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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Cleanup unused test files. #3905

Closed samuelklee closed 6 years ago

samuelklee commented 6 years ago

The following one-liner (which I Googled, so I cannot vouch that this is the best way to do things) revealed 245Mb of files that are unused in master:

for ff in `find src/test/resources -name "*"`; do file=`basename $ff`; git grep -l $file >/dev/null; rcode=$?; if [[ $rcode -ne 0 ]]; then echo $ff; fi; done

Note I didn't search in all branches, but I figure we can always recommit those files. Also, any index files, etc. should be retained if necessary.

CNV team will delete their files, but I'll leave it up to engine and the other teams about how much we want to remove.

src/test/resources/dbsnp_132.b36.excluding_sites_after_129.chr1_1k.vcf.idx src/test/resources/empty.vcf.idx src/test/resources/exampleFASTA.fasta.fai src/test/resources/fastaWithoutDict.fasta.fai src/test/resources/fastaWithoutFai.dict src/test/resources/hg19micro.dict src/test/resources/hg19micro.fasta.fai src/test/resources/hg19mini.dict src/test/resources/hg19mini.fasta.fai src/test/resources/Homo_sapiens_assembly19_chr1_1M.dict src/test/resources/Homo_sapiens_assembly19_chr1_1M.fasta.fai src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf.idx src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf.idx src/test/resources/human_g1k_v37.chr17_1Mb.dict src/test/resources/human_g1k_v37.chr17_1Mb.fasta.fai src/test/resources/iupacFASTA.dict src/test/resources/iupacFASTA.fasta.fai src/test/resources/joint_calling.chr1_1M.1kg_samples.10samples.noINFO.vcf.idx src/test/resources/large/1000G.phase3.broad.withGenotypes.chr20.10100000.vcf.idx src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram.bai src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/model_final/bias_covariates_ARD_coefficients.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/model_final/mean_bias_covariates_matrix.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/model_final/mean_bias_covariates_norm2.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/model_final/target_specific_mean_log_bias.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/model_final/target_specific_unexplained_variance.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/bias_covariates_ARD_coefficients_history.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/copy_ratio_max_likelihood_estimate_matrix.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/copy_ratio_precision_matrix.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/copy_ratio_Viterbi_matrix.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/log_likelihood_history.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/sample_bias_latent_posteriors.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/sample_log_likelihoods.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/sample_read_depth_posteriors.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/sample_specific_unexplained_variance.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/segments/SM-74NEG.seg src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/segments/SM-74P2T.seg src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/segments/SM-74P35.seg src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/total_covariate_bias_matrix.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/posteriors_final/total_unexplained_variance_matrix.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wgs_pon/model_final/bias_covariates_ARD_coefficients.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wgs_pon/model_final/mean_bias_covariates_matrix.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wgs_pon/model_final/mean_bias_covariates_norm2.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wgs_pon/model_final/target_specific_mean_log_bias.tsv src/test/resources/large/cnv_germline_workflows_test_files/inputs/wgs_pon/model_final/target_specific_unexplained_variance.tsv src/test/resources/large/cnv/realistic-targets.tab src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list src/test/resources/large/cnv_somatic_workflows_test_files/wes-do-gc.pon.hdf5 src/test/resources/large/cnv_somatic_workflows_test_files/wes-no-gc.pon.hdf5 src/test/resources/large/cnv/truncated-realistic-targets.tab src/test/resources/large/dbsnp_138.b37.1.1-65M.vcf.idx src/test/resources/large/dbsnp_138.b37.20.21.vcf.blockgz.gz.tbi src/test/resources/large/expected.NA12878.RNAseq.splitNcigarReads.bai src/test/resources/large/expected.NA12878.RNAseq.splitNcigarReads.doNotFixOverhangs.bai src/test/resources/large/expected.NA12878.RNAseq.splitNcigarReads.maxBasesInOverhang5.bai src/test/resources/large/expected.NA12878.RNAseq.splitNcigarReads.maxMismatchesInOverhang0.bai src/test/resources/large/gencode.v19.LargeFile.gtf.idx src/test/resources/large/gencode.v26.primary_assembly.annotation.XYZ.gtf.idx src/test/resources/large/gvcfs/CEUTrio.20.21.gatk3.4.g.vcf.idx src/test/resources/large/gvcfs/combined.gatk3.7_30_ga4f720357.g.vcf.gz.tbi src/test/resources/large/gvcfs/combined.gatk3.7.g.vcf.gz.tbi src/test/resources/large/gvcfs/gatk3.7_30_ga4f720357.24_sample.21.g.vcf.idx src/test/resources/large/gvcfs/HG00096.g.vcf.gz.tbi src/test/resources/large/gvcfs/HG00268.g.vcf.gz.tbi src/test/resources/large/gvcfs/NA19625.g.vcf.gz.tbi src/test/resources/large/Homo_sapiens_assembly38.20.21.dict src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta.fai src/test/resources/large/human_g1k_v37.20.21.fasta.amb src/test/resources/large/human_g1k_v37.20.21.fasta.ann src/test/resources/large/human_g1k_v37.20.21.fasta.bwt src/test/resources/large/human_g1k_v37.20.21.fasta.pac src/test/resources/large/human_g1k_v37.20.21.fasta.sa src/test/resources/large/K-562.duplicateMarked.chr20.bai src/test/resources/large/mutect/dream_synthetic_bams/normal_3.bam.bai src/test/resources/large/mutect/dream_synthetic_bams/normal_4.bam.bai src/test/resources/large/mutect/dream_synthetic_bams/normal.bam.bai src/test/resources/large/mutect/dream_synthetic_bams/tumor_3.bam.bai src/test/resources/large/mutect/dream_synthetic_bams/tumor_4.bam.bai src/test/resources/large/mutect/dream_synthetic_bams/tumor.bam.bai src/test/resources/large/NA12878.RNAseq.bai src/test/resources/large/SVIntegrationTest.bam.bai src/test/resources/large/very-small-gnomad.vcf.idx src/test/resources/large/VQSR/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.20.1M-10M.vcf.idx src/test/resources/large/VQSR/combined.phase1.chr20.raw.indels.filtered.sites.1M-10M.vcf.idx src/test/resources/large/VQSR/dbsnp_132_b37.leftAligned.20.1M-10M.vcf.idx src/test/resources/large/VQSR/expected/snpRecal.scattered.vcf.idx src/test/resources/large/VQSR/expected/snpSampledRecal.vcf.idx src/test/resources/large/VQSR/indelRecal.vcf.idx src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf.idx src/test/resources/large/VQSR/phase1.projectConsensus.chr20.1M-10M.raw.snps.vcf.idx src/test/resources/large/VQSR/sites_r27_nr.b37_fwd.20.1M-10M.vcf.idx src/test/resources/large/VQSR/snpRecal.vcf.idx src/test/resources/NA12878.chr17_69k_70k.dictFix.bam.bai src/test/resources/NA12878.chr17_69k_70k.dictFix.cram.crai src/test/resources/org/broadinstitute/hellbender/engine/ambiguityCodes.dict src/test/resources/org/broadinstitute/hellbender/engine/ambiguityCodes.fasta.fai src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10000000-10000020.with.unmapped.bam.bai src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam.bai src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram.crai src/test/resources/org/broadinstitute/hellbender/engine/cramtestWrongRef.dict src/test/resources/org/broadinstitute/hellbender/engine/cramtestWrongRef.fasta.fai src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram.bai src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram.crai src/test/resources/org/broadinstitute/hellbender/engine/example_features.bed.idx src/test/resources/org/broadinstitute/hellbender/engine/example_variants_noSequenceDict.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/example_variants_withSequenceDict.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_gvcf.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/FeatureInput/vcfWithIndex.vcf src/test/resources/org/broadinstitute/hellbender/engine/FeatureInput/vcfWithIndex.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/FeatureInput/vcfWithOutIndex.vcf src/test/resources/org/broadinstitute/hellbender/engine/GCSTests/expected_ReadWalkerGCSSupportIntegrationTest_bam_multiple_intervals.bai src/test/resources/org/broadinstitute/hellbender/engine/GCSTests/expected_ReadWalkerGCSSupportIntegrationTest_bam_multiple_intervals_with_unmapped.bai src/test/resources/org/broadinstitute/hellbender/engine/GCSTests/expected_ReadWalkerGCSSupportIntegrationTest_bam_single_interval.bai src/test/resources/org/broadinstitute/hellbender/engine/GCSTests/expected_ReadWalkerGCSSupportIntegrationTest_bam_unmapped_only.bai src/test/resources/org/broadinstitute/hellbender/engine/GCSTests/expected_ReadWalkerGCSSupportIntegrationTest_bam_wholefile.bai src/test/resources/org/broadinstitute/hellbender/engine/GCSTests/expected_VariantWalkerGCSSupportIntegrationTest_vcf_multiple_intervals.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/GCSTests/expected_VariantWalkerGCSSupportIntegrationTest_vcf_single_interval.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/GCSTests/expected_VariantWalkerGCSSupportIntegrationTest_vcf_wholefile.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/GenomicsDBIntegration/tiny.g.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/minimal_bcf_file.bcf.idx src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed.idx src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf3_file.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf4_file.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1_WithOverlap.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2_WithOverlap.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/splitVariants_1.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/splitVariants_2.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf.idx src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam.bai src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam.bai src/test/resources/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSink/directoryWithNoPartFiles src/test/resources/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSink/directoryWithNoPartFiles/_SUCCESS src/test/resources/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSink/fragments_test src/test/resources/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSink/fragments_test/part-r-00001 src/test/resources/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSink/fragments_test/part-r-00002 src/test/resources/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSink/fragments_test/part-r-00003 src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.bam.bai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectAlignmentSummaryMetrics/summary_alignment_bisulfite_test.sam src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectAlignmentSummaryMetrics/summary_alignment_stats_test2.sam src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectAlignmentSummaryMetrics/summary_alignment_stats_test.bam src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectAlignmentSummaryMetrics/summary_alignment_stats_test.cram src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectAlignmentSummaryMetrics/summary_alignment_stats_test.fasta.fai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectAlignmentSummaryMetrics/summary_alignment_stats_test_multiple.sam src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectAlignmentSummaryMetrics/summary_alignment_stats_test.sam src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectBaseDistributionByCycle/example_pfFail_reads.bam.bai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectBaseDistributionByCycle/first5000a.bai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectBaseDistributionByCycle/originalQuals.chr1.1-1K.bam.bai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectBaseDistributionByCycle/unmapped.bam.bai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectBaseDistributionByCycle/valid.cram.crai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectBaseDistributionByCycle/valid.dict src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectBaseDistributionByCycle/valid.fasta.fai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectQualityYieldMetrics/collect_quality_yield_metrics.bam src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectQualityYieldMetrics/collect_quality_yield_metrics.cram src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectQualityYieldMetrics/valid.cram.crai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectQualityYieldMetrics/valid.dict src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectQualityYieldMetrics/valid.fasta.fai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/MeanQualityByCycle/example_pfFail_reads.bam.bai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/MeanQualityByCycle/first5000a.bai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/MeanQualityByCycle/unmapped.bam.bai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/QualityScoreDistribution/example_pfFail_reads.bam.bai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/QualityScoreDistribution/first5000a.bai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/QualityScoreDistribution/originalQuals.chr1.1-1K.bam.bai src/test/resources/org/broadinstitute/hellbender/metrics/analysis/QualityScoreDistribution/unmapped.bam.bai src/test/resources/org/broadinstitute/hellbender/tools/add_comments_to_bam.bam src/test/resources/org/broadinstitute/hellbender/tools/add_comments_to_bam.sam src/test/resources/org/broadinstitute/hellbender/tools/ArtificallyContaminatedBams/contamination.case.2.txt src/test/resources/org/broadinstitute/hellbender/tools/ArtificallyContaminatedBams/contamination.case.3.txt src/test/resources/org/broadinstitute/hellbender/tools/ArtificallyContaminatedBams/contamination.case.4.txt src/test/resources/org/broadinstitute/hellbender/tools/ArtificallyContaminatedBams/contamination.case.5.txt src/test/resources/org/broadinstitute/hellbender/tools/ArtificallyContaminatedBams/contamination.case.6.txt src/test/resources/org/broadinstitute/hellbender/tools/ArtificallyContaminatedBams/contamination.case.7.txt src/test/resources/org/broadinstitute/hellbender/tools/ArtificallyContaminatedBams/contamination.case.8.txt src/test/resources/org/broadinstitute/hellbender/tools/ArtificallyContaminatedBams/contamination.case.broken.1.txt src/test/resources/org/broadinstitute/hellbender/tools/ArtificallyContaminatedBams/contamination.case.broken.2.txt src/test/resources/org/broadinstitute/hellbender/tools/ArtificallyContaminatedBams/contamination.case.broken.3.txt src/test/resources/org/broadinstitute/hellbender/tools/ArtificallyContaminatedBams/contamination.case.broken.4.txt src/test/resources/org/broadinstitute/hellbender/tools/ArtificallyContaminatedBams/contamination.case.broken.5.txt src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.fakeSitesForTesting.b37.chr17.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.fakeSitesForTesting.b37.chr20.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.manyObservations.full.table.gz src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.manyObservations.piece.table.gz src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.noMD.noBQSR.bam.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.noMD.noBQSR.cram.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.noMD.noBQSR.md.bqsr.bam.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.4379150-4379157.bam.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b36.excluding_sites_after_129.chr1_1k.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.20.10m-10m100.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.excluding_sites_after_129.ch20.1m-1m1k.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.noMD.noBQSR.md.bqsr.bam.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.postRecalibrated.txt src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.recalibrated.DIQ.bam.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m20k.NA12878.2inputs.recal.txt src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m20k.NA12878.indels_context_size_4.recal.txt src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m20k.NA12878.low_quality_tail_5.recal.txt src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m20k.NA12878.mismatches_context_size_4.recal.txt src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m20k.NA12878.quantizing_levels_6.recal.txt src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m20k.NA12878.recal.txt src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.bqsr.qq-1.alternate.bam.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.bqsr.qq6.alternate.bam.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.reads.pipeline.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.reads.pipeline.cram.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam.bai src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.sharded.bam/part-r-00001.bam 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src/test/resources/org/broadinstitute/hellbender/tools/walkers/rnaseq/ASEReadCounter/NA12878.chr20_2444518_2637800.RNAseq.warnings.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/UnmarkDuplicates/allDuplicates.bam.bai src/test/resources/org/broadinstitute/hellbender/tools/walkers/ValidateVariants/complexEvents_incompatibleDict.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/ValidateVariants/complexEvents_lexDict.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/ValidateVariants/complexEvents.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/ValidateVariants/gvcf.basepairResolution.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/ValidateVariants/NA12891.AS.chr20snippet_BAD_INCOMPLETE_REGION.g.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/ValidateVariants/NA12891.AS.chr20snippet.BAD_MISSING_NON_REF.g.vcf.idx 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src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/synthetic.challenge.set1.tumor-vs-synthetic.challenge.set1.normal-filtered.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/CEUtriMixedPloidyTest.vcf src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/CEUtrioPopPriorsTest_chr1.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/CEUtrioTest_chr1.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testFamilyPriors_chr1.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testFamilyPriors.vcf src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testSingleParentFamily_chr1.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testSingleParentFamily.vcf src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/NA12878.Jan2013.haplotypeCaller.subset.indels.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/testFamilyPriors_chr20.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/threeMemberNonTrioTest_chr1.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/threeMemberNonTrioTest_chr20.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/261_S01_raw_variants_gvcf.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/complexExample1.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/diploid-multisample-sac.g.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_DiscordanceNoSampleSpecified.vcf src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_FileWithoutInfoLineInHeaderWithOverride.vcf src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_SelectMultiAllelicExcludeNonVar.vcf src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/filteringDepthInFormat.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/haploid-multisample.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/selectVariantsInfoField.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/test.dup.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/tetra-diploid.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/tetraploid-multisample-sac.g.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/tetraploid-multisample.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2DiscordanceConcordance.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/UpdateVCFSequenceDictionary/exampleBAM.sam src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/UpdateVCFSequenceDictionary/exampleFASTA.fasta.fai src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/expected.soap_gatk_annotated.AMD.table src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/multiallelic_gt.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/multiallelic.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/soap_gatk_annotated.noChr_lines.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/soap_gatk_annotated.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/vcfexample2.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/vcfexample.noSamples.vcf.idx src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/vcfexample.withMLE.vcf.idx src/test/resources/org/broadinstitute/hellbender/utils/IndexUtils/test_bed_for_index.bed.idx src/test/resources/org/broadinstitute/hellbender/utils/IndexUtils/test_variants_for_index.g.vcf.idx src/test/resources/org/broadinstitute/hellbender/utils/IndexUtils/test_variants_for_index.vcf.bgz.tbi src/test/resources/org/broadinstitute/hellbender/utils/read/comparator_test_with_unmapped.bam.bai src/test/resources/org/broadinstitute/hellbender/utils/read/ReadUtils/print_reads.fasta.fai src/test/resources/org/broadinstitute/hellbender/utils/samples/SampleUtils/emptySamples.samples src/test/resources/org/broadinstitute/hellbender/utils/samples/SampleUtils/overlapsWithSamples2.samples src/test/resources/org/broadinstitute/hellbender/utils/samples/SampleUtils/samples1.samples src/test/resources/org/broadinstitute/hellbender/utils/samples/SampleUtils/samples2.samples src/test/resources/org/broadinstitute/hellbender/utils/SequenceDictionaryUtils/test2.dict src/test/resources/org/broadinstitute/hellbender/utils/SequenceDictionaryUtils/test2.fasta.fai src/test/resources/org/broadinstitute/hellbender/utils/SequenceDictionaryUtils/test2.intervals src/test/resources/org/broadinstitute/hellbender/utils/SequenceDictionaryUtils/test2.sorted.bam.bai src/test/resources/org/broadinstitute/hellbender/utils/SequenceDictionaryUtils/test2.vcf.idx src/test/resources/org/broadinstitute/hellbender/utils/SequenceDictionaryUtils/test.dict src/test/resources/org/broadinstitute/hellbender/utils/SequenceDictionaryUtils/test.fasta.fai src/test/resources/org/broadinstitute/hellbender/utils/SequenceDictionaryUtils/test.sorted.bam.bai src/test/resources/org/broadinstitute/hellbender/utils/SequenceDictionaryUtils/test_variants_for_index.vcf.bgz.tbi src/test/resources/org/broadinstitute/hellbender/utils/SequenceDictionaryUtils/test.vcf.idx src/test/resources/org/broadinstitute/hellbender/utils/test/SamAssertionUtilsUnitTest/file1.bam.bai src/test/resources/problematicFASTA.dict src/test/resources/problematicFASTA.fasta.fai

samuelklee commented 6 years ago

Hmm, I think we'll also have to check for files that are duplicated in our resources.

droazen commented 6 years ago

@samuelklee This is a very dangerous/misleading check! Most of the files in your list are actually in use in the test suite, and their presence is inferred from the path to the file(s) they are associated with. For example, vcf index files are loading indirectly by our readers, using the path to the vcf to infer the path to the index.

samuelklee commented 6 years ago

Yup, I mentioned index files above. And of course tests should still pass after deletion...

droazen commented 6 years ago

It's not just index files -- many paths to test files are constructed programmatically rather than hardcoded into the source. And some files are used by out-of-band tests, such as our jenkins tests.

samuelklee commented 6 years ago

Ah OK...well definitely don't delete those, then!

droazen commented 6 years ago

Closing -- 99% of the files in the list above are actually in use (and I don't want people deleting test data using this approach, as it's not a reliable way of checking for usage of files).

samuelklee commented 6 years ago

113 / 643 of them were CNV test files that I deleted in #3907, which is a shade bit more than 1%... only a small fraction of these are loaded dynamically or are index/dict files, which tests will catch (and they have already, now that I check---6 / 113).

I will concede that it is likely that most of the remaining files are index files, etc., but I do see a few more bams, etc. that could stand deletion.

I'm curious as to what the best way to do this sort of thing actually is!