diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index 7e96b609e..7c567f511 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -34,10 +34,7 @@ import org.broadinstitute.sting.gatk.filters.ReadFilter; import org.broadinstitute.sting.gatk.walkers.Attribution; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.ApplicationDetails; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.GATKDocUtils; -import org.broadinstitute.sting.utils.help.GATKDoclet; +import org.broadinstitute.sting.utils.help.*; import org.broadinstitute.sting.utils.text.TextFormattingUtils; import java.util.*; @@ -178,7 +175,7 @@ public class CommandLineGATK extends CommandLineExecutable { Formatter formatter = new Formatter(additionalHelp); formatter.format("For a full description of this walker, see its GATKdocs at:%n"); - formatter.format("%s%n", GATKDocUtils.helpLinksToGATKDocs(walkerType)); + formatter.format("%s%n", HelpUtils.helpLinksToGATKDocs(walkerType)); return additionalHelp.toString(); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index 902f9d308..bf490e28c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -1,10 +1,11 @@ package org.broadinstitute.sting.gatk.refdata; +import net.sf.samtools.util.SequenceUtil; import org.broad.tribble.Feature; +import org.broad.tribble.annotation.Strand; import org.broad.tribble.dbsnp.DbSNPFeature; import org.broad.tribble.gelitext.GeliTextFeature; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; @@ -92,6 +93,67 @@ public class VariantContextAdaptors { // -------------------------------------------------------------------------------------------------------------- private static class DBSnpAdaptor implements VCAdaptor { + private static boolean isSNP(DbSNPFeature feature) { + return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact"); + } + + private static boolean isMNP(DbSNPFeature feature) { + return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range"); + } + + private static boolean isInsertion(DbSNPFeature feature) { + return feature.getVariantType().contains("insertion"); + } + + private static boolean isDeletion(DbSNPFeature feature) { + return feature.getVariantType().contains("deletion"); + } + + private static boolean isIndel(DbSNPFeature feature) { + return isInsertion(feature) || isDeletion(feature) || isComplexIndel(feature); + } + + public static boolean isComplexIndel(DbSNPFeature feature) { + return feature.getVariantType().contains("in-del"); + } + + /** + * gets the alternate alleles. This method should return all the alleles present at the location, + * NOT including the reference base. This is returned as a string list with no guarantee ordering + * of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest + * frequency). + * + * @return an alternate allele list + */ + public static List getAlternateAlleleList(DbSNPFeature feature) { + List ret = new ArrayList(); + for (String allele : getAlleleList(feature)) + if (!allele.equals(String.valueOf(feature.getNCBIRefBase()))) ret.add(allele); + return ret; + } + + /** + * gets the alleles. This method should return all the alleles present at the location, + * including the reference base. The first allele should always be the reference allele, followed + * by an unordered list of alternate alleles. + * + * @return an alternate allele list + */ + public static List getAlleleList(DbSNPFeature feature) { + List alleleList = new ArrayList(); + // add ref first + if ( feature.getStrand() == Strand.POSITIVE ) + alleleList = Arrays.asList(feature.getObserved()); + else + for (String str : feature.getObserved()) + alleleList.add(SequenceUtil.reverseComplement(str)); + if ( alleleList.size() > 0 && alleleList.contains(feature.getNCBIRefBase()) + && !alleleList.get(0).equals(feature.getNCBIRefBase()) ) + Collections.swap(alleleList, alleleList.indexOf(feature.getNCBIRefBase()), 0); + + return alleleList; + } + /** * Converts non-VCF formatted dbSNP records to VariantContext. * @return DbSNPFeature. @@ -102,18 +164,18 @@ public class VariantContextAdaptors { @Override public VariantContext convert(String name, Object input, ReferenceContext ref) { DbSNPFeature dbsnp = (DbSNPFeature)input; - if ( ! Allele.acceptableAlleleBases(DbSNPHelper.getReference(dbsnp)) ) + if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) ) return null; - Allele refAllele = Allele.create(DbSNPHelper.getReference(dbsnp), true); + Allele refAllele = Allele.create(dbsnp.getNCBIRefBase(), true); - if ( DbSNPHelper.isSNP(dbsnp) || DbSNPHelper.isIndel(dbsnp) || DbSNPHelper.isMNP(dbsnp) || dbsnp.getVariantType().contains("mixed") ) { + if ( isSNP(dbsnp) || isIndel(dbsnp) || isMNP(dbsnp) || dbsnp.getVariantType().contains("mixed") ) { // add the reference allele List alleles = new ArrayList(); alleles.add(refAllele); // add all of the alt alleles boolean sawNullAllele = refAllele.isNull(); - for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) { + for ( String alt : getAlternateAlleleList(dbsnp) ) { if ( ! Allele.acceptableAlleleBases(alt) ) { //System.out.printf("Excluding dbsnp record %s%n", dbsnp); return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java deleted file mode 100644 index a2132cee5..000000000 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java +++ /dev/null @@ -1,169 +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 org.broadinstitute.sting.gatk.refdata.features; - -import net.sf.samtools.util.SequenceUtil; -import org.broad.tribble.annotation.Strand; -import org.broad.tribble.dbsnp.DbSNPFeature; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; - -/** - * this class contains static helper methods for DbSNP - */ -public class DbSNPHelper { - - private DbSNPHelper() {} // don't make a DbSNPHelper - - public static String rsIDOfFirstRealVariant(List VCs, VariantContext.Type type) { - if ( VCs == null ) - return null; - - String rsID = null; - for ( VariantContext vc : VCs ) { - if ( vc.getType() == type ) { - rsID = vc.getID(); - break; - } - } - - return rsID; - } - - /** - * get the -1 * (log 10 of the error value) - * - * @return the log based error estimate - */ - public static double getNegLog10PError(DbSNPFeature feature) { - return 4; // -log10(0.0001) - } - - // - // What kind of variant are we? - // - // ---------------------------------------------------------------------- - public static boolean isSNP(DbSNPFeature feature) { - return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact"); - } - - public static boolean isMNP(DbSNPFeature feature) { - return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range"); - } - - public static String toMediumString(DbSNPFeature feature) { - String s = String.format("%s:%d:%s:%s", feature.getChr(), feature.getStart(), feature.getRsID(), Utils.join("",feature.getObserved())); - if (isSNP(feature)) s += ":SNP"; - if (isIndel(feature)) s += ":Indel"; - if (isHapmap(feature)) s += ":Hapmap"; - if (is2Hit2Allele(feature)) s += ":2Hit"; - return s; - } - - public static boolean isInsertion(DbSNPFeature feature) { - return feature.getVariantType().contains("insertion"); - } - - public static boolean isDeletion(DbSNPFeature feature) { - return feature.getVariantType().contains("deletion"); - } - - public static boolean isIndel(DbSNPFeature feature) { - return DbSNPHelper.isInsertion(feature) || DbSNPHelper.isDeletion(feature) || DbSNPHelper.isComplexIndel(feature); - } - - public static boolean isComplexIndel(DbSNPFeature feature) { - return feature.getVariantType().contains("in-del"); - } - - public static boolean isHapmap(DbSNPFeature feature) { - return feature.getValidationStatus().contains("by-hapmap"); - } - - public static boolean is2Hit2Allele(DbSNPFeature feature) { - return feature.getValidationStatus().contains("by-2hit-2allele"); - } - - public static boolean is1000genomes(DbSNPFeature feature) { - return feature.getValidationStatus().contains("by-1000genomes"); - } - - public static boolean isMQ1(DbSNPFeature feature) { - return feature.getWeight() == 1; - } - - /** - * gets the alternate alleles. This method should return all the alleles present at the location, - * NOT including the reference base. This is returned as a string list with no guarantee ordering - * of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest - * frequency). - * - * @return an alternate allele list - */ - public static List getAlternateAlleleList(DbSNPFeature feature) { - List ret = new ArrayList(); - for (String allele : getAlleleList(feature)) - if (!allele.equals(String.valueOf(feature.getNCBIRefBase()))) ret.add(allele); - return ret; - } - - public static boolean onFwdStrand(DbSNPFeature feature) { - return feature.getStrand() == Strand.POSITIVE; - } - - public static String getReference(DbSNPFeature feature) { - return feature.getNCBIRefBase(); - } - - public static String toSimpleString(DbSNPFeature feature) { - return String.format("%s:%s:%s", feature.getRsID(), feature.getObserved(), (feature.getStrand() == Strand.POSITIVE) ? "+" : "-"); - } - - /** - * gets the alleles. This method should return all the alleles present at the location, - * including the reference base. The first allele should always be the reference allele, followed - * by an unordered list of alternate alleles. - * - * @return an alternate allele list - */ - public static List getAlleleList(DbSNPFeature feature) { - List alleleList = new ArrayList(); - // add ref first - if ( onFwdStrand(feature) ) - alleleList = Arrays.asList(feature.getObserved()); - else - for (String str : feature.getObserved()) - alleleList.add(SequenceUtil.reverseComplement(str)); - if ( alleleList.size() > 0 && alleleList.contains(getReference(feature)) && !alleleList.get(0).equals(getReference(feature)) ) - Collections.swap(alleleList, alleleList.indexOf(getReference(feature)), 0); - - return alleleList; - } -} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index 6243a6cc0..4d8be4800 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -26,7 +26,6 @@ package org.broadinstitute.sting.gatk.walkers; import org.broad.tribble.Feature; -import org.broad.tribble.dbsnp.DbSNPFeature; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; @@ -34,9 +33,6 @@ import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; -import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper; -import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index a7837813a..01926a7f3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -29,15 +29,11 @@ import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationInterfaceManager; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -158,7 +154,7 @@ public class VariantAnnotatorEngine { private void annotateDBs(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc, Map infoAnnotations) { for ( Map.Entry, String> dbSet : dbAnnotations.entrySet() ) { if ( dbSet.getValue().equals(VCFConstants.DBSNP_KEY) ) { - String rsID = DbSNPHelper.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType()); + String rsID = VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType()); infoAnnotations.put(VCFConstants.DBSNP_KEY, rsID != null); // annotate dbsnp id if available and not already there if ( rsID != null && (!vc.hasID() || vc.getID().equals(VCFConstants.EMPTY_ID_FIELD)) ) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java index 51fe543df..60f0fcb0a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java @@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature; +import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java index 90e6fcd77..3046ef925 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java @@ -42,50 +42,190 @@ import java.io.PrintStream; /** * Emits a data file containing information about callable, uncallable, poorly mapped, and other parts of the genome * - * @Author depristo - * @Date May 7, 2010 + *

+ * A very common question about a NGS set of reads is what areas of the genome are considered callable. The system + * considers the coverage at each locus and emits either a per base state or a summary interval BED file that + * partitions the genomic intervals into the following callable states: + *

+ *
REF_N
+ *
the reference base was an N, which is not considered callable the GATK
+ *
CALLABLE
+ *
the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE
+ *
NO_COVERAGE
+ *
absolutely no reads were seen at this locus, regardless of the filtering parameters
+ *
LOW_COVERAGE
+ *
there were less than min. depth bases at the locus, after applying filters
+ *
EXCESSIVE_COVERAGE
+ *
more than -maxDepth read at the locus, indicating some sort of mapping problem
+ *
POOR_MAPPING_QUALITY
+ *
more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads
+ *
+ *

+ * + *

Input

+ *

+ * A BAM file containing exactly one sample. + *

+ * + *

Output

+ *

+ *

    + *
  • -o: a OutputFormatted (recommended BED) file with the callable status covering each base
    • + *
  • -summary: a table of callable status x count of all examined bases
    • + *
+ *

+ * + *

Examples

+ * 
+ *     -T CallableLociWalker \
+ *     -I my.bam \
+ *     -summary my.summary \
+ *     -o my.bed
+ *
+ * + * would produce a BED file (my.bed) that looks like: + * + * 
+ *     20 10000000 10000864 CALLABLE
+ *     20 10000865 10000985 POOR_MAPPING_QUALITY
+ *     20 10000986 10001138 CALLABLE
+ *     20 10001139 10001254 POOR_MAPPING_QUALITY
+ *     20 10001255 10012255 CALLABLE
+ *     20 10012256 10012259 POOR_MAPPING_QUALITY
+ *     20 10012260 10012263 CALLABLE
+ *     20 10012264 10012328 POOR_MAPPING_QUALITY
+ *     20 10012329 10012550 CALLABLE
+ *     20 10012551 10012551 LOW_COVERAGE
+ *     20 10012552 10012554 CALLABLE
+ *     20 10012555 10012557 LOW_COVERAGE
+ *     20 10012558 10012558 CALLABLE
+ *     et cetera...
+ *
+ * as well as a summary table that looks like: + * + * 
+ *                        state nBases
+ *                        REF_N 0
+ *                     CALLABLE 996046
+ *                  NO_COVERAGE 121
+ *                 LOW_COVERAGE 928
+ *           EXCESSIVE_COVERAGE 0
+ *         POOR_MAPPING_QUALITY 2906
+ *
+ * + * @author Mark DePristo + * @since May 7, 2010 */ @By(DataSource.REFERENCE) public class CallableLociWalker extends LocusWalker { @Output PrintStream out; - @Argument(fullName = "maxLowMAPQ", shortName = "mlmq", doc = "Maximum value for MAPQ to be considered a problematic mapped read. The gap between this value and mmq are reads that are not sufficiently well mapped for calling but aren't indicative of mapping problems.", required = false) + /** + * Callable loci summary counts (see outputs) will be written to this file. + */ + @Output(fullName = "summary", shortName = "summary", doc = "Name of file for output summary", required = true) + File summaryFile; + + /** + * The gap between this value and mmq are reads that are not sufficiently well mapped for calling but + * aren't indicative of mapping problems. For example, if maxLowMAPQ = 1 and mmq = 20, then reads with + * MAPQ == 0 are poorly mapped, MAPQ >= 20 are considered as contributing to calling, where + * reads with MAPQ >= 1 and < 20 are not bad in and of themselves but aren't sufficiently good to contribute to + * calling. In effect this reads are invisible, driving the base to the NO_ or LOW_COVERAGE states + */ + @Argument(fullName = "maxLowMAPQ", shortName = "mlmq", doc = "Maximum value for MAPQ to be considered a problematic mapped read.", required = false) byte maxLowMAPQ = 1; - @Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth. Defaults to 50.", required = false) + /** + * Reads with MAPQ > minMappingQuality are treated as usable for variation detection, contributing to the CALLABLE + * state. + */ + @Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth.", required = false) byte minMappingQuality = 10; - @Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth. Defaults to 20.", required = false) + /** + * Bases with less than minBaseQuality are viewed as not sufficiently high quality to contribute to the CALLABLE state + */ + @Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth.", required = false) byte minBaseQuality = 20; + /** + * If the number of QC+ bases (on reads with MAPQ > minMappingQuality and with base quality > minBaseQuality) exceeds this + * value and is less than maxDepth the site is considered CALLABLE. + */ @Argument(fullName = "minDepth", shortName = "minDepth", doc = "Minimum QC+ read depth before a locus is considered callable", required = false) int minDepth = 4; + /** + * If the QC+ depth exceeds this value the site is considered to have EXCESSIVE_DEPTH + */ @Argument(fullName = "maxDepth", shortName = "maxDepth", doc = "Maximum read depth before a locus is considered poorly mapped", required = false) int maxDepth = -1; + /** + * We don't want to consider a site as POOR_MAPPING_QUALITY just because it has two reads, and one is MAPQ. We + * won't assign a site to the POOR_MAPPING_QUALITY state unless there are at least minDepthForLowMAPQ reads + * covering the site. + */ @Argument(fullName = "minDepthForLowMAPQ", shortName = "mdflmq", doc = "Minimum read depth before a locus is considered a potential candidate for poorly mapped", required = false) int minDepthLowMAPQ = 10; - @Argument(fullName = "maxFractionOfReadsWithLowMAPQ", shortName = "frlmq", doc = "Maximum read depth before a locus is considered poorly mapped", required = false) + /** + * If the number of reads at this site is greater than minDepthForLowMAPQ and the fraction of reads with low mapping quality + * exceeds this fraction then the site has POOR_MAPPING_QUALITY. + */ + @Argument(fullName = "maxFractionOfReadsWithLowMAPQ", shortName = "frlmq", doc = "If the fraction of reads at a base with low mapping quality exceeds this value, the site may be poorly mapped", required = false) double maxLowMAPQFraction = 0.1; - @Argument(fullName = "format", shortName = "format", doc = "Output format for the system: either BED or STATE_PER_BASE", required = false) + /** + * The output of this walker will be written in this format. The recommended option is BED. + */ + @Argument(fullName = "format", shortName = "format", doc = "Output format", required = false) OutputFormat outputFormat; - @Argument(fullName = "summary", shortName = "summary", doc = "Name of file for output summary", required = true) - File summaryFile; + public enum OutputFormat { + /** + * The output will be written as a BED file. There's a BED element for each + * continuous run of callable states (i.e., CALLABLE, REF_N, etc). This is the recommended + * format + */ + BED, - public enum OutputFormat { BED, STATE_PER_BASE } + /** + * Emit chr start stop state quads for each base. Produces a potentially disasterously + * large amount of output. + */ + STATE_PER_BASE + } + + public enum CalledState { + /** the reference base was an N, which is not considered callable the GATK */ + REF_N, + /** the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE */ + CALLABLE, + /** absolutely no reads were seen at this locus, regardless of the filtering parameters */ + NO_COVERAGE, + /** there were less than min. depth bases at the locus, after applying filters */ + LOW_COVERAGE, + /** more than -maxDepth read at the locus, indicating some sort of mapping problem */ + EXCESSIVE_COVERAGE, + /** more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads */ + POOR_MAPPING_QUALITY + } //////////////////////////////////////////////////////////////////////////////////// // STANDARD WALKER METHODS //////////////////////////////////////////////////////////////////////////////////// + @Override public boolean includeReadsWithDeletionAtLoci() { return true; } + @Override public void initialize() { + if ( getToolkit().getSamples().size() > 1 ) + throw new UserException.BadArgumentValue("-I", "CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: " + getToolkit().getSamples()); + try { PrintStream summaryOut = new PrintStream(summaryFile); summaryOut.close(); @@ -94,15 +234,15 @@ public class CallableLociWalker extends LocusWalker { if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) ) return 0; - String rsID = dbsnp == null ? null : DbSNPHelper.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP); + String rsID = dbsnp == null ? null : VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP); Collection contexts = getVariantContexts(tracker, ref); diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java rename to public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java index 5e536d4c1..e328c9286 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.refdata.features.beagle; +package org.broadinstitute.sting.utils.codecs.beagle; /* * Copyright (c) 2010 The Broad Institute * diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java rename to public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java index e6832754d..0aa9ecba2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java @@ -22,7 +22,7 @@ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.features.beagle; +package org.broadinstitute.sting.utils.codecs.beagle; import org.broad.tribble.Feature; import org.broadinstitute.sting.utils.variantcontext.Allele; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java index fef6c4ea0..c30da828e 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java @@ -117,7 +117,7 @@ public class CGVarCodec implements FeatureCodec { return new VariantContext("CGI", array[3], start, end, alleles, VariantContext.NO_NEG_LOG_10PERROR, null, attrs); } - public Class getFeatureType() { + public Class getFeatureType() { return VariantContext.class; } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java index 90878dee7..535f607a1 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java @@ -82,7 +82,7 @@ public class RawHapMapCodec implements FeatureCodec { headerLine); } - public Class getFeatureType() { + public Class getFeatureType() { return RawHapMapFeature.class; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java rename to public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java index cec40b5bd..391715c63 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java @@ -1,6 +1,5 @@ -package org.broadinstitute.sting.gatk.refdata.features.refseq; +package org.broadinstitute.sting.utils.codecs.refseq; -import org.apache.commons.io.filefilter.FalseFileFilter; import org.broad.tribble.Feature; import org.broad.tribble.TribbleException; import org.broad.tribble.readers.LineReader; @@ -104,7 +103,7 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec getFeatureType() { return RefSeqFeature.class; } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java rename to public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java index a38d45428..c04ca8592 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.refdata.features.refseq; +package org.broadinstitute.sting.utils.codecs.refseq; import org.broad.tribble.Feature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/Transcript.java b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/Transcript.java rename to public/java/src/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java index d8bf12810..3e8a4fb34 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/Transcript.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java @@ -1,53 +1,53 @@ -package org.broadinstitute.sting.gatk.refdata.features.refseq; - -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.HasGenomeLocation; - -import java.util.List; - -/** - * Created by IntelliJ IDEA. - * User: asivache - * Date: Sep 22, 2009 - * Time: 5:22:30 PM - * To change this template use File | Settings | File Templates. - */ -public interface Transcript extends HasGenomeLocation { - - /** Returns id of the transcript (RefSeq NM_* id) */ - public String getTranscriptId(); - /** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */ - public int getStrand(); - /** Returns transcript's full genomic interval (includes all exons with UTRs) */ - public GenomeLoc getLocation(); - /** Returns genomic interval of the coding sequence (does not include - * UTRs, but still includes introns, since it's a single interval on the DNA) - */ - public GenomeLoc getCodingLocation(); - /** Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc, - * but the implementation can decide otherwise) - */ - public String getGeneName(); - /** Number of exons in this transcript */ - public int getNumExons(); - /** Genomic location of the n-th exon; expected to throw an exception (runtime) if n is out of bounds */ - public GenomeLoc getExonLocation(int n); - - /** Returns the list of all exons in this transcript, as genomic intervals */ - public List getExons(); - - /** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */ - public boolean overlapsP (GenomeLoc that); - - /** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript. - * NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons, - * but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript. - * @see #overlapsExonP - */ - public boolean overlapsCodingP (GenomeLoc that); - - /** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */ - public boolean overlapsExonP (GenomeLoc that); - - -} +package org.broadinstitute.sting.utils.codecs.refseq; + +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.HasGenomeLocation; + +import java.util.List; + +/** + * Created by IntelliJ IDEA. + * User: asivache + * Date: Sep 22, 2009 + * Time: 5:22:30 PM + * To change this template use File | Settings | File Templates. + */ +public interface Transcript extends HasGenomeLocation { + + /** Returns id of the transcript (RefSeq NM_* id) */ + public String getTranscriptId(); + /** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */ + public int getStrand(); + /** Returns transcript's full genomic interval (includes all exons with UTRs) */ + public GenomeLoc getLocation(); + /** Returns genomic interval of the coding sequence (does not include + * UTRs, but still includes introns, since it's a single interval on the DNA) + */ + public GenomeLoc getCodingLocation(); + /** Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc, + * but the implementation can decide otherwise) + */ + public String getGeneName(); + /** Number of exons in this transcript */ + public int getNumExons(); + /** Genomic location of the n-th exon; expected to throw an exception (runtime) if n is out of bounds */ + public GenomeLoc getExonLocation(int n); + + /** Returns the list of all exons in this transcript, as genomic intervals */ + public List getExons(); + + /** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */ + public boolean overlapsP (GenomeLoc that); + + /** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript. + * NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons, + * but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript. + * @see #overlapsExonP + */ + public boolean overlapsCodingP (GenomeLoc that); + + /** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */ + public boolean overlapsExonP (GenomeLoc that); + + +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java rename to public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java index 43e2c3ff5..f4048d37d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.features.sampileup; +package org.broadinstitute.sting.utils.codecs.sampileup; import org.broad.tribble.Feature; import org.broad.tribble.FeatureCodec; @@ -35,7 +35,7 @@ import java.util.ArrayList; import java.util.regex.Matcher; import java.util.regex.Pattern; -import static org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature.VariantType; +import static org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature.VariantType; /** * A Tribble encoder / decoder for SAM pileup data. diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java rename to public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java index 378f26934..eb33243e3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.features.sampileup; +package org.broadinstitute.sting.utils.codecs.sampileup; import net.sf.samtools.util.StringUtil; import org.broad.tribble.Feature; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java rename to public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java index 039b8adde..f6861e585 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.features.samread; +package org.broadinstitute.sting.utils.codecs.samread; import net.sf.samtools.Cigar; import net.sf.samtools.TextCigarCodec; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadFeature.java rename to public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java index 7f12b2b2f..fc1bf89af 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadFeature.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.refdata.features.samread; +package org.broadinstitute.sting.utils.codecs.samread; import org.broad.tribble.Feature; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java index eada8521f..b5efb49a7 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java @@ -222,7 +222,7 @@ public class SnpEffCodec implements FeatureCodec, SelfScopingFeatureCodec { return null; } - public Class getFeatureType() { + public Class getFeatureType() { return SnpEffFeature.class; } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java index e169dbdfc..284c43e90 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java @@ -178,7 +178,7 @@ public class SoapSNPCodec implements FeatureCodec, NameAwareCodec { /** * @return VariantContext */ - public Class getFeatureType() { + public Class getFeatureType() { return VariantContext.class; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java rename to public/java/src/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java index 745ccdd9f..6fe1907e3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.refdata.features.table; +package org.broadinstitute.sting.utils.codecs.table; import org.broad.tribble.Feature; import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java rename to public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java index ab1ac59d8..2ce7c679e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.refdata.features.table; +package org.broadinstitute.sting.utils.codecs.table; import org.broad.tribble.Feature; import org.broad.tribble.readers.LineReader; @@ -51,7 +51,7 @@ public class TableCodec implements ReferenceDependentFeatureCodec { } @Override - public Class getFeatureType() { + public Class getFeatureType() { return TableFeature.class; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java rename to public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java index ca73ee960..a85849f0b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.refdata.features.table; +package org.broadinstitute.sting.utils.codecs.table; import org.broad.tribble.Feature; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index cb505c717..19f58ddaa 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -263,7 +263,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, * * @return the type of record */ - public Class getFeatureType() { + public Class getFeatureType() { return VariantContext.class; } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java index f43891e77..c0a04c81f 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java @@ -180,4 +180,19 @@ public class VCFUtils { return new HashSet(map.values()); } + + public static String rsIDOfFirstRealVariant(List VCs, VariantContext.Type type) { + if ( VCs == null ) + return null; + + String rsID = null; + for ( VariantContext vc : VCs ) { + if ( vc.getType() == type ) { + rsID = vc.getID(); + break; + } + } + + return rsID; + } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java index ce03c8093..214a1716a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java @@ -71,7 +71,7 @@ public abstract class DocumentedGATKFeatureHandler { * @return */ public String getDestinationFilename(ClassDoc doc, Class clazz) { - return GATKDocUtils.htmlFilenameForClass(clazz); + return HelpUtils.htmlFilenameForClass(clazz); } /** diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java deleted file mode 100644 index 8efeecd7b..000000000 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java +++ /dev/null @@ -1,48 +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 org.broadinstitute.sting.utils.help; - -/** - * @author depristo - * @since 8/8/11 - */ -public class GATKDocUtils { - private final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/"; - private final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/"; - private final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/"; - - public static String htmlFilenameForClass(Class c) { - return c.getName().replace(".", "_") + ".html"; - } - - public static String helpLinksToGATKDocs(Class c) { - String classPath = htmlFilenameForClass(c); - StringBuilder b = new StringBuilder(); - b.append("release version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n"); - b.append("stable version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n"); - b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n"); - return b.toString(); - } -} diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java index 4527c6afe..da4e7bdaf 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java @@ -32,6 +32,10 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils; import java.lang.reflect.Field; public class HelpUtils { + public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/"; + public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/"; + public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/"; + protected static boolean implementsInterface(ProgramElementDoc classDoc, Class... interfaceClasses) { for (Class interfaceClass : interfaceClasses) if (assignableToClass(classDoc, interfaceClass, false)) @@ -74,4 +78,17 @@ public class HelpUtils { String.format("%s.%s", containingPackage.name(), doc.name()) : String.format("%s", doc.name()); } + + public static String htmlFilenameForClass(Class c) { + return c.getName().replace(".", "_") + ".html"; + } + + public static String helpLinksToGATKDocs(Class c) { + String classPath = htmlFilenameForClass(c); + StringBuilder b = new StringBuilder(); + b.append("release version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n"); + b.append("stable version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n"); + b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n"); + return b.toString(); + } } \ No newline at end of file diff --git a/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java index 79e9172dd..013a37a88 100755 --- a/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java @@ -26,7 +26,6 @@ package org.broadinstitute.sting.commandline; import org.broad.tribble.Feature; -import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.testng.Assert; @@ -35,7 +34,6 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; -import javax.script.Bindings; import java.util.List; import java.util.EnumSet; /** diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java index f782580e2..85ae1e1f7 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java @@ -10,7 +10,7 @@ import org.testng.Assert; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature; +import org.broadinstitute.sting.utils.codecs.table.TableFeature; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java index bd4f93d24..d45f6e667 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java @@ -4,7 +4,7 @@ import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature; +import org.broadinstitute.sting.utils.codecs.table.TableFeature; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType; diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java index fbd30bc8a..1e39fd26f 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java @@ -31,7 +31,7 @@ import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature; +import org.broadinstitute.sting.utils.codecs.table.TableFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java index 5d662ffed..90262b9c1 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java @@ -29,8 +29,8 @@ import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broad.tribble.Feature; import org.broad.tribble.FeatureCodec; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.refdata.features.table.BedTableCodec; -import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature; +import org.broadinstitute.sting.utils.codecs.table.BedTableCodec; +import org.broadinstitute.sting.utils.codecs.table.TableFeature; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec; import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;