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• Arabidopsis-C99826.embl
• Arabidopsis-C99826.fna
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• attribute_after_dot.gff3
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• bar.fas
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• BLOSUM62
• blosum62.c
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• broken_hmmer.hmm
• cds_check_fail_1.gff3
• cds_check_fail_2.gff3
• cds_check_fail_3.gff3
• cds_check_fail_4.gff3
• cds_check_succ_1.gff3
• cds_check_succ_10.gff3
• cds_check_succ_11.gff3
• cds_check_succ_12.gff3
• cds_check_succ_2.gff3
• cds_check_succ_3.gff3
• cds_check_succ_4.gff3
• cds_check_succ_5.gff3
• cds_check_succ_6.gff3
• cds_check_succ_7.gff3
• cds_check_succ_8.gff3
• cds_check_succ_9.gff3
• cds_feature_with_multiple_parents.gff3
• cds_feature_with_multiple_parents_tidied.gff3
• cds_with_multiple_parents_1.gff3
• cds_with_multiple_parents_1_tidied.gff3
• cds_with_multiple_parents_2.gff3
• cds_with_multiple_parents_2_tidied.gff3
• Copysorttest.embl
• Copysorttest.fna
• Copysorttest.gbk
• corrupt.fas
• corrupt.gff3
• corrupt_gff3_header.txt
• corrupt_large.gff3
• corrupt_target_attribute.gff3
• corruptpatternfile.fna
• csa_example_consensus_spliced_alignments.gff3
• csa_example_spliced_alignments.gff3
• csr_testcase.fastq
• csr_testcase_r0.fastq
• csr_testcase_r10.fastq
• csr_testcase_r23.fastq
• csr_testcase_r96.fastq
• custom_streams_ref.txt
• cycle_simple.gff3
• dbxref.gff3
• dbxref_invalid.gff3
• dbxref_invalid2.gff3
• description_test.fastq
• description_test2.fastq
• dna_hmmer.hmm
• double_free.gff3
• Duplicate.embl
• Duplicate.fna
• Duplicate.gbk
• Duplicate.shreddered
• duplicate.XRF_abbr
• duplicate_attribute.gff3
• duplicate_attribute_fixed.gff3
• dust.fna
• dust.link5.out
• dust.out
• dust.threshold3.out
• dust.window32.out
• dynbuf.gff3
• Ecoli-section1.fna
• Ecoli-section2.fna
• ecolicmp-neg.of
• ecolicmp-se.of
• ecolicmp.of
• ecolicmp250.of
• eden.gff3
• eden.linesorted.gff3
• eden_only_annotation.gff3
• embl_test1.embl
• embl_test2.embl
• embl_test3.embl
• embl_test4.embl
• embl_test5.embl
• embl_test5.fas
• embl_test6.embl
• empty.gff3
• empty_attribute.gff3
• empty_attribute_name.gff3
• empty_attribute_value.gff3
• empty_file
• empty_id_attribute.gff3
• empty_other_attribute.gff3
• empty_parent_attribute.gff3
• empty_seq.fas
• encode_known_genes_Mar07.gff3
• encode_known_genes_Mar07.seqids
• example_1.bam
• example_1.fa
• example_1.fa.fai
• example_1.sam.extract
• example_1.sam.gz
• example_1.sorted.bam
• example_1.sorted.bam.bai
• fail_arrow_width.style
• fail_background_color.style
• fail_block_caption_font_size.style
• fail_block_caption_space.style
• fail_collapse.style
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• fail_fill.style
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• fail_split.style
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• fail_track_caption_space.style
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• fail_track_vspace.style
• fail_unit.style
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• fasta_seq.fas
• fasta_seq.gff3
• fastq_long.fastq
• fastq_problem.fasta
• fastq_problem.fastq.gz
• fastq_problem2.fasta
• fastq_problem2.fastq.gz
• fib25.fas.gz
• filter_luafilter_filtered_LTR.gff3
• filter_luafilter_filtered_orf_frame.gff3
• filter_luafilter_filtered_orf_pos.gff3
• filter_luafilter_filtered_orfs.gff3
• filter_luafilter_test.gff3
• filter_luafilter_test_no_frame_attribute.gff3
• filter_nh_file01.gff3
• filter_nh_file02.gff3
• filter_nh_file03.gff3
• filter_nh_file04.gff3
• filter_targetbest_complex_test.gff3
• filter_targetbest_complex_test.out
• filter_targetbest_multiple_test.gff3
• filter_targetbest_simple_test.gff3
• filter_targetbest_simple_test.out
• foo.32.des
• foo.32.esq
• foo.32.info_map
• foo.32.info_nomap
• foo.32.sds
• foo.32.ver0.al1
• foo.32.ver0.esq
• foo.64.des
• foo.64.esq
• foo.64.info_map
• foo.64.info_nomap
• foo.64.sds
• foo.64.ver0.al1
• foo.64.ver0.esq
• foo.fas
• foo_width4.fas
• foobar.fas
• foofoo.fas
• foofoofoo.fas
• foorcfoo.fas
• foorcfoofoo.fas
• frompos.fas
• gap_fail1.gff3
• gap_fail2.gff3
• gap_fail3.gff3
• gap_fail4.gff3
• gap_fail5.gff3
• gap_fail6.gff3
• gap_fail7.gff3
• genbank_test.gbk
• genbank_test1.gbk
• genbank_test2.fas
• genbank_test2.gbk
• genbank_test3.gbk
• genbank_test4.gbk
• genbank_test5.gbk
• genbank_test6.gbk
• genbank_test7.gbk
• genbank_test8.gbk
• genome_stream_stdin.gff3
• gff3_file_1_short.txt
• gff3_file_1_short_sorted.txt
• gff3_numeric_a.gff
• gff3_numeric_mixed.gff3
• gff3_numeric_mixed.out
• gff3_numeric_only.gff3
• gff3_numeric_only.out
• gmap2gff3_prob.gmap
• gmap2gff3_prob.out
• graphics_curve_test_coords.txt
• graphics_test.out
• gt.supp
• gt_bioseq_fail_1.fas
• gt_bioseq_fail_2.fas
• gt_bioseq_fail_3.fas
• gt_bioseq_fail_4.fas
• gt_bioseq_fail_5.fas
• gt_bioseq_fail_6.fas
• gt_bioseq_fail_7.fas
• gt_bioseq_seqlengthdistri.out
• gt_bioseq_succ_1.fas
• gt_bioseq_succ_2.fas
• gt_bioseq_succ_3.fas
• gt_bioseq_succ_3.gc
• gt_bioseq_succ_3.out1
• gt_bioseq_succ_3.out2
• gt_bioseq_succ_3.out3
• gt_cds_descrange_multi.fas
• gt_cds_descrange_multi.in
• gt_cds_descrange_multi.out
• gt_cds_descrange_multi_fail_1.fas
• gt_cds_descrange_multi_fail_2.fas
• gt_cds_descrange_wrong_id.fas
• gt_cds_descrange_wrong_range.fas
• gt_cds_nostartcodon_nofinalstopcodon.in
• gt_cds_nostartcodon_nofinalstopcodon.out
• gt_cds_test_1.fas
• gt_cds_test_1.in
• gt_cds_test_1.out
• gt_cds_test_10.fas
• gt_cds_test_10.in
• gt_cds_test_10.out
• gt_cds_test_11.fas
• gt_cds_test_11.in
• gt_cds_test_11.out
• gt_cds_test_12.fas
• gt_cds_test_12.in
• gt_cds_test_12.out
• gt_cds_test_13.fas
• gt_cds_test_13.in
• gt_cds_test_13.out
• gt_cds_test_14.fas
• gt_cds_test_14.in
• gt_cds_test_14.out
• gt_cds_test_2.fas
• gt_cds_test_2.in
• gt_cds_test_2.out
• gt_cds_test_3.fas
• gt_cds_test_3.in
• gt_cds_test_3.out
• gt_cds_test_4.fas
• gt_cds_test_4.in
• gt_cds_test_4.out
• gt_cds_test_5.fas
• gt_cds_test_5.in
• gt_cds_test_5.out
• gt_cds_test_6.fas
• gt_cds_test_6.in
• gt_cds_test_6.out
• gt_cds_test_7.fas
• gt_cds_test_7.in
• gt_cds_test_7.out
• gt_cds_test_8.fas
• gt_cds_test_8.in
• gt_cds_test_8.out
• gt_cds_test_9.fas
• gt_cds_test_9.in
• gt_cds_test_9.out
• gt_cds_test_descrange.fas
• gt_cds_test_descrange.in
• gt_cds_test_descrange.out
• gt_chseqids_test_1.chseqids
• gt_chseqids_test_1.gff3
• gt_chseqids_test_1.out
• gt_chseqids_test_2.chseqids
• gt_chseqids_test_2.gff3
• gt_chseqids_test_2.out
• gt_chseqids_test_3.chseqids
• gt_chseqids_test_3.gff3
• gt_chseqids_test_4.chseqids
• gt_chseqids_test_4.gff3
• gt_chseqids_test_4.out
• gt_chseqids_test_5.chseqids
• gt_chseqids_test_5.gff3
• gt_chseqids_test_5.out
• gt_chseqids_test_5.sorted_out
• gt_chseqids_test_6.chseqids
• gt_chseqids_test_6.gff3
• gt_chseqids_test_6.out
• gt_csa_prob_1.debug
• gt_csa_prob_1.in
• gt_csa_prob_1.out
• gt_csa_prob_2.debug
• gt_csa_prob_2.in
• gt_csa_prob_2.out
• gt_csa_prob_3.debug
• gt_csa_prob_3.in
• gt_csa_prob_3.out
• gt_csa_prob_4.debug
• gt_csa_prob_4.in
• gt_csa_prob_4.out
• gt_csa_prob_5.in
• gt_csa_prob_5.out
• gt_csa_prob_6.in
• gt_csa_prob_6.out
• gt_csa_test_1.in
• gt_encseq_col_test1.fasta
• gt_encseq_eqlen_last_empty.fas
• gt_eval_ltr_prob_1.out
• gt_eval_ltr_prob_1.prediction
• gt_eval_ltr_prob_1.reality
• gt_eval_ltr_test_1.in
• gt_eval_ltr_test_1.out
• gt_eval_ltr_test_2.out
• gt_eval_ltr_test_2.prediction
• gt_eval_ltr_test_2.reality
• gt_eval_ltr_test_3.out
• gt_eval_ltr_test_3.prediction
• gt_eval_ltr_test_3.reality
• gt_eval_ltr_test_4.out
• gt_eval_ltr_test_4.prediction
• gt_eval_ltr_test_4.reality
• gt_eval_ltr_test_5.out
• gt_eval_ltr_test_5.prediction
• gt_eval_ltr_test_5.reality
• gt_eval_ltr_test_6.out
• gt_eval_ltr_test_6.prediction
• gt_eval_ltr_test_6.reality
• gt_eval_ltr_test_7.out
• gt_eval_ltr_test_7.prediction
• gt_eval_ltr_test_7.reality
• gt_eval_ltr_test_8.out
• gt_eval_ltr_test_8.prediction
• gt_eval_ltr_test_8.reality
• gt_eval_ltr_test_9.out
• gt_eval_ltr_test_9.prediction
• gt_eval_ltr_test_9.reality
• gt_eval_prob_1.out
• gt_eval_prob_1.out_swapped
• gt_eval_prob_1.prediction
• gt_eval_prob_1.reality
• gt_eval_test_1.in
• gt_eval_test_1.out
• gt_eval_test_10.in
• gt_eval_test_10.out
• gt_eval_test_2.nuc
• gt_eval_test_2.out
• gt_eval_test_2.prediction
• gt_eval_test_2.reality
• gt_eval_test_3.nuc
• gt_eval_test_3.out
• gt_eval_test_3.prediction
• gt_eval_test_3.reality
• gt_eval_test_4.nuc
• gt_eval_test_4.out
• gt_eval_test_4.prediction
• gt_eval_test_4.reality
• gt_eval_test_5.nuc
• gt_eval_test_5.out
• gt_eval_test_5.prediction
• gt_eval_test_5.reality
• gt_eval_test_6.nuc
• gt_eval_test_6.out
• gt_eval_test_6.prediction
• gt_eval_test_6.reality
• gt_eval_test_7.nuc
• gt_eval_test_7.out
• gt_eval_test_7.prediction
• gt_eval_test_7.reality
• gt_eval_test_8.nuc
• gt_eval_test_8.out
• gt_eval_test_8.prediction
• gt_eval_test_8.reality
• gt_eval_test_9.in
• gt_eval_test_9.out
• gt_evalviz_test.out
• gt_evalviz_test.prediction
• gt_evalviz_test.reality
• gt_extractfeat_mappings.fas
• gt_extractfeat_mappings.gff3
• gt_extractfeat_mappings.md5.gff3
• gt_extractfeat_mappings_md5.fas
• gt_extractfeat_mappings_ref.fas
• gt_extractfeat_mappings_ref.md5.fas
• gt_extractfeat_mappings_sep1.fas
• gt_extractfeat_mappings_sep2.fas
• gt_extractfeat_mappings_seprm.lua
• gt_extractfeat_mappings_seprm_bar.fas
• gt_extractfeat_mappings_seprm_baz.fas
• gt_extractfeat_mappings_seprm_foo.fas
• gt_extractfeat_mappings_seprm_quux.fas
• gt_extractfeat_matchdescstart_1.fas
• gt_extractfeat_matchdescstart_1.gff3
• gt_extractfeat_matchdescstart_1.out
• gt_extractfeat_matchdescstart_2.fas
• gt_extractfeat_phase.fas
• gt_extractfeat_phase.gff3
• gt_extractfeat_phase.out
• gt_extractfeat_phase_fix.gff3
• gt_extractfeat_phase_fix.out
• gt_extractfeat_retainids.fas
• gt_extractfeat_retainids.gff3
• gt_extractfeat_retainids_join.fas
• gt_extractfeat_seqid.fas
• gt_extractfeat_seqid_target.fas
• gt_extractfeat_seqid_target.gff3
• gt_extractfeat_succ_1.fas
• gt_extractfeat_succ_1.fas.gz
• gt_extractfeat_succ_1.gff3
• gt_extractfeat_succ_1.out
• gt_extractfeat_succ_2.fas
• gt_extractfeat_succ_2.gff3
• gt_extractfeat_succ_2.out1
• gt_extractfeat_succ_2.out2
• gt_extractfeat_succ_2.out3
• gt_extractfeat_succ_3.fas
• gt_extractfeat_succ_3.gff3
• gt_extractfeat_succ_3.out
• gt_extractfeat_target.fas
• gt_fingerprint_extract.out
• gt_gff3_addintrons_overlapping_exons.gff3
• gt_gff3_addintrons_overlapping_exons_with_introns.gff3
• gt_gff3_fail_1.gff3
• gt_gff3_illegal_feature_start.gff3
• gt_gff3_illegal_region_start.gff3
• gt_gff3_linesort.in.gff3
• gt_gff3_linesort.out.gff3
• gt_gff3_linesort2.in.gff3
• gt_gff3_linesort2.out.gff3
• gt_gff3_offset_test.gff3
• gt_gff3_offset_test.out-1
• gt_gff3_offset_test.out-999
• gt_gff3_offset_test.out1000
• gt_gff3_offsetfile_test.gff3
• gt_gff3_offsetfile_test.offsetfile
• gt_gff3_offsetfile_test.out
• gt_gff3_phases1.gff3
• gt_gff3_phases1.out
• gt_gff3_phases2.gff3
• gt_gff3_phases3.gff3
• gt_gff3_phases3.out
• gt_gff3_phases4.gff3
• gt_gff3_phases5.gff3
• gt_gff3_phases6.gff3
• gt_gff3_phases7.gff3
• gt_gff3_prob_1.gff3
• gt_gff3_prob_10.in
• gt_gff3_prob_10.out
• gt_gff3_prob_11.in
• gt_gff3_prob_11.out
• gt_gff3_prob_12.gff3
• gt_gff3_prob_13.gff3
• gt_gff3_prob_2.in
• gt_gff3_prob_2.out
• gt_gff3_prob_3.gff3
• gt_gff3_prob_4.gff3
• gt_gff3_prob_5.in
• gt_gff3_prob_5.out
• gt_gff3_prob_6.in
• gt_gff3_prob_7.in
• gt_gff3_prob_7.sorted
• gt_gff3_prob_7.unsorted
• gt_gff3_prob_8.in
• gt_gff3_prob_8.out
• gt_gff3_prob_9.in
• gt_gff3_prob_9.out
• gt_gff3_range_check.gff3
• gt_gff3_range_check2.gff3
• gt_gff3_range_check3.gff3
• gt_gff3_test_1.in
• gt_gff3_test_1.out
• gt_gff3_test_10.gff3
• gt_gff3_test_11.gff3
• gt_gff3_test_12.gff3
• gt_gff3_test_13.gff3
• gt_gff3_test_14.gff3
• gt_gff3_test_15.gff3
• gt_gff3_test_15.out
• gt_gff3_test_16.gff3
• gt_gff3_test_17.gff3
• gt_gff3_test_18.gff3
• gt_gff3_test_19.gff3
• gt_gff3_test_2.gff3
• gt_gff3_test_20.gff3
• gt_gff3_test_21.gff3
• gt_gff3_test_22.gff3
• gt_gff3_test_23.gff3
• gt_gff3_test_24.gff3
• gt_gff3_test_25.gff3
• gt_gff3_test_25.out
• gt_gff3_test_26.gff3
• gt_gff3_test_27.gff3
• gt_gff3_test_3.gff3
• gt_gff3_test_4.gff3
• gt_gff3_test_5.gff3
• gt_gff3_test_6.gff3
• gt_gff3_test_7.gff3
• gt_gff3_test_8.gff3
• gt_gff3_test_9.gff3
• gt_gff3_undefined_range.gff3
• gt_gff3_undefined_range_parent.gff3
• gt_gff3_undefined_range_tidy.gff3
• gt_gff3_whitespace_problem.gff3
• gt_gtf_to_gff3_test.gff3
• gt_gtf_to_gff3_test.gtf
• gt_gtf_to_gff3_test_fail_no_flank.gtf
• gt_gtf_to_gff3_test_inconsistent_strand1.gtf
• gt_gtf_to_gff3_test_inconsistent_strand2.gtf
• gt_gtf_to_gff3_test_stop_codon_in_cds.gff3
• gt_gtf_to_gff3_test_stop_codon_in_cds.gtf
• gt_gtf_to_gff3_test_stop_codon_in_cds2.gff3
• gt_gtf_to_gff3_test_stop_codon_in_cds2.gtf
• gt_linspace_align_affine_test_1.fas
• gt_linspace_align_affine_test_2.fas
• gt_linspace_align_affine_test_3.fas
• gt_linspace_align_global_affine_special_cases.out
• gt_linspace_align_global_affine_test_1.out
• gt_linspace_align_global_affine_test_2.out
• gt_linspace_align_global_linear_special_cases.out
• gt_linspace_align_global_test_1.out
• gt_linspace_align_global_test_2.out
• gt_linspace_align_local_affine_special_cases.out
• gt_linspace_align_local_affine_test_1.out
• gt_linspace_align_local_linear_special_cases.out
• gt_linspace_align_local_test_1.out
• gt_linspace_align_local_test_2.out
• gt_linspace_align_local_test_3.out
• gt_linspace_align_special_cases_test_1.fas
• gt_linspace_align_special_cases_test_2.fas
• gt_linspace_align_test_1.fas
• gt_linspace_align_test_2.fas
• gt_linspace_align_test_3.fas
• gt_linspace_align_test_4.fas
• gt_loccheck_containment_fail.gff3
• gt_merge_prob_1.in1
• gt_merge_prob_1.in2
• gt_merge_prob_1.out
• gt_merge_prob_2.in1
• gt_merge_prob_2.in2
• gt_merge_prob_2.out
• gt_mmapandread_test_1.in
• gt_mmapandread_test_2.in
• gt_mmapandread_test_3.in
• gt_mmapandread_test_4.in
• gt_mutate_test_1.fas
• gt_mutate_test_1.out
• gt_mutate_test_2.fas
• gt_mutate_test_2.out
• gt_mutate_test_both.out
• gt_regioncov_test_1.out
• gt_regioncov_test_2.out
• gt_select_encode.out
• gt_select_test.out
• gt_select_test_contain.1000-8999
• gt_select_test_contain.1000-9000
• gt_select_test_contain.1001-9000
• gt_seqlensort_test.fas
• gt_seqlensort_test_sorted.fas
• gt_seqorder_test.fas
• gt_seqorder_test_revsort.fas
• gt_seqorder_test_sort.fas
• gt_seqorder_test_sorthdr.fas
• gt_seqorder_test_sortlength.fas
• gt_sequniq_rev_bug.fas
• gt_sequniq_rev_bug.out
• gt_sketch_multiline_without_parent.gff3
• gt_sketch_textwidth.gff3
• gt_sketch_textwidth_0.recmaps
• gt_sketch_textwidth_1.recmaps
• gt_sketch_textwidth_2.recmaps
• gt_splicesiteinfo_prob_1.gff3
• gt_splicesiteinfo_test_1.fas
• gt_splicesiteinfo_test_1.gff3
• gt_splicesiteinfo_test_1.out
• gt_splicesiteinfo_test_2.fas
• gt_splicesiteinfo_test_2.gff3
• gt_splicesiteinfo_test_2.out
• gt_splicesiteinfo_test_3.gff3
• gt_splicesiteinfo_test_4.fas
• gt_splicesiteinfo_test_4.gff3
• gt_splicesiteinfo_test_4.out
• gt_splicesiteinfo_test_5.fas
• gt_splicesiteinfo_test_5.gff3
• gt_splicesiteinfo_test_5.out
• gt_splicesiteinfo_test_6.gff3
• gt_splicesiteinfo_test_6.mapping
• gt_stat_cdslengthdistri.out
• gt_stat_exonnumberdistri_encode.out
• gt_stat_exonnumberdistri_standard.out
• gt_stat_source.out
• gt_stat_test_1.out
• gt_stat_test_2.out
• gt_stat_test_3.out
• gt_stat_test_4.out
• gt_stat_test_5.out
• gt_stat_test_6.out
• gt_translate.in
• gt_translate.out
• gt_uniq_test_1.gff3
• gt_uniq_test_1.out
• gt_uniq_test_2.gff3
• gt_uniq_test_2.out
• gt_uniq_test_3.gff3
• gt_uniq_test_3.out
• gt_uniq_test_4.gff3
• gt_uniq_test_4.out
• gt_uniq_test_5.gff3
• gt_uniq_test_5.out
• gt_uniq_test_6.gff3
• gt_uniq_test_6.out
• gt_view.sh
• gt_view_prob_1.gff3
• gt_view_prob_2.gff3
• header.gff3
• header_3_1_21.gff3
• identity_score_matrix
• illegal_is_circular_value.gff3
• illegal_uppercase_attribute.gff3
• inconsistent_sequence_ids.gff3
• interfeat_pseudo.gff3
• interfeat_pseudo.out
• invalidregex.XRF_abbr
• invalidtag.XRF_abbr
• is_circular_example.gff3
• is_circular_example_with_sequence_region.gff3
• linesort_test_1.gff3
• linesort_test_1.out
• linesort_test_2.gff3
• linesort_test_2.out
• linesort_test_3.gff3
• linesort_test_3.out
• lua_aaseq.fas
• lua_dnaseq.fas
• marker.fas
• marker.out
• match_part_gap.gff3
• matchtool_blast.db
• matchtool_blast.match
• matchtool_blast.match.bz2
• matchtool_blast.match.gz
• matchtool_blast.out
• matchtool_blast_corrupt.match
• matchtool_blast_empty.match
• matchtool_blast_empty.out
• matchtool_blast_neg.match
• matchtool_blast_too_few.match
• matchtool_blast_too_many.match
• matchtool_blastalln.out
• matchtool_blastallp.out
• matchtool_blastn.db
• matchtool_blastn.out
• matchtool_blastn.query
• matchtool_blastp.db
• matchtool_blastp.out
• matchtool_blastp.query
• matchtool_open.match
• matchtool_open.match.bz2
• matchtool_open.match.gz
• matchtool_open.out
• matchtool_open_corrupt.match
• matchtool_open_empty.match
• matchtool_open_empty.out
• matchtool_open_neg.match
• matchtool_open_too_few.match
• matchtool_open_too_many.match
• matchtool_see-ext.match
• md5_seqid_missing_seqid.gff3
• md5_seqid_too_short.gff3
• md5_seqid_wrong_separator.gff3
• merge_with_seq.gff3
• mergefeat.gff3
• mergefeat.out
• mergefeat_no_merge.gff3
• meta_directives.gff3
• mini_peptide_repeats.fas
• minimal_fasta.gff3
• minimal_fasta_without_directive.gff3
• missing_gff3_header.gff3
• missingabbr.XRF_abbr
• multi_feature_different_sequence_id.gff3
• multi_feature_multi.gff3
• multi_feature_orphan_fail.gff3
• multi_feature_orphan_succ.gff3
• multi_feature_simple.gff3
• multi_feature_simple_reverted.gff3
• multi_feature_undefined_parent.gff3
• multi_feature_with_different_parent_1.gff3
• multi_feature_with_different_parent_1_tidy.gff3
• multi_feature_with_different_parent_2.gff3
• multi_feature_with_different_parent_2_tidy.gff3
• multiple_header_lines.gff3
• multiple_top_level_parents.gff3
• not_sorted.gff3
• nowildcardatend.fna
• nowildcardatend_rev.fna
• order_sketch_out.txt
• orphaned_parent.gff3
• png_devel_1.gff3
• png_devel_10.gff3
• png_devel_11.gff3
• png_devel_12.gff3
• png_devel_2.gff3
• png_devel_3.gff3
• png_devel_4.gff3
• png_devel_5.gff3
• png_devel_6.gff3
• png_devel_7.gff3
• png_devel_8.gff3
• png_devel_9.gff3
• png_prob_1.gff3
• png_prob_2.gff3
• png_prob_3.gff3
• png_prob_4.gff3
• png_prob_5.gff3
• png_test_1.gff3
• png_test_3.gff3
• problematic.fas
• pseudo_feature_minimal.gff3
• Q1.gz
• query-fwd.match
• query-rev.match
• Query1
• Query2
• Query3
• Random-Small.embl
• Random-Small.fna
• Random-Small.gbk
• Random.embl
• Random.fna
• Random.gbk
• Random.magicmatch
• Random159.embl
• Random159.fna
• Random159.gbk
• Random160.embl
• Random160.fna
• Random160.gbk
• Random80.fna
• RandomN.embl
• RandomN.fna
• RandomN.gbk
• RandomN.magicmatch
• rcr_testreads.fq
• rcr_testreads_on_seq.bam
• rcr_testreads_on_seq.bam.bai
• rcr_testreads_on_seq.sam
• rcr_testseq.fa
• rcr_testseq.fa.fai
• Reads1.fna
• Reads2-spmitv.txt
• Reads2.fna
• Reads3.fna
• Reference1
• Reference2
• regionmapping_1.lua
• regionmapping_2.lua
• regionmapping_3.lua
• regionmapping_4.lua
• regionmapping_5.lua
• regionmapping_6.lua
• Repfind-example.fna
• resetsource.gff3
• resetsource.out
• retain_1.gff3
• retain_2.gff3
• retain_both.gff3
• retainids.gff3
• reverse_feature_order.gff3
• reverse_feature_order.out
• reverse_feature_order_multiple_parents.gff3
• reverse_feature_order_multiple_parents.out
• reverse_standard_gene_as_tree.gff3
• revision_numbers.gff3
• revision_numbers.out
• sain.fna
• Scaffold_102.fa
• Scaffold_102.gff3
• Scaffold_102.joined.out
• Scaffold_102.out
• script_example.out
• script_filter_output.txt
• see-ext-ani-at1MB-U8.txt
• see-ext-at1MB-400-al-from-dtrace.matches
• see-ext-at1MB-400-cigar.matches
• see-ext-at1MB-400-cigarX.matches
• see-ext-at1MB-400-dtrace.matches
• see-ext-at1MB-400-evalue-bitscore.matches
• see-ext-at1MB-400-seqdesc.matches
• see-ext-at1MB-400-seqlength.matches
• see-ext-at1MB-400-trace.matches
• see-ext-at1MB-500-al.matches
• see-ext-at1MB-500-alignment-seed_in_algn.matches
• see-ext-at1MB-500-failed_seed.matches
• see-ext-at1MB-Atinsert100-evalue-bitscore-cigar-seqlength.matches
• see-ext-at1MB-Atinsert100-evalue-bitscore-cigarX-seqlength.matches
• see-ext-at1MB-maxmat250.matches
• see-ext-at1MB-mincoverage200-tabsep.matches
• see-ext-at1MB-U8-200-al-from-dtrace.matches
• see-ext-at1MB-u8-failed_seed-evalue.matches
• see-ext-at1MB-u8-maxmat30.matches
• see-ext-at1MB-u8.matches
• see-ext-at1MB.matches
• see-ext-fastq_long-u8.matches
• see-ext-fastq_long.matches
• see-ext-paired-u8.matches
• see-ext-paired.matches
• see-ext-U8-evalue-bitscore.matches
• seedextend1.out.gz
• seedextend2.out.gz
• seedextend3.out
• self_referential.gff3
• seqfilter_prot_wildcard.fas
• seqfilter_prot_wildcard_no_wildcards.fas
• sequence_region_1.gff3
• sequence_region_2.gff3
• sequence_region_joined.gff3
• sequence_region_negative_end.gff3
• sequence_region_negative_start.gff3
• shorten_desc.clipped.fas
• shorten_desc.embl
• shorten_desc.fas
• shorten_desc.gbk
• shorthand.XRF_abbr
• simple_orphan.gff3
• Small.embl
• Small.fna
• Small.gbk
• small_poly.fas
• Smalldup.fna
• solid_color_reads.fastq
• splice_site_prob.gff3
• splice_site_prob.out
• Splintoptions
• standard_fasta_example.fas
• standard_fasta_example.gff3
• standard_fasta_example_only_annotation.gff3
• standard_fasta_example_rejoined.gff3
• standard_fasta_example_with_id.gff3
• standard_fasta_example_with_id.out
• standard_gene_as_dag.gff3
• standard_gene_as_dag_sorted.gff3
• standard_gene_as_tree.blocks
• standard_gene_as_tree.gff3
• standard_gene_as_tree.header
• standard_gene_as_tree.hotspots
• standard_gene_as_tree.recmaps
• standard_gene_as_tree.types
• standard_gene_simple.gff3
• standard_gene_with_introns_as_tree.gff3
• sw100K1.fsa
• sw100K1.magicmatch
• sw100K2.fsa
• sw100K2.magicmatch
• target_attribute_swapped_range.gff3
• target_attribute_without_strand.gff3
• terminator_separation.gff3
• test.XRF_abbr
• test1.fasta
• test1.fastq
• test10_multiline.fastq
• test2_wrong_begin.fastq
• test3_different_seqnames.fastq
• test4_different_seqlengths.fastq
• test5_tricky.fastq
• test6_premature_end.fastq
• test7_empty_seq.fastq
• test9_uneven_length.fastq
• test_1_multiset.txt
• test_1_result.txt
• test_1_text.txt
• test_2_multiset.txt
• test_2_result.txt
• test_2_text.txt
• test_3_multiset.txt
• test_3_result.txt
• test_3_text.txt
• testspec.lua
• testspec_fi.lua
• trackname1.out
• trackname1.style
• transcript.gff3
• transcript.png
• transcript.style
• transient_edges_bug.gff3
• trembl-difflenkey.faa
• trembl-emptykey.faa
• trembl-eqlen.faa
• trembl-keys.txt
• trembl-wrongkey.txt
• trembl.faa
• trkeys-result.txt
• trkeys.txt
• tRNA.dos.fas
• trna_glutamine.embl
• trna_glutamine.fna
• trna_glutamine.gbk
• trna_glutamine.out
• TTT-small-wrongchar.embl
• TTT-small-wrongchar.fna
• TTT-small-wrongchar.gbk
• TTT-small.embl
• TTT-small.fna
• TTT-small.gbk
• TTTN.fna
• two_fasta_seqs.gff3
• two_fasta_seqs_without_sequence_regions.gff3
• U89959_cds.fas
• U89959_cds.gff3
• U89959_cds_1.fas
• U89959_cds_10.fas
• U89959_cds_11.fas
• U89959_cds_12.fas
• U89959_cds_13.fas
• U89959_cds_14.fas
• U89959_cds_16.fas
• U89959_cds_2.fas
• U89959_cds_21.fas
• U89959_cds_22.fas
• U89959_cds_23.fas
• U89959_cds_24.fas
• U89959_cds_25.fas
• U89959_cds_3.fas
• U89959_cds_4.fas
• U89959_cds_5.fas
• U89959_cds_6.fas
• U89959_cds_9.fas
• U89959_csas.gff3
• U89959_csas.gff3md5
• U89959_csas.gff3md5old
• U89959_ests.checklist
• U89959_ests.checklist_uniq
• U89959_ests.fas
• U89959_ests.magicmatch
• U89959_ests_gi_8690080_soft_masked.fas
• U89959_ests_gi_8690080_unmasked.checklist
• U89959_ests_no_wildcards.fas
• U89959_ests_unique.fas
• U89959_genomic.fas
• U89959_genomic.magicmatch
• U89959_ginums.corrupt
• U89959_ginums.out
• U89959_ginums.txt
• U89959_sas.gff3
• U89959_sas.gff3md5
• U89959_sas.gff3md5old
• U89959_sas.minus_targets
• undefined_parent.gff3
• unknown_meta_directive.gff3
• unknown_meta_directive_without_argument.gff3
• unsorted_gff3_file.txt
• uppercase_attributes.gff3
• Verysmall.embl
• Verysmall.fna
• Verysmall.gbk
• wildcardatend.fna
• wildcardatend_rev.fna