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data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/variantcontext/filter/CompoundFilterTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/variantcontext/filter/FilteringVariantContextIteratorTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/variantcontext/filter/GenotypeQualityFilterTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/variantcontext/filter/HeterozygosityFilterTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilterTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/variantcontext/filter/PassingVariantFilterTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/variantcontext/filter/SnpFilterTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriterUnitTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/variantcontext/writer/TabixOnTheFlyIndexCreationTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/variantcontext/writer/VCFWriterUnitTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilderUnitTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/variantcontext/writer/VariantContextWritersUnitTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/AbstractVCFCodecTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/IndexFactoryUnitTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFCodec42FeaturesTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFCodec43FeaturesTest.java: Java source, UTF-8 Unicode text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFCompoundHeaderLineUnitTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFEncoderTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFFileReaderTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFHeaderLineTranslatorUnitTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFHeaderLineUnitTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java: Variant Call Format (VCF) version 4.2\n" +, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFHeaderVersionTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFIteratorTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFMergerTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFStandardHeaderLinesUnitTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFTextTransformerTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFUtilsTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/PrintVariantsExampleTest.java: Java source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/java/htsjdk/HtsjdkTest.java: Perl5 module source, ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMCigarOverflowTest/CigarOverflowTest.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 513 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMCigarOverflowTest/cigar-64k.sam.gz: gzip compressed data, was "cigar-64k.sam", last modified: Tue Feb 13 15:05:01 2018, max compression, from Unix, original size modulo 2^32 1434684 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 28268 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai: SAMtools BAI (BAM indexing format), with 45 reference sequences data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.csi: Blocked GNU Zip Format (BGZF; gzip compatible), block length 19615 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.iii: Blocked GNU Zip Format (BGZF; gzip compatible), block length 19616 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/long_references.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 4809 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/long_references.bam.csi: Blocked GNU Zip Format (BGZF; gzip compatible), block length 104 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/uncompressed_index.bam.bai: SAMtools BAI (BAM indexing format), with 86 reference sequences data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/uncompressed_index.bam.csi: data data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SAMIntegerTagTest/variousAttributes.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 229 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SAMIntegerTagTest/variousAttributes.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/Chromosome1to10.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 3707 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/Chromosome5to9.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 1990 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/chr11sub_file1.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/chr11sub_file2.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/expected_output.sam: Sequence Alignment/Map (SAM), with header version 1.6 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file1.sam: Sequence Alignment/Map (SAM), with header version 1.6 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file2.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file3.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file4.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/expected_output.sam: Sequence Alignment/Map (SAM), with header version 1.6 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/unsorted_input/1.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/unsorted_input/2.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.dict: Sequence Alignment/Map (SAM), with header version 1.5 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.fasta: ASCII text 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Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/duplicated_reads_out_of_order.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/hanging_tab.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/inappropriate_mate_cigar_string.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_coord_sort_order.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_mate_cigar_string.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_platform_unit.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_queryname_sort_order.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/mate_cigar_and_no_oqs.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/mate_cigar_and_oqs.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/missing_fields.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/missing_platform_unit.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.cram: CRAM version 3.0 (identified as nm_tag_validation.cr\225\004) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.fa: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.fa.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/not_stored_qualities.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 144 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/not_stored_qualities.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/not_stored_qualities_more_than_100.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/seq_qual_len_mismatch.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/ValidateSamFileTest/test_samfile_version_1pt5.bam: 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data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/block_compressed.sam.gz.gzi: data data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/compressed.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 278 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/compressed.sam.gz: gzip compressed data, was "uncompressed.sam", last modified: Wed Nov 17 16:27:28 2010, from Unix, original size modulo 2^32 671 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/coordinate_sorted.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram: CRAM version 2.1 (identified as /home/chris/projects\207\021) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.first.8000.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 16689 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.cram: CRAM version 2.1 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.cram.bai: SAMtools BAI (BAM indexing format), with 1 reference sequences data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.dict: Sequence Alignment/Map (SAM), with header version 1.4 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.fa: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.fa.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.fasta: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/GRCh38mini.fa: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/GRCh38mini.fa.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.0-unMapped.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.0-unMapped.cram.crai: gzip compressed data, from Unix, original size modulo 2^32 99 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.1-unMapped.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.1-unMapped.cram.crai: gzip compressed data, from Unix, original size modulo 2^32 120 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram.crai: gzip compressed data, from Unix, original size modulo 2^32 209 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.unmapped.orig.bai: SAMtools BAI (BAM indexing format), with 2 reference sequences data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.unmapped.orig.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 18914 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/NA12878.unmapped.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/amb#amb.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/amb#amb.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/amb.fa: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/amb.fa.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ambiguityCodes.fasta: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ambiguityCodes.fasta.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/auxf#values.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/auxf#values.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/auxf#values.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/auxf.alteredForMD5test.fa: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/auxf.alteredForMD5test.fa.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/auxf.fa: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/auxf.fa.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#bounds.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#bounds.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#bounds.sam: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#clip.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#clip.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#clip.sam: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#noseq.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#noseq.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#noseq.sam: Sequence Alignment/Map (SAM), ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#pad1.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#pad1.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#pad1.sam: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#pad2.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#pad2.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#pad2.sam: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#pad3.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#pad3.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#pad3.sam: Sequence Alignment/Map (SAM), ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#unknown.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#unknown.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1#unknown.sam: Sequence Alignment/Map (SAM), ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1.fa: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1.fa.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c1WithRG.bam: Sequence Alignment/Map (SAM), ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c2#pad.2.1.cram: CRAM version 2.1 (identified as c2#pad.2.1.cram) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c2#pad.3.0.cram: CRAM version 3.0 (identified as c2#pad.3.0.cram) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c2#pad.sam: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c2.fa: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/c2.fa.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#1.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#1.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#1.sam: Sequence Alignment/Map (SAM), ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#1000.2.1.cram: CRAM version 2.1 (identified as ce#1000.2.1.cram) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#1000.3.0.cram: CRAM version 3.0 (identified as ce#1000.3.0.cram) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#1000.sam: Sequence Alignment/Map (SAM), ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#2.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#2.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#2.sam: Sequence Alignment/Map (SAM), ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#5.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#5.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#5.sam: Sequence Alignment/Map (SAM), ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#5b.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#5b.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#5b.sam: Sequence Alignment/Map (SAM), ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#containsInvalidRecords.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#large_seq.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#large_seq.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#large_seq.sam: ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#supp.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#supp.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#supp.sam: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#tag_depadded.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#tag_depadded.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#tag_depadded.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#tag_padded.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#tag_padded.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#tag_padded.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#unmap.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#unmap.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#unmap.sam: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#unmap1.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#unmap1.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#unmap1.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#unmap2.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#unmap2.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce#unmap2.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram: CRAM version 2.1 (identified as /Users/cmn/projects/T\004) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram.bai: SAMtools BAI (BAM indexing format), with 4 reference sequences data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/cramQueryTestEmpty.cram: CRAM version 2.1 (identified as /Users/cmn/projects/?\010) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/cramQueryTestEmpty.cram.bai: SAMtools BAI (BAM indexing format), with 4 reference sequences data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram: CRAM version 2.1 (identified as /home/chris/projects\201\021) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram.bai: SAMtools BAI (BAM indexing format), with 2 reference sequences data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/cramQueryWithCRAI.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/cramQueryWithCRAI.cram.crai: gzip compressed data, from Unix, original size modulo 2^32 47 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.dict: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.dict: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.dict: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.fasta: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.fasta.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/io/bzip2-test.bz2: bzip2 compressed data, block size = 900k data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/mateResolutionTest1.sam: Sequence Alignment/Map (SAM), with header version 1.5 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/mateResolutionTest2.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/md#1.2.1.cram: CRAM version 2.1 (identified as md#1.2.1.cram) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/md#1.3.0.cram: CRAM version 3.0 (identified as md#1.3.0.cram) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/md#1.sam: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/md.fa: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/md.fa.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.cram: CRAM version 3.0 (identified as lane1.edited.sorted.\247\001) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.cram.crai: gzip compressed data, from Unix, original size modulo 2^32 89 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.dict: Sequence Alignment/Map (SAM), with header version 1.0 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa.fai: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram: CRAM version 3.0 (identified as file:///Users/cnorma\233\007) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram.bai: SAMtools BAI (BAM indexing format), with 1 reference sequences data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/referenceEmbedded.NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/referenceNotRequired.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/referenceNotRequired.cram.crai: gzip compressed data, from Unix data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/samtoolsSliceMD5WithAmbiguityCodesTest.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/test.cram: CRAM version 2.1 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/test.cram.bai: SAMtools BAI (BAM indexing format), with 1 reference sequences data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/test2.cram: CRAM version 2.1 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#blank.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#blank.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#blank.sam: empty data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#large_aux.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#large_aux.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#large_aux.sam: Sequence Alignment/Map (SAM), ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#large_aux2.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#large_aux2.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#large_aux2.sam: Sequence Alignment/Map (SAM), ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#minimal.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#minimal.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#minimal.sam: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#pair.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#pair.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#pair.sam: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#repeated.2.1.cram: CRAM version 2.1 (identified as xx#repeated.2.1.cram\233') data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#repeated.3.0.cram: CRAM version 3.0 (identified as xx#repeated.3.0.cram\347) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#repeated.sam: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#rg.2.1.cram: CRAM version 2.1 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#rg.3.0.cram: CRAM version 3.0 (identified as -) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#rg.sam: Sequence Alignment/Map (SAM), with header version 1.4 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/cram/xx#tlen.2.1.cram: CRAM version 2.1 (identified as xx#tlen.2.1.cram) 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data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/interval_list/shortExampleWithEmptyLine.interval_list: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/large.txt: Variant Call Format (VCF) version 4.1, ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/sites.bed: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/soapsnp.txt: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/split/test.bin.part1: data data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/split/test.bin.part2: data data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/split/test.bin.part3: data data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/split/test.bin.split: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/tabix/4featuresHG38Header.vcf: Variant Call Format (VCF) version 4.2, ASCII text, with very long lines 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data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/tabix/testTabixIndex.vcf.gz: Blocked GNU Zip Format (BGZF; gzip compatible), block length 343 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/tabix/trioDup.vcf: Variant Call Format (VCF) version 3.3, ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/tabix/trioDup.vcf.gz: Blocked GNU Zip Format (BGZF; gzip compatible), block length 1324 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/tabix/trioDup.vcf.gz.tbi: Blocked GNU Zip Format (BGZF; gzip compatible), block length 295 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/test: cannot open `data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/test' (No such file or directory) with: cannot open `with' (No such file or directory) spaces.vcf: cannot open `spaces.vcf' (No such file or directory) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/test.bed: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/test.gff: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/test.tabix.bed: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/test.tabix.bed.gz: Blocked GNU Zip Format (BGZF; gzip compatible), block length 87 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/test.tabix.bed.gz.tbi: Blocked GNU Zip Format (BGZF; gzip compatible), block length 92 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/test.tabix.bed.idx: data data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/test.vcf: Variant Call Format (VCF) version 4.1, ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/test.vcf.bgz: Blocked GNU Zip Format (BGZF; gzip compatible), block length 820 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/test.vcf.gz: gzip compressed data, was "test.vcf", last modified: Thu Apr 30 13:19:14 2015, from Unix, original size modulo 2^32 1645 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/testGeliText.txt: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/testIntervalList.list: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/tmp/.gitignore: empty data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/trioDup.vcf: Variant Call Format (VCF) version 3.3, ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/vcfexample.vcf: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/vcfexample.vcf.gz: Blocked GNU Zip Format (BGZF; gzip compatible), block length 442 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/vcfexample.vcf.gz.tbi: Blocked GNU Zip Format (BGZF; gzip compatible), block length 85 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/vcfexample.vcf.truncated.gz: Blocked GNU Zip Format (BGZF; gzip compatible), block length 442 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/vcfexample.vcf.truncated.hdr.gz: Blocked GNU Zip Format (BGZF; gzip compatible), block length 442 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/BCFVersion22Uncompressed.bcf: Binary Call Format (BCF) version 2.2 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/HiSeq.10000.vcf: Variant Call Format (VCF) version 4.0, ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/HiSeq.10000.vcf.bgz: Blocked GNU Zip Format (BGZF; gzip compatible), block length 16687 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/HiSeq.10000.vcf.bgz.tbi: Blocked GNU Zip Format (BGZF; gzip compatible), block length 2515 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/Homo_sapiens_assembly38.tile_db_header.vcf: Variant Call Format (VCF) version 4.1, ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf: Variant Call Format (VCF) version 4.1, ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/NA12891.fp.vcf: Variant Call Format (VCF) version 4.1, ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/NA12891.vcf: Variant Call Format (VCF) version 4.1, ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/NA12891.vcf.gz: Blocked GNU Zip Format (BGZF; gzip compatible), block length 3126 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/VCF4HeaderTest.vcf: Variant Call Format (VCF) version 4.0, ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/VQSR.mixedTest.recal: Variant Call Format (VCF) version 4.1, ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/Vcf4.2WithSourceVersionInfoFields.vcf: Variant Call Format (VCF) version 4.2, ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/VcfThatLacksAnIndex: cannot open `data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/VcfThatLacksAnIndex' (No such file or directory) but: cannot open `but' (No such file or directory) has: cannot open `has' (No such file or directory) a: cannot open `a' (No such file or directory) space.vcf: cannot open `space.vcf' (No such file or directory) data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/VcfThatLacksAnIndex.bcf: Binary Call Format (BCF) version 2.1 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/VcfThatLacksAnIndex.vcf: Variant Call Format (VCF) version 4.1, ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/VcfThatLacksAnIndex.vcf.bgz: Blocked GNU Zip Format (BGZF; gzip compatible), block length 820 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/VcfThatLacksAnIndex.vcf.gz: gzip compressed data, was "test.vcf", last modified: Thu Apr 30 13:19:14 2015, from Unix, original size modulo 2^32 1645 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/breakpoint.vcf: Variant Call Format (VCF) version 4.1, ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/corrupt_file_that_starts_with_#.vcf: ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/dbsnp_135.b37.1000.vcf: Variant Call Format (VCF) version 4.1, ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/diagnosis_targets_testfile.vcf: Variant Call Format (VCF) version 4.1, ASCII text, with very long lines data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/ex2.bgzf.bcf.csi: Blocked GNU Zip Format (BGZF; gzip compatible), block length 101 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/ex2.vcf: Variant Call Format (VCF) version 4.1, ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/phased.vcf: Variant Call Format (VCF) version 4.1, ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/phased.vcf.idx: data data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/serialization_test.bcf: Binary Call Format (BCF) version 2.1 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/serialization_test.bcf.idx: data data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/structuralvariants.vcf: Variant Call Format (VCF) version 4.2, ASCII text data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/test.vcf.bgz: Blocked GNU Zip Format (BGZF; gzip compatible), block length 820 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/test.vcf.bgz.tbi: Blocked GNU Zip Format (BGZF; gzip compatible), block length 117 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/test.vcf.gz: gzip compressed data, was "test.vcf", last modified: Thu Apr 30 13:19:14 2015, from Unix, original size modulo 2^32 1645 data/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/variant/test1.vcf: Variant Call Format (VCF) version 4.1, ASCII text, with very long lines 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