Re-committing the following changes from Dec 18:
Refactored interval specific arguments out of GATKArgumentCollection into InvtervalArgumentCollection such that it can be used in other CommandLinePrograms. Updated SelectHeaders to print out full interval arguments. Added RemoteFile.createUrl(Date expiration) to enable creation of presigned URLs for download over http: or file:.
This commit is contained in:
Khalid Shakir
parent
4fb3e48099
commit
4ffb43079f
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@ -57,6 +57,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.gatk.walkers.TreeReducible;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
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import org.broadinstitute.sting.utils.interval.IntervalSetRule;
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import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
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import org.broadinstitute.variant.vcf.*;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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@ -180,18 +182,47 @@ public class SelectHeaders extends RodWalker<Integer, Integer> implements TreeRe
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headerLines = new LinkedHashSet<VCFHeaderLine>(getSelectedHeaders(headerLines));
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// Optionally add in the intervals.
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if (includeIntervals && getToolkit().getArguments().intervals != null) {
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for (IntervalBinding<Feature> intervalBinding : getToolkit().getArguments().intervals) {
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String source = intervalBinding.getSource();
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if (source == null)
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continue;
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File file = new File(source);
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if (file.exists()) {
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headerLines.add(new VCFHeaderLine(VCFHeader.INTERVALS_KEY, FilenameUtils.getBaseName(file.getName())));
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} else {
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headerLines.add(new VCFHeaderLine(VCFHeader.INTERVALS_KEY, source));
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if (includeIntervals) {
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IntervalArgumentCollection intervalArguments = getToolkit().getArguments().intervalArguments;
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if (intervalArguments.intervals != null) {
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for (IntervalBinding<Feature> intervalBinding : intervalArguments.intervals) {
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String source = intervalBinding.getSource();
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if (source == null)
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continue;
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File file = new File(source);
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if (file.exists()) {
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headerLines.add(new VCFHeaderLine(VCFHeader.INTERVALS_KEY, FilenameUtils.getBaseName(file.getName())));
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} else {
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headerLines.add(new VCFHeaderLine(VCFHeader.INTERVALS_KEY, source));
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}
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}
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}
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if (intervalArguments.excludeIntervals != null) {
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for (IntervalBinding<Feature> intervalBinding : intervalArguments.excludeIntervals) {
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String source = intervalBinding.getSource();
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if (source == null)
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continue;
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File file = new File(source);
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if (file.exists()) {
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headerLines.add(new VCFHeaderLine(VCFHeader.EXCLUDE_INTERVALS_KEY, FilenameUtils.getBaseName(file.getName())));
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} else {
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headerLines.add(new VCFHeaderLine(VCFHeader.EXCLUDE_INTERVALS_KEY, source));
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}
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}
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}
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if (intervalArguments.intervalMerging != IntervalMergingRule.ALL) {
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headerLines.add(new VCFHeaderLine(VCFHeader.INTERVAL_MERGING_KEY, String.valueOf(intervalArguments.intervalMerging)));
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}
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if (intervalArguments.intervalSetRule != IntervalSetRule.UNION) {
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headerLines.add(new VCFHeaderLine(VCFHeader.INTERVAL_SET_RULE_KEY, String.valueOf(intervalArguments.intervalSetRule)));
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}
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if (intervalArguments.intervalPadding != 0) {
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headerLines.add(new VCFHeaderLine(VCFHeader.INTERVAL_PADDING_KEY, String.valueOf(intervalArguments.intervalPadding)));
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}
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}
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TreeSet<String> vcfSamples = new TreeSet<String>(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
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@ -0,0 +1,70 @@
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/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.commandline;
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import org.broad.tribble.Feature;
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import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
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import org.broadinstitute.sting.utils.interval.IntervalSetRule;
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import java.util.List;
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public class IntervalArgumentCollection {
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/**
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* Using this option one can instruct the GATK engine to traverse over only part of the genome. This argument can be specified multiple times.
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* One may use samtools-style intervals either explicitly (e.g. -L chr1 or -L chr1:100-200) or listed in a file (e.g. -L myFile.intervals).
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* Additionally, one may specify a rod file to traverse over the positions for which there is a record in the file (e.g. -L file.vcf).
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* To specify the completely unmapped reads in the BAM file (i.e. those without a reference contig) use -L unmapped.
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*/
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@Input(fullName = "intervals", shortName = "L", doc = "One or more genomic intervals over which to operate. Can be explicitly specified on the command line or in a file (including a rod file)", required = false)
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public List<IntervalBinding<Feature>> intervals = null;
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/**
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* Using this option one can instruct the GATK engine NOT to traverse over certain parts of the genome. This argument can be specified multiple times.
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* One may use samtools-style intervals either explicitly (e.g. -XL chr1 or -XL chr1:100-200) or listed in a file (e.g. -XL myFile.intervals).
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* Additionally, one may specify a rod file to skip over the positions for which there is a record in the file (e.g. -XL file.vcf).
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*/
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@Input(fullName = "excludeIntervals", shortName = "XL", doc = "One or more genomic intervals to exclude from processing. Can be explicitly specified on the command line or in a file (including a rod file)", required = false)
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public List<IntervalBinding<Feature>> excludeIntervals = null;
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/**
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* How should the intervals specified by multiple -L or -XL arguments be combined? Using this argument one can, for example, traverse over all of the positions
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* for which there is a record in a VCF but just in chromosome 20 (-L chr20 -L file.vcf -isr INTERSECTION).
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*/
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@Argument(fullName = "interval_set_rule", shortName = "isr", doc = "Indicates the set merging approach the interval parser should use to combine the various -L or -XL inputs", required = false)
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public IntervalSetRule intervalSetRule = IntervalSetRule.UNION;
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/**
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* Should abutting (but not overlapping) intervals be treated as separate intervals?
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*/
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@Argument(fullName = "interval_merging", shortName = "im", doc = "Indicates the interval merging rule we should use for abutting intervals", required = false)
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public IntervalMergingRule intervalMerging = IntervalMergingRule.ALL;
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/**
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* For example, '-L chr1:100' with a padding value of 20 would turn into '-L chr1:80-120'.
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*/
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@Argument(fullName = "interval_padding", shortName = "ip", doc = "Indicates how many basepairs of padding to include around each of the intervals specified with the -L/--intervals argument", required = false)
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public int intervalPadding = 0;
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}
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@ -55,7 +55,6 @@ import org.broadinstitute.sting.gatk.samples.SampleDBBuilder;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.*;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.interval.IntervalUtils;
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@ -361,7 +360,6 @@ public class GenomeAnalysisEngine {
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* Returns a list of active, initialized read transformers
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*
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* @param walker the walker we need to apply read transformers too
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* @return a non-null list of read transformers
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*/
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public void initializeReadTransformers(final Walker walker) {
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final List<ReadTransformer> activeTransformers = new ArrayList<ReadTransformer>();
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@ -672,41 +670,7 @@ public class GenomeAnalysisEngine {
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* Setup the intervals to be processed
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*/
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protected void initializeIntervals() {
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// return if no interval arguments at all
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if ( argCollection.intervals == null && argCollection.excludeIntervals == null )
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return;
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// Note that the use of '-L all' is no longer supported.
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// if include argument isn't given, create new set of all possible intervals
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final Pair<GenomeLocSortedSet, GenomeLocSortedSet> includeExcludePair = IntervalUtils.parseIntervalBindingsPair(
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this.referenceDataSource,
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argCollection.intervals,
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argCollection.intervalSetRule, argCollection.intervalMerging, argCollection.intervalPadding,
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argCollection.excludeIntervals);
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final GenomeLocSortedSet includeSortedSet = includeExcludePair.getFirst();
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final GenomeLocSortedSet excludeSortedSet = includeExcludePair.getSecond();
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// if no exclude arguments, can return parseIntervalArguments directly
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if ( excludeSortedSet == null )
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intervals = includeSortedSet;
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// otherwise there are exclude arguments => must merge include and exclude GenomeLocSortedSets
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else {
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intervals = includeSortedSet.subtractRegions(excludeSortedSet);
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// logging messages only printed when exclude (-XL) arguments are given
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final long toPruneSize = includeSortedSet.coveredSize();
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final long toExcludeSize = excludeSortedSet.coveredSize();
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final long intervalSize = intervals.coveredSize();
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logger.info(String.format("Initial include intervals span %d loci; exclude intervals span %d loci", toPruneSize, toExcludeSize));
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logger.info(String.format("Excluding %d loci from original intervals (%.2f%% reduction)",
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toPruneSize - intervalSize, (toPruneSize - intervalSize) / (0.01 * toPruneSize)));
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}
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logger.info(String.format("Processing %d bp from intervals", intervals.coveredSize()));
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intervals = IntervalUtils.parseIntervalArguments(this.referenceDataSource, argCollection.intervalArguments);
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}
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/**
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@ -26,11 +26,7 @@
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package org.broadinstitute.sting.gatk.arguments;
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import net.sf.samtools.SAMFileReader;
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import org.broad.tribble.Feature;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Hidden;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.IntervalBinding;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
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import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod;
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@ -38,8 +34,6 @@ import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
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import org.broadinstitute.sting.gatk.samples.PedigreeValidationType;
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import org.broadinstitute.sting.utils.QualityUtils;
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import org.broadinstitute.sting.utils.baq.BAQ;
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import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
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import org.broadinstitute.sting.utils.interval.IntervalSetRule;
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import java.io.File;
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import java.util.ArrayList;
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@ -100,41 +94,8 @@ public class GATKArgumentCollection {
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@Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually", required = false)
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public List<String> readFilters = new ArrayList<String>();
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/**
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* Using this option one can instruct the GATK engine to traverse over only part of the genome. This argument can be specified multiple times.
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* One may use samtools-style intervals either explicitly (e.g. -L chr1 or -L chr1:100-200) or listed in a file (e.g. -L myFile.intervals).
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* Additionally, one may specify a rod file to traverse over the positions for which there is a record in the file (e.g. -L file.vcf).
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* To specify the completely unmapped reads in the BAM file (i.e. those without a reference contig) use -L unmapped.
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*/
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@Input(fullName = "intervals", shortName = "L", doc = "One or more genomic intervals over which to operate. Can be explicitly specified on the command line or in a file (including a rod file)", required = false)
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public List<IntervalBinding<Feature>> intervals = null;
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/**
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* Using this option one can instruct the GATK engine NOT to traverse over certain parts of the genome. This argument can be specified multiple times.
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* One may use samtools-style intervals either explicitly (e.g. -XL chr1 or -XL chr1:100-200) or listed in a file (e.g. -XL myFile.intervals).
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* Additionally, one may specify a rod file to skip over the positions for which there is a record in the file (e.g. -XL file.vcf).
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*/
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@Input(fullName = "excludeIntervals", shortName = "XL", doc = "One or more genomic intervals to exclude from processing. Can be explicitly specified on the command line or in a file (including a rod file)", required = false)
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public List<IntervalBinding<Feature>> excludeIntervals = null;
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/**
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* How should the intervals specified by multiple -L or -XL arguments be combined? Using this argument one can, for example, traverse over all of the positions
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* for which there is a record in a VCF but just in chromosome 20 (-L chr20 -L file.vcf -isr INTERSECTION).
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*/
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@Argument(fullName = "interval_set_rule", shortName = "isr", doc = "Indicates the set merging approach the interval parser should use to combine the various -L or -XL inputs", required = false)
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public IntervalSetRule intervalSetRule = IntervalSetRule.UNION;
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/**
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* Should abutting (but not overlapping) intervals be treated as separate intervals?
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*/
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@Argument(fullName = "interval_merging", shortName = "im", doc = "Indicates the interval merging rule we should use for abutting intervals", required = false)
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public IntervalMergingRule intervalMerging = IntervalMergingRule.ALL;
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/**
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* For example, '-L chr1:100' with a padding value of 20 would turn into '-L chr1:80-120'.
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*/
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@Argument(fullName = "interval_padding", shortName = "ip", doc = "Indicates how many basepairs of padding to include around each of the intervals specified with the -L/--intervals argument", required = false)
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public int intervalPadding = 0;
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@ArgumentCollection
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public IntervalArgumentCollection intervalArguments = new IntervalArgumentCollection();
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@Input(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false)
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public File referenceFile = null;
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@ -32,6 +32,7 @@ import net.sf.picard.util.IntervalList;
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import net.sf.samtools.SAMFileHeader;
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import org.apache.log4j.Logger;
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import org.broad.tribble.Feature;
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import org.broadinstitute.sting.commandline.IntervalArgumentCollection;
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import org.broadinstitute.sting.commandline.IntervalBinding;
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import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
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import org.broadinstitute.sting.utils.GenomeLoc;
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@ -534,6 +535,47 @@ public class IntervalUtils {
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}
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}
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public static GenomeLocSortedSet parseIntervalArguments(final ReferenceDataSource referenceDataSource, IntervalArgumentCollection argCollection) {
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GenomeLocSortedSet intervals = null;
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// return if no interval arguments at all
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if ( argCollection.intervals == null && argCollection.excludeIntervals == null )
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return intervals;
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// Note that the use of '-L all' is no longer supported.
