From 64e2d3a8af2c7b46d3a2d7bf046a925cf14b6aeb Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Tue, 29 Jan 2019 17:08:26 -0500 Subject: [PATCH] A port of FastaAlternateReferenceMaker and FastaReferenceMaker from GATK3 (#5549) * Ported FastaAlternateReferenceMaker and FastaReferenceMaker from GATK3 * Added a new walker type ReferenceWalker, and a new tool CountBasesInReference to demonstrate it * Made changes to the close behavior in FastaWriter, and added additional buffering Resolves #4891 --- .../hellbender/engine/ReferenceContext.java | 3 +- .../hellbender/engine/ReferenceWalker.java | 107 +++++++ .../examples/ExampleReferenceWalker.java | 81 ++++++ .../walkers/fasta/CountBasesInReference.java | 37 +++ .../fasta/FastaAlternateReferenceMaker.java | 262 ++++++++++++++++++ .../walkers/fasta/FastaReferenceMaker.java | 144 ++++++++++ .../hellbender/utils/BaseUtils.java | 34 +++ .../hellbender/utils/SimpleInterval.java | 2 - .../hellbender/utils/help/HelpConstants.java | 2 - .../iterators/IntervalLocusIterator.java | 7 +- .../utils/reference/FastaReferenceWriter.java | 28 +- ...ExampleReferenceWalkerIntegrationTest.java | 36 +++ .../GenomicsDBImportIntegrationTest.java | 23 +- .../CountBasesInReferenceIntegrationTest.java | 38 +++ ...lternateReferenceMakerIntegrationTest.java | 155 +++++++++++ .../FastaReferenceMakerIntegrationTest.java | 69 +++++ .../ReblockGVCFIntegrationTest.java | 4 +- .../hellbender/utils/BaseUtilsUnitTest.java | 29 ++ .../FastaReferenceWriterUnitTest.java | 139 +++++----- .../ExampleReferenceWalker/example.dict | 2 + .../ExampleReferenceWalker/example.fasta | 6 + .../ExampleReferenceWalker/example.fasta.fai | 1 + .../ExampleReferenceWalker/example.vcf | 26 ++ .../ExampleReferenceWalker/example.vcf.idx | Bin 0 -> 307 bytes .../ExampleReferenceWalker/veryspecific.bam | Bin 0 -> 637 bytes .../veryspecific.bam.bai | Bin 0 -> 96 bytes .../ExampleReferenceWalker/veryspecific.sam | 5 + .../NA12878.WGS.b37.chr20.firstMB.vcf.gz | Bin 0 -> 23749 bytes .../NA12878.WGS.b37.chr20.firstMB.vcf.gz.tbi | Bin 0 -> 570 bytes .../NA12878.chr1_10mb_11mb.slx.indels.vcf | 5 + .../NA12878.chr1_10mb_11mb.slx.indels.vcf.idx | Bin 0 -> 2211 bytes ...nate_reference_contiguous_diff_contig.dict | 3 + ...ate_reference_contiguous_diff_contig.fasta | 6 + ...reference_contiguous_diff_contig.fasta.fai | 2 + ...nate_reference_contiguous_same_contig.dict | 2 + ...ate_reference_contiguous_same_contig.fasta | 5 + ...reference_contiguous_same_contig.fasta.fai | 1 + .../expected_no_mask.dict | 2 + .../expected_no_mask.fasta | 3 + .../expected_no_mask.fasta.fai | 1 + .../expected_snp1.dict | 2 + .../expected_snp1.fasta | 3 + .../expected_snp1.fasta.fai | 1 + .../expected_snp1_mask2.dict | 2 + .../expected_snp1_mask2.fasta | 3 + .../expected_snp1_mask2.fasta.fai | 1 + .../expected_snp1_mask2_priority.dict | 2 + .../expected_snp1_mask2_priority.fasta | 3 + .../expected_snp1_mask2_priority.fasta.fai | 1 + .../expected_snp2.dict | 2 + .../expected_snp2.fasta | 3 + .../expected_snp2.fasta.fai | 1 + .../expected_snp2_mask1.dict | 2 + .../expected_snp2_mask1.fasta | 3 + .../expected_snp2_mask1.fasta.fai | 1 + .../expected_snp2_mask1_priority.dict | 2 + .../expected_snp2_mask1_priority.fasta | 3 + .../expected_snp2_mask1_priority.fasta.fai | 1 + .../expected_snp_mask.dict | 2 + .../expected_snp_mask.fasta | 3 + .../expected_snp_mask.fasta.fai | 1 + .../expected_snpsAndIndels.dict | 2 + .../expected_snpsAndIndels.fasta | 3 + .../expected_snpsAndIndels.fasta.fai | 1 + .../expected_snpsAndIndels_mask1.dict | 2 + .../expected_snpsAndIndels_mask1.fasta | 3 + .../expected_snpsAndIndels_mask1.fasta.fai | 1 + ...expected_snpsAndIndels_mask1_priority.dict | 2 + ...xpected_snpsAndIndels_mask1_priority.fasta | 3 + ...ted_snpsAndIndels_mask1_priority.fasta.fai | 1 + .../expected_snpsAndIndels_mask2.fasta | 3 + .../expected_snpsAndIndels_maskOverlaps.dict | 2 + .../expected_snpsAndIndels_maskOverlaps.fasta | 3 + ...ected_snpsAndIndels_maskOverlaps.fasta.fai | 1 + ...d_snpsAndIndels_maskOverlaps_priority.dict | 2 + ..._snpsAndIndels_maskOverlaps_priority.fasta | 3 + ...sAndIndels_maskOverlaps_priority.fasta.fai | 1 + .../expected_test_iupac.dict | 2 + .../expected_test_iupac.fasta | 90 ++++++ .../expected_test_iupac.fasta.fai | 1 + .../iupac_sample_NA1.dict | 2 + .../iupac_sample_NA1.fasta | 2 + .../iupac_sample_NA1.fasta.fai | 1 + .../iupac_sample_NA2.dict | 1 + .../iupac_sample_NA2.fasta | 2 + .../iupac_sample_NA2.fasta.fai | 1 + .../iupac_sample_NA3.dict | 2 + .../iupac_sample_NA3.fasta | 2 + .../iupac_sample_NA3.fasta.fai | 1 + .../overlapsIndelsMask.vcf | 164 +++++++++++ .../overlapsIndelsMask.vcf.idx | Bin 0 -> 2104 bytes .../FastaAlternateReferenceMaker/snps.vcf | 163 +++++++++++ .../FastaAlternateReferenceMaker/snps.vcf.idx | Bin 0 -> 2159 bytes .../FastaAlternateReferenceMaker/snps2.vcf | 163 +++++++++++ .../snps2.vcf.idx | Bin 0 -> 2164 bytes .../snpsAndIndels.vcf | 167 +++++++++++ .../snpsAndIndels.vcf.idx | Bin 0 -> 2212 bytes .../spanningDel.delOnly.starFirst.vcf | 116 ++++++++ .../spanningDel.delOnly.starFirst.vcf.idx | Bin 0 -> 348 bytes .../FastaReferenceMaker/reference_only.dict | 4 + .../FastaReferenceMaker/reference_only.fasta | 28 ++ .../reference_only.fasta.fai | 3 + ...eference_only_contiguous_diff_contigs.dict | 3 + ...ference_only_contiguous_diff_contigs.fasta | 6 + ...nce_only_contiguous_diff_contigs.fasta.fai | 2 + ...reference_only_contiguous_same_contig.dict | 2 + ...eference_only_contiguous_same_contig.fasta | 5 + ...ence_only_contiguous_same_contig.fasta.fai | 1 + .../testutils/ArgumentsBuilder.java | 9 + .../hellbender/testutils/FastaTestUtils.java | 33 +++ .../testutils/GenomicsDBTestUtils.java | 3 +- 111 files changed, 2212 insertions(+), 112 deletions(-) create mode 100644 src/main/java/org/broadinstitute/hellbender/engine/ReferenceWalker.java create mode 100644 src/main/java/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker.java create mode 100644 src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/CountBasesInReference.java create mode 100644 src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker.java create mode 100644 src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker.java create mode 100644 src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalkerIntegrationTest.java create mode 100644 src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/CountBasesInReferenceIntegrationTest.java create mode 100644 src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMakerIntegrationTest.java create mode 100644 src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMakerIntegrationTest.java create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/veryspecific.bam create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/veryspecific.bam.bai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/veryspecific.sam create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/NA12878.WGS.b37.chr20.firstMB.vcf.gz create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/NA12878.WGS.b37.chr20.firstMB.vcf.gz.tbi create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/NA12878.chr1_10mb_11mb.slx.indels.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/NA12878.chr1_10mb_11mb.slx.indels.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_alternate_reference_contiguous_diff_contig.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_alternate_reference_contiguous_diff_contig.fasta create mode 100644 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create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp_mask.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp_mask.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp_mask.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask2.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_test_iupac.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_test_iupac.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_test_iupac.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA2.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA2.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA2.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/overlapsIndelsMask.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/overlapsIndelsMask.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps2.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snps2.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snpsAndIndels.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/snpsAndIndels.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/spanningDel.delOnly.starFirst.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/spanningDel.delOnly.starFirst.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_diff_contigs.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_diff_contigs.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_diff_contigs.fasta.fai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_same_contig.dict create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_same_contig.fasta create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_same_contig.fasta.fai create mode 100644 src/testUtils/java/org/broadinstitute/hellbender/testutils/FastaTestUtils.java diff --git a/src/main/java/org/broadinstitute/hellbender/engine/ReferenceContext.java b/src/main/java/org/broadinstitute/hellbender/engine/ReferenceContext.java index d0ee38eb375..4ad4fff65ac 100644 --- a/src/main/java/org/broadinstitute/hellbender/engine/ReferenceContext.java +++ b/src/main/java/org/broadinstitute/hellbender/engine/ReferenceContext.java @@ -2,13 +2,12 @@ import htsjdk.samtools.SAMSequenceRecord; import htsjdk.samtools.reference.ReferenceSequence; +import org.broadinstitute.hellbender.exceptions.GATKException; import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.exceptions.GATKException; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.iterators.ByteArrayIterator; -import java.util.Arrays; import java.util.Iterator; /** diff --git a/src/main/java/org/broadinstitute/hellbender/engine/ReferenceWalker.java b/src/main/java/org/broadinstitute/hellbender/engine/ReferenceWalker.java new file mode 100644 index 00000000000..9d7228747af --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/engine/ReferenceWalker.java @@ -0,0 +1,107 @@ +package org.broadinstitute.hellbender.engine; + +import org.broadinstitute.hellbender.engine.filters.CountingReadFilter; +import org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalker; +import org.broadinstitute.hellbender.utils.SimpleInterval; +import org.broadinstitute.hellbender.utils.iterators.IntervalLocusIterator; + +/** + * A reference walker is a tool which processes each base in a given reference. Each base can be processed individually + * or in a context of multiple bases in a window. Reads and Feature tracks can optionally be included as well. The + * reference bases to process can be subset to a given set of intervals. + * + * ReferenceWalker authors must implement the apply() method to process each position, and may optionally implement + * {@link #onTraversalStart()} and/or {@link #onTraversalSuccess()}. + * + * Tool authors may also implement {@link #getReferenceWindow(SimpleInterval)} to provide additional bases of context + * around each position. + * + * See the {@link ExampleReferenceWalker} walker for an example. + */ +public abstract class ReferenceWalker extends GATKTool { + + @Override + public String getProgressMeterRecordLabel() { return "bases"; } + + @Override + public final boolean requiresReference() { return true; } + + /** + * Initialize data sources for traversal. + * + * Marked final so that tool authors don't override it. Tool authors should override onTraversalStart() instead. + */ + @Override + protected final void onStartup() { + super.onStartup(); + } + + /** + * Implementation of reference-locus-based traversal. + * Subclasses can override to provide own behavior but default implementation should be suitable for most uses. + */ + @Override + public void traverse() { + final CountingReadFilter readFilter = makeReadFilter(); + + for(final SimpleInterval locus : getIntervalIterator()){ + final SimpleInterval referenceWindow = getReferenceWindow(locus); + final ReferenceContext referenceContext = new ReferenceContext(reference, locus, referenceWindow); + apply(referenceContext, + new ReadsContext(reads, referenceContext.getWindow(), readFilter), // Will create an empty ReadsContext if reads == null + new FeatureContext(features, referenceContext.getWindow())); // Will create an empty FeatureContext if features == null + + progressMeter.update(referenceContext.getInterval()); + }; + + } + + /** + * Determine the window to use when creating the ReferenceContext in apply. This determines which reference bases are + * seen at each position, as well as which reads / features are considered to overlap the reference site. + * + * The default implementation returns the single reference locus passed that is passed in, but subclasses may override + * this method in order to change the window size. + * + * @param locus the current locus being processed in the traversal + * @return the window to use when creating the ReferenceContext that is passed into {@link #apply(ReferenceContext, ReadsContext, FeatureContext)} + */ + protected SimpleInterval getReferenceWindow(SimpleInterval locus){ + return locus; + } + + private Iterable getIntervalIterator(){ + return () -> new IntervalLocusIterator(getTraversalIntervals().iterator()); + } + + /** + * Process an individual reference locus (with optional contextual information). Must be implemented by tool authors. + * In general, tool authors should simply stream their output from apply(), and maintain as little internal state + * as possible. + * + * @param referenceContext Reference bases at the current locus. The window around the single locus is provided by {@link #getReferenceWindow(SimpleInterval)} + * Additional bases my be retrieved by invoking the by invoking {@link ReferenceContext#setWindow} + * on this object before calling {@link ReferenceContext#getBases}, however this will not effect + * the set of reads and features that are considered overlapping which are based on the preset + * window passed in. + * @param readsContext Reads spanning the current reference window. Will be an empty, but non-null, context object + * if there is no backing source of Read data (in which case all queries on it will return an + * empty List). + * @param featureContext Features spanning the current reference window. Will be an empty, but non-null, context object + * if there is no backing source of Feature data (in which case all queries on it will return an + * empty List). + * + */ + public abstract void apply(ReferenceContext referenceContext, ReadsContext readsContext, FeatureContext featureContext ); + + /** + * Shutdown data sources. + * + * Marked final so that tool authors don't override it. Tool authors should override {@link #onTraversalSuccess()} instead. + */ + @Override + protected final void onShutdown() { + // Overridden only to make final so that concrete tool implementations don't override + super.onShutdown(); + } +} diff --git a/src/main/java/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker.java b/src/main/java/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker.java new file mode 100644 index 00000000000..870fb36a135 --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker.java @@ -0,0 +1,81 @@ +package org.broadinstitute.hellbender.tools.examples; + +import com.google.common.annotations.VisibleForTesting; +import htsjdk.variant.variantcontext.VariantContext; +import org.broadinstitute.barclay.argparser.Argument; +import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; +import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; +import org.broadinstitute.hellbender.cmdline.programgroups.ExampleProgramGroup; +import org.broadinstitute.hellbender.engine.*; +import org.broadinstitute.hellbender.utils.SimpleInterval; + +import java.util.Comparator; +import java.util.HashMap; +import java.util.Map; +import java.util.Map.Entry; + +/** + * Counts the number of times each reference context is seen as well as how many times it's overlapped by reads and variants. + * Why you would want to do this is a mystery. + * + * This is a toy example to illustrate how to implement a ReferenceWalker. + */ +@CommandLineProgramProperties( + summary = "Example of how to implement a ReferenceWalker that uses reads and features as well as a custom window", + oneLineSummary = "Example of how to implement a ReferenceWalker", + programGroup = ExampleProgramGroup.class, + omitFromCommandLine = true) +public class ExampleReferenceWalker extends ReferenceWalker { + + @Argument(fullName = StandardArgumentDefinitions.VARIANT_LONG_NAME, + shortName = StandardArgumentDefinitions.VARIANT_SHORT_NAME, + doc="variants to count overlaps of") + private FeatureInput variants; + + @VisibleForTesting + final Map contextCounts = new HashMap<>(); + + @Override + protected SimpleInterval getReferenceWindow(SimpleInterval locus) { + // add one base of padding to each side of each reference locus. + return new SimpleInterval(locus.getContig(), Math.max(locus.getStart() -1, 1), locus.getStart()+1); + } + + @Override + public void apply(ReferenceContext referenceContext, ReadsContext readsContext, FeatureContext featureContext) { + final byte[] bases = referenceContext.getBases(); + final String baseString = new String(bases); + final OverlapCounts counts = contextCounts.getOrDefault(baseString, new OverlapCounts()); + if(readsContext.iterator().hasNext()){ + counts.overlappedByReads++; + } + + if(!featureContext.getValues(variants).isEmpty()){ + counts.overlappedByVariants++; + } + + counts.timesSeen++; + + contextCounts.put(baseString, counts); + } + + @Override + public Object onTraversalSuccess(){ + contextCounts.entrySet().stream() + .sorted(Comparator.comparing(Entry::getKey)) + .forEachOrdered(entry -> System.out.println(entry.getKey() + " " + entry.getValue().toString())); + return 0; + } + + @VisibleForTesting + static class OverlapCounts { + long timesSeen = 0; + long overlappedByReads = 0; + long overlappedByVariants = 0; + + @Override + public String toString(){ + return String.format("Seen: %d Reads %d Variants %d", timesSeen, overlappedByReads, overlappedByVariants); + } + } +} diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/CountBasesInReference.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/CountBasesInReference.java new file mode 100644 index 00000000000..d532f7ef5be --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/CountBasesInReference.java @@ -0,0 +1,37 @@ +package org.broadinstitute.hellbender.tools.walkers.fasta; + +import com.google.common.annotations.VisibleForTesting; +import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; +import org.broadinstitute.barclay.help.DocumentedFeature; +import org.broadinstitute.hellbender.engine.FeatureContext; +import org.broadinstitute.hellbender.engine.ReadsContext; +import org.broadinstitute.hellbender.engine.ReferenceContext; +import org.broadinstitute.hellbender.engine.ReferenceWalker; +import picard.cmdline.programgroups.ReferenceProgramGroup; + +@DocumentedFeature +@CommandLineProgramProperties( + oneLineSummary = "Count the numbers of each base in a reference file", + summary = "Count the number of times each individual base occurs in a reference file.", + programGroup = ReferenceProgramGroup.class +) +public class CountBasesInReference extends ReferenceWalker { + @VisibleForTesting + final long[] baseCounts = new long[256]; + + @Override + public void apply(ReferenceContext referenceContext, ReadsContext read, FeatureContext featureContext) { + baseCounts[referenceContext.getBase()]++; + } + + @Override + public Object onTraversalSuccess(){ + for (int i = 0; i < baseCounts.length; i++) { + final long count = baseCounts[i]; + if (count > 0){ + System.out.println((char)i + " : " + count ); + } + } + return 0; + } +} diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker.java new file mode 100644 index 00000000000..2c3b38f0a9d --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker.java @@ -0,0 +1,262 @@ +package org.broadinstitute.hellbender.tools.walkers.fasta; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFHeader; +import org.broadinstitute.barclay.argparser.Argument; +import org.broadinstitute.barclay.argparser.CommandLineException; +import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; +import org.broadinstitute.barclay.help.DocumentedFeature; +import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; +import org.broadinstitute.hellbender.engine.FeatureContext; +import org.broadinstitute.hellbender.engine.FeatureInput; +import org.broadinstitute.hellbender.engine.ReadsContext; +import org.broadinstitute.hellbender.engine.ReferenceContext; +import org.broadinstitute.hellbender.exceptions.UserException; +import org.broadinstitute.hellbender.utils.BaseUtils; +import org.broadinstitute.hellbender.utils.SimpleInterval; +import org.broadinstitute.hellbender.utils.Utils; +import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; +import picard.cmdline.programgroups.ReferenceProgramGroup; + +import java.util.ArrayList; +import java.util.List; +import java.util.Optional; + + +/** + * Generate an alternative reference sequence over the specified interval + * + *

Given a variant callset, this tool replaces the reference bases at variation sites with the bases supplied in the + * corresponding callset records. Additionally, it allows for one or more "snp-mask" VCFs to set overlapping bases to 'N'.

+ * + *

The output format can be partially controlled using the provided command-line arguments. + * Specify intervals with the usual -L argument to output only the reference bases within your intervals. + * Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a + * separate fasta sequence (named numerically in order).

+ * + *

Caveats

+ *
    + *
  • If there are multiple variants that start at a site, it chooses one of them randomly.
    • + *
  • When there are overlapping indels (but with different start positions) only the first will be chosen.
    • + *
  • This tool works only for SNPs and for simple indels (but not for things like complex substitutions).
    • + *
+ + *

Input

+ *

+ * The reference, requested intervals, and any number of variant files. + *

+ * + *

Output

+ *

+ * A FASTA file representing the requested intervals. + *

+ * + *

Usage example

+ * 
+ * gatk FastaAlternateReferenceMaker \
+ *   -R reference.fasta \
+ *   -O output.fasta \
+ *   -L input.intervals \
+ *   -V input.vcf \
+ *
+ *   [--snp-mask mask.vcf]
+ *
+ * + */ +@DocumentedFeature +@CommandLineProgramProperties(summary = "Create an alternative fasta reference by inserting variants from a vcf into an existing reference sequence.", + oneLineSummary = "Create an alternative reference by combining a fasta with a vcf.", + programGroup = ReferenceProgramGroup.class) +public class FastaAlternateReferenceMaker extends FastaReferenceMaker { + + //Pre-allocated as a lame optimization + private static final byte[] NO_BASES = {}; + private static final byte[] N_BYTES = {'N'}; + private static final byte[] n_BYTES = {'n'}; + private static final byte[] A_BYTES = {'A'}; + private static final byte[] a_BYTES = {'a'}; + private static final byte[] G_BYTES = {'G'}; + private static final byte[] g_BYTES = {'g'}; + private static final byte[] C_BYTES = {'C'}; + private static final byte[] c_BYTES = {'c'}; + private static final byte[] T_BYTES = {'T'}; + private static final byte[] t_BYTES = {'t'}; + + private static final String EMPTY_BASE = " "; + + /** + * Variants from this input file are used by this tool to construct an alternate reference. + */ + @Argument(fullName= StandardArgumentDefinitions.VARIANT_LONG_NAME, + shortName = StandardArgumentDefinitions.VARIANT_SHORT_NAME, + doc="A source of variants to merge with the reference sequence.") + protected FeatureInput variants; + + public static final String SNP_MASK_LONG_NAME = "snp-mask"; + + /** + * SNPs from this file are used as a mask (inserting N's in the sequence) when constructing the alternate reference + */ + @Argument(fullName= SNP_MASK_LONG_NAME, doc="SNP mask VCF file", optional=true) + protected FeatureInput snpmask; + + public static final String SNP_MASK_PRIORITY_LONG_NAME = "snp-mask-priority"; + /** + * Gives priority to a SNP mask over an input VCF for a site. Only has an effect if the --snp-mask argument is used. + */ + @Argument(fullName= SNP_MASK_PRIORITY_LONG_NAME, doc="Give the snp mask priority over the input VCF.", optional=true) + protected boolean snpmaskPriority = false; + + public static final String USE_IUPAC_SAMPLE_LONG_NAME = "use-iupac-sample"; + /** + * This option will generate an error if the specified sample does not exist in the VCF. + * Non-diploid (or non-called) genotypes are ignored. + */ + @Argument(fullName= USE_IUPAC_SAMPLE_LONG_NAME, doc = "If specified, heterozygous SNP sites will be output using IUPAC ambiguity codes given the genotypes for this sample", optional=true) + private String iupacSample = null; + + private int deletionBasesRemaining = 0; + + @Override + public void onTraversalStart() { + super.onTraversalStart(); + + if (snpmaskPriority && snpmask == null){ + throw new CommandLineException("Cannot specify --" + SNP_MASK_PRIORITY_LONG_NAME + " without " + " --" + SNP_MASK_LONG_NAME); + } + + if ( iupacSample != null ) { + final VCFHeader variantHeader = (VCFHeader) getHeaderForFeatures(variants); + final ArrayList samples = variantHeader.getSampleNamesInOrder(); + if( samples == null || !samples.contains(iupacSample)) { + throw new UserException.BadInput("the IUPAC sample specified is not present in the provided VCF file"); + } + } + } + + @Override + public void apply(final ReferenceContext ref, final ReadsContext reads, final FeatureContext features) { + final byte[] bases = handlePosition(ref.getInterval(), ref.getBase(), features); + final SimpleInterval interval = ref.getInterval(); + if( bases.length == 0){ + advancePosition(interval); + } else { + for( byte base : bases) { + addToReference(interval, base); + } + } + } + + private byte[] handlePosition(SimpleInterval interval, byte base, FeatureContext features) { + if (deletionBasesRemaining > 0) { + deletionBasesRemaining--; + return NO_BASES; + } + + // If we have a mask at this site, use it + if ( snpmaskPriority ){ + if (isMasked(features) ) + return N_BYTES; + } + + // Check to see if we have a called snp + for ( final VariantContext vc : features.getValues(variants) ) { + if ( vc.isFiltered() || vc.getStart() != interval.getStart() ) + continue; + + if ( vc.isSimpleDeletion()) { + deletionBasesRemaining = vc.getReference().length() - 1; + // delete the next n bases, not this one + return baseToByteArray(base); + } else if ( vc.isSimpleInsertion() || vc.isSNP() ) { + // Get the first alt allele that is not a spanning deletion. If none present, use the empty allele + final Optional optionalAllele = getFirstConcreteAltAllele(vc.getAlternateAlleles()); + final Allele allele = optionalAllele.orElseGet(() -> Allele.create(EMPTY_BASE, false)); + if ( vc.isSimpleInsertion() ) { + return allele.getBases(); + } else { + final String iupacBase = (iupacSample != null) ? getIUPACBase(vc.getGenotype(iupacSample)) : allele.toString(); + return iupacBase.getBytes(); + } + } + } + + if ( !snpmaskPriority ){ + if ( isMasked(features)) { + return N_BYTES; + } + } + + // if we got here then we're just ref + return baseToByteArray(base); + } + + private byte[] baseToByteArray(byte base) { + switch(base) { + case 'A': return A_BYTES; + case 'a': return a_BYTES; + case 'C': return C_BYTES; + case 'c': return c_BYTES; + case 'G': return G_BYTES; + case 'g': return g_BYTES; + case 'T': return T_BYTES; + case 't': return t_BYTES; + case 'N': return N_BYTES; + case 'n': return n_BYTES; + default: return new byte[]{base}; + } + } + + /** + * Get the first non-symbolic, non-spanning deletion, called allele + * @param altAlleles the alternate alleles + * @return the first non spanning deletion allele or null + */ + private Optional getFirstConcreteAltAllele(final List altAlleles ) { + return altAlleles.stream() + .filter(allele -> !allele.isSymbolic()) + .filter(allele -> !GATKVCFConstants.isSpanningDeletion(allele)) + .filter(Allele::isCalled) + .findFirst(); + } + + /** + * Mask a SNP (inserting N's in the sequence) + * + * @param features the Reference Metadata available at a particular site in the genome + * @return mask at the locus or null if no SNP at that locus + */ + private boolean isMasked(final FeatureContext features){ + return features.getValues(snpmask).stream().anyMatch(VariantContext::isSNP); + } + + /** + * Returns the IUPAC encoding for the given genotype or the reference base if not possible + * + * @param genotype the genotype to encode + * @return non-null, non-empty String of bases + */ + private String getIUPACBase(final Genotype genotype) { + Utils.nonNull(genotype, () -> "The genotype is null for sample " + iupacSample); + + // If we have a spanning deletion, if both alleles are spanning deletions, use the empty allele. Otherwise, use the allele that is not a + // spanning deletion. + if ( genotype.getAlleles().contains(Allele.SPAN_DEL) ) { + if ( genotype.isHomVar() ) { + return EMPTY_BASE; + } else { + return genotype.getAllele(0).equals(Allele.SPAN_DEL) ? genotype.getAllele(1).getBaseString() : genotype.getAllele(0).getBaseString(); + } + } + + if ( !genotype.isHet() ) { + return genotype.getAllele(0).getBaseString(); + } + + final byte allele1 = genotype.getAllele(0).getBases()[0]; + final byte allele2 = genotype.getAllele(1).getBases()[0]; + return new String(new byte[] {BaseUtils.basesToIUPAC(allele1, allele2)}); + } +} \ No newline at end of file diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker.java new file mode 100644 index 00000000000..2ce549a3791 --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker.java @@ -0,0 +1,144 @@ +package org.broadinstitute.hellbender.tools.walkers.fasta; + +import com.google.common.primitives.Bytes; +import it.unimi.dsi.fastutil.bytes.ByteArrayList; +import org.broadinstitute.barclay.argparser.Argument; +import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; +import org.broadinstitute.barclay.help.DocumentedFeature; +import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; +import org.broadinstitute.hellbender.engine.FeatureContext; +import org.broadinstitute.hellbender.engine.ReadsContext; +import org.broadinstitute.hellbender.engine.ReferenceContext; +import org.broadinstitute.hellbender.engine.ReferenceWalker; +import org.broadinstitute.hellbender.exceptions.UserException; +import org.broadinstitute.hellbender.utils.SimpleInterval; +import org.broadinstitute.hellbender.utils.io.IOUtils; +import org.broadinstitute.hellbender.utils.reference.FastaReferenceWriter; +import picard.cmdline.programgroups.ReferenceProgramGroup; + +import java.io.IOException; +import java.nio.file.Path; + +/** + * Create a subset of a FASTA reference sequence + * + *

This tool creates a new reference in FASTA format consisting of only those positions or intervals + * provided in the input data set. The output format can be partially controlled using the provided command-line + * arguments. Specify intervals with the usual -L argument to output only the reference bases within your intervals. + * Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a + * separate fasta sequence (named numerically in order).

+ * + *

Input

+ *

+ * The reference and requested intervals. + *

+ * + *

Output

+ *

+ * A fasta file representing the requested intervals. Each interval has a description line starting with a greater-than (">") symbol followed by sequence data. + * The description begins with the contig name followed by the beginning position on the contig. + * 

+ * For example, the fasta file for contig 1 and intervals 1:3-1:4 and 1:6-1:9
+ * >1 1:3
+ * AT
+ * >1 1:6
+ * GGGG
+ *
+ *

+ * + *

Usage example

+ * 
+ * gatk FastaReferenceMaker \
+ *   -R reference.fasta \
+ *   -O output.fasta \
+ *   -L input.intervals
+ *
+ * + */ +@DocumentedFeature +@CommandLineProgramProperties( + summary = "Create snippets of a fasta file by subsetting to an interval list", + oneLineSummary = "Create snippets of a fasta file", + programGroup = ReferenceProgramGroup.class +) +public class FastaReferenceMaker extends ReferenceWalker { + + @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, + shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, + doc = "Path to write the output fasta to") + protected String output; + + public static final String LINE_WIDTH_LONG_NAME = "line-width"; + @Argument(fullName= LINE_WIDTH_LONG_NAME, doc="Maximum length of sequence to write per line", optional=true) + public int basesPerLine = FastaReferenceWriter.DEFAULT_BASES_PER_LINE; + + protected FastaReferenceWriter writer; + private int contigCount = 0; + private int currentSequenceStartPosition = 0; + private SimpleInterval lastPosition = null; + private ByteArrayList sequence = new ByteArrayList(10000); + + @Override + public void onTraversalStart() { + final Path path = IOUtils.getPath(output); + try { + writer = new FastaReferenceWriter(path, basesPerLine, true, true); + } catch (IOException e) { + throw new UserException.CouldNotCreateOutputFile("Couldn't create " + output + ", encountered exception: " + e.getMessage(), e); + } + } + + @Override + public void apply(ReferenceContext referenceContext, ReadsContext read, FeatureContext featureContext) { + addToReference(referenceContext.getInterval(), referenceContext.getBase()); + } + + protected void addToReference(SimpleInterval interval, byte base) { + advancePosition(interval); + sequence.add(base); + } + + protected void advancePosition(SimpleInterval interval) { + if(lastPosition == null ){ + initializeNewSequence(interval); + } else if ( !lastPosition.withinDistanceOf(interval, 1)) { + finalizeSequence(); + initializeNewSequence(interval); + } + lastPosition = interval; + } + + private void finalizeSequence() { + final String description = lastPosition.getContig() + ":" + currentSequenceStartPosition + "-" + lastPosition.getEnd(); + try { + writer.appendSequence(String.valueOf(contigCount), description, basesPerLine, Bytes.toArray(sequence)); + } catch (IOException e) { + throw new UserException.CouldNotCreateOutputFile("Failed while writing " + output + ".", e); + } + } + + private void initializeNewSequence(SimpleInterval interval) { + lastPosition = interval; + contigCount++; + currentSequenceStartPosition = lastPosition.getStart(); + sequence.clear(); + } + + @Override + public Object onTraversalSuccess(){ + finalizeSequence(); + return null; + } + + @Override + public void closeTool() { + super.closeTool(); + try{ + writer.close(); + } catch (IllegalStateException e){ + //sink this + } catch (IOException e) { + throw new UserException("Failed to write fasta due to " + e.getMessage(), e); + } + } +} \ No newline at end of file diff --git a/src/main/java/org/broadinstitute/hellbender/utils/BaseUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/BaseUtils.java index 4464afc9c33..ea9ab25a05d 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/BaseUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/BaseUtils.java @@ -285,4 +285,38 @@ public static byte getComplement(final byte base) { } return Integer.compare(o1.length, o2.length); }; + + /** + * Converts a pair of bases to their IUPAC ambiguity code + * + * @param base1 1st base + * @param base2 2nd base + * @return byte + */ + public static byte basesToIUPAC(final byte base1, final byte base2) { + // ensure that the bases come in order + if (base2 < base1) { + return basesToIUPAC(base2, base1); + + } + // ensure that the bases are regular ones + if (!isRegularBase(base1) || !isRegularBase(base2)) { + return Base.N.base; + } + + // IUPAC codes are not needed if the bases are identical + if (basesAreEqual(base1, base2)) { + return base1; + } + + if (base1 == Base.A.base) { + return (byte) (base2 == Base.C.base ? 'M' : (base2 == Base.G.base ? 'R' : 'W')); + } + + if (base1 == Base.C.base) { + return (byte) (base2 == Base.G.base ? 'S' : 'Y'); + } + // the only possibility left is G/T + return 'K'; + } } diff --git a/src/main/java/org/broadinstitute/hellbender/utils/SimpleInterval.java b/src/main/java/org/broadinstitute/hellbender/utils/SimpleInterval.java index cad25b71893..4d61fe05092 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/SimpleInterval.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/SimpleInterval.java @@ -4,8 +4,6 @@ import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; import htsjdk.samtools.util.Locatable; -import org.apache.logging.log4j.LogManager; -import org.apache.logging.log4j.Logger; import org.broadinstitute.hellbender.exceptions.GATKException; import org.broadinstitute.hellbender.exceptions.UserException; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/help/HelpConstants.java b/src/main/java/org/broadinstitute/hellbender/utils/help/HelpConstants.java index 95b2d5fa099..e552745a934 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/help/HelpConstants.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/help/HelpConstants.java @@ -3,9 +3,7 @@ import org.broadinstitute.hellbender.utils.Utils; import java.util.HashMap; -import java.util.HashSet; import java.util.Map; -import java.util.Set; public final class HelpConstants { diff --git a/src/main/java/org/broadinstitute/hellbender/utils/iterators/IntervalLocusIterator.java b/src/main/java/org/broadinstitute/hellbender/utils/iterators/IntervalLocusIterator.java index f4482798219..870ff5a7d8d 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/iterators/IntervalLocusIterator.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/iterators/IntervalLocusIterator.java @@ -1,11 +1,12 @@ package org.broadinstitute.hellbender.utils.iterators; -import org.broadinstitute.hellbender.utils.IntervalUtils; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.Utils; - -import java.util.*; +import java.util.Collections; +import java.util.Iterator; +import java.util.List; +import java.util.NoSuchElementException; /** * Returns a SimpleInterval for each locus in a set of intervals. I.e. returns each genomic point location in an interval list. diff --git a/src/main/java/org/broadinstitute/hellbender/utils/reference/FastaReferenceWriter.java b/src/main/java/org/broadinstitute/hellbender/utils/reference/FastaReferenceWriter.java index b81be29cf8f..146039c2d22 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/reference/FastaReferenceWriter.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/reference/FastaReferenceWriter.java @@ -10,11 +10,7 @@ import org.broadinstitute.hellbender.utils.param.ParamUtils; import org.codehaus.plexus.util.StringUtils; -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStream; -import java.io.OutputStreamWriter; -import java.io.Writer; +import java.io.*; import java.nio.charset.Charset; import java.nio.file.Files; import java.nio.file.Path; @@ -254,7 +250,7 @@ public FastaReferenceWriter(final Path fastaFile, final int basesPerLine, final // for the sake of avoiding creating output if basesPerLine is invalid. this.defaultBasePerLine = checkBasesPerLine(basesPerLine); - this.fastaStream = new CountingOutputStream(Files.newOutputStream(Utils.nonNull(fastaFile))); + this.fastaStream = new CountingOutputStream(new BufferedOutputStream(Files.newOutputStream(Utils.nonNull(fastaFile)))); this.indexWriter = indexFile == null ? new NullWriter() : new OutputStreamWriter(Files.newOutputStream(indexFile), CHARSET); final BufferedWriter dictWriter = new BufferedWriter(dictFile == null ? new NullWriter() : new OutputStreamWriter(Files.newOutputStream(dictFile), CHARSET)); this.dictWriter = dictWriter; @@ -509,7 +505,7 @@ private void closeSequence() { if (currentSequenceName != null) { if (currentBasesCount == 0) { - throw new IllegalStateException("no base was added"); + throw new IllegalStateException("startSequence was called but no base was added"); } sequenceNamesAndSizes.put(currentSequenceName, currentBasesCount); writeIndexEntry(); @@ -681,18 +677,22 @@ private void assertIsNotClosed() { *

* * @throws IOException if such exception is thrown when closing output writers and output streams. + * @throws IllegalStateException if closing without writing any sequences or closing when writing a sequence is in progress */ public void close() throws IOException { if (!closed) { - closeSequence(); - if (sequenceNamesAndSizes.isEmpty()) { - throw new IllegalStateException("no sequences where added to the reference"); + try { + closeSequence(); + if (sequenceNamesAndSizes.isEmpty()) { + throw new IllegalStateException("no sequences where added to the reference"); + } + } finally { + closed = true; + fastaStream.close(); + indexWriter.close(); + dictWriter.close(); } - fastaStream.close(); - indexWriter.close(); - dictWriter.close(); - closed = true; } } diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalkerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalkerIntegrationTest.java new file mode 100644 index 00000000000..16746bc3599 --- /dev/null +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalkerIntegrationTest.java @@ -0,0 +1,36 @@ +package org.broadinstitute.hellbender.tools.examples; + +import org.broadinstitute.hellbender.CommandLineProgramTest; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.testng.Assert; +import org.testng.annotations.Test; + +import java.util.Map; + +public class ExampleReferenceWalkerIntegrationTest extends CommandLineProgramTest { + + @Test + public void testExampleReferenceWalker(){ + final ArgumentsBuilder args = new ArgumentsBuilder(); + args.addReference( getTestFile(("example.fasta"))); + args.addInput(getTestFile("veryspecific.bam")); + args.addVCF(getTestFile("example.vcf")); + + final ExampleReferenceWalker exampleReferenceWalker = new ExampleReferenceWalker(); + exampleReferenceWalker.instanceMain(args.getArgsArray()); + + final Map contextCounts = exampleReferenceWalker.contextCounts; + final ExampleReferenceWalker.OverlapCounts aaaCounts = contextCounts.get("AAA"); + final ExampleReferenceWalker.OverlapCounts nnnCounts = contextCounts.get("NNN"); + final ExampleReferenceWalker.OverlapCounts aacCounts = contextCounts.get("AAC"); + assertCountsEqual(aaaCounts, 78, 9, 3 ); + assertCountsEqual(nnnCounts, 78, 1, 0); + assertCountsEqual(aacCounts, 1, 0, 1); + } + + private static void assertCountsEqual(ExampleReferenceWalker.OverlapCounts counts, long seen, long reads, long variants){ + Assert.assertEquals(counts.timesSeen, seen); + Assert.assertEquals(counts.overlappedByReads, reads); + Assert.assertEquals(counts.overlappedByVariants, variants); + } +} diff --git a/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java index 95312cdbb0d..3743000dc1f 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java @@ -16,14 +16,13 @@ import org.broadinstitute.hellbender.Main; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.IntervalUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.BaseTest; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.gcs.BucketUtils; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; -import org.broadinstitute.hellbender.testutils.BaseTest; -import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; import org.genomicsdb.GenomicsDBUtils; @@ -36,7 +35,9 @@ import java.io.File; import java.io.IOException; -import java.nio.file.*; +import java.nio.file.Files; +import java.nio.file.Paths; +import java.nio.file.StandardCopyOption; import java.util.*; import java.util.stream.Collectors; @@ -286,7 +287,7 @@ private File runCombineGVCFs(final List inputs, final List args.addArgument("L", interval.toString())); + intervals.forEach(args::addInterval); Arrays.stream(extraArgs).forEach(args::add); Utils.resetRandomGenerator(); @@ -451,7 +452,7 @@ private void writeToGenomicsDB(final List vcfInputs, final List args.addArgument("L", IntervalUtils.locatableToString(interval))); + intervals.forEach(args::addInterval); vcfInputs.forEach(vcf -> args.addArgument("V", vcf)); args.addArgument("batch-size", String.valueOf(batchSize)); args.addArgument(GenomicsDBImport.VCF_INITIALIZER_THREADS_LONG_NAME, String.valueOf(threads)); @@ -581,7 +582,7 @@ public void testSampleNameWithSpaces() throws IOException { ArgumentsBuilder args = new ArgumentsBuilder() .addArgument(GenomicsDBImport.BATCHSIZE_ARG_LONG_NAME, String.valueOf(2)) .addFileArgument(GenomicsDBImport.SAMPLE_NAME_MAP_LONG_NAME, outOfOrderSampleMap) - .addArgument("L", IntervalUtils.locatableToString(SMALLER_INTERVAL.get(0))) + .addInterval(SMALLER_INTERVAL.get(0)) .addArgument(GenomicsDBImport.WORKSPACE_ARG_LONG_NAME, workspace); runCommandLine(args); @@ -593,7 +594,7 @@ public void testSampleNameWithSpaces() throws IOException { public void testSampleNameOrdering(final ArgumentsBuilder args) throws IOException { final String workspace = createTempDir("gendbtest").getAbsolutePath() + "/workspace"; - args.addArgument("L", IntervalUtils.locatableToString(INTERVAL.get(0))) + args.addInterval(INTERVAL.get(0)) .addArgument(GenomicsDBImport.WORKSPACE_ARG_LONG_NAME, workspace); runCommandLine(args); @@ -685,7 +686,7 @@ public void testRenamingSamples(final Map renamingMap, final int .addArgument(GenomicsDBImport.WORKSPACE_ARG_LONG_NAME, new File(workspace).getAbsolutePath()) .addArgument(GenomicsDBImport.VCF_INITIALIZER_THREADS_LONG_NAME, String.valueOf(threads)) .addArgument(GenomicsDBImport.BATCHSIZE_ARG_LONG_NAME, String.valueOf(batchSize)) - .addArgument("L", IntervalUtils.locatableToString(INTERVAL.get(0))); + .addInterval(INTERVAL.get(0)); runCommandLine(args); final Set expectedSampleNames = sampleMap.keySet(); @@ -741,7 +742,7 @@ public void testCantSpecifyVCFAndSampleNameFile(){ .addArgument(GenomicsDBImport.SAMPLE_NAME_MAP_LONG_NAME, createInOrderSampleMap().getAbsolutePath()) .addArgument(StandardArgumentDefinitions.VARIANT_LONG_NAME, HG_00096) .addArgument(GenomicsDBImport.WORKSPACE_ARG_LONG_NAME, createTempDir("workspace").getAbsolutePath()) - .addArgument("L", IntervalUtils.locatableToString(INTERVAL.get(0))); + .addInterval(INTERVAL.get(0)); runCommandLine(args); } diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/CountBasesInReferenceIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/CountBasesInReferenceIntegrationTest.java new file mode 100644 index 00000000000..feb75b44893 --- /dev/null +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/CountBasesInReferenceIntegrationTest.java @@ -0,0 +1,38 @@ +package org.broadinstitute.hellbender.tools.walkers.fasta; + +import org.broadinstitute.hellbender.CommandLineProgramTest; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.testng.Assert; +import org.testng.annotations.Test; + +import java.io.File; + +public class CountBasesInReferenceIntegrationTest extends CommandLineProgramTest { + + @Test + public void testCountBasesInReferenceWithInterval(){ + final ArgumentsBuilder args = new ArgumentsBuilder(); + args.addReference(new File(hg19MiniReference)) + .addArgument("L", "1:5000-6000"); + final CountBasesInReference walker = new CountBasesInReference(); + walker.instanceMain(args.getArgsArray()); + final long[] baseCounts = walker.baseCounts; + + Assert.assertEquals(baseCounts['N'], 1001L); + } + + @Test + public void testCountBasesInReferenceFull(){ + final ArgumentsBuilder args = new ArgumentsBuilder(); + args.addReference(new File(hg19MiniReference)); + final CountBasesInReference walker = new CountBasesInReference(); + walker.instanceMain(args.getArgsArray()); + final long[] baseCounts = walker.baseCounts; + + Assert.assertEquals(baseCounts['A'], 4546); + Assert.assertEquals(baseCounts['C'], 4995); + Assert.assertEquals(baseCounts['G'], 4559); + Assert.assertEquals(baseCounts['T'], 3900); + Assert.assertEquals(baseCounts['N'], 46000); + } +} \ No newline at end of file diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMakerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMakerIntegrationTest.java new file mode 100644 index 00000000000..7fdcfbaeb15 --- /dev/null +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMakerIntegrationTest.java @@ -0,0 +1,155 @@ +package org.broadinstitute.hellbender.tools.walkers.fasta; + +import org.broadinstitute.hellbender.CommandLineProgramTest; +import org.broadinstitute.hellbender.exceptions.UserException; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.FastaTestUtils; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.io.File; + +public class FastaAlternateReferenceMakerIntegrationTest extends CommandLineProgramTest { + private final File spanningDelTestFile = getTestFile("spanningDel.delOnly.starFirst.vcf"); + private final File iupacTestFile = getTestFile("NA12878.WGS.b37.chr20.firstMB.vcf.gz"); + private final File snp1 = getTestFile("snps.vcf"); + private final File snp2 = getTestFile("snps2.vcf"); + private final File snpsAndIndels = getTestFile("snpsAndIndels.vcf"); + private final File overlapsIndels = getTestFile("overlapsIndelsMask.vcf"); + + @Test + public void testAlternateReferenceContiguousSameContig() { + // Show that FastaAlternateReferenceMaker behaves the same as FastaReferenceMaker across contiguous intervals on the same contig. + // Note that there are variant locations in this interval. + ArgumentsBuilder args = new ArgumentsBuilder(); + final File out = createTempFile("test", "fasta"); + args.addVCF(getTestFile("NA12878.chr1_10mb_11mb.slx.indels.vcf")) + .addReference(new File(b37Reference)) + .addArgument("L", "1:10,000,100-10,000,200") + .addArgument("L", "1:10,000,201-10,000,301") + .addOutput(out); + runCommandLine(args); + FastaTestUtils.assertFastaFilesContainTheSameSequence(out.toPath(), getTestFile("expected_alternate_reference_contiguous_same_contig.fasta").toPath()); + } + + @Test + public void testAlternateReferenceContiguousDiffContigs() { + // Show that FastaAlternateReferenceMaker behaves the same as FastaReferenceMaker across contiguous intervals on different contigs. + // Note that there are variant locations in this interval. + ArgumentsBuilder args = new ArgumentsBuilder(); + final File out = createTempFile("test", "fasta"); + args.addVCF(getTestFile("NA12878.chr1_10mb_11mb.slx.indels.vcf")) + .addReference(new File(b37Reference)) + .addArgument("L", "1:10,000,100-10,000,200") + .addArgument("L", "2:10,000,201-10,000,301") + .addOutput(out); + runCommandLine(args); + FastaTestUtils.assertFastaFilesContainTheSameSequence(out.toPath(), getTestFile("expected_alternate_reference_contiguous_diff_contig.fasta").toPath()); + } + + @DataProvider + public Object[][] getSnpMaskVariants(){ + return new Object[][]{ + {snp1, snp2, getTestFile("expected_snp1_mask2.fasta"), false}, + {snp1, snp2, getTestFile("expected_snp1_mask2_priority.fasta"), true}, + {snp2, snp1, getTestFile("expected_snp2_mask1.fasta"), false}, + {snp2, snp1, getTestFile("expected_snp2_mask1_priority.fasta"), true}, + {snpsAndIndels, snp1, getTestFile("expected_snpsAndIndels_mask1.fasta"), false}, + {snpsAndIndels, snp1, getTestFile("expected_snpsAndIndels_mask1_priority.fasta"), true}, + {snpsAndIndels, overlapsIndels, getTestFile("expected_snpsAndIndels_maskOverlaps.fasta"), false}, + {snpsAndIndels, overlapsIndels, getTestFile("expected_snpsAndIndels_maskOverlaps_priority.fasta"), true}, + }; + } + + @Test(dataProvider = "getSnpMaskVariants") + public void testSnpMask(File vcf, File mask, File expected, boolean priority) { + ArgumentsBuilder args = new ArgumentsBuilder(); + final File out = createTempFile("test", "fasta"); + args.addVCF(vcf) + .addReference(new File(b37Reference)) + .addFileArgument(FastaAlternateReferenceMaker.SNP_MASK_LONG_NAME, mask) + .addArgument("L", "1:10,000,000-10,000,100") + .addBooleanArgument(FastaAlternateReferenceMaker.SNP_MASK_PRIORITY_LONG_NAME, priority) + .addOutput(out); + runCommandLine(args); + FastaTestUtils.assertFastaFilesContainTheSameSequence(out.toPath(), expected.toPath()); + } + + @DataProvider + public Object[][] noMask() { + return new Object[][]{ + {snp1, getTestFile("expected_snp1.fasta")}, + {snp2, getTestFile("expected_snp2.fasta")}, + }; + } + + @Test(dataProvider = "noMask") + public void testNoMask(File vcf, File expected) { + ArgumentsBuilder args = new ArgumentsBuilder(); + final File out = createTempFile("test", "fasta"); + args.addVCF(vcf) + .addReference(new File(b37Reference)) + .addArgument("L", "1:10,000,000-10,000,100") + .addOutput(out); + runCommandLine(args); + FastaTestUtils.assertFastaFilesContainTheSameSequence(out.toPath(), expected.toPath()); + } + + @Test(expectedExceptions = UserException.BadInput.class) + public void testBadIupacInput() { + ArgumentsBuilder args = new ArgumentsBuilder(); + args.addVCF(iupacTestFile) + .addOutput( createTempFile("alternate", "fasta")) + .addReference(new File(b37Reference)) + .addArgument(FastaAlternateReferenceMaker.USE_IUPAC_SAMPLE_LONG_NAME, "SAMPLE_DOESNT_EXIST"); + runCommandLine(args); + } + + @Test + public void testIupac() { + final File out = createTempFile("alternate", "fasta"); + ArgumentsBuilder args = new ArgumentsBuilder(); + args.addVCF(iupacTestFile) + .addOutput(out) + .addReference(new File(b37Reference)) + .addArgument(FastaAlternateReferenceMaker.USE_IUPAC_SAMPLE_LONG_NAME, "NA12878") + .addArgument("L", "20:61050-66380"); + + runCommandLine(args); + FastaTestUtils.assertFastaFilesContainTheSameSequence(out.toPath(), getTestFile("expected_test_iupac.fasta").toPath()); + } + + @Test + void testSpanDel() { + final File out = createTempFile("alternate", "fasta"); + ArgumentsBuilder args = new ArgumentsBuilder(); + args.addVCF(spanningDelTestFile) + .addOutput(out) + .addReference(new File(b37Reference)) + .addArgument("L", "1:1273247"); + runCommandLine(args); + FastaTestUtils.assertFastaFilesContainTheSameSequence(out.toPath(), getTestFile("iupac_sample_NA3.fasta").toPath()); + } + + @DataProvider(name = "iupacSample") + public Object[][] getIupacSampleData() { + return new Object[][]{ + {"NA1", getTestFile("iupac_sample_NA1.fasta")}, + // {"NA2", getTestFile("iupac_sample_NA2.fasta")}, this test disabled because gatk4 won't write a fasta with an empty reference sequence + {"NA3", getTestFile("iupac_sample_NA3.fasta")} + }; + } + + @Test(dataProvider = "iupacSample") + void testSpanDelIUPAC(final String sample, final File expected) { + final ArgumentsBuilder args = new ArgumentsBuilder(); + final File out = createTempFile("alternate", "fasta"); + args.addVCF(spanningDelTestFile) + .addOutput(out) + .addReference(new File(b37Reference)) + .addArgument("L", "1:1273247") + .addArgument("use-iupac-sample", sample); + runCommandLine(args); + FastaTestUtils.assertFastaFilesContainTheSameSequence(out.toPath(), expected.toPath()); + } +} \ No newline at end of file diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMakerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMakerIntegrationTest.java new file mode 100644 index 00000000000..f7bb2b436ae --- /dev/null +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMakerIntegrationTest.java @@ -0,0 +1,69 @@ +package org.broadinstitute.hellbender.tools.walkers.fasta; + +import org.broadinstitute.hellbender.CommandLineProgramTest; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.BaseTest; +import org.broadinstitute.hellbender.testutils.FastaTestUtils; +import org.testng.Assert; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.util.Arrays; +import java.util.List; + +public class FastaReferenceMakerIntegrationTest extends CommandLineProgramTest { + + @DataProvider + public Object[][] getFastaParameters(){ + return new Object[][]{ + {Arrays.asList("1:10,000,100-10,000,500", "1:10,100,000-10,101,000", "1:10,900,000-10,900,001"), getTestFile("reference_only.fasta")}, + {Arrays.asList("1:10,000,100-10,000,200", "1:10,000,201-10,000,301"), getTestFile("reference_only_contiguous_same_contig.fasta")}, + {Arrays.asList("1:10,000,100-10,000,200", "2:10,000,201-10,000,301"), getTestFile("reference_only_contiguous_diff_contigs.fasta")} + }; + } + + @Test(dataProvider = "getFastaParameters") + public void runMakeFastaTest(List intervals, File expected) throws IOException { + ArgumentsBuilder args = new ArgumentsBuilder(); + final File out = BaseTest.createTempFile("subset", ".fasta"); + args.addReference(new File(b37Reference)) + .addOutput(out); + intervals.forEach(interval -> args.addArgument("L", interval)); + runCommandLine(args); + + FastaTestUtils.assertFastaFilesContainTheSameSequence(out.toPath(), expected.toPath()); + } + + + @DataProvider + public Object[][] getBasesPerLine(){ + return new Object[][]{ + {13}, {60}, {100} + }; + } + + @Test(dataProvider = "getBasesPerLine") + public void testBasePerLine(int basesPerLine) throws IOException { + ArgumentsBuilder args = new ArgumentsBuilder(); + final File out = BaseTest.createTempFile("subset", ".fasta"); + final File hg19mini = new File(hg19MiniReference); + args.addReference(hg19mini) + .addOutput(out) + .addArgument(FastaReferenceMaker.LINE_WIDTH_LONG_NAME, String.valueOf(basesPerLine)); + + runCommandLine(args); + + FastaTestUtils.assertFastaFilesContainTheSameSequence(out.toPath(), hg19mini.toPath()); + final List lines = Files.readAllLines(out.toPath()); + for(int i = 0; i < lines.size(); i++){ + String line = lines.get(i); + if(!line.startsWith(">")){ + Assert.assertTrue(line.length() == basesPerLine || i == lines.size()-1 || lines.get(i+1).startsWith(">")); + } + } + + } +} \ No newline at end of file diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java index 9cc4d922b2f..2465790ef1e 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java @@ -5,8 +5,6 @@ import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.engine.FeatureDataSource; -import org.broadinstitute.hellbender.utils.IntervalUtils; -import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.testutils.CommandLineProgramTester; import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; @@ -49,7 +47,7 @@ public void testGVCFReblockingIsContiguous() throws Exception { final ArgumentsBuilder args2 = new ArgumentsBuilder(); args2.addArgument("R", b37_reference_20_21); args2.addArgument("V", output.getAbsolutePath()); - args2.addArgument("L", IntervalUtils.locatableToString(new SimpleInterval("20:60001-1000000"))); + args2.addArgument("L", "20:60001-1000000"); args2.add("-gvcf"); validator.runCommandLine(args2); //will throw a UserException if GVCF isn't contiguous diff --git a/src/test/java/org/broadinstitute/hellbender/utils/BaseUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/BaseUtilsUnitTest.java index 80280a204d3..1decd368e3d 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/BaseUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/BaseUtilsUnitTest.java @@ -165,4 +165,33 @@ public Object[][] baseComparatorData() { } return result; } + + @Test + public void testConvertBasesToIUPAC() { + for ( final BaseUtils.Base b : BaseUtils.Base.values() ) { + if ( BaseUtils.isRegularBase(b.base) ) { + Assert.assertEquals(BaseUtils.basesToIUPAC(b.base, b.base), b.base, "testing same base"); + } + } + + Assert.assertEquals(BaseUtils.basesToIUPAC((byte)'X', (byte)'X'), 'N', "testing non-standard base"); + testIUPACBaseBothDirections('A', 'X' , 'N'); + + Assert.assertEquals(BaseUtils.basesToIUPAC((byte) 'T', (byte) 'T'), 'T', "testing same base"); + + testIUPACBaseBothDirections('A', 'C', 'M'); + testIUPACBaseBothDirections('A', 'T', 'W'); + testIUPACBaseBothDirections('A', 'G', 'R'); + testIUPACBaseBothDirections('C', 'G', 'S'); + testIUPACBaseBothDirections('C', 'T', 'Y'); + testIUPACBaseBothDirections('G', 'T', 'K'); + + } + + protected void testIUPACBaseBothDirections(char base1, char base2, char expected) { + byte base1Byte = (byte) base1; + byte base2Byte = (byte) base2; + Assert.assertEquals(BaseUtils.basesToIUPAC(base1Byte, base2Byte), expected, "testing " + base1 + "/" + base2 + "==" + expected); + Assert.assertEquals(BaseUtils.basesToIUPAC(base2Byte, base1Byte), expected, "testing " + base2 + "/" + base1 + "==" + expected); + } } diff --git a/src/test/java/org/broadinstitute/hellbender/utils/reference/FastaReferenceWriterUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/reference/FastaReferenceWriterUnitTest.java index 064dd6f4c8b..ffe7f7c30cc 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/reference/FastaReferenceWriterUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/reference/FastaReferenceWriterUnitTest.java @@ -15,12 +15,7 @@ import org.testng.annotations.DataProvider; import org.testng.annotations.Test; -import java.io.BufferedReader; -import java.io.File; -import java.io.FileOutputStream; -import java.io.IOException; -import java.io.InputStreamReader; -import java.io.OutputStream; +import java.io.*; import java.net.URISyntaxException; import java.nio.file.Path; import java.security.GeneralSecurityException; @@ -40,6 +35,69 @@ */ public class FastaReferenceWriterUnitTest extends GATKBaseTest { + public static void assertOutput(final Path path, final boolean mustHaveIndex, final boolean mustHaveDictionary, + final boolean withDescriptions, final SAMSequenceDictionary dictionary, final int defaultBpl, + final Map bases, final Map basesPerLine) + throws IOException { + assertFastaContent(path, withDescriptions, dictionary, defaultBpl, bases, basesPerLine); + if (mustHaveDictionary) { + assertFastaDictionaryContent(ReferenceSequenceFileFactory.getDefaultDictionaryForReferenceSequence(path), dictionary); + } + if (mustHaveIndex) { + assertFastaIndexContent(path, ReferenceSequenceFileFactory.getFastaIndexFileName(path), dictionary, bases); + } + } + + public static void assertFastaContent(final Path path, final boolean withDescriptions, final SAMSequenceDictionary dictionary, final int defaultBpl, + final Map bases, final Map basesPerLine) + throws IOException { + try (final BufferedReader reader = new BufferedReader(new InputStreamReader(path.getFileSystem().provider().newInputStream(path)))) { + for (final SAMSequenceRecord sequence : dictionary.getSequences()) { + final String description = String.format("index=%d\tlength=%d", + dictionary.getSequenceIndex(sequence.getSequenceName()), sequence.getSequenceLength()); + final String expectedHeader = FastaReferenceWriter.HEADER_START_CHAR + sequence.getSequenceName() + + ((withDescriptions) ? FastaReferenceWriter.HEADER_NAME_AND_DESCRIPTION_SEPARATOR + description : ""); + Assert.assertTrue(reader.readLine().startsWith(expectedHeader)); + final byte[] expectedBases = bases.get(sequence.getSequenceName()); + final int bpl_ = basesPerLine.get(sequence.getSequenceName()); + final int bpl = bpl_ < 0 ? (defaultBpl < 0 ? FastaReferenceWriter.DEFAULT_BASES_PER_LINE : defaultBpl) : bpl_; + int offset = 0; + while (offset < expectedBases.length) { + final int expectedLength = Math.min(expectedBases.length - offset, bpl); + final byte[] expectedBaseLine = SequenceUtil.upperCase( + Arrays.copyOfRange(expectedBases, offset, offset + expectedLength)); + final byte[] actualBaseLine = SequenceUtil.upperCase(reader.readLine().getBytes()); + Assert.assertEquals(actualBaseLine, expectedBaseLine); + offset += expectedLength; + } + } + } + } + + public static void assertFastaIndexContent(final Path path, final Path indexPath, final SAMSequenceDictionary dictionary, + final Map bases) { + final FastaSequenceIndex index = new FastaSequenceIndex(indexPath); + final IndexedFastaSequenceFile indexedFasta = new IndexedFastaSequenceFile(path, index); + for (final SAMSequenceRecord sequence : dictionary.getSequences()) { + final String name = sequence.getSequenceName(); + final int length = sequence.getSequenceLength(); + final ReferenceSequence start = indexedFasta.getSubsequenceAt(name, 1, Math.min(length, 30)); + final ReferenceSequence end = indexedFasta.getSubsequenceAt(name, Math.max(1, length - 29), length); + final int middlePos = Math.max(1, Math.min(length, length / 2)); + final ReferenceSequence middle = indexedFasta.getSubsequenceAt(name, middlePos, Math.min(middlePos + 29, length)); + Assert.assertEquals(start.getBases(), Arrays.copyOfRange(bases.get(name), 0, start.length())); + Assert.assertEquals(end.getBases(), Arrays.copyOfRange(bases.get(name), Math.max(0, length - 30), length)); + Assert.assertEquals(middle.getBases(), Arrays.copyOfRange(bases.get(name), middlePos - 1, middlePos - 1 + middle.length())); + } + } + + public static void assertFastaDictionaryContent(final Path dictPath, final SAMSequenceDictionary dictionary) { + final ReadsDataSource readsDataSource = new ReadsDataSource(dictPath); + final SAMFileHeader actualHeader = readsDataSource.getHeader(); + final SAMSequenceDictionary actualDictionary = actualHeader.getSequenceDictionary(); + dictionary.assertSameDictionary(actualDictionary); + } + @Test(expectedExceptions = IllegalStateException.class) public void testEmptySequence() throws IOException { final File testOutput = createTempFile("fwr-test", ".fasta"); @@ -218,7 +276,7 @@ public Object[][] invalidDescriptionData() { public void testWriter(final SAMSequenceDictionary dictionary, final boolean withIndex, final boolean withDictionary, final boolean withDescriptions, final int defaultBpl, final int minBpl, final int maxBpl, final int seed) - throws IOException, GeneralSecurityException, URISyntaxException { + throws IOException { final Map bases = new LinkedHashMap<>(dictionary.getSequences().size()); final Map bpl = new LinkedHashMap<>(dictionary.getSequences().size()); final Random rdn = new Random(seed); @@ -337,7 +395,7 @@ private void generateRandomBasesAndBpls(SAMSequenceDictionary dictionary, int mi - private void writeReference(final FastaReferenceWriter writer, final boolean withDescriptions, + private static void writeReference(final FastaReferenceWriter writer, final boolean withDescriptions, final Random rdn, final SAMSequenceDictionary dictionary, final Map seqs, final Map basesPerLine) @@ -404,71 +462,6 @@ private void writeReference(final FastaReferenceWriter writer, final boolean wit } } - private void assertOutput(final Path path, final boolean mustHaveIndex, final boolean mustHaveDictionary, - final boolean withDescriptions, final SAMSequenceDictionary dictionary, final int defaultBpl, - final Map bases, final Map basesPerLine) - throws GeneralSecurityException, IOException, URISyntaxException { - assertFastaContent(path, withDescriptions, dictionary, defaultBpl, bases, basesPerLine); - if (mustHaveDictionary) { - assertFastaDictionaryContent(ReferenceSequenceFileFactory.getDefaultDictionaryForReferenceSequence(path), dictionary); - } - if (mustHaveIndex) { - assertFastaIndexContent(path, ReferenceSequenceFileFactory.getFastaIndexFileName(path), dictionary, bases); - } - } - - private void assertFastaContent(final Path path, final boolean withDescriptions, final SAMSequenceDictionary dictionary, final int defaultBpl, - final Map bases, final Map basesPerLine) - throws IOException { - try (final BufferedReader reader = new BufferedReader(new InputStreamReader(path.getFileSystem().provider().newInputStream(path)))) { - for (final SAMSequenceRecord sequence : dictionary.getSequences()) { - final String description = String.format("index=%d\tlength=%d", - dictionary.getSequenceIndex(sequence.getSequenceName()), sequence.getSequenceLength()); - final String expectedHeader = - FastaReferenceWriter.HEADER_START_CHAR + sequence.getSequenceName() - + ((withDescriptions) ? FastaReferenceWriter.HEADER_NAME_AND_DESCRIPTION_SEPARATOR + description : ""); - Assert.assertEquals(reader.readLine(), expectedHeader); - final byte[] expectedBases = bases.get(sequence.getSequenceName()); - final int bpl_ = basesPerLine.get(sequence.getSequenceName()); - final int bpl = bpl_ < 0 ? (defaultBpl < 0 ? FastaReferenceWriter.DEFAULT_BASES_PER_LINE : defaultBpl) : bpl_; - int offset = 0; - while (offset < expectedBases.length) { - final int expectedLength = Math.min(expectedBases.length - offset, bpl); - final byte[] expectedBaseLine = SequenceUtil.upperCase(Arrays.copyOfRange(expectedBases, offset, offset + expectedLength)); - final byte[] actualBaseLine = SequenceUtil.upperCase(reader.readLine().getBytes()); - Assert.assertEquals(actualBaseLine, expectedBaseLine); - offset += expectedLength; - } - } - } - } - - private void assertFastaIndexContent(final Path path, final Path indexPath, final SAMSequenceDictionary dictionary, - final Map bases) - throws IOException { - final FastaSequenceIndex index = new FastaSequenceIndex(indexPath); - final IndexedFastaSequenceFile indexedFasta = new IndexedFastaSequenceFile(path, index); - for (final SAMSequenceRecord sequence : dictionary.getSequences()) { - final String name = sequence.getSequenceName(); - final int length = sequence.getSequenceLength(); - final ReferenceSequence start = indexedFasta.getSubsequenceAt(name, 1, Math.min(length, 30)); - final ReferenceSequence end = indexedFasta.getSubsequenceAt(name, Math.max(1, length - 29), length); - final int middlePos = Math.max(1, Math.min(length, length / 2)); - final ReferenceSequence middle = indexedFasta.getSubsequenceAt(name, middlePos, Math.min(middlePos + 29, length)); - Assert.assertEquals(start.getBases(), Arrays.copyOfRange(bases.get(name), 0, start.length())); - Assert.assertEquals(end.getBases(), Arrays.copyOfRange(bases.get(name), Math.max(0, length - 30), length)); - Assert.assertEquals(middle.getBases(), Arrays.copyOfRange(bases.get(name), middlePos - 1, middlePos - 1 + middle.length())); - } - } - - private void assertFastaDictionaryContent(final Path dictPath, final SAMSequenceDictionary dictionary) - throws IOException, GeneralSecurityException, URISyntaxException { - final ReadsDataSource readsDataSource = new ReadsDataSource(dictPath); - final SAMFileHeader actualHeader = readsDataSource.getHeader(); - final SAMSequenceDictionary actualDictionary = actualHeader.getSequenceDictionary(); - dictionary.assertSameDictionary(actualDictionary); - } - @DataProvider(name = "testData") public Object[][] testData() { // data-signature: (SAMSequenceDictionary dictionary, boolean withDescriptions, int defaultBpl, int minBpl, int maxBpl, int seed diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.dict b/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.dict new file mode 100644 index 00000000000..dcec775543f --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.dict @@ -0,0 +1,2 @@ +@HD VN:1.6 +@SQ SN:1 LN:400 M5:f9f1dd3e58bd7fb781819cf22639251e UR:file:/Users/louisb/Workspace/gatk/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.fasta new file mode 100644 index 00000000000..8434b8826af --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.fasta @@ -0,0 +1,6 @@ +>1 very short reference +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT \ No newline at end of file diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.fasta.fai new file mode 100644 index 00000000000..f03689c440e --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.fasta.fai @@ -0,0 +1 @@ +1 400 24 80 81 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.vcf new file mode 100644 index 00000000000..0e654b54b5d --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.vcf @@ -0,0 +1,26 @@ +##fileformat=VCFv4.2 +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +1 84 . 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a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1.fasta new file mode 100644 index 00000000000..bcf491f98f2 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1.fasta @@ -0,0 +1,3 @@ +>1 1:10000000 +AACCCCATCTCTACAATAAATGAAAATATTAGCTGGGCATTGTGGTGTGTGCTTGTAGTC +CCAGCTACTTGGCGGGCTGAGGTGGGAGAATCATCCAAGCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1.fasta.fai new file mode 100644 index 00000000000..33f57fd5d73 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1.fasta.fai @@ -0,0 +1 @@ +1 101 14 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2.dict new file mode 100644 index 00000000000..831ca1fcc32 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:101 M5:0c62618ad31bc3745ab01e59073a2145 UR:file:/Users/louisb/Workspace/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2.fasta new file mode 100644 index 00000000000..c71a9576c86 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2.fasta @@ -0,0 +1,3 @@ +>1 1:10000000 +AACCCCATCTCTACAATAAATGAAAATATTAGCTGGGCATTGTGGTGTGTGCTTGTAGTC +CCAGCTACTTGGCGGGNTGAGGTGGGAGAATCATCCAAGCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2.fasta.fai new file mode 100644 index 00000000000..33f57fd5d73 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2.fasta.fai @@ -0,0 +1 @@ +1 101 14 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2_priority.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2_priority.dict new file mode 100644 index 00000000000..98788bc7b2d --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2_priority.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:101 M5:facb25ff6a96440373bf5428abe616a1 UR:file:/Users/louisb/Workspace/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2_priority.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2_priority.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2_priority.fasta new file mode 100644 index 00000000000..33286c1f1ec --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2_priority.fasta @@ -0,0 +1,3 @@ +>1 1:10000000 +AACCCCNTCTCTACAATAAATGAAAATATTAGCTGGGCATNGTGGTGTGTGCTTGTAGTC +CCAGCTACTTGGCGGGNTGAGGTGGGAGAATCATCCAAGCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2_priority.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2_priority.fasta.fai new file mode 100644 index 00000000000..33f57fd5d73 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp1_mask2_priority.fasta.fai @@ -0,0 +1 @@ +1 101 14 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2.dict new file mode 100644 index 00000000000..c38b58977bc --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:101 M5:673f1f9474cd09efedebc64b6644c78f UR:file:/Users/louisb/Workspace/gatk/FastaAlternateReferenceMaker/expected_snp2.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2.fasta new file mode 100644 index 00000000000..8f139e81c75 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2.fasta @@ -0,0 +1,3 @@ +>1 1:10000000 +AACCCCATCTCTACAATAAATTAAAATATTAGCTGGGCATTGTGGTGTGTGCTTGTAGTC +CCAGCTACTTGGCGGGATGAGGTGGGAGAATCATCCAAGCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2.fasta.fai new file mode 100644 index 00000000000..33f57fd5d73 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2.fasta.fai @@ -0,0 +1 @@ +1 101 14 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1.dict new file mode 100644 index 00000000000..2558023a0d8 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:101 M5:a4f6c011bf2331baf9c75f1fe1ee2d95 UR:file:/Users/louisb/Workspace/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1.fasta new file mode 100644 index 00000000000..972d466e3c1 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1.fasta @@ -0,0 +1,3 @@ +>1 1:10000000 +AACCCCATCTCTACAATAAATNAAAATATTAGCTGGGCATTGTGGTGTGTGCTTGTAGTC +CCAGCTACTTGGCGGGATGAGGTGGGAGAATCATCCAAGCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1.fasta.fai new file mode 100644 index 00000000000..33f57fd5d73 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1.fasta.fai @@ -0,0 +1 @@ +1 101 14 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.dict new file mode 100644 index 00000000000..da43dd7f267 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:101 M5:3f17f93d6a70c11a6a5a31149eb25363 UR:file:/Users/louisb/Workspace/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.fasta new file mode 100644 index 00000000000..1e402f88f3e --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.fasta @@ -0,0 +1,3 @@ +>1 1:10000000 +AACCCCNTCTCTACAATAAATNAAAATATTAGCTGGGCATNGTGGTGTGTGCTTGTAGTC +CCAGCTACTTGGCGGGATGAGGTGGGAGAATCATCCAAGCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.fasta.fai new file mode 100644 index 00000000000..33f57fd5d73 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp2_mask1_priority.fasta.fai @@ -0,0 +1 @@ +1 101 14 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp_mask.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp_mask.dict new file mode 100644 index 00000000000..8655f943675 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp_mask.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:101 M5:706b03a33b4a74ba44953ebb62c56e29 UR:file:/Users/louisb/Workspace/gatk/FastaAlternateReferenceMaker/expected_snp_mask.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp_mask.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp_mask.fasta new file mode 100644 index 00000000000..a8dd0f991b1 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp_mask.fasta @@ -0,0 +1,3 @@ +>1 1:10000000 +AACCCCATCTCTACAATAAATGAAAATATTAGCTGGGCATGGTGGTGTGTGCTTGTAGTC +CCAGCTACTTGGCGGGCTGAGGTGGGAGAATCATCCAAGCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp_mask.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp_mask.fasta.fai new file mode 100644 index 00000000000..33f57fd5d73 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snp_mask.fasta.fai @@ -0,0 +1 @@ +1 101 14 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels.dict new file mode 100644 index 00000000000..db49ef33e2a --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:95 M5:fbfd08abb257112c4e8a349d1c0bf3f7 UR:file:/Users/louisb/Workspace/gatk/FastaAlternateReferenceMaker/expected_snpsAndIndels.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels.fasta new file mode 100644 index 00000000000..f47f27ce109 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels.fasta @@ -0,0 +1,3 @@ +>1 1:10000000 +AACCCCATCTCTACAATAAATGAAAAAGCTGGGCATTGTGGTGTGTGCATAGTCCCAGCT +ACTTGGCGGGCTGAGGTGGGAGAATCATCCAAGCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels.fasta.fai new file mode 100644 index 00000000000..733c0cdda37 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels.fasta.fai @@ -0,0 +1 @@ +1 95 14 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.dict new file mode 100644 index 00000000000..b5d87fff927 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:95 M5:fbfd08abb257112c4e8a349d1c0bf3f7 UR:file:/Users/louisb/Workspace/gatk/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.fasta new file mode 100644 index 00000000000..f47f27ce109 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.fasta @@ -0,0 +1,3 @@ +>1 1:10000000 +AACCCCATCTCTACAATAAATGAAAAAGCTGGGCATTGTGGTGTGTGCATAGTCCCAGCT +ACTTGGCGGGCTGAGGTGGGAGAATCATCCAAGCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.fasta.fai new file mode 100644 index 00000000000..733c0cdda37 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1.fasta.fai @@ -0,0 +1 @@ +1 95 14 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.dict new file mode 100644 index 00000000000..eb92c48fcc4 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:95 M5:fc6ceea2cd802bc8deca9d24da9505a6 UR:file:/Users/louisb/Workspace/gatk/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.fasta new file mode 100644 index 00000000000..3ef8b741176 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.fasta @@ -0,0 +1,3 @@ +>1 1:10000000 +AACCCCNTCTCTACAATAAATNAAAAAGCTGGGCATNGTGGTGTGTGCATAGTCCCAGCT +ACTTGGCGGGCTGAGGTGGGAGAATCATCCAAGCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.fasta.fai new file mode 100644 index 00000000000..733c0cdda37 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask1_priority.fasta.fai @@ -0,0 +1 @@ +1 95 14 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask2.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask2.fasta new file mode 100644 index 00000000000..812e31afff6 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_mask2.fasta @@ -0,0 +1,3 @@ +>1 1:10000000 +AACCCCATCTCTACAATAAATGAAAAAGCTGGGCATTGTGGTGTGTGCATAGTCCCAGCT +ACTTGGCGGGNTGAGGTGGGAGAATCATCCAAGCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.dict new file mode 100644 index 00000000000..4e7ac5efc73 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:95 M5:cc9e3cd4a56921da39ccb38260350580 UR:file:/Users/louisb/Workspace/gatk/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.fasta new file mode 100644 index 00000000000..637d65531b7 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.fasta @@ -0,0 +1,3 @@ +>1 1:10000000 +AACCCCATCTCTACAATAAATGAAAAAGCTGGGCATTGTGGTGTGTGNATAGTCCCAGCT +ACTTGGCGGGCTGAGGTGGGAGAATCATCCAAGCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.fasta.fai new file mode 100644 index 00000000000..733c0cdda37 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps.fasta.fai @@ -0,0 +1 @@ +1 95 14 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.dict new file mode 100644 index 00000000000..112c5d91614 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:99 M5:b0c42fcbbea5cc1987b3352d66642ca0 UR:file:/Users/louisb/Workspace/gatk/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.fasta new file mode 100644 index 00000000000..68c5123abf0 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.fasta @@ -0,0 +1,3 @@ +>1 1:10000000 +AACCCCATCTCTACAATAAATGAAANNATTAGCTGGGCATTGTGGTGTGTGNNTAGTCCC +AGCTACTTGGCGGGCTGAGGTGGGAGAATCATCCAAGCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.fasta.fai new file mode 100644 index 00000000000..939f7b8e704 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_snpsAndIndels_maskOverlaps_priority.fasta.fai @@ -0,0 +1 @@ +1 99 14 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_test_iupac.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_test_iupac.dict new file mode 100644 index 00000000000..b058e0e17c6 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_test_iupac.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:5331 M5:f09cbb7d1d84301472b166f3ebb93809 UR:file:/Users/louisb/Workspace/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_test_iupac.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_test_iupac.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_test_iupac.fasta new file mode 100644 index 00000000000..d2c5182ab75 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_test_iupac.fasta @@ -0,0 +1,90 @@ +>1 20:61050 +CAGATATACTTCACAGCCCACGCTGACTCTGCCAAGCACAGACAACCAYTGGGCCCCAGG +GGAGCTGCAGGTCTCCTGGTCACCTAATCTTTTTTTTTTTTATACTTTAAGTTTTGGGGT +ACATGTGCACAACGTGCAGGTTACATATGTATACATGTGCCATGTTCATGTGCTGCACCC +ATTAACTCGTCATTTAACATTAGGTATATCTCCTAATGCTATCCCTCCCCCCTCCCCCCA +CCCCACAACAGGCCCTGGTGCCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCAT +GCCCTTTGCAGGGACATGGATGAAGCTGGAAACCATCATTCTCAGCAAACTATCAAACTA +TCACAAGGACAAAAAACCAAACACTGCATGTTTTCACTCATAGGTGGGAATTGAATAATG +AGAACACATGGACACAGGAAGGGGAACATCACACATCGGGACCTAATCTTAAGCTAAGTG +TGGCTAAGAGCCTATCTGCTGGCCTTTACTATTAAGCACTGCCCACTGGATTGCAGCCTG +AATTACACCGCCAAACAAATACTGTTTCAGCATACATTACCAGTGAAACCCAATGCAGGA +ACATAGTCAAAAATAAACACCTGGCATAGAGACTTGGCCCTCTGAAAACACCCAGAAAAA +AGCCAGCTATATTCAACATACATCACTGTCAAAATATCAAGGAAAATGAAGAAGAATAAA +ACAAAAAGTCAAAACCAAATGATAGGAACTTCAAAAAGATAAAGTAACACCAGCTGTCTT +AGATGAGAAAGAATCAGCACACATTCTTGCAATTCAAAAAGTCAGAATGTCTCCTTACCT +CCAAACAATCATACTAGCTCTCATCAGATTGAAATGGCTGAAATGACAGACATAGAATTC +ATGATCTGGAAGGTAAGGAAGCTCAAGAACATTCAGGAGAAAGTTGAAACCCAGTCCAAG +GAAGCCAGTAAAGCAATCCAAGAGTACAGAGATAACATAGCCATTTTAAGAAAGAACCAA +AAGAAACTTCTGCAATTGACAAATTCATTATAGGAATTTTGTAATACATTCAGAAGCATT +AACAACAGAATAGATCAAGTTGAGGAAAGAATCTCAGAGCTCAAAGATCAGTCCTTTGAA +TCAACACAGTCAGACAAAACTAAAGAAAAAAATTTAAAAATAAAACCTCTAAAAAAATAT +GGAATTATGTAAAGATACCAAACTTACAACTTATGGGCATTCCTGAAAGAGGAGAAAGAA +TAAGTAACTTGGAAAACATATTTGAGGATAGTCCATGAAAATTTCCCCAATCTCCCTAGA +GAGGCTGACATGCAAATTCAAGAAATGCAAATAACCCCTGTGAGATAACTACAAGATAAC +TATCCCCAAGACACATAGTCATAAGATTCTCCAAGGTCAACGTGAAAGAAAAAAATCTTA +AGGGCAGCTAGAGAAAAGCCTGAGGTCACTTATGAAGGGAAGCTCATCAGACTAACAGCA +GACTTCTCAGCAGAAACCTTACAAACCAAGCAAGATTAGGGGCCTATTTTTAGCATCCTT +AAAGAAAAGAAATTTCAGTGAAGAATTCCATATCCTGCAAAACTAAGCTTCATAAAAGAA +GGAGAAATAGGCTGGGCATGGTGGCTCACACCTGTAATACCAGCATTTTGGGAGGCTCAG +GCAGGAGGATTGCTTGAGCTCAAGAGTTTGAGACCAGCCTGGGCAACATGGCAAAACCCT +GTCTCTTCTAAAAATACAAAAATTACCTGGGCAAGACTCCATCACAAACAAACTAACAAA +CCAAAACTATCAGGTACTATGCTCACTACCTGGGTGACAAAATCATTTTTACACCAAACC +CAGTGACAAGCAATTTACCCATGTAACAAACCTGCATGTGTATCCCCTGAACCTAAAATA +AAAGTTAAAAAAAAAAGAACTTTCATCAACATTTCTTGCAGTGAAGGTATGTTAGTGATG +AACATTCTCTGCTTTTATTGCCTGAAAATATCTTTATTTTGTATTCATATTTGACATATA +TTCTCACTGGGCATAAAAATTCTAAATTACAAGTTTTTCCCCTTTTTTGTATTAAAAATT +TCATTCCAATATCTTTCATATTGCCTTATTTGTAATGATGCCTTCTATCCTTCTTATCTT +TGTTCCATTTATAAGAAGTGTTCCCCAACCCCAGMCTGATTAAAACCATTTTTTTAATTA +AAAAAGCAAAAGAAAGAAACATTTTTATCTGAAGCTGTCTCAGACTCAGACACCACCCAA +TCTTCAGATTTCAAATAGCTTATACTCAAACATTTGGTAATATCAGCCCCTTAATGGTCT +TCCTGGAGGGCAGATGCATTCTAGAGATGAGAACACGATCATGATTACGAATGCTACCAC +CACTACGAACGCACAAAAGTCACTGGTGTGATCCTTTCTCAGAACACTGTGGTAACTTCT +GGACATTCTCTGCTGTTATCATTGCTTCTTCCTTCTGGGTTTTTTTCCCCCTTATATGGG +CAGATAATTTTCTCCATTGGAATGAAAAAGTCTTGCTTCATGCTCTTTAACTGTGTGACC +TTGGGCGTATTACTTTACTTTGGGGCAAACCATTTTCCTTCTTGAGGACCAAATGTGCTC +TTTTATAAAACGAGCAGTTAGAATTAGATTGTCTCTCTGGACACGGCTTATGTTGACAAC +CTGGATCACATTAGAGGATCACACTGAGACCTTTATGTCGGCCTCAGTTCCTCCATCTGT +AAAGTAGAGGTTGGGCTTAGATTATAGATGATAAAGACACCAACTTTCCTGGAAAGGATT +CTGGAAAGGATTCTGAACTTAGGCTCAGCCTCAGTAAGAAGGAGTTCTGTGATTAAACAG +GGATGCCCACACATCAGCAACAGAAATGGGCAGGTCAACCATGTATGCTGTGCCTCAGTG +AAGATTTTATGCTATGCTGTGCATTTGATATCCATTCTCTATATTTGATATCCAATCTAA +GATTATCTAGAAGGTCCTTTCCAAGACACTGATGAGATACATCTGTATAAATATATAACT +CAGGATGAAAGCAACTTTTAACATTTAGCGTGTGCCTCTGCCTCTGATCTGATTACAGCC +CACAGAGAAATATAAACAATACACAATACAGGCTAATGAAGAAGGGTGATAAGATTTTTT +TTTTTTTTTGAGACGGAATTTCACTCTTGTCACCCAGGCTGGAGTGCAATGGTGCAATCT +TGGCTCACTGCAACCTTCGCCTCCCGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGT +AGATGGGATTGGAGGTGCCCACCACCACGCCCGGCTAATTTTTGTATTTTTTAGTAGAGA +CAGGGTTTCACCATGTTGTCCACGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCAG +CCTCAGCCTCCCAAAGTGCTAGGATTACAGGTGTGAGCCACTGCAACCGGCCAAGGGTGA +TAAGATTTTAAAAATTTATTTAAAATACAGAAATTTCAAAAAGAGAGAAGTGCAGTGATA +GCAAAATTGATGCAAACTGTGCAAGCATGAAATCTATTTTATAGCTGAATCTACTTTTCT +TGGTCCCAAGATTCTATTTCCATTGGTTTTCAAATAGTTAATTCTATTGTTTTTTCAGGG +AGATTACTAAAATCACTAATAATTATTTTCCTACTGACACAAAATCTAAAAAGCACCATA +TAGACCTTCTCTCTCCATCTCCCCTTATCCTTATGTCACCTTACCCTACCCCAATACTCC +AATGGCAGAGTATCTACCCATGGCAGAGTAGAGAATATGTACACTAACAAAACCAGATGC +ACAGAGGTGGGGTATCCATCTCTGACTTGGCTGAGCTAGTCTAAGGAAGGAAGGCTCTGT +GGCCATTGTCCTTGGAAGTCATTCTCACAGGTTGGTGGTATTCTCAAGTAGGTGGTGCTT +GAGTGGCCCAAGAGCACCCACATGCTGCTATGCATTTTTCTGACAACCTCTTTATGATCT +CTGACTTTGGCAGATCATCTTGCATCTCTCAATTGGAGAGTCACTTTTCTTATCTCCACA +GAAAATTCTTAATCAAGCTCCTGGTTTTCCTTTATAGCTTCTACTTTTTAAACTCACTTC +TCCAACTTCACCGCTACATCTCTGACAGATGAGAACATTAGAGATTCCCTGTTTTTCAAA +AACAAAACAAAACTCAGCAAAACTATAAATATACTAAGGGTAAGTCTGTATTATCTCCTG +CCAAAATACACCACCCTGCATTTTTTTAAATTTTTATCTTTTGTAGGTACATAGTAGGTG +TCTATATTTGTGGGGTACATGAGATGTTTTGATACAAGCATGCAATGCATAATAACCACA +TCATGGAAAATGGGGTATCCATCCCCTCAAGCATTTATCCTTTGTGTTACAAATTATCTA +ATTATACTTTATTATTTTAAAATGTACAATTAAATTATTTTTGACTATAGTCACCTCGTT +ATGCTATTAAATACCAGGTCTTATTCATTCTTTCTAACTATTTTTTGTACCCAGTAACCA +TCCTCACCTTCCCACACACGCCCACCACCTTTCCCAGCCTCTGATAACCATCCTTCTACT +CTCTATCTCCCTTGAATTCAGTAGTTTTGATTTTTAGATTTCACAAATAAGTGAGAACAT +GCAATATTTGTCTTTATGTTCCTGGCTTATTTCACTTAGCATAATGGCCTCCAGTTCCAT +CCATGTTATTGCAAATGACAGCATCTCTTTCTTTTTTATGGCTGAATAATACTCCACTGT +GTATAAGTTCCACATTTTCTTTATCCACTCATTTGTTGATTGACACTTACRTTGCTTCTA +AATCTTGGCTATTGTGAATAGTGCTGCAACAAGCACAGGTGTGCAGATATCTATTCAATA +TTCTTATTTCCTTTTGGAGGGGAGTGTGTACCTAGCAGTGGGATTGCTGGATTGTATGGT +AACTCTATTTTCAGTTTTTTTAGGAACCTCCAAACTGTTCTCCATAGTGGTTGTACTATC +TTACGTTCACACCAGTAGCATACAAGGGTTTCCCTTTCTCCAAATCCTTGCCAGCATTTG +CTATTGCCTGTCTTTTGGATAAAAGCCATTTTAACTGGAGTGAGATGATATTCCATTGTA +GCTTGATTTTCATTTCTCTGATGATCAGTGATTTTGAGCACCTTTTCATCTGCCTGTTTG +CCATTTGTATGTCTTCTTTTGAGAATATCTATTCAGATACTTTGCCCATTTTTAAGTTGG +ATCATTAGATTTTTTTCCTATAGAATTGTTTGAGCTCTTTRTATTTCCTGT diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_test_iupac.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_test_iupac.fasta.fai new file mode 100644 index 00000000000..72a4546698e --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/expected_test_iupac.fasta.fai @@ -0,0 +1 @@ +1 5331 12 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.dict new file mode 100644 index 00000000000..644c9d969c4 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:1 M5:b9ece18c950afbfa6b0fdbfa4ff731d3 UR:file:/Users/louisb/Workspace/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.fasta new file mode 100644 index 00000000000..61763682496 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.fasta @@ -0,0 +1,2 @@ +>1 1:1273247 +T diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.fasta.fai new file mode 100644 index 00000000000..83f731e8ace --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA1.fasta.fai @@ -0,0 +1 @@ +1 1 13 1 2 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA2.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA2.dict new file mode 100644 index 00000000000..530deb275ac --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA2.dict @@ -0,0 +1 @@ +@HD VN:1.5 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA2.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA2.fasta new file mode 100644 index 00000000000..4e82c549e59 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA2.fasta @@ -0,0 +1,2 @@ +>1 1:1273247 + diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA2.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA2.fasta.fai new file mode 100644 index 00000000000..3eac6fe3a19 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA2.fasta.fai @@ -0,0 +1 @@ +1 0 13 0 2 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.dict new file mode 100644 index 00000000000..cfd70b1ee54 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:1 M5:dfcf28d0734569a6a693bc8194de62bf UR:file:/Users/louisb/Workspace/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.fasta new file mode 100644 index 00000000000..3b18766eea4 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.fasta @@ -0,0 +1,2 @@ +>1 1:1273247 +G diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.fasta.fai new file mode 100644 index 00000000000..83f731e8ace --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/iupac_sample_NA3.fasta.fai @@ -0,0 +1 @@ +1 1 13 1 2 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/overlapsIndelsMask.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/overlapsIndelsMask.vcf new file mode 100644 index 00000000000..8d568434c3d --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker/overlapsIndelsMask.vcf @@ -0,0 +1,164 @@ 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+GAGTGAGACTCCTACTCAAAAAAAAACAAAAAACAAAAAACAAACCACAAAACTTTCCAG +GTAACTTATTAAAACATGTTTTTTGTTTGTTTTGAGACAGAGTCTTGCTCTGTCGCCCAG +GCTGGAGTGCAGTGGAGCAATCTCAGCTCACTGCAAGCTCCGCCTCCCGGGTTCACACCA +TTCTCCTGCCTCAGCCTCCCGAGTAGCTAGGACTATAGGCACCCGCCACCACGCCCAGCT +TATTTTTTTTGTATTTTTTAGTAGAGACGGGGTTTCATCGTGTTAGCCAGGATGGTCTCG +ATCTCCTGACCTCGTGATCCGCCCACCTCAGCCTCCCAAAG +>2 1:10100000 +GACACCAAAAATACCAAGGACTGTGATTAACCCAGTTTTGATGATCAGTTAGCTGTGAAG +GAGGGGAGGGGAGGAGAGATGGAGAAATGACACCTTGGTTTCTAGCTATGGAGAAGGATA +GATAAGGGTTGAATAAGGAATTCCAGAGAAGCAGCAGATTTTGGAGAAAGCACATGTTTC +TTTTTTTTTTTTTCGTCTTTTGAGACAGGGTCTCCCTCTGTCGCCCAGGCTGGAGTGCAG +TGGCGCAACCTCAGCTCACTGCAACCTCTGCCCCCTGGGTTCAAGTGATTCTCCTGCCTC +AGCCTTCCAAGTAGCTGCCAGCCATGCCCAGCTAATTTTTTAATTTTTAGTAGAGACGGT +GTTTCACCATATTGGCCAGGCTGGTCTTGAACTCCAGACCTTGGTGATCCGCCTGCCATG +GCCTCCCAAAGTGCTGGGATTACAGGTGTCAGCTACCACGCCAGGCCTCCGGCTAATTTT +TGTATATTTTGTAGAGACAGGGTCTTGCCATGTTGCCCAGGCTGGTCTCAAACTCCTGGG +CTCAAGTGATCTGCCCACCTCAGCCTCCCAGAGTGCTGAGATTGCAAGTTTAATTTTGGA +CCACCAAAAAGATGAGTCCACATGTAGACCCCCACTCTGGCCTTGGTGCTCTAACATCTC +CATTTCTTTCTTCTTTTTTCTTTTTTTTTTTTTGAGATGGAGTTTCGCTCTTGTTGCCCA +GGCTGGAGTGCAATGGCGCGATCTCAGCTCGCTGCAACCTCTGCCTCCCAGGTTCAAGCG +ATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAAGCATGTACCACCATGCCTGGC +TAATTTTTTTGTATTTTTATTAGAGACGGGATTTCTCCATGTTGGCTTGGCGGGTCTCAA +ACTCTTGACCTTAGGTGATCTGCCTGCCTCAGCCTCCCAAAGTGCTGGGATTACCGGCGT +GAGCCACCGCACCCAGCCTAACATCCCCACCTCTTTGACCA +>3 1:10900000 +CT diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only.fasta.fai new file mode 100644 index 00000000000..280dc2e189f --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only.fasta.fai @@ -0,0 +1,3 @@ +1 401 14 60 61 +2 1001 436 60 61 +3 2 1468 2 3 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_diff_contigs.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_diff_contigs.dict new file mode 100644 index 00000000000..14bc064c515 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_diff_contigs.dict @@ -0,0 +1,3 @@ +@HD VN:1.5 +@SQ SN:1 LN:101 M5:8c41aecb370a27de4a5eea543bb5b5a3 UR:file:/Users/louisb/Workspace/gatk/test_reference_only_contiguous_diff_contigs.fasta +@SQ SN:2 LN:101 M5:151f2cbc5ef6bcf8dd21284da7f812cf UR:file:/Users/louisb/Workspace/gatk/test_reference_only_contiguous_diff_contigs.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_diff_contigs.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_diff_contigs.fasta new file mode 100644 index 00000000000..8d46c3fc964 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_diff_contigs.fasta @@ -0,0 +1,6 @@ +>1 1:10000100 +CTTGGAGGCAGAGGTTGCAGTGAGCTGAGATTGTGACACTGCACTCCAGCCTGGGAGACA +GAGTGAGACTCCTACTCAAAAAAAAACAAAAAACAAAAAAC +>2 2:10000201 +TAAAACAGTCAGATCTCATGAGAACTCCCTCACTATCACAAGAACAGCATGGGGGAAACT +GCCCCCATGATCCAGTCACCTCCCACTAGGTCCCTCCCTCC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_diff_contigs.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_diff_contigs.fasta.fai new file mode 100644 index 00000000000..2d3913cb646 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_diff_contigs.fasta.fai @@ -0,0 +1,2 @@ +1 101 14 60 61 +2 101 131 60 61 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_same_contig.dict b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_same_contig.dict new file mode 100644 index 00000000000..23e8707e138 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_same_contig.dict @@ -0,0 +1,2 @@ +@HD VN:1.5 +@SQ SN:1 LN:202 M5:f2db2997e9aa1590b41c8c93029fc5bc UR:file:/Users/louisb/Workspace/gatk/reference_only_contiguous_same_contig.fasta diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_same_contig.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_same_contig.fasta new file mode 100644 index 00000000000..7bd493f0020 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_same_contig.fasta @@ -0,0 +1,5 @@ +>1 1:10000100 +CTTGGAGGCAGAGGTTGCAGTGAGCTGAGATTGTGACACTGCACTCCAGCCTGGGAGACA +GAGTGAGACTCCTACTCAAAAAAAAACAAAAAACAAAAAACAAACCACAAAACTTTCCAG +GTAACTTATTAAAACATGTTTTTTGTTTGTTTTGAGACAGAGTCTTGCTCTGTCGCCCAG +GCTGGAGTGCAGTGGAGCAATC diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_same_contig.fasta.fai b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_same_contig.fasta.fai new file mode 100644 index 00000000000..5d6ec3ffe06 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker/reference_only_contiguous_same_contig.fasta.fai @@ -0,0 +1 @@ +1 202 14 60 61 diff --git a/src/testUtils/java/org/broadinstitute/hellbender/testutils/ArgumentsBuilder.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/ArgumentsBuilder.java index f01cc05e91e..ad7afb48b11 100644 --- a/src/testUtils/java/org/broadinstitute/hellbender/testutils/ArgumentsBuilder.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/ArgumentsBuilder.java @@ -1,7 +1,9 @@ package org.broadinstitute.hellbender.testutils; +import htsjdk.samtools.util.Locatable; import org.apache.commons.lang3.StringUtils; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; +import org.broadinstitute.hellbender.utils.IntervalUtils; import org.broadinstitute.hellbender.utils.Utils; import java.io.File; @@ -133,6 +135,13 @@ public ArgumentsBuilder addArgument(final String argumentName) { return this; } + public ArgumentsBuilder addInterval(Locatable interval){ + Utils.nonNull(interval); + add("-L"); + add(IntervalUtils.locatableToString(interval)); + return this; + } + /** * Add an argument with a given value to this builder without splitting the value string into multiple arguments at whitespace. * This is specifically to allow arguments with values that contain whitespace. diff --git a/src/testUtils/java/org/broadinstitute/hellbender/testutils/FastaTestUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/FastaTestUtils.java new file mode 100644 index 00000000000..3596ffd41f1 --- /dev/null +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/FastaTestUtils.java @@ -0,0 +1,33 @@ +package org.broadinstitute.hellbender.testutils; + +import htsjdk.samtools.SAMSequenceRecord; +import org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile; +import org.testng.Assert; + +import java.nio.file.Path; + +/** + * Utilities for comparing Fasta files. + */ +public final class FastaTestUtils { + + private FastaTestUtils() {} + + /** + * Assert that two fasta files contain the same sequences, with the same names, in the same order. + * This is different from exact file equality because they may have different sequence descriptions and line lengths. + */ + public static void assertFastaFilesContainTheSameSequence(Path actualFasta, Path expectedFasta){ + try(final CachingIndexedFastaSequenceFile actual = new CachingIndexedFastaSequenceFile(actualFasta, 100000, true, true); + final CachingIndexedFastaSequenceFile expected = new CachingIndexedFastaSequenceFile(expectedFasta,10000, true, true)) + { + actual.getSequenceDictionary().assertSameDictionary(expected.getSequenceDictionary()); + for( SAMSequenceRecord record : actual.getSequenceDictionary().getSequences()){ + final byte[] actualBases = actual.getSequence(record.getSequenceName()).getBases(); + final byte[] expectedBases = expected.getSequence(record.getSequenceName()).getBases(); + Assert.assertEquals(actualBases, expectedBases, "Bases in reference were different.\n" + + new String(actualBases) + "\n" +new String(expectedBases)); + } + } + } +} diff --git a/src/testUtils/java/org/broadinstitute/hellbender/testutils/GenomicsDBTestUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/GenomicsDBTestUtils.java index ddeb97a0238..4743ee299f1 100644 --- a/src/testUtils/java/org/broadinstitute/hellbender/testutils/GenomicsDBTestUtils.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/GenomicsDBTestUtils.java @@ -2,7 +2,6 @@ import htsjdk.samtools.util.Locatable; import org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport; -import org.broadinstitute.hellbender.utils.IntervalUtils; import org.broadinstitute.hellbender.utils.io.IOUtils; import java.io.File; @@ -54,7 +53,7 @@ public static File createTempGenomicsDB(final List gvcfs, final Locatable final String workspace = new File(workspaceDir, "workspace").getAbsolutePath(); args.addArgument(GenomicsDBImport.WORKSPACE_ARG_LONG_NAME, workspace); - args.addArgument("L", IntervalUtils.locatableToString(interval)); + args.addInterval(interval); importer.runCommandLine(args); return new File(workspace); }