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- addintrons.gff3
- addintrons.out
- additional_attribute.gff3
- all_node_types.gff3
- Arabidopsis-C99826.embl
- Arabidopsis-C99826.fna
- Arabidopsis-C99826.gbk
- at-C99887-fwd.fna
- at-C99887-rev.fna
- at-C99930.fna
- at100K1
- at1MB
- Atinsert.embl
- Atinsert.fna
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- Atinsert_seqrange_13-17_rev.fna
- Atinsert_seqrange_3-7.fna
- Atinsert_single_3.fna
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- attribute_after_dot.gff3
- attribute_w_multiple_equals.gff3
- bar.fas
- bigfonts.style
- blank_attributes.gff3
- BLOSUM62
- blosum62.c
- BLOSUM62.gth
- BLOSUM62.out
- 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
- fail_default_stroke_color.style
- fail_fill.style
- fail_group_by_parent.style
- fail_max_capt_show_width.style
- fail_max_num_lines.style
- fail_max_show_width.style
- fail_min_len_block.style
- fail_ruler_text.style
- fail_rulerfontsize.style
- fail_rulerspace.style
- fail_show_bar_height.style
- fail_show_block_captions.style
- fail_show_grid.style
- fail_show_margins.style
- fail_show_track_captions.style
- fail_split.style
- fail_stroke.style
- fail_stroke_width.style
- fail_style.style
- fail_track_caption_font_size.style
- fail_track_caption_space.style
- fail_track_title_color.style
- fail_track_vspace.style
- fail_unit.style
- fail_vspace.style
- 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
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