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// if include argument isn't given, create new set of all possible intervals
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final Pair<GenomeLocSortedSet, GenomeLocSortedSet> includeExcludePair = IntervalUtils.parseIntervalBindingsPair(
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referenceDataSource,
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argCollection.intervals,
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argCollection.intervalSetRule, argCollection.intervalMerging, argCollection.intervalPadding,
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argCollection.excludeIntervals);
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final GenomeLocSortedSet includeSortedSet = includeExcludePair.getFirst();
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final GenomeLocSortedSet excludeSortedSet = includeExcludePair.getSecond();
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// if no exclude arguments, can return parseIntervalArguments directly
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if ( excludeSortedSet == null )
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intervals = includeSortedSet;
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// otherwise there are exclude arguments => must merge include and exclude GenomeLocSortedSets
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else {
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intervals = includeSortedSet.subtractRegions(excludeSortedSet);
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// logging messages only printed when exclude (-XL) arguments are given
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final long toPruneSize = includeSortedSet.coveredSize();
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final long toExcludeSize = excludeSortedSet.coveredSize();
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final long intervalSize = intervals.coveredSize();
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logger.info(String.format("Initial include intervals span %d loci; exclude intervals span %d loci", toPruneSize, toExcludeSize));
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logger.info(String.format("Excluding %d loci from original intervals (%.2f%% reduction)",
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toPruneSize - intervalSize, (toPruneSize - intervalSize) / (0.01 * toPruneSize)));
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}
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logger.info(String.format("Processing %d bp from intervals", intervals.coveredSize()));
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return intervals;
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}
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public static Pair<GenomeLocSortedSet, GenomeLocSortedSet> parseIntervalBindingsPair(
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final ReferenceDataSource referenceDataSource,
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final List<IntervalBinding<Feature>> intervals,
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@ -73,6 +73,10 @@ public class VCFHeader {
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public static final String REFERENCE_KEY = "reference";
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public static final String CONTIG_KEY = "contig";
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public static final String INTERVALS_KEY = "intervals";
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public static final String EXCLUDE_INTERVALS_KEY = "excludeIntervals";
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public static final String INTERVAL_MERGING_KEY = "interval_merging";
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public static final String INTERVAL_SET_RULE_KEY = "interval_set_rule";
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public static final String INTERVAL_PADDING_KEY = "interval_padding";
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// were the input samples sorted originally (or are we sorting them)?
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private boolean samplesWereAlreadySorted = true;
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@ -1068,7 +1068,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
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List<IntervalBinding<Feature>> intervalArgs = new ArrayList<IntervalBinding<Feature>>(1);
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intervalArgs.add(new IntervalBinding<Feature>(picardIntervalFile.getAbsolutePath()));
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IntervalUtils.loadIntervals(intervalArgs, argCollection.intervalSetRule, argCollection.intervalMerging, argCollection.intervalPadding, genomeLocParser);
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IntervalUtils.loadIntervals(intervalArgs, argCollection.intervalArguments.intervalSetRule, argCollection.intervalArguments.intervalMerging, argCollection.intervalArguments.intervalPadding, genomeLocParser);
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}
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@Test(expectedExceptions=UserException.class, dataProvider="invalidIntervalTestData")
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@ -1081,7 +1081,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
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List<IntervalBinding<Feature>> intervalArgs = new ArrayList<IntervalBinding<Feature>>(1);
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intervalArgs.add(new IntervalBinding<Feature>(gatkIntervalFile.getAbsolutePath()));
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IntervalUtils.loadIntervals(intervalArgs, argCollection.intervalSetRule, argCollection.intervalMerging, argCollection.intervalPadding, genomeLocParser);
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IntervalUtils.loadIntervals(intervalArgs, argCollection.intervalArguments.intervalSetRule, argCollection.intervalArguments.intervalMerging, argCollection.intervalArguments.intervalPadding, genomeLocParser);
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}
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private File createTempFile( String tempFilePrefix, String tempFileExtension, String... lines ) throws Exception {
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@ -27,6 +27,8 @@ package org.broadinstitute.sting.queue.util
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import java.io.File
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import org.broadinstitute.sting.utils.io.FileExtension
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||||
import java.util.Date
|
||||
import java.net.URL
|
||||
|
||||
/**
|
||||
* An extension of java.io.File that can be pulled from or pushed to a remote location.
|
||||
|
|
@ -35,5 +37,6 @@ trait RemoteFile extends File with FileExtension {
|
|||
def pullToLocal()
|
||||
def pushToRemote()
|
||||
def deleteRemote()
|
||||
def createUrl(expiration: Date): URL
|
||||
def remoteDescription: String
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue