| Next changeset 1:449e9aeded2d (2019-06-23) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty |
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added:
macros.xml nanopolish_polya.xml test-data/30xpolyA-small-subset-results.tsv test-data/30xpolyA-small-subset-sequencing_summary.txt test-data/30xpolyA-small-subset-win-results-t3.tsv test-data/30xpolyA-small-subset-win-results.tsv test-data/30xpolyA-small-subset.fastq test-data/30xpolyA-small-subset.sorted.bam test-data/all_fasta.loc test-data/all_fasta.loc.sample test-data/draft.fa test-data/draft_single_seq.fa test-data/enolase_reference.fas test-data/eventalign-summary.txt test-data/fast5_files.tar test-data/fast5_files.tar.bz2 test-data/fast5_files.tar.gz test-data/fast5_files_30xpolyA-small-subset.tar test-data/fast5_files_30xpolyA-small-subset.tar.bz2 test-data/fast5_files_30xpolyA-small-subset.tar.gz test-data/methylation_calls.tsv test-data/polished.fa test-data/reads-draft.eventalign.sam test-data/reads.fasta test-data/reads.fasta.index test-data/reads.fasta.index.fai test-data/reads.fasta.index.gzi test-data/reads.fasta.index.readdb test-data/reads.sorted.bam test-data/t2-eventalign-summary.txt test-data/t2-polished.fa test-data/t2-variants.vcf test-data/t3_polished.fa test-data/t3_variants.vcf test-data/t4_polished.fa test-data/t4_variants.vcf test-data/variants.vcf tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 7739a9b0dd83 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jun 19 07:00:20 2019 -0400 |
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| @@ -0,0 +1,28 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.11.1">nanopolish</requirement> + <yield/> + </requirements> + </xml> + +<!-- index outputs + <data name="output_index" format="nanopolish_index" from_work_dir="reads.fasta.index" /> + <data name="output_index_fai" format="nanopolish_index_fai" from_work_dir="reads.fasta.index.fai" /> + <data name="output_index_gzi" format="nanopolish_index_gzi" from_work_dir="reads.fasta.index.gzi" /> + <data name="output_index_readdb" format="nanopolish_index_readdb" from_work_dir="reads.fasta.index.readdb" /> + --> +<!-- <output name="output_index" file="reads.fasta.index" /> + <output name="output_index_fai" file="reads.fasta.index.fai" /> + <output name="output_index_gzi" file="reads.fasta.index.gzi" /> + <output name="output_index_readdb" file="reads.fasta.index.readdb" /> + --> + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nmeth.3444</citation> + <citation type="doi">10.1038/nmeth.4184</citation> + <yield /> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 7739a9b0dd83 nanopolish_polya.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nanopolish_polya.xml Wed Jun 19 07:00:20 2019 -0400 |
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| @@ -0,0 +1,126 @@ +<tool id="nanopolish_polya" name="Nanopolish polyA" version="0.1.0"> + <description>- Estimate the length of the poly-A tail on direct RNA reads.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input_merged' reads.fasta && + + #if $input_reads_raw.extension == 'fast5': + mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 && + + #else if $input_reads_raw.extension == 'fast5.tar': + ln -s '$input_reads_raw' fast5_files.tar && + mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files && + + #else if $input_reads_raw.extension == 'fast5.tar.bz2': + ln -s '$input_reads_raw' fast5_files.tar.bz2 && + mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files && + + #else: + ln -s '$input_reads_raw' fast5_files.tar.gz && + mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files && + + #end if + + nanopolish index + -d fast5_files/ + #if $adv.input_seq_summary: + -s '$adv.input_seq_summary' + #end if + reads.fasta && + + ln -s '$b' reads.bam && + ln -s '${b.metadata.bam_index}' reads.bam.bai && + #if $reference_source.reference_source_selector == 'history': + ln -f -s '$reference_source.ref_file' genome.fa && + #else: + ln -f -s '$reference_source.ref_file.fields.path' genome.fa && + #end if + + nanopolish polya + -r reads.fasta + -b reads.bam + -g genome.fa + --threads "\${GALAXY_SLOTS:-4}" + #if $w and str($w).strip(): + -w "${w}" + #end if + > polya_results.tsv + ]]></command> + <inputs> + <!-- index inputs --> + <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> + <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/> + + <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> + <options from_data_table="all_fasta"> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> + + <section name="adv" title="Optional data inputs"> + <!-- optional inputs --> + <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/> + </section> + + <param argument="-w" type="text" optional="true" + label="only compute the poly-A lengths for reads in window STR (format: ctg:start_id-end_id)" /> + + </inputs> + + <outputs> + <data name="polya_results" format="tabular" from_work_dir="polya_results.tsv" label="called methylation sites" /> + </outputs> + <tests> + <test> + <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" /> + <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files_30xpolyA-small-subset.tar.gz" /> + <param name="b" value="30xpolyA-small-subset.sorted.bam" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="enolase_reference.fas" /> + <!-- <param name="w" value="tig00000001:200000-202000" /> --> + <output name="polya_results" file="30xpolyA-small-subset-results.tsv" /> + </test> + <test> + <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" /> + <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files_30xpolyA-small-subset.tar.gz" /> + <param name="b" value="30xpolyA-small-subset.sorted.bam" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="enolase_reference.fas" /> + <param name="w" value="YHR174W:600-900" /> + <output name="polya_results" file="30xpolyA-small-subset-win-results.tsv" /> + </test> + <test> + <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" /> + <param name="input_reads_raw" ftype="fast5.tar" value="fast5_files_30xpolyA-small-subset.tar" /> + <param name="b" value="30xpolyA-small-subset.sorted.bam" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="enolase_reference.fas" /> + <param name="w" value="YHR174W:600-900" /> + <output name="polya_results" file="30xpolyA-small-subset-win-results-t3.tsv" /> + </test> + </tests> + <help><![CDATA[ + Usage: nanopolish polya [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa + Estimate the length of the poly-A tail on direct RNA reads + + Quickstart tutorial and manual available at: + http://nanopolish.readthedocs.io/en/latest/quickstart_polya.html + + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 7739a9b0dd83 test-data/30xpolyA-small-subset-results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/30xpolyA-small-subset-results.tsv Wed Jun 19 07:00:20 2019 -0400 |
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| @@ -0,0 +1,14 @@ +readname contig position leader_start adapter_start polya_start transcript_start read_rate polya_length qc_tag +453f3f3e-d22f-4d9c-81a6-8576e23390ed YHR174W 0 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +3aa5f5e9-ff35-4e5d-a45b-f933ba6f53e1 YHR174W 1 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +453f3f3e-d22f-4d9c-81a6-8576e23390ed YHR174W 9 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +4ed8103e-7338-4869-99a4-864f10adb88f YHR174W 44 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +487eedb2-d957-4fa9-8c18-22d18d9d579e YHR174W 116 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +f2b2e374-e463-4642-aaa3-f5a360b1f781 YHR174W 344 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +ab761bb7-ca33-4f3b-a83a-1b3964a9fcba YHR174W 371 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +adc50c94-789e-4c49-b20d-1f1598a27bec YHR174W 459 79.0 7649.0 11378.0 13048.0 115.85 59.19 PASS +caae9035-fa35-4e56-8f2c-4defa2785f30 YHR174W 575 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +3789435a-c50f-44f0-a383-50412f7c5153 YHR174W 605 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +56f62749-403c-454d-930b-83d9057ce93f YHR174W 635 70.0 5844.0 9869.0 10678.0 125.50 28.67 PASS +a3237e11-476a-498e-beee-e79ef5c2f4ca YHR174W 909 174.0 1249.0 4232.0 5123.0 111.56 27.96 PASS +6134c169-e914-432a-a81d-77181378c671 YHR174W 911 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD |
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| diff -r 000000000000 -r 7739a9b0dd83 test-data/30xpolyA-small-subset-sequencing_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/30xpolyA-small-subset-sequencing_summary.txt Wed Jun 19 07:00:20 2019 -0400 |
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| @@ -0,0 +1,14 @@ +filename read_id run_id channel start_time duration num_events passes_filtering template_start num_events_template template_duration num_called_template sequence_length_template mean_qscore_template strand_score_template calibration_strand_genome_template calibration_strand_identity_template calibration_strand_accuracy_template calibration_strand_speed_bps_template +MINICOL596_20180206_FAH55913_MN19174_sequencing_throughput_LS_RNA_21456_30xpolyA_11237_read_1111_ch_186_strand.fast5 a3237e11-476a-498e-beee-e79ef5c2f4ca 0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f 186 4706.06607 6.69256 1317 True 0.1328 1317 6.55976 1317 458 9.089 -0.0007 filtered_out -1.0 -1.0 0.0 +MINICOL596_20180206_FAH55913_MN19174_sequencing_throughput_LS_RNA_21456_30xpolyA_11237_read_1111_ch_114_strand.fast5 4d5344d1-618d-4116-9955-58937325ab81 0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f 114 5212.87815 16.99203 3123 True 1.43592 3123 15.55611 3123 1339 9.793 -0.0002 YHR174W 0.9687249660491943 0.900820255279541 0.0 +MINICOL596_20180206_FAH55913_MN19174_sequencing_throughput_LS_RNA_21456_30xpolyA_11237_read_1111_ch_117_strand.fast5 ed326f39-888c-4def-9336-5ea9998f8ff8 0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f 117 4600.60259 16.66335 3319 True 0.1328 3319 16.53054 3319 1376 9.102 -0.0002 YHR174W 0.9599359035491943 0.8940298557281494 0.0 +MINICOL596_20180206_FAH55913_MN19174_sequencing_throughput_LS_RNA_21456_30xpolyA_11237_read_1111_ch_398_strand.fast5 b9566e59-7f55-430b-a650-50e4e25efd8f 0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f 398 4906.15405 19.28918 3142 True 3.63977 3142 15.6494 3142 1316 9.558 -0.0003 YHR174W 0.972016453742981 0.874167263507843 0.0 +MINICOL596_20180206_FAH55913_MN19174_sequencing_throughput_LS_RNA_21456_30xpolyA_11237_read_1111_ch_178_strand.fast5 0681af58-5bc3-49b1-a7df-899a5fb96608 0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f 178 4751.95153 18.94721 3518 True 1.42331 3518 17.5239 3518 1345 9.458 -0.0004 YHR174W 0.9727782011032104 0.9060402512550354 0.0 +MINICOL596_20180206_FAH55913_MN19174_sequencing_throughput_LS_RNA_21456_30xpolyA_11237_read_1111_ch_470_strand.fast5 56f62749-403c-454d-930b-83d9057ce93f 0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f 470 4876.32371 12.34097 1820 True 3.27556 1820 9.06541 1820 693 9.147 -0.0009 filtered_out -1.0 -1.0 0.0 +MINICOL596_20180206_FAH55913_MN19174_sequencing_throughput_LS_RNA_21456_30xpolyA_11237_read_1111_ch_124_strand.fast5 9fb6716f-89a8-4995-9c11-8206052e21aa 0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f 124 5102.39708 21.16202 3491 True 3.77656 3491 17.38546 3491 1317 9.076 -0.0002 YHR174W 0.9644300937652588 0.8990203738212585 0.0 +MINICOL596_20180206_FAH55913_MN19174_sequencing_throughput_LS_RNA_21456_30xpolyA_11237_read_1111_ch_185_strand.fast5 ad1abf81-31b4-4d68-8805-39bc5dd2854c 0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f 185 4035.69256 18.64608 3134 True 3.03818 3134 15.6079 3134 1347 8.833 -0.0004 YHR174W 0.9604200124740601 0.869787871837616 0.0 +MINICOL596_20180206_FAH55913_MN19174_sequencing_throughput_LS_RNA_21456_30xpolyA_11237_read_1111_ch_481_strand.fast5 adc50c94-789e-4c49-b20d-1f1598a27bec 0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f 481 5763.81906 14.04117 2061 True 3.77722 2061 10.26394 2061 880 9.785 -0.0006 filtered_out -1.0 -1.0 0.0 +MINICOL596_20180206_FAH55913_MN19174_sequencing_throughput_LS_RNA_21456_30xpolyA_11237_read_1111_ch_5_strand.fast5 92f23fd6-df21-40a3-8089-971ab76d1928 0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f 5 5409.94754 17.43991 3133 True 1.83466 3133 15.60525 3133 1312 8.486 -0.0004 YHR174W 0.950647234916687 0.8781763911247253 0.0 +MINICOL596_20180206_FAH55913_MN19174_sequencing_throughput_LS_RNA_21456_30xpolyA_11237_read_1111_ch_70_strand.fast5 abb19cf7-f443-4d7a-9267-60cbcc63c1ea 0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f 70 5222.23705 17.76726 3285 True 1.40438 3285 16.36288 3285 1343 9.19 -0.0006 YHR174W 0.9666136503219604 0.8987435102462769 0.0 +MINICOL596_20180206_FAH55913_MN19174_sequencing_throughput_LS_RNA_21456_30xpolyA_11237_read_1111_ch_83_strand.fast5 25f527d1-40ac-4f1e-9e9a-51c19ebe469e 0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f 83 4816.32869 17.37616 3189 True 1.4917 3189 15.88446 3189 1324 8.695 -0.0002 YHR174W 0.9548022747039795 0.8769459128379822 0.0 +MINICOL596_20180206_FAH55913_MN19174_sequencing_throughput_LS_RNA_21456_30xpolyA_11237_read_1111_ch_469_strand.fast5 5247b83c-27db-483f-a2bb-4b2a27b97488 0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f 469 5135.93293 33.82802 6747 True 0.22709 6747 33.60093 6747 1385 9.436 -0.0001 YHR174W 0.9835293889045715 0.9275147914886475 0.0 |
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| diff -r 000000000000 -r 7739a9b0dd83 test-data/30xpolyA-small-subset-win-results-t3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/30xpolyA-small-subset-win-results-t3.tsv Wed Jun 19 07:00:20 2019 -0400 |
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| @@ -0,0 +1,12 @@ +readname contig position leader_start adapter_start polya_start transcript_start read_rate polya_length qc_tag +453f3f3e-d22f-4d9c-81a6-8576e23390ed YHR174W 0 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +3aa5f5e9-ff35-4e5d-a45b-f933ba6f53e1 YHR174W 1 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +453f3f3e-d22f-4d9c-81a6-8576e23390ed YHR174W 9 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +4ed8103e-7338-4869-99a4-864f10adb88f YHR174W 44 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +487eedb2-d957-4fa9-8c18-22d18d9d579e YHR174W 116 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +f2b2e374-e463-4642-aaa3-f5a360b1f781 YHR174W 344 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +ab761bb7-ca33-4f3b-a83a-1b3964a9fcba YHR174W 371 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +adc50c94-789e-4c49-b20d-1f1598a27bec YHR174W 459 79.0 7649.0 11378.0 13048.0 115.85 59.19 PASS +caae9035-fa35-4e56-8f2c-4defa2785f30 YHR174W 575 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +3789435a-c50f-44f0-a383-50412f7c5153 YHR174W 605 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +56f62749-403c-454d-930b-83d9057ce93f YHR174W 635 70.0 5844.0 9869.0 10678.0 125.50 28.67 PASS |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/30xpolyA-small-subset-win-results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/30xpolyA-small-subset-win-results.tsv Wed Jun 19 07:00:20 2019 -0400 |
| b |
| @@ -0,0 +1,12 @@ +readname contig position leader_start adapter_start polya_start transcript_start read_rate polya_length qc_tag +453f3f3e-d22f-4d9c-81a6-8576e23390ed YHR174W 0 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +3aa5f5e9-ff35-4e5d-a45b-f933ba6f53e1 YHR174W 1 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +453f3f3e-d22f-4d9c-81a6-8576e23390ed YHR174W 9 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +4ed8103e-7338-4869-99a4-864f10adb88f YHR174W 44 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +487eedb2-d957-4fa9-8c18-22d18d9d579e YHR174W 116 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +f2b2e374-e463-4642-aaa3-f5a360b1f781 YHR174W 344 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +ab761bb7-ca33-4f3b-a83a-1b3964a9fcba YHR174W 371 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +adc50c94-789e-4c49-b20d-1f1598a27bec YHR174W 459 79.0 7649.0 11378.0 13048.0 115.85 59.19 PASS +caae9035-fa35-4e56-8f2c-4defa2785f30 YHR174W 575 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +3789435a-c50f-44f0-a383-50412f7c5153 YHR174W 605 -1.0 -1.0 -1.0 -1.0 -1.00 -1.00 READ_FAILED_LOAD +56f62749-403c-454d-930b-83d9057ce93f YHR174W 635 70.0 5844.0 9869.0 10678.0 125.50 28.67 PASS |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/30xpolyA-small-subset.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/30xpolyA-small-subset.fastq Wed Jun 19 07:00:20 2019 -0400 |
| b |
| b'@@ -0,0 +1,48 @@\n+@6134c169-e914-432a-a81d-77181378c671 runid=0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f read=1000 ch=11 start_time=2018-02-06T15:03:43Z\n+AAGGAAGCUUGGUCUCACUUUCAAGACCGCUGGUAUCCAAAUUGUUGCUGAUGAUUUGACUGUCACCAACCCAGCUAGAAUUGCUACCGCCAAAAGAAGGCUGCUGACGCUUUGUUGUUGAAGGUUAACCAAUUGGUACCUUCGAUGGCUCCAUCAAGGCUGCUCAAGACUUUCGCUGCUUAUUGGCUGCUUUCAUGGUUUCCAGAUCUGGUGAAACUGAAGACACUUCAUUGUGACUUGGUUGUCGGUCAAAAGAACUGGUCAAUCAAGACUGGUGCUCCAGCUAGAUCCGAAAGAUUGGCUAAGUUGAACCAAUUAGAAUCGAAGAAGAAUUGGUGACAAGGCUGUCUACGCCGGUGAAAAAUUCCUUUGUGACAAGUUGUAUCGCGUGAGUAGUGAACCGUGGCAAUCA\n++\n+$%\'\'()&&*+0/&&#%%\'),)&&9,-/1013:43558.::/67*,5,1/.\'\'\'\')0314352&&\'*-.47702356,,,3,+&&\'\'*+*--&\'-.&-*\')(*+676500)*+-*010-&\'(\'+),.,0-2:0-),(%\'(,)*&*&&%$%\'3211--0/0+13/0.0+++*,-,(*+/.0$%$)),&$\'*%*-)&\'&++*+(,,/()000720027-,,.500202))))*-*(*+)((*-,(),/+/21*+35/)+2,-.6/+/4*/-22+,,,32/,,-/,.-./103+.,883+,,,/1,-/10,))++,,81+,%&\'1---3-+.-*+0++13--204+-,**-+))**.4/32+*)1/.*%&(\'%$#&\'()*20231/-+,**((*+*+*\',/-1)(\'%%%&$)+$%%\n+@3aa5f5e9-ff35-4e5d-a45b-f933ba6f53e1 runid=0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f read=1000 ch=165 start_time=2018-02-06T14:26:34Z\n+UAGAUUGUCUGUUGGUCGCUGGCUGUCUAAAGUUUACGCUAGAUUCGUCUACGACCCGUGGUAACCCCAUCGUGAAGUCGAAUUAACCACCGAAAAGGUGUUUCAGAUCUGUUCCACACUGGUGCCCACCGGUGUCCGGGUUUGGAAAUGAGAGAUGAAGACAAUCCAAGUGAUGGGUAAGGGUGUUAUGAACGCUGUCAACAACGUCAACACGUUUGCUGCUGCUUUGCCAAGGCCAACCAAGAUGUUAAGGACCAAAGAGCCGUCGAUGACUUUGUUGUCUUUGGAUGGUACCGCCAACAAGUCCAGGUAAGGUGCUGCCGCUAUCUUGGUGUUCUCCAUGGCCGCUGCUAGAGCCGCUGCUGCUGAAAAGAACGUCCAUUGUACCAACUUGACUUGUCUAAGUCCAAGACCCUCUCCAUACGUUUUGCCAGUUCCACUCUUGAACGUUUUGAACGGUGGUCCCACGCUGGUGGUGCUUUGGCUUUGCAAGAAUCUUUGAUUGCUCCAACUGGUGCUAAGACCUUCGCUGAAGCCAUGAGAAACUGUCAAGUUUACCACAACUUGAAGUCUUUGACCAAGAAGAGAUCGGUGCUUUGCCGGUAUUCCGGUGACGAAGGUGGUGUUGCUCCAAAACAUUCAAUCGCUGAAGAAGCUUUGGACUUGAUUGUUGACGCUAUCUCAAGGCUGCUGGUACGGUAAGGUCAAGAUCGGUUUGGACUGUGCUUCUCCUCUGAAUUCUUUCAAGGACAGACAGUACGACUUGACCAAGAACCCAGAAUCUGACAAUCCAAGUGGUUGGCUGGGUGUCGAAUUGGCUGUUUUGUACCUACUCCUCUGAUGAAGAGUACCCAAUUGUCUCCAUGAAGAUCCAUCAUUGCUGAAGAUGCUGGAAGCUUGGACCACUUCUCAAGACCGCUGGUAUCCAAAUUGUUGCUGAUGACUUGACUGUCAACCCAGCUAGAAUUGCUACCGAAAGAAGAAUCGCUGACGCUUUGUUGAAGGUUAACCAAAUCGGUACCUUGUCUUGAAUCCAUCAAGGCUGUUCUGAGACUUCGCUGCCAACUGUGGUGCUUCGGUUUCCCAUCCACAGAUCUGGUGAAACUGAAGACACUUCAUUGCUGACUUGGUUGUCGGUUUGAGAACUGGUCAAAAUCAAGACUGGUGCUCCAGCUAGAUCCGAAAGAUUGGCUAAGUUGAUUAAUUGUUGAGAAUCGAAGAAUGACAAGCUGUCUACGCCAGUGAAUUCCACCACGGUGACAAGUUGUAUCGUGAGUGAUCGUGCAAAAAAUAAUAU\n++\n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n+@caae9035-fa35-4e56-8f2c-4defa2785f30 runid=0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f read=1000 ch=155 start_time=2018-02-06T14:38:41Z\n+CCAACUUGAAGUCUUUGACCAAGUAGAGAGAUCGGUGCUCUGCCGGUAACGUCGUCGGUGACGAAGGUGGUGUUGCUCCAAACAUUCAAACCGCUGGAGAAGCUUUGGACUUGAUUGUUGACGCUAUCAAGGCUGCUGGUCACGA'..b"GUCUACGCCGGUGGAAACUUCCACCACGGUGACGGUUGUAUCGUCGUGAGUAGUGAACCGCAGCAAAAAAACACCAUUCAACCCGCCCCACCUAUCCCAAAAUUA\n++\n+%*'+*(+,+1/6.)&%%&$&+&&++('/'(..55008090/+1+32701+)*+*+5444/0.+))+-()&'(*&,*,,',,.0.1-('&%%%&+*)+'(+2(+.,2+-3.+,0+++.5/*-5.4.''')+-5/4076--()4**0.24/1,1.7..932312.1.,02*+()-+,')'%&(++)(*+*6.*+-,,,.,62-,2(),+,5+,1)*-)76((,-3-4/-*-*((-/+,.-3475843477591,*.,3/..434-71.-40...175,+*'+'()+*++,1/)(.60,14011-+&'(('-+/.-.04+2/*+0++-031202.,-+*,./,.0+*,,.1+.,*''&$%%&'&*%,((()10#)*)+'*,*,10.-**,3+-*(&&%%&%&())*+*---,&'(%$$'&(3898)&%$'&'*'%&)&*((+,,,$(($&%(+(&)-,%$%\n+@56f62749-403c-454d-930b-83d9057ce93f runid=0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f read=1111 ch=470 start_time=2018-02-06T14:42:46Z\n+ACGCCCCGCCCAGAGGUGGUUGCUCCAAACAUUCAAACCGUUGAGGAAGCUUGACACUGAUUGUUGACAAUGUUCAAGGCUGCUGGUCACGACGGUAAGGUCAAGAUUAGAGUUGGACUGUGCUUUCCAUUGAAUUCUUCAAGGACGGUAAGUACGACUUGGACUUAGAACCCAGAAUUUGACAAAUCCAAGUAGCUGACUGGUGUCGAAUUGGCUGACAUGUACAACCACCUGAUGAAGAGAUACCCAAUUGUCUCCUCCGAAGAUCCAUUUGCUAAGAUGACUGGGAAGCUAAGUCUCACUUUCAAGACCGCUGGUAUCCAAAUUGUUGCUGAUGACUUGACUGUCACCAACCCAGCUAGAAUUGCUACCGCCAUCGAAAAGGCUGCUGACGCUUUGUUGUUGAGUUAACCAAAUCGGUACCUUGUCUGAAUCCAUUCAAGGCUGCUCGAGACUUCGUUGCCAACUGGGGUGUCUAGUUUUCCCACAGAUCUGGUGAAGGUAAGACAUCAUUGCUGACUUUGGUCGGUCGGUUUGAGAACUGGUCAAAUCUGGAUGGUGCUCCAGCUAGAUCCGAAGAUUGGCUAAGUUGAACCAAUUGUUGAGAAUCAGAAGAAAUUGGGUGACAAGGCUGUCUACGCCGGUGAAUUCCACGACAAGUUGUAUCGCGUGAGUAGUGAUCGCAAAAAACAU\n++\n+'%#%&'&%%)+$$&('&''&&&&'*),4-''*)&*.,--)),*)('+'%%(+**'%$('),13./,+*)(')+)&3.-.*+2*36/++**),.)..0-*2)(,20,.*'('')/)0426--+))+*''%'*/00/,&*))*-.,+-(/&$%0,,,+,)0445/+-(--1-03-)-.1+(.)*+/1)*4/0*)(-+/045315-11*))*3+2)2('()'**((&()(.)(+*+./113.*,)--06857/8+*+'(*($''%&2',01,*0*.+*'&)(+*+,+*31+)1,-0*()&%'()+)+)&'5003-.0125321736:443132.)11336621311131/,+.0/1861-+..**+4,4.-)'(,(+1*'$&*24-)+&')-100+*&,.-*6./0-)))*.-.2.45...16612-.//0**(3*)7.*)(%'&/)*6501*))))+*+&'(+(,*()%-103,+,-01*,/-*(+.-)+024406963+)&*'')+(**)%%%*****+.(),.),(&(&*)6/50+*,*03001750.7+-)'%)((',+/./0000/02313.1003--.4+2++,/)),,3132.1-/+10./.-/*&&'(0+06.1225/..*)+,('&&''%&&'')+'/.,/.,)+*(+,++.2031)''%'%&(((''%$(())'$%$'+360(+$#\n+@adc50c94-789e-4c49-b20d-1f1598a27bec runid=0c640f6d456ec16c9dfc0e1a607256f68c2b0c2f read=1111 ch=481 start_time=2018-02-06T14:57:33Z\n+GCUGUUUUGAACGGUGGUUCCCACGCUGGUGGUGCUUUGGCUUUGCAAGAAUUCAUGAUUGCUCCAACUGGUGCUAAGACCUCGCUGAAGCCAUGAGAAUUGGUUCGAAGGUCUACCACAACUUGAAGUCUUUGACCAAGAAGAGAUAUGGUGCUUCUGCCGGUAACGUCGGUGACGAAGGUGGUGUUGCUCCAAAACUAUCAAACCGCUGAAGAAGCUUUGGACUUGAUUGUUGGCGCUAUCAAGGCUGCUGGUCACGACGGUAAGGUCAAGAUGGUUUUGGACAAUGUUUCCUCUGAAUUCUCAAGGACGGUGAGUACGACUUGGACAUCAAGAACCCAGAAUCUGACAAAUCCAAGUGGUUGACUGGUGUCGAAUUGGGUGACCGUACCACUCCUUGAUGAAGAGAGAUACCCAAUUGUCUCCAUGAAGAUCCAUUUGCUGAAGAUGACUAAGGAAGCUAAGUCUCACUUCAAGACCGCUGGUAUCCAAAUUGUUGCUGAUGACUUGACUGUCACCAACCCAGCUAGAAUCGUUCGCCAUCGAAAAGAAGGCUGCUGACGCUUUGUUGUUGAAGGUGGUUAACCAAAUCGGUACCUUGUCUGAAUCCAUCAAGGCUGCUCAAGACUUUGCAGCCAACUGGGUGUCAUGGUUUCCCACAGAUUUGGUGAAACUGAAGACACUUCAUUGCUGACUUGGUUGUCGGUUUGAGAACUGGUCAAAUCAAGACUGGUGCUCCAGCUAGAUCCGAAAGAUUGGCUAAGUUGAACCAAUUGUUGAGAAUCGAAGAAGAAUUGGGUGACAAGGCUGUCUACGCCGGUGAAUUCCACCACGGUGACAAGUUGUAUCGCGUGAAGUGAACCGUAAGCAAAAAGAAACC\n++\n+$%%&(201*+1(())//23-83*+*(02/.3/1/,-+-.,*1020/46,.0,+,--..17-,,1+0'%+422368766++)%(&'++-0)-)'$%'(/3/56/8,,))'*'*%&%*)'-'+'(**/,0*)*56334081,,*)*(*,-.221,+/(&'(-2-5010-//376311///+/+*4./0750///05.51&&&)&(66331/,,,+&+)''/52+0,+,1303769,.*(%&((),/,1-+-0).0.,,-./,%*))-/*.)*,6...)1+:6*8,++/003'-*'+)(-.1.*)&)').).)+*'&%$&&%((())*,-+)&(*/2*+6+96412/)%'),+.6.,157/,,//++0-.-042234,/2/-3/(.1*('+**1.+*)(*%&)))*..-+)))*+,0:473/3()()/0--,3--,.2,+,+-)$,)./-.49+)'&&*-*2+/3'','&&&&(',%%(++0.-//4//0+600:61204/-,(,-/())*-655660+*,/,107.,,-,,+.3+%&&+').+(&&%'+1/)+.,.-/626110.(+..''/,0/**)*('-*,)(*(*/8**+(./.412.)(&,,-1)*/&()*,-,)*833144/,&,/*'+*-223+).+33+,3,*)+-2/'*0)%'+**))),3,-410*)*0/,.+++)*%&(5.4574402),*/(-3613/*+./250,,6,*8:--4:5...-62--*(+**+,/13(('*&+33*-30-3,--360+)(-).0/30.30113834203..40+60)*)3-(/0+3,.,,-++$''(&)-+000).&(&*$')&*'424334//3+('&%%%%((*+(&'')(*((&'()(+378/)65*(#\n" |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/30xpolyA-small-subset.sorted.bam |
| b |
| Binary file test-data/30xpolyA-small-subset.sorted.bam has changed |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Wed Jun 19 07:00:20 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +draft draft draft ${__HERE__}/draft.fa \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc.sample Wed Jun 19 07:00:20 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +draft draft draft ${__HERE__}/draft.fa \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/draft.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/draft.fa Wed Jun 19 07:00:20 2019 -0400 |
| b |
| b'@@ -0,0 +1,46213 @@\n+>tig00000001 len=4376233 reads=23096 covStat=7751.73 gappedBases=no class=contig suggestRepeat=no suggestCircular=no\n+AGATGCTTTGAAAGAAACGCAGAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAG\n+GCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTGAAAAGAAAATGTCCCACAGGTACAGATAGAGTTGCTGCTTATCATACTCACGGTGCAGATA\n+GTCATGGCGATTATGTTGATGAATTTTTTCAAGTAGCGATAAAATCTTGTAAGAAGTAAAGATAATAATCTTGAAGCATTTTATCTCGCAACACCTGATG\n+GACGATTTGAGGCGCTTAATAATAAAGGAGAATATATTTTATCAGAAATAGTGTCCCGGGATTGAGTTCAGTATGCATACCGTATCATGATTAATTTTAG\n+TGCTTTTATTAGTGGGGCCTATAGGAGATTCAATGAAATATAGTTCAATATTTTCGATGCTTTCATTTTTATACTATTTGCCTGTAATGAGACAGCTGTT\n+TACGGTTCTGATGAAAACATTATTTTTATGAGGTATGTGGAAAAATTACATTTAGATAAATACTCTGTTAAAAATACGGTAAAACTGAAACAATGGCGAT\n+ACAATTAGCTGAAATATATGTTAGGTATCGCTATGGCGAACGGATTGCAGAAGAAAAACCATATTTAATTACGGAACTACCAGATAGTTGGGTTGTTGAG\n+GGAGCAAAGTTACCTTATGAAGTTGCGGGTGGTGTATTTATTATAGAAATTAATAAGAAAAATGGATGTGTTTTGAATTTCCTACATAGTAAATAATGCT\n+GGCGCTGATGGATGCGGATGGAAACATTGCGTGGAGCGGGGAGTATGATGAGTGGGGCAACCAGCTGAATGAAGAGAACCCGCATCACCTGCACCAGCCG\n+TACCGGCTGCCGGGGCAGCAGTATGATAAGGAGTCGGGGCTGTACTACAACCGGAACCGGTACTACGATCCGTTGCAGGGCGGTATATCACCAGGACCCG\n+ATAGGGCTGAGGGGGATGGAGTCTGTATGCGTATCCGCTGAATCCGGTGAATGGTATTGATCCATTAGGTTAAGTCCCGCAGATGTAGCGCTAATAAGAA\n+GAAAAGATCAACTAAACCATCAAAGAGCATGGGATATATTATCTGATACTTATGAAGATATGAAGAGATTAAATTTAGGTGGGACTGATCAATTTTTCCA\n+TTGTATGGCATTTTGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTA\n+AATCTGTTCGGTATGTACGGCAGAAAAGTAAAGCTATCCCATTCTGAAATGATTGAAGATAATAAAAAGACTTGGCTGTAAATGACCATGGGTTGACATG\n+TCCATCAACAACAGATTGCTCAGATAGATGTAGTGATTATATTAATCCAGCATAAAAAACGATAAAGGCTTTACAAGATGCTGGCTATCTCAAGTAATCT\n+ATCAAAGATGATAATATTTATTTTTGCTATTATAATCATTGTTGTTTTATGCGTAATTACTTATCTTTATTTATACAAAGATGAATCTCTTGTAAGTAAA\n+CATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAA\n+TGTAGAAGATGATTATTTTTTCTTATTTTCCCTAACAAATGATGATGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAA\n+TCGTATCAAAGAATGATCCAGATACAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGGCAAGGGATGGTGTAAACCTTTTTTGTTGGTGAAATTAAT\n+GTTACGCATTATTTTATAACAAATATTGGAGCTGGATTGCCTGATGCTTGTGCAGAGTAATTGCTTGAATTAAGAGTCTATCCCATATCGAAGTCGTCAA\n+CTTCGTAGTGAGGAAAAGTAAAATTCCTGACTGAGAAAAGACATGTCGGCTATTGTGTAAAGCCATATAGCTCAGACGATGAATATCTACTCGTATTCAG\n+TTGTTTATTGAGGGTGAGTTCCGACCCTGAAACAACAAATAAAATGAACAGTCAGAGAGTTTACATAGAATTGCACTGGTCTTTTACGATATCTGACATT\n+GTGTAATACATATTCAGCCATGCATTAATTAAAATGTTACGTGTTTAATGTGAGTCCCTATCTGAAAATAAATAATCCTTCCGGATTAAAATAAATTCTT\n+GCCGGGAAAGAAAGAGGAAATAAACCATTAGCGGAAAACCAGCGGCACGCCAGGGTGACATGCCCCAGTACGGCGGCCCGATAGTCCAGGGTTCAGCGGG\n+GTACTGATAGTCGCGCCGACTGCATCGAGAACTCCATACAACTTTTACGGAACGTCACCTGATAAAATTTGTTCAGTATCGTCTTTGAGATTCTCAAGGT\n+TATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAACCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGA\n+CGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTC\n+AGCGACCAGTTCGCGGTAACGATAAAACGTATCACGCGAAACGCCCATGATTTTACAGGCTTTTGATACGTTGCTGAGTTCTTCAGCCAGATTGAGCAAA\n+CCGGCTTTGTGTTTGATGACGGGATTGGCAGTATGAAGCATGAGAGTTACCTCTTGTTTTGGATAAGGATTCGACACTCATATCAAAACCGGTAACTCTC\n+AACCTTTCAAGGCCATGTGTCAGATCAAGTCGCGACTAATACAAATACGTCCCTCATTACCGCGCCTTAACCCATTCCGCCACTTCCGCCCACTCACCGC\n+GAAAGACAACTTTTTCCGCTTTTTCTCAAGCTGATAGCGATACATCGGGTCGTAATATTCTTCAAGTAACGGCACCAGCCAGGCCAGATGACCGTCGGTG\n+CTGCCGGTGGTGAGTTGCGTTGTCAGTGCTGCATCCAGCCTTGCAGCCAGTTCGTTATAGCGCTGTAGCCCCAGCCGACGCTTAATCGCCGAAAGTCCGT\n+GATGCAGGTATTCGCAATACTCCTGCCAGCCCTGTTCGTCGCCGTACGCGTGGGTAAAATCATGATGCATACGCAAGAAATACTCTTCGTTCAGGCGCTC\n+AAGACGGATCTCAAACGGATCTTCTACCACCGCAATCGCCGCCTGAGTCATTCGCTCGCGCAGGCATTCCGGCAGGTGATTCGAACCGATCATCCGGCTT\n+TCGTCTTCCAGCACCCACAGGCGCAAATTCTGACGGGCGTCGGTTTTAGCATTTCGGCAGCCAGCAGGTTTTCAAAACTCGCCTGGCTAAGTTGTGGTTG\n+TAACGTGCGACCAAACGCCGAACCGCGATGACGCGCCAACCCTTCCAGATCAACACCGTTCGGCTGTTGCTGCACTAACAGCGTTTTACCGCTGCCGGTA\n+CAACCGCCAATCAGCACTATCGGTTTTGTGCCAGTTCAATAGTCGCCTGAATCGCGGTCTGGCGCAGTGCCTTATAACCGCCTTCCACCAGCGGATAATC\n+AATCCCCGCTGCATGCAACCAGCTTTGCACAATATGTGAGCGCTGACCGCCACGGGCGCAGCAGAGAATACCTTGCGGATTTTGCA'..b'ATTCGATTCGCCTGTAAGCATCAGAATGATGTTCGGCATATAGCGCAAGTCCTTCCAGTTTGGGCAAAG\n+CATCAGCCAGATGTAGGCTATGTGGATCTACCAGGTCCACAACCATTTTGCCATCCTGTTCGGCAAAGAACAGGAAATCGGGACGAACAATCTTGTACTG\n+TTCAGCTTCAACATAAGCGATTCCCAGTGACGACTGCCCTGTGTACTGTGGATTACGATACCAGAAAGCAAATCCTTCACGTTTGGTTTCGATCTCAAAA\n+CCTTGGTTTCCCAATGGTTCAACAGAGCCGGATAGTTCCCGCTTTCGTCACACAACAAATGGTGTTTCCAGACTGGAAGGTCAGCTTCCTTTTCACCTTC\n+ACGCACCCTGGTCATTTCAAACTTGTTCGCCGGCCTGACCAGATCCACATCCTGCGGTTCGGTACTCATTTCGACGATTTGACGATAGGCCTCTTTACGC\n+TCATCTTTCAACGACTTGATTTGCGGTGTGTACTCGGCCAGCCACGCCTTCGCCAGTCTATCGGCCTCGCCATCGAAGTAATCCTGCACCTCCATCACCA\n+GCCCCATGCCAGCAACGGTAACACGAGCCTCCATGATTGCTTCCAGATATTCCTCTGCATCCTCTTCTCGATCCGCAACCTTATCGGCCAGATATTCGAC\n+ATAGGTACGTGAAACATCCGGGCTGAAAATTCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTGAGGTGCTCCAGTGGCTTCTGTTTC\n+TATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCACTGCCGTAAAACATG\n+GCAACTGCAGTTCACTTACACCGCTTCTCAACCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTTGGATGCCGGGCAACCGCCCGCATT\n+ATGGGCGTTGGCCTCAACACGATTTTCCGCCATTTAAAAACTCAGGCCGCAGTCGGTAACCTCGCGCATACAGCCGGGCAGTGACGTCATCGTCTGCGCG\n+GAAATGGACGAACAGTGGGGATACGTCGGGGCTAAATCGCGCCAGCGCTGGCTGTTTACGCGTATGACAGGCTCCGGAAGACGGTTGTTGCGCACGTATT\n+CGGTGAACGCACTATGGCGACGCTGGGGCGTCTTATGAGCCTGCTGTCACCCTTTGACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCC\n+CGCCTGAAGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAA\n+GTCGCTGTCGTTCTCAAAATCGGTGGAGCAGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGTAA\n+CAGATATATCGCCTCCATCACCGCTGAAGTAATGAAGTAAGGCAGCAAGCCTCGCCATGTTCTCCGCCATTTTAGAAGCATAATCCTTAAAATCATAAAG\n+AAGGCCAATCATTCTCATTTCTGACTCGACCTGGTTGTAGAATTCGATCCAATGTCTTTCTGCTTCTGCAGAGAATCGGAGGCAGATACGATTATTTTCA\n+CACACGGACGGGTTTGCCTCCACCTTTGTAAGAAAGAATTGTGAAATGGGGTTGCAAATGAATAATTACACATATAAAGTGAATTTTAATTCAATAAGTG\n+GCGTTCGCCATGCGAGGATAAAATGTCCGATTTATACAAAAACACTTTCTGAAACTGCTCGACTTTACCCTGCACAGTTCACTTCTCTGCTGACCCTTGC\n+CGCACAGCTCAAAGCCGATAAAAAATGGCAAGGAAGTACAGAAGCTTACCGGTAAAACATCGCGCTCATCTTCGAAAAGACTCGACTCGTACCCGTTGCT\n+CTTTCGAAGTTGCCGCATTTGACCAGGGCGCGCGCGTTACCTATTTAGGGCCGAGCGGCAGCCAGATTGGGCATAAAGAGTCAATTAAGGACACCGCGCG\n+GGTTCTCGGGCGGATGTATGACGGCATTCAGTATCGCGGTCACGGCCAGGAAGTGGTCGAAACGCTGGCGCAGTATGCGGGCGTGCCGGTGTGGAACGGG\n+CTGACCAACGAGTTCCACCCGACCCAGCTGCTGGCGGACCTGATGACCATGCAGGAGCACCTGCCGGGCAAGGCGTTTAACGAGATGACGCTGGTCTACG\n+CGGGCGATGCGCGCAACAACATGGGCAACTCGATGCTGGAAGCGGCGGCGCTGACCGGGCTGGATCTGCGCCTGTTGGCCCCGAAAGCCTGCTGGCCGGA\n+AGAGAGCCTGGTGGCGGAGTGCAGCGCGCTGGCGGAGAAGCACGGCGGGAAAATTACTCTGACGGAAGACGTGGCGGCAGGCGTTAAGGGCGCGGACTTT\n+ATCTATACCGACGTGTGGGTGTCGATGGGCGAGGCCAAAGAGAAGTGGGCAGAGCGGATTGCGCTGCTGCGCGGGTATCAGGTGAACGCGCAGATGATGG\n+CGCTGACCGACAACCCGAACGTGAAGTTCCTGCACTGTCTGCCGGCGTTCCATGACGACCAGACTACGCTCGGCAAGCAGATGGCGAAGGAGTTCGATCT\n+GCACGGCGGGATGGAGGTGACGGACGAGGTGTTTGAGTCGGCGGCGAGCATCGTGTTCGACCAGGCGGAAAACCGGATGCATACGATTAAGGCGGTGATG\n+ATGGCAACGCTTGGGGATTGGGTCCGCTGCGCGTTGGTGCCTCACCCGGCCCTCTCCCACAGGAGAGGGAGAACACCGGCTCCATTTCATTGATTTTTCA\n+TCCCGAAAAGGTACGTTTTCGCCTTAATTCCAGCGTGGACATGCCAGCATTATGCCGATTATTCAGTCTGTTGAACGTGCGTTGCAGATCCTCGACCTGT\n+TCAACGAGCAGGCCACCGAGCTTAAGATCACCGACATCAGCAAACTGATGGGGCTGAGCAAGAGTACCCTCCACTCGCTGCTAAAACCCTGCAGCTTCAC\n+GGCTATATCGATCAGAACCCGGAGAACGGCAAGTATCGCCTCGGCATGAAGCTGGTCGAGCGCGGCCATTTTGTCGTGGGCTCCATCGATATTCGGCAGA\n+AGGCAAAGGCTGGCTGACGGAGCTGTCCCGGCGGACCGGGCAGACCACCCATCTGGGGATCCTGGACGGGCGTGAAGGGTCTATATCGAGAAGATTGAAG\n+GCAAGCTGGCCGCCATCGCCTATTCACGCATCGGCCGCCGCCTGCCGGTGCACGCCACCGCCATCGGCAAGGTGTTGATTGCCTGGCTGGGCGAGGCCGA\n+GCTGAACGCCCTGCTGGAGGGCTATCAGTACACTACCTTTACGCCCGCCACCCTCGCGTCTCGCGAAGCCTTAATGAGCGCCCTGGCGCAGACCCGCGCG\n+CAAGGCTACGCCCTGGACAGCGAAGAGAACGAGCAGGGCGTGCGCTGCGTGGCGGTGCCGGTGTGGAACCACGAGTCCCGCGTCATCGCCGCCCTGAGCC\n+TGTCGACGCTGACCTCCCGCGTGGACGACGCGGGCTGGCTAATTTCCGCGAGCAGCTTCAGCAGGCCGGGCTCGCGCTCTCGCGCGCTGGGCTACCGGCC\n+TGAGCCGTTAGACCGGCTCGTAGGTGAAGTAGTCGAAGTCCGCGTAGCAGCCGTCGCTGATGTCCTCGGTGCAGGCCCACAAACGCGCCGGTGAAGAAGC\n+CGCGCCCGCCGATGTAGTCGTCCGACAGCTTCCACGCCTCATACGTCACCGGCACGGTGTGCCACGTCTCGCCATCAAACGAGTAGCTGTAGCGGTAGAC\n+CAGCGTATCCACGTCCACCCGCAGCCAGACGCTCTCCGCATGTTCCGGCAC\n' |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/draft_single_seq.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/draft_single_seq.fa Wed Jun 19 07:00:20 2019 -0400 |
| b |
| b'@@ -0,0 +1,3000 @@\n+>tig00000001 len=4376233 reads=23096 covStat=7751.73 gappedBases=no class=contig suggestRepeat=no suggestCircular=no\n+AGATGCTTTGAAAGAAACGCAGAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAG\n+GCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTGAAAAGAAAATGTCCCACAGGTACAGATAGAGTTGCTGCTTATCATACTCACGGTGCAGATA\n+GTCATGGCGATTATGTTGATGAATTTTTTCAAGTAGCGATAAAATCTTGTAAGAAGTAAAGATAATAATCTTGAAGCATTTTATCTCGCAACACCTGATG\n+GACGATTTGAGGCGCTTAATAATAAAGGAGAATATATTTTATCAGAAATAGTGTCCCGGGATTGAGTTCAGTATGCATACCGTATCATGATTAATTTTAG\n+TGCTTTTATTAGTGGGGCCTATAGGAGATTCAATGAAATATAGTTCAATATTTTCGATGCTTTCATTTTTATACTATTTGCCTGTAATGAGACAGCTGTT\n+TACGGTTCTGATGAAAACATTATTTTTATGAGGTATGTGGAAAAATTACATTTAGATAAATACTCTGTTAAAAATACGGTAAAACTGAAACAATGGCGAT\n+ACAATTAGCTGAAATATATGTTAGGTATCGCTATGGCGAACGGATTGCAGAAGAAAAACCATATTTAATTACGGAACTACCAGATAGTTGGGTTGTTGAG\n+GGAGCAAAGTTACCTTATGAAGTTGCGGGTGGTGTATTTATTATAGAAATTAATAAGAAAAATGGATGTGTTTTGAATTTCCTACATAGTAAATAATGCT\n+GGCGCTGATGGATGCGGATGGAAACATTGCGTGGAGCGGGGAGTATGATGAGTGGGGCAACCAGCTGAATGAAGAGAACCCGCATCACCTGCACCAGCCG\n+TACCGGCTGCCGGGGCAGCAGTATGATAAGGAGTCGGGGCTGTACTACAACCGGAACCGGTACTACGATCCGTTGCAGGGCGGTATATCACCAGGACCCG\n+ATAGGGCTGAGGGGGATGGAGTCTGTATGCGTATCCGCTGAATCCGGTGAATGGTATTGATCCATTAGGTTAAGTCCCGCAGATGTAGCGCTAATAAGAA\n+GAAAAGATCAACTAAACCATCAAAGAGCATGGGATATATTATCTGATACTTATGAAGATATGAAGAGATTAAATTTAGGTGGGACTGATCAATTTTTCCA\n+TTGTATGGCATTTTGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTA\n+AATCTGTTCGGTATGTACGGCAGAAAAGTAAAGCTATCCCATTCTGAAATGATTGAAGATAATAAAAAGACTTGGCTGTAAATGACCATGGGTTGACATG\n+TCCATCAACAACAGATTGCTCAGATAGATGTAGTGATTATATTAATCCAGCATAAAAAACGATAAAGGCTTTACAAGATGCTGGCTATCTCAAGTAATCT\n+ATCAAAGATGATAATATTTATTTTTGCTATTATAATCATTGTTGTTTTATGCGTAATTACTTATCTTTATTTATACAAAGATGAATCTCTTGTAAGTAAA\n+CATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAA\n+TGTAGAAGATGATTATTTTTTCTTATTTTCCCTAACAAATGATGATGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAA\n+TCGTATCAAAGAATGATCCAGATACAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGGCAAGGGATGGTGTAAACCTTTTTTGTTGGTGAAATTAAT\n+GTTACGCATTATTTTATAACAAATATTGGAGCTGGATTGCCTGATGCTTGTGCAGAGTAATTGCTTGAATTAAGAGTCTATCCCATATCGAAGTCGTCAA\n+CTTCGTAGTGAGGAAAAGTAAAATTCCTGACTGAGAAAAGACATGTCGGCTATTGTGTAAAGCCATATAGCTCAGACGATGAATATCTACTCGTATTCAG\n+TTGTTTATTGAGGGTGAGTTCCGACCCTGAAACAACAAATAAAATGAACAGTCAGAGAGTTTACATAGAATTGCACTGGTCTTTTACGATATCTGACATT\n+GTGTAATACATATTCAGCCATGCATTAATTAAAATGTTACGTGTTTAATGTGAGTCCCTATCTGAAAATAAATAATCCTTCCGGATTAAAATAAATTCTT\n+GCCGGGAAAGAAAGAGGAAATAAACCATTAGCGGAAAACCAGCGGCACGCCAGGGTGACATGCCCCAGTACGGCGGCCCGATAGTCCAGGGTTCAGCGGG\n+GTACTGATAGTCGCGCCGACTGCATCGAGAACTCCATACAACTTTTACGGAACGTCACCTGATAAAATTTGTTCAGTATCGTCTTTGAGATTCTCAAGGT\n+TATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAACCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGA\n+CGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTC\n+AGCGACCAGTTCGCGGTAACGATAAAACGTATCACGCGAAACGCCCATGATTTTACAGGCTTTTGATACGTTGCTGAGTTCTTCAGCCAGATTGAGCAAA\n+CCGGCTTTGTGTTTGATGACGGGATTGGCAGTATGAAGCATGAGAGTTACCTCTTGTTTTGGATAAGGATTCGACACTCATATCAAAACCGGTAACTCTC\n+AACCTTTCAAGGCCATGTGTCAGATCAAGTCGCGACTAATACAAATACGTCCCTCATTACCGCGCCTTAACCCATTCCGCCACTTCCGCCCACTCACCGC\n+GAAAGACAACTTTTTCCGCTTTTTCTCAAGCTGATAGCGATACATCGGGTCGTAATATTCTTCAAGTAACGGCACCAGCCAGGCCAGATGACCGTCGGTG\n+CTGCCGGTGGTGAGTTGCGTTGTCAGTGCTGCATCCAGCCTTGCAGCCAGTTCGTTATAGCGCTGTAGCCCCAGCCGACGCTTAATCGCCGAAAGTCCGT\n+GATGCAGGTATTCGCAATACTCCTGCCAGCCCTGTTCGTCGCCGTACGCGTGGGTAAAATCATGATGCATACGCAAGAAATACTCTTCGTTCAGGCGCTC\n+AAGACGGATCTCAAACGGATCTTCTACCACCGCAATCGCCGCCTGAGTCATTCGCTCGCGCAGGCATTCCGGCAGGTGATTCGAACCGATCATCCGGCTT\n+TCGTCTTCCAGCACCCACAGGCGCAAATTCTGACGGGCGTCGGTTTTAGCATTTCGGCAGCCAGCAGGTTTTCAAAACTCGCCTGGCTAAGTTGTGGTTG\n+TAACGTGCGACCAAACGCCGAACCGCGATGACGCGCCAACCCTTCCAGATCAACACCGTTCGGCTGTTGCTGCACTAACAGCGTTTTACCGCTGCCGGTA\n+CAACCGCCAATCAGCACTATCGGTTTTGTGCCAGTTCAATAGTCGCCTGAATCGCGGTCTGGCGCAGTGCCTTATAACCGCCTTCCACCAGCGGATAATC\n+AATCCCCGCTGCATGCAACCAGCTTTGCACAATATGTGAGCGCTGACCGCCACGGGCGCAGCAGAGAATACCTTGCGGATTTTGCAG'..b'GTAGTCGGCGTCACAAAAGGTGCGGTCTTACGGAATTTTCCGTAAAGTTCGGTACTCTGAGTAAGTAGAGATAAATTCTTCAGGAGAGAAGCCA\n+TGAAGTGGCAACAACGTGTTCGTGTCGCAACGGGTCTAAGTTGCTGGCAGATTATGTTGCATTTACTGGTAGTGGCGCTGCTGGTGGTGGGCTGGATGAG\n+TAAGACTCTGGTTCACGTCGGCGTGGGATTATGCGCACTGTATTGTGTCACGGTAGTGATGATGCTGGTGTTTCAGCGCCACCCCGAGCAACGCTGGCGT\n+GAGGTGGCAGACGTGCTGGAAGAGCTGACCACGACCTGGTATTTTGGCGCAGCGCTGATTGTGCTGTGGCTGTTGTCCCGCGTTCTGGAAAACAACTTTT\n+GCTGGCAATTGCAGGGCTGGCAATCCTTGCCGGCCCGGCGGTAGTGTCTTTGCTGGCGAAAGATAAGAAGTTACATCACCTTACGTCTAAACATCGCGTA\n+CGCCGCTGACCCTGTCGTGGCCGTTATCACCAGTAGCGGCCACAAACTATTCCACACAATATCCAGACTCGCATCCTTCAAATAAATCTGCTTGGTAATG\n+TCCGTAAAGTGGCGAATAGGGTTAATCCACGTCAGGTTTTGCAGCCATACCGGCATGTTTTCCACCGGAGAAACGTAACCGGAAAGGAGAATGGCGGGCA\n+TCATAAAGACAAACACGCCGATAAACGCCTGCTGTTGTGTTGAACAGAGTGATGAAATCAACAGACCGAATCCCACCAGCGATAAACCATAAATCACCAT\n+CGTAAAGTAGAACAGCGCCAGCGATCCGGCGAAGGGATTTGATACGCCCAGATACCAATCGCCAGCACAATGGTGGCCTGGAAGGTGGCGACAATTAACG\n+CCGGTACGGCTTTGCCGATGAAGATCTGCCAGGTGGTGAGCGGCGAAACCAGTAGCTGATCGAGCGTACCTTGTTCACGTTCGCGGGCGACGGAAAGTGA\n+AGTGACGATCATTACGCCGATAGTGGTGATCATGGCGATCAGTGACGGCACCACAAACCATTTGTAGTCGAGATTCGGGTTATACCAGTTGCGTACCACC\n+AGCTCGCTGTTGTTAGGTTTCGGTTTTCCTTCCAGCAGCTCCTGCTGATAATTTTGACGATCTGTTGCAGGTAGTTGGCGGCAATTTGCGCACTGTTGGA\n+GTTACGCCCGTCGAGGATCAACTGCAAAGGCGCGGTCTGGAAGGTATCCAGTTTGCGCGAGAAGTCAGCCGGGAAACGCACCAGTAGTAACGCCTTTGTG\n+TGTCGATGGTTGGGCGGATCTCCTGTGGGCTTTTCAGCAGCAGCACATGAGTAAAGGCGCTGGCGCGGGCAAAACGTTGGGTCAGCTCCACCGAATGCTC\n+GCCGTTATCTTCATCGTAGATGGCGATGGTGGCGTTAGTCACTTCCAGCGTGGCGGCGAACGGGAACAGGATCACCTGAATTAGCACGGGTAAAATCAGA\n+ATCGCGCGGGTTTGCGGTTCGCGCAGCAACGACTGCAACTCTTTGCGGATTAACGTCCATAAGCGATGAAACATGCTCTTCTCCTAATCCAGCCGACGTT\n+TGGTTTTCAGCCACGTCAGGCCGATAAACATCACCGCCGAAGCGATCAAAAACAGCACGTTTACCACCAGCACCACTGGAATATTCCCGGCGAGGAACAG\n+GCTTTGCAGGGTGCTGACGAAATAACGAGCGGGAATAATGTACGTCACCGCGCGGATCACCGCGGGCATACTGTCGATCTGAAAAATAAAGCCGGAAAGC\n+ATAATCGACGGCAGAAAAGCGGCGTTCAGGGCGACCTGAGCGGCATTGAACTGGTTGCGGGTAATCGTGGAAATCAGCAGCCCCATCCCCAGGGTACTGA\n+GTAAAACAGGCTGGAGATAAAAACAGAATCAGCAGCGACCCGCGATACGGCACGCCGAGAATAAACACTGACACCAGCATACACAGCAACATCGCCAGCA\n+TCCCGAGAAAGTAATAAGGGATCAGCTTACACAGCAGCAGTTCCGTGCGGGTAATCTCCGTAGAGAGCAGAGCCTCCATGGTGCCGCGTTCCCATTCTCG\n+CGCCACCACCAGCGAGGTGAGAATCGCGCCGATGACCGTCATGATAATGGTCACCGCACCGGGGATAATGAAGTGCTGGCTAATCGCCGCCGGGTTAAAC\n+CAGTAGCGGGTTTGTACATCAATAAGCGGTTCAAAAGTCTGCCCGTTGTCCTCCGCTCGCTGCATTTGCCAGATCTGCCAGATCCCTTCGACATACCCTG\n+TACAAAGTTAGCGGTATTCGGCTCACTGCCGTCGGTGATCACCTGAATCGGTGCGGTGGCGTTGGCGCGCTCCATCTGTTCCGCAAAATCCACCGGAATA\n+ACCACCAGACCGCGAATTTTCCCCGCCTGCATTTTGGCGATCAGTTCCTGACGGTTATCGCTGATGGTGGCGTCGATGTAGGGCGAACCGGTCATGGTGT\n+GGTGAAATCCAGCGCCGCTTCGCTACGCTGTTCCAGTAAAATCCCGACCCGCAGCTTGCTGGAGTCGAGGTTAATGCCGTAACCAAAATAAACAGCAGTA\n+GCAGCGGGATCACTACCGCAATCAGCCAGCTACTCGGATCGCGAACGATCTGCCGCGTCTCTTTAACGCACAGCGCCCGTACGCGACGCCAGGACAGGAT\n+CGGGTTACTCATTGCTATGCTCCTTATCCCAGTCGTGGATCAACTGAATAAAGGCTTGCTCCATGGTGGGATCGGGTTGCTCATCGTTAGCCGACTGTGC\n+TTTCAAATCGTCCGGCGTGCCGCTGGCGATTAATTTCCCGCGGTACACCAGGCCGATGCGGTCGCAATATTCCGCTTCATCCATAAAGTGGGTGGTGACC\n+ATCACCGTGACGCCTTTCTCTACCATGCTGTTGATGTGCAGCCAAAATTCACGGCGGGTGAGGGGTCAACGCCGGAAGTCGGTTCGTCGAGAAACAGAAT\n+GTCCGGTTCATGCATCAGCGAACAGGCCAGCGCCAGCCGCTGTTTAAAACCTAATGGCAGTTCATCGGTGGCGTGGGAGGCGATACTTTTCAGGCCGAAC\n+GCCTCGCTCATGCGGGAGATTTTTCGTTCTGCGCCCGACCGCGTAAGCCATACACACCAGAGAAAAAGCGTAAATTCTGTTCGACCGTCAGGTTACCGTA\n+GAGCGAAAATTTTTGCGCCATATAGCCGAGATGCTGGCGCGCTTTACCGGAACTCTCTTTCAGATCCATCCCCAGCACCAGCGCCTGGCCGGAAGTCGGC\n+ACCAGCAAACCGCACATCATCTTAAAGGTGGTCGATTTACCCGCGCCGTTTGGCCCCAGCAAACCAAAAATCTCCCCACGTTTAACGGCAAAGTTGACGT\n+GATCGGTGGCGGCAAAATCCCCAAATTTCTTGGTCAGTTCTTTCGCTTCGATCACCGTCTCGCCGGGTGTGCCTTCTACCGTATGTAATATTGCGCCCAG\n+CGGCGATTCCGAGGTTCCGGCACCGCCCAGCAAATCAATAAACGCATCTTCAAAACGCGGCGTAGTTTCGTTGATGTTGATTTCCGGCATCCCGTCGGCA\n+TGGCGAATATCGTCTGGTGTGGCCTCTTTTTGAGGATCAGACGTACCGATTTCCCCTGAATCATGCCGTCGCTGACCTGCGGCAGTTTCAAGGCGCGTTG\n+CAACAGTTTGCGGTTGCCCTCGTGTGGACTGGTCATCAGAAAGCTGCGTCCGGCCATGGTTTGTGTCAGGGCTTTTGGTTCTCCCTGATACAGCAACTCG\n+CCTTCGTTCATCAGTAACACGTCACGGCACTGCTCGGCTTCGTCGAGATACGAGGTACTCCAGAGGATTAACATCCCTTCGCCCGCCAGCTCATGCACCA\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/enolase_reference.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/enolase_reference.fas Wed Jun 19 07:00:20 2019 -0400 |
| b |
| @@ -0,0 +1,23 @@ +>YHR174W +ATGGCTGTCTCTAAAGTTTACGCTAGATCCGTCTACGACTCCCGTGGTAACCCAACCGTC +GAAGTCGAATTAACCACCGAAAAGGGTGTTTTCAGATCCATTGTTCCATCTGGTGCCTCC +ACCGGTGTCCACGAAGCTTTGGAAATGAGAGATGAAGACAAATCCAAGTGGATGGGTAAG +GGTGTTATGAACGCTGTCAACAACGTCAACAACGTCATTGCTGCTGCTTTCGTCAAGGCC +AACCTAGATGTTAAGGACCAAAAGGCCGTCGATGACTTCTTGTTGTCTTTGGATGGTACC +GCCAACAAGTCCAAGTTGGGTGCTAACGCTATCTTGGGTGTCTCCATGGCCGCTGCTAGA +GCCGCTGCTGCTGAAAAGAACGTCCCATTGTACCAACATTTGGCTGACTTGTCTAAGTCC +AAGACCTCTCCATACGTTTTGCCAGTTCCATTCTTGAACGTTTTGAACGGTGGTTCCCAC +GCTGGTGGTGCTTTGGCTTTGCAAGAATTCATGATTGCTCCAACTGGTGCTAAGACCTTC +GCTGAAGCCATGAGAATTGGTTCCGAAGTTTACCACAACTTGAAGTCTTTGACCAAGAAG +AGATACGGTGCTTCTGCCGGTAACGTCGGTGACGAAGGTGGTGTTGCTCCAAACATTCAA +ACCGCTGAAGAAGCTTTGGACTTGATTGTTGACGCTATCAAGGCTGCTGGTCACGACGGT +AAGGTCAAGATCGGTTTGGACTGTGCTTCCTCTGAATTCTTCAAGGACGGTAAGTACGAC +TTGGACTTCAAGAACCCAGAATCTGACAAATCCAAGTGGTTGACTGGTGTCGAATTAGCT +GACATGTACCACTCCTTGATGAAGAGATACCCAATTGTCTCCATCGAAGATCCATTTGCT +GAAGATGACTGGGAAGCTTGGTCTCACTTCTTCAAGACCGCTGGTATCCAAATTGTTGCT +GATGACTTGACTGTCACCAACCCAGCTAGAATTGCTACCGCCATCGAAAAGAAGGCTGCT +GACGCTTTGTTGTTGAAGGTTAACCAAATCGGTACCTTGTCTGAATCCATCAAGGCTGCT +CAAGACTCTTTCGCTGCCAACTGGGGTGTTATGGTTTCCCACAGATCTGGTGAAACTGAA +GACACTTTCATTGCTGACTTGGTTGTCGGTTTGAGAACTGGTCAAATCAAGACTGGTGCT +CCAGCTAGATCCGAAAGATTGGCTAAGTTGAACCAATTGTTGAGAATCGAAGAAGAATTG +GGTGACAAGGCTGTCTACGCCGGTGAAAACTTCCACCACGGTGACAAGTTGTAA |
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| diff -r 000000000000 -r 7739a9b0dd83 test-data/fast5_files_30xpolyA-small-subset.tar.gz |
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| diff -r 000000000000 -r 7739a9b0dd83 test-data/methylation_calls.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/methylation_calls.tsv Wed Jun 19 07:00:20 2019 -0400 |
| b |
| b'@@ -0,0 +1,16999 @@\n+chromosome\tstrand\tstart\tend\tread_name\tlog_lik_ratio\tlog_lik_methylated\tlog_lik_unmethylated\tnum_calling_strands\tnum_motifs\tsequence\n+tig00000001\t+\t191153\t191157\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-6.31\t-130.59\t-124.28\t1\t2\tTATTACGACCGCTGA\n+tig00000001\t+\t191181\t191181\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.75\t-101.63\t-100.88\t1\t1\tTTTGGCGTTGA\n+tig00000001\t+\t191196\t191215\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-11.45\t-223.51\t-212.05\t1\t3\tCAGTGCGGCAAACAGCGGATAGAACGGGCT\n+tig00000001\t+\t191229\t191229\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-5.42\t-101.51\t-96.09\t1\t1\tGGAGGCGTGCA\n+tig00000001\t+\t191244\t191244\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.28\t-82.87\t-80.59\t1\t1\tAAAGGCGTTGT\n+tig00000001\t+\t191255\t191273\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-9.25\t-167.61\t-158.35\t1\t3\tTCATGCGTTTGTGCGGTACATAACGCTGT\n+tig00000001\t+\t191354\t191354\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-4.06\t-98.18\t-94.12\t1\t1\tGATTGCGTAAC\n+tig00000001\t+\t191369\t191374\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-1.70\t-119.73\t-118.02\t1\t2\tATACCCGGATCGTTCT\n+tig00000001\t+\t191399\t191420\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-14.84\t-212.15\t-197.31\t1\t4\tAACAGCGGCGAACAGTCCGCCATCATCGGAAT\n+tig00000001\t+\t191440\t191440\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.39\t-97.48\t-95.10\t1\t1\tATAGCCGACCC\n+tig00000001\t+\t191502\t191524\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-7.13\t-196.90\t-189.78\t1\t5\tCTTGGCGGGCGTTATAAATCGTACCGTCGTAGG\n+tig00000001\t+\t191548\t191562\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t2.03\t-164.90\t-166.93\t1\t3\tCACAGCGAGGCGGAAAGGACGAGCC\n+tig00000001\t+\t191576\t191595\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-16.47\t-198.51\t-182.04\t1\t5\tTTGCCCGCTGCGGTGCGACTTCCGCGATCA\n+tig00000001\t+\t191606\t191606\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.43\t-106.24\t-105.81\t1\t1\tGCTCACGCAGG\n+tig00000001\t+\t191632\t191632\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-5.03\t-101.77\t-96.74\t1\t1\tCAGTGCGCATC\n+tig00000001\t+\t191646\t191646\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.52\t-102.26\t-101.75\t1\t1\tGCCACCGATAA\n+tig00000001\t+\t191659\t191671\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-6.16\t-155.98\t-149.82\t1\t3\tCCATACGGGTTACGTGCCGTTTC\n+tig00000001\t+\t191686\t191686\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-1.12\t-84.86\t-83.73\t1\t1\tTAAACCGGTGT\n+tig00000001\t+\t191710\t191715\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-1.66\t-141.17\t-139.51\t1\t2\tAGCAACGCTCCGTGGT\n+tig00000001\t+\t191741\t191741\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.49\t-76.49\t-74.01\t1\t1\tTATTGCGATCA\n+tig00000001\t+\t191764\t191764\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.28\t-106.49\t-104.21\t1\t1\tTCACCCGGTGT\n+tig00000001\t+\t191778\t191778\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-8.95\t-111.16\t-102.21\t1\t1\tCAGGGCGTTTA\n+tig00000001\t+\t191820\t191820\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-1.97\t-129.21\t-127.24\t1\t1\tTAAAACGAAGT\n+tig00000001\t+\t191835\t191835\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.83\t-101.24\t-100.41\t1\t1\tTTTATCGGCAT\n+tig00000001\t+\t191854\t191854\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-3.07\t-94.72\t-91.65\t1\t1\tTTTGCCGCATG\n+tig00000001\t+\t191878\t191886\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-11.48\t-176.19\t-164.71\t1\t3\tCATGGCGCGCCTTCGTGAA\n+tig00000001\t+\t191901\t191919\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-5.54\t-179.90\t-174.37\t1\t5\tCAGATCGCCCATCGCTACGTCGGCGTTGC\n+tig00000001\t+\t191931\t191944\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-19.26\t-177.78\t-158.53\t1\t3\tCAAGTCGGCACGGAACAGCGCCTC\n+tig00000001\t+\t191977\t192002\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-8.41\t-244.04\t-235.63\t1\t6\tTTCCCCGCCGGATGGCGACGGAAAATTCGCCGCCCT\n+tig00000001\t+\t192027\t192029\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.80\t-105.66\t-104.86\t1\t2\tTCAAACGCGCTGT\n+tig00000001\t+\t192053\t192064\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.40\t-160.39\t-157.99\t1\t3\tATAATCGACCAGTGCGCGGAAG\n+tig00000001\t+\t192079\t192079\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-7.16\t-99.97\t-92.81\t1\t1\tGTGGGCGCAGT\n+tig00000001\t+\t192107\t192107\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.87\t-96.22\t-95.35\t1\t1\tGGCAGCGGTTT\n+tig00000001\t+\t192121\t192121\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.94\t-100.94\t-100.00\t1\t1\tACTGGCGACCA\n+tig00000001\t+\t192136\t192146\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-4.34\t-143.10\t-138.77\t1\t4\tATTCTCGTCGCGATTC'..b'7cd320d229a4\t-1.02\t-218.40\t-217.38\t1\t4\tCATCACGCGCATCACCACGCCGGATG\n+tig00000001\t-\t202851\t202854\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.97\t-151.89\t-150.93\t1\t2\tGGCATCGGCGTTTT\n+tig00000001\t-\t202884\t202903\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-3.39\t-239.50\t-236.10\t1\t3\tGTTAACGTCAGCCACCGGGCCTGACGGGCT\n+tig00000001\t-\t202916\t202919\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-5.57\t-158.84\t-153.27\t1\t2\tAAATACGCCGGGAA\n+tig00000001\t-\t202940\t202940\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.01\t-137.40\t-137.40\t1\t1\tGGGGCCGTCTG\n+tig00000001\t-\t202966\t202985\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.70\t-224.43\t-223.73\t1\t4\tCCTGACGGCGATATCACCCGCTACCGTTAT\n+tig00000001\t-\t203017\t203022\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t0.16\t-138.31\t-138.47\t1\t2\tCCCTGCGCAACGGAAG\n+tig00000001\t-\t203035\t203042\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.21\t-179.23\t-179.03\t1\t2\tGCCACCGGCAGCCGGAAA\n+tig00000001\t-\t203055\t203068\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t3.76\t-206.83\t-210.60\t1\t3\tCATGACGTGGAGCCGTTACGGTCA\n+tig00000001\t-\t203098\t203098\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t1.17\t-125.07\t-126.23\t1\t1\tTGTTCCGGTTA\n+tig00000001\t-\t203111\t203111\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.97\t-148.33\t-147.36\t1\t1\tTAACCCGCTAT\n+tig00000001\t-\t203126\t203126\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-7.02\t-103.83\t-96.81\t1\t1\tATGACCGTTTT\n+tig00000001\t-\t203142\t203155\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-6.70\t-214.24\t-207.54\t1\t4\tGGTGACGGCGGTGCACCGCGAGGA\n+tig00000001\t-\t203177\t203192\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.92\t-216.14\t-215.23\t1\t4\tAGTACCGCGCATACGACAGCCGTGGA\n+tig00000001\t-\t203209\t203209\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-2.79\t-123.73\t-120.94\t1\t1\tATTGCCGTGAA\n+tig00000001\t-\t203220\t203220\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-1.36\t-114.22\t-112.86\t1\t1\tAGACACGCAGG\n+tig00000001\t-\t203235\t203237\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-4.35\t-124.77\t-120.42\t1\t2\tTGAAACGCGGTAT\n+tig00000001\t-\t203251\t203257\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-5.88\t-153.96\t-148.09\t1\t3\tTACAACGCCGCCGGTGA\n+tig00000001\t-\t203272\t203272\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-1.72\t-105.43\t-103.71\t1\t1\tACCACCGTCAT\n+tig00000001\t-\t203283\t203287\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t0.27\t-130.94\t-131.20\t1\t2\tTGCCCCGGACGGCAG\n+tig00000001\t-\t203299\t203299\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.22\t-118.31\t-118.09\t1\t1\tAGAAACGGGAC\n+tig00000001\t-\t203311\t203316\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-10.31\t-125.90\t-115.59\t1\t2\tCAGTACGATGCGTGGG\n+tig00000001\t-\t203340\t203357\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-11.70\t-169.31\t-157.61\t1\t4\tTACCACGCAGGGCGGTCTGACGCGCAGT\n+tig00000001\t-\t203371\t203393\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.98\t-246.59\t-245.61\t1\t4\tGAATACGATGCTGCCGGACGGGTCATCCGCCTG\n+tig00000001\t-\t203410\t203410\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t3.62\t-109.90\t-113.52\t1\t1\tGAAAACGGCAG\n+tig00000001\t-\t203429\t203447\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-12.27\t-220.57\t-208.29\t1\t4\tCCTTCCGTTACGATGTACTCGACCGGCTG\n+tig00000001\t-\t203464\t203486\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-2.89\t-240.35\t-237.45\t1\t4\tGAAACCGGCTTTGACGGCCGCACACAGCGTTAT\n+tig00000001\t-\t203497\t203506\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-3.73\t-154.07\t-150.34\t1\t2\tCACCACGACCTGACCGGCAA\n+tig00000001\t-\t203519\t203524\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-7.21\t-149.81\t-142.60\t1\t2\tTTATCCGCAGCGAGGA\n+tig00000001\t-\t203560\t203609\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-7.10\t-430.95\t-423.84\t1\t8\tTATGACGAAGCAGACCGCCTCACGCACCGCACCGTGAATGGCGAAACCGCAGAGCGGTGG\n+tig00000001\t-\t203623\t203629\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-1.64\t-163.12\t-161.49\t1\t3\tTATGACGAACGCGGCTG\n+tig00000001\t-\t203659\t203676\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.40\t-230.02\t-229.62\t1\t3\tATCAGCGAAGGGCACCGGGTGACGGTGC\n+tig00000001\t-\t203705\t203710\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-7.62\t-166.05\t-158.43\t1\t2\tAAGGCCGCCTCGCCAG\n+tig00000001\t-\t203727\t203727\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.50\t-190.77\t-190.27\t1\t1\tCCTGACGGTGC\n+tig00000001\t-\t203739\t203745\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.18\t-205.41\t-205.23\t1\t2\tTCATCCGCAGACGAATG\n+tig00000001\t-\t203781\t203788\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t0.12\t-163.10\t-163.22\t1\t2\tACATGCGTACAACGCACA\n' |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/polished.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/polished.fa Wed Jun 19 07:00:20 2019 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>tig00000001\n+AGATGCTTTGAAAGAAACGCAGAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTGAAAAGAAAATGTCCCACAGGTACAGATAGAGTTGCTGCTTATCATACTCACGGTGCAGATAGTCATGGCGATTATGTTGATGAATTTTTTCAAGTAGCGATAAAATCTTGTAAGAAGTAAAGATAATAATCTTGAAGCATTTTATCTCGCAACACCTGATGGACGATTTGAGGCGCTTAATAATAAAGGAGAATATATTTTATCAGAAATAGTGTCCCGGGATTGAGTTCAGTATGCATACCGTATCATGATTAATTTTAGTGCTTTTATTAGTGGGGCCTATAGGAGATTCAATGAAATATAGTTCAATATTTTCGATGCTTTCATTTTTATACTATTTGCCTGTAATGAGACAGCTGTTTACGGTTCTGATGAAAACATTATTTTTATGAGGTATGTGGAAAAATTACATTTAGATAAATACTCTGTTAAAAATACGGTAAAACTGAAACAATGGCGATACAATTAGCTGAAATATATGTTAGGTATCGCTATGGCGAACGGATTGCAGAAGAAAAACCATATTTAATTACGGAACTACCAGATAGTTGGGTTGTTGAGGGAGCAAAGTTACCTTATGAAGTTGCGGGTGGTGTATTTATTATAGAAATTAATAAGAAAAATGGATGTGTTTTGAATTTCCTACATAGTAAATAATGCTGGCGCTGATGGATGCGGATGGAAACATTGCGTGGAGCGGGGAGTATGATGAGTGGGGCAACCAGCTGAATGAAGAGAACCCGCATCACCTGCACCAGCCGTACCGGCTGCCGGGGCAGCAGTATGATAAGGAGTCGGGGCTGTACTACAACCGGAACCGGTACTACGATCCGTTGCAGGGCGGTATATCACCAGGACCCGATAGGGCTGAGGGGGATGGAGTCTGTATGCGTATCCGCTGAATCCGGTGAATGGTATTGATCCATTAGGTTAAGTCCCGCAGATGTAGCGCTAATAAGAAGAAAAGATCAACTAAACCATCAAAGAGCATGGGATATATTATCTGATACTTATGAAGATATGAAGAGATTAAATTTAGGTGGGACTGATCAATTTTTCCATTGTATGGCATTTTGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGTAAAGCTATCCCATTCTGAAATGATTGAAGATAATAAAAAGACTTGGCTGTAAATGACCATGGGTTGACATGTCCATCAACAACAGATTGCTCAGATAGATGTAGTGATTATATTAATCCAGCATAAAAAACGATAAAGGCTTTACAAGATGCTGGCTATCTCAAGTAATCTATCAAAGATGATAATATTTATTTTTGCTATTATAATCATTGTTGTTTTATGCGTAATTACTTATCTTTATTTATACAAAGATGAATCTCTTGTAAGTAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTCTTATTTTCCCTAACAAATGATGATGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGGCAAGGGATGGTGTAAACCTTTTTTGTTGGTGAAATTAATGTTACGCATTATTTTATAACAAATATTGGAGCTGGATTGCCTGATGCTTGTGCAGAGTAATTGCTTGAATTAAGAGTCTATCCCATATCGAAGTCGTCAACTTCGTAGTGAGGAAAAGTAAAATTCCTGACTGAGAAAAGACATGTCGGCTATTGTGTAAAGCCATATAGCTCAGACGATGAATATCTACTCGTATTCAGTTGTTTATTGAGGGTGAGTTCCGACCCTGAAACAACAAATAAAATGAACAGTCAGAGAGTTTACATAGAATTGCACTGGTCTTTTACGATATCTGACATTGTGTAATACATATTCAGCCATGCATTAATTAAAATGTTACGTGTTTAATGTGAGTCCCTATCTGAAAATAAATAATCCTTCCGGATTAAAATAAATTCTTGCCGGGAAAGAAAGAGGAAATAAACCATTAGCGGAAAACCAGCGGCACGCCAGGGTGACATGCCCCAGTACGGCGGCCCGATAGTCCAGGGTTCAGCGGGGTACTGATAGTCGCGCCGACTGCATCGAGAACTCCATACAACTTTTACGGAACGTCACCTGATAAAATTTGTTCAGTATCGTCTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAACCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATAAAACGTATCACGCGAAACGCCCATGATTTTACAGGCTTTTGATACGTTGCTGAGTTCTTCAGCCAGATTGAGCAAACCGGCTTTGTGTTTGATGACGGGATTGGCAGTATGAAGCATGAGAGTTACCTCTTGTTTTGGATAAGGATTCGACACTCATATCAAAACCGGTAACTCTCAACCTTTCAAGGCCATGTGTCAGATCAAGTCGCGACTAATACAAATACGTCCCTCATTACCGCGCCTTAACCCATTCCGCCACTTCCGCCCACTCACCGCGAAAGACAACTTTTTCCGCTTTTTCTCAAGCTGATAGCGATACATCGGGTCGTAATATTCTTCAAGTAACGGCACCAGCCAGGCCAGATGACCGTCGGTGCTGCCGGTGGTGAGTTGCGTTGTCAGTGCTGCATCCAGCCTTGCAGCCAGTTCGTTATAGCGCTGTAGCCCCAGCCGACGCTTAATCGCCGAAAGTCCGTGATGCAGGTATTCGCAATACTCCTGCCAGCCCTGTTCGTCGCCGTACGCGTGGGTAAAATCATGATGCATACGCAAGAAATACTCTTCGTTCAGGCGCTCAAGACGGATCTCAAACGGATCTTCTACCACCGCAATCGCCGCCTGAGTCATTCGCTCGCGCAGGCATTCCGGCAGGTGATTCGAACCGATCATCCGGCTTTCGTCTTCCAGCACCCACAGGCGCAAATTCTGACGGGCGTCGGTTTTAGCATTTCGGCAGCCAGCAGGTTTTCAAAACTCGCCTGGCTAAGTTGTGGTTGTAACGTGCGACCAAACGCCGAACCGCGATGACGCGCCAACCCTTCCAGATCAACACCGTTCGGCTGTTGCTGCACTAACAGCGTTTTACCGCTGCCGGTACAACCGCCAATCAGCACTATCGGTTTTGTGCCAGTTCAATAGTCGCCTGAATCGCGGTCTGGCGCAGTGCCTTATAACCGCCTTCCACCAGCGGATAATCAATCCCCGCTGCATGCAACCAGCTTTGCACAATATGTGAGCGCTGACCGCCACGGGCGCAGCAGAGAATACCTTGCGGATTTTGCAGGCACGCTGCCCGCCAGGCGTCCATGCGCTGCTGACGAATTTCACCCGCCACCAGTTTATGTCCCAGCGCCAGCGCTGCGTCTGAGCCTTGCTGTTTATAGCAGGTGCCAACGGCGGCGCGTTCATCGTTATTCATTAACGGCAGATTGATAGCGGCGGGCATTGCGCCGTGCTCAAACTCG'..b'GGTAAAGCCTTTGTGAATATTGATGGTGAGCACCTTGAACGAAAATTGTTGTGTTTGATCGGGCATAATTTTCCTGTCTTTGCCTCTTATCTCATTGAAATAGTGTAGTCGGCGTCACAAAAGGTGCGGTCTTACGGAATTTTCCGTAAAGTTCGGTACTCTGAGTAAGTAGAGATAAATTCTTCAGGAGAGAAGCCATGAAGTGGCAACAACGTGTTCGTGTCGCAACGGGTCTAAGTTGCTGGCAGATTATGTTGCATTTACTGGTAGTGGCGCTGCTGGTGGTGGGCTGGATGAGTAAGACTCTGGTTCACGTCGGCGTGGGATTATGCGCACTGTATTGTGTCACGGTAGTGATGATGCTGGTGTTTCAGCGCCACCCCGAGCAACGCTGGCGTGAGGTGGCAGACGTGCTGGAAGAGCTGACCACGACCTGGTATTTTGGCGCAGCGCTGATTGTGCTGTGGCTGTTGTCCCGCGTTCTGGAAAACAACTTTTGCTGGCAATTGCAGGGCTGGCAATCCTTGCCGGCCCGGCGGTAGTGTCTTTGCTGGCGAAAGATAAGAAGTTACATCACCTTACGTCTAAACATCGCGTACGCCGCTGACCCTGTCGTGGCCGTTATCACCAGTAGCGGCCACAAACTATTCCACACAATATCCAGACTCGCATCCTTCAAATAAATCTGCTTGGTAATGTCCGTAAAGTGGCGAATAGGGTTAATCCACGTCAGGTTTTGCAGCCATACCGGCATGTTTTCCACCGGAGAAACGTAACCGGAAAGGAGAATGGCGGGCATCATAAAGACAAACACGCCGATAAACGCCTGCTGTTGTGTTGAACAGAGTGATGAAATCAACAGACCGAATCCCACCAGCGATAAACCATAAATCACCATCGTAAAGTAGAACAGCGCCAGCGATCCGGCGAAGGGATTTGATACGCCCAGATACCAATCGCCAGCACAATGGTGGCCTGGAAGGTGGCGACAATTAACGCCGGTACGGCTTTGCCGATGAAGATCTGCCAGGTGGTGAGCGGCGAAACCAGTAGCTGATCGAGCGTACCTTGTTCACGTTCGCGGGCGACGGAAAGTGAAGTGACGATCATTACGCCGATAGTGGTGATCATGGCGATCAGTGACGGCACCACAAACCATTTGTAGTCGAGATTCGGGTTATACCAGTTGCGTACCACCAGCTCGCTGTTGTTAGGTTTCGGTTTTCCTTCCAGCAGCTCCTGCTGATAATTTTGACGATCTGTTGCAGGTAGTTGGCGGCAATTTGCGCACTGTTGGAGTTACGCCCGTCGAGGATCAACTGCAAAGGCGCGGTCTGGAAGGTATCCAGTTTGCGCGAGAAGTCAGCCGGGAAACGCACCAGTAGTAACGCCTTTGTGTGTCGATGGTTGGGCGGATCTCCTGTGGGCTTTTCAGCAGCAGCACATGAGTAAAGGCGCTGGCGCGGGCAAAACGTTGGGTCAGCTCCACCGAATGCTCGCCGTTATCTTCATCGTAGATGGCGATGGTGGCGTTAGTCACTTCCAGCGTGGCGGCGAACGGGAACAGGATCACCTGAATTAGCACGGGTAAAATCAGAATCGCGCGGGTTTGCGGTTCGCGCAGCAACGACTGCAACTCTTTGCGGATTAACGTCCATAAGCGATGAAACATGCTCTTCTCCTAATCCAGCCGACGTTTGGTTTTCAGCCACGTCAGGCCGATAAACATCACCGCCGAAGCGATCAAAAACAGCACGTTTACCACCAGCACCACTGGAATATTCCCGGCGAGGAACAGGCTTTGCAGGGTGCTGACGAAATAACGAGCGGGAATAATGTACGTCACCGCGCGGATCACCGCGGGCATACTGTCGATCTGAAAAATAAAGCCGGAAAGCATAATCGACGGCAGAAAAGCGGCGTTCAGGGCGACCTGAGCGGCATTGAACTGGTTGCGGGTAATCGTGGAAATCAGCAGCCCCATCCCCAGGGTACTGAGTAAAACAGGCTGGAGATAAAAACAGAATCAGCAGCGACCCGCGATACGGCACGCCGAGAATAAACACTGACACCAGCATACACAGCAACATCGCCAGCATCCCGAGAAAGTAATAAGGGATCAGCTTACACAGCAGCAGTTCCGTGCGGGTAATCTCCGTAGAGAGCAGAGCCTCCATGGTGCCGCGTTCCCATTCTCGCGCCACCACCAGCGAGGTGAGAATCGCGCCGATGACCGTCATGATAATGGTCACCGCACCGGGGATAATGAAGTGCTGGCTAATCGCCGCCGGGTTAAACCAGTAGCGGGTTTGTACATCAATAAGCGGTTCAAAAGTCTGCCCGTTGTCCTCCGCTCGCTGCATTTGCCAGATCTGCCAGATCCCTTCGACATACCCTGTACAAAGTTAGCGGTATTCGGCTCACTGCCGTCGGTGATCACCTGAATCGGTGCGGTGGCGTTGGCGCGCTCCATCTGTTCCGCAAAATCCACCGGAATAACCACCAGACCGCGAATTTTCCCCGCCTGCATTTTGGCGATCAGTTCCTGACGGTTATCGCTGATGGTGGCGTCGATGTAGGGCGAACCGGTCATGGTGTGGTGAAATCCAGCGCCGCTTCGCTACGCTGTTCCAGTAAAATCCCGACCCGCAGCTTGCTGGAGTCGAGGTTAATGCCGTAACCAAAATAAACAGCAGTAGCAGCGGGATCACTACCGCAATCAGCCAGCTACTCGGATCGCGAACGATCTGCCGCGTCTCTTTAACGCACAGCGCCCGTACGCGACGCCAGGACAGGATCGGGTTACTCATTGCTATGCTCCTTATCCCAGTCGTGGATCAACTGAATAAAGGCTTGCTCCATGGTGGGATCGGGTTