindowMakerIterator.advance() to filter down that stream of + * loci to only those covered by the given interval list. + * + * Example: + * Incoming stream of reads: A:chr20:1-5, B:chr20:2-6, C:chr20:2-7, D:chr20:3-8, E:chr20:5-10 + * Incoming intervals: chr20:3-7 + * + * Locus iterator by state will produce the following stream of data: + * chr1:1 {A}, chr1:2 {A,B,C}, chr1:3 {A,B,C,D}, chr1:4 {A,B,C,D}, chr1:5 {A,B,C,D,E}, + * chr1:6 {B,C,D,E}, chr1:7 {C,D,E}, chr1:8 {D,E}, chr1:9 {E}, chr1:10 {E} + * + * WindowMakerIterator will then filter the incoming stream, emitting the following stream: + * chr1:3 {A,B,C,D}, chr1:4 {A,B,C,D}, chr1:5 {A,B,C,D,E}, chr1:6 {B,C,D,E}, chr1:7 {C,D,E} * * @author mhanna * @version 0.1 diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java index d99e7c353..1d14a7f35 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java @@ -102,7 +102,9 @@ public class TraverseLoci extends TraversalEngine,Locu } /** - * Gets the best view of loci for this walker given the available data. + * Gets the best view of loci for this walker given the available data. The view will function as a 'trigger track' + * of sorts, providing a consistent interface so that TraverseLoci doesn't need to be reimplemented for any new datatype + * that comes along. * @param walker walker to interrogate. * @param dataProvider Data which which to drive the locus view. * @return A view of the locus data, where one iteration of the locus view maps to one iteration of the traversal. From 5af373a3a13a3558d758fb280e8cdced5c4bc949 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Wed, 8 Feb 2012 14:39:55 -0500 Subject: [PATCH 14/14] BQSR with indels integrated! * added support to base before deletion in the pileup * refactored covariates to operate on mismatches, insertions and deletions at the same time * all code is in private so original BQSR is still working as usual in public * outputs a molten CSV with mismatches, insertions and deletions, time to play! * barely tested, passes my very simple tests... haven't tested edge cases. --- .../sting/gatk/iterators/LocusIteratorByState.java | 4 ++-- .../SNPGenotypeLikelihoodsCalculationModel.java | 7 +++++-- .../org/broadinstitute/sting/utils/NGSPlatform.java | 12 +++++++++++- .../sting/utils/pileup/AbstractReadBackedPileup.java | 6 +++--- .../utils/pileup/ExtendedEventPileupElement.java | 2 +- .../sting/utils/pileup/PileupElement.java | 9 ++++++++- .../pileup/ReadBackedExtendedEventPileupImpl.java | 2 +- .../sting/utils/pileup/ReadBackedPileupImpl.java | 4 ++-- .../sting/utils/sam/ArtificialSAMUtils.java | 4 ++-- .../sting/utils/sam/GATKSAMRecordUnitTest.java | 4 ++-- 10 files changed, 37 insertions(+), 17 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java index 316a20a70..6edae3816 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java @@ -470,7 +470,7 @@ public class LocusIteratorByState extends LocusIterator { if (op == CigarOperator.D) { if (readInfo.includeReadsWithDeletionAtLoci()) { // only add deletions to the pileup if we are authorized to do so - pile.add(new PileupElement(read, readOffset, true, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart()))); + pile.add(new PileupElement(read, readOffset, true, nextOp == CigarOperator.D, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart()))); size++; nDeletions++; if (read.getMappingQuality() == 0) @@ -479,7 +479,7 @@ public class LocusIteratorByState extends LocusIterator { } else { if (!filterBaseInRead(read, location.getStart())) { - pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart()))); + pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.D, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart()))); size++; if (read.getMappingQuality() == 0) nMQ0Reads++; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index ea53c815d..6171b01eb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -39,7 +39,10 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; import org.broadinstitute.sting.utils.variantcontext.*; -import java.util.*; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel { @@ -212,7 +215,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC public class BAQedPileupElement extends PileupElement { public BAQedPileupElement( final PileupElement PE ) { - super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeInsertion(), PE.isNextToSoftClip()); + super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeDeletion(), PE.isBeforeInsertion(), PE.isNextToSoftClip()); } @Override diff --git a/public/java/src/org/broadinstitute/sting/utils/NGSPlatform.java b/public/java/src/org/broadinstitute/sting/utils/NGSPlatform.java index 4f01f2b7a..597dc4803 100644 --- a/public/java/src/org/broadinstitute/sting/utils/NGSPlatform.java +++ b/public/java/src/org/broadinstitute/sting/utils/NGSPlatform.java @@ -87,7 +87,7 @@ public enum NGSPlatform { /** * Returns the NGSPlatform corresponding to the PL tag in the read group * @param plFromRG -- the PL field (or equivalent) in a ReadGroup object - * @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match + * @return an NGSPlatform object matching the PL field of the header, or UNKNOWN if there was no match */ public static final NGSPlatform fromReadGroupPL(final String plFromRG) { if ( plFromRG == null ) return UNKNOWN; @@ -105,4 +105,14 @@ public enum NGSPlatform { return UNKNOWN; } + + /** + * checks whether or not the requested platform is listed in the set (and is not unknown) + * + * @param platform the read group string that describes the platform used + * @return true if the platform is known (i.e. it's in the list and is not UNKNOWN) + */ + public static final boolean isKnown (final String platform) { + return fromReadGroupPL(platform) != UNKNOWN; + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java index 82e403842..70ad70f43 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java @@ -177,7 +177,7 @@ public abstract class AbstractReadBackedPileup pileup = new UnifiedPileupElementTracker(); for (GATKSAMRecord read : reads) { - pileup.add(createNewPileupElement(read, offset, false, false, false)); // only used to create fake pileups for testing so ancillary information is not important + pileup.add(createNewPileupElement(read, offset, false, false, false, false)); // only used to create fake pileups for testing so ancillary information is not important } return pileup; @@ -204,7 +204,7 @@ public abstract class AbstractReadBackedPileup createNewPileup(GenomeLoc loc, PileupElementTracker pileupElementTracker); - protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip); + protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip); // -------------------------------------------------------- // diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java index 921da2a1f..506442d03 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java @@ -48,7 +48,7 @@ public class ExtendedEventPileupElement extends PileupElement { public ExtendedEventPileupElement(GATKSAMRecord read, int offset, int eventLength, String eventBases, Type type) { - super(read, offset, type == Type.DELETION, false, false); // extended events are slated for removal + super(read, offset, type == Type.DELETION, false, false, false); // extended events are slated for removal this.read = read; this.offset = offset; this.eventLength = eventLength; diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java index a4830223e..9df22700e 100755 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java @@ -24,6 +24,7 @@ public class PileupElement implements Comparable { protected final GATKSAMRecord read; protected final int offset; protected final boolean isDeletion; + protected final boolean isBeforeDeletion; protected final boolean isBeforeInsertion; protected final boolean isNextToSoftClip; @@ -33,6 +34,7 @@ public class PileupElement implements Comparable { * @param read the read we are adding to the pileup * @param offset the position in the read for this base. All deletions must be left aligned! (-1 is only allowed for reads starting with insertions) * @param isDeletion whether or not this base is a deletion + * @param isBeforeDeletion whether or not this base is before a deletion * @param isBeforeInsertion whether or not this base is before an insertion * @param isNextToSoftClip whether or not this base is next to a soft clipped base */ @@ -40,13 +42,14 @@ public class PileupElement implements Comparable { "read != null", "offset >= -1", "offset <= read.getReadLength()"}) - public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeInsertion, final boolean isNextToSoftClip) { + public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeDeletion, final boolean isBeforeInsertion, final boolean isNextToSoftClip) { if (offset < 0 && isDeletion) throw new ReviewedStingException("Pileup Element cannot create a deletion with a negative offset"); this.read = read; this.offset = offset; this.isDeletion = isDeletion; + this.isBeforeDeletion = isBeforeDeletion; this.isBeforeInsertion = isBeforeInsertion; this.isNextToSoftClip = isNextToSoftClip; } @@ -55,6 +58,10 @@ public class PileupElement implements Comparable { return isDeletion; } + public boolean isBeforeDeletion() { + return isBeforeDeletion; + } + public boolean isBeforeInsertion() { return isBeforeInsertion; } diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java index df334f557..357195daa 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java @@ -96,7 +96,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup< } @Override - protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) { + protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) { throw new UnsupportedOperationException("Not enough information provided to create a new pileup element"); } diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java index 20b100001..7a6ebef21 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java @@ -71,7 +71,7 @@ public class ReadBackedPileupImpl extends AbstractReadBackedPileup= right.getAlignmentStart() && pos <= right.getAlignmentEnd()) { - pileupElements.add(new PileupElement(right, pos - rightStart, false, false, false)); + pileupElements.add(new PileupElement(right, pos - rightStart, false, false, false, false)); } } diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java index 729503f84..520fb7040 100755 --- a/public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java @@ -42,8 +42,8 @@ public class GATKSAMRecordUnitTest extends BaseTest { @Test public void testReducedReadPileupElement() { - PileupElement readp = new PileupElement(read, 0, false, false, false); - PileupElement reducedreadp = new PileupElement(reducedRead, 0, false, false, false); + PileupElement readp = new PileupElement(read, 0, false, false, false, false); + PileupElement reducedreadp = new PileupElement(reducedRead, 0, false, false, false, false); Assert.assertFalse(readp.getRead().isReducedRead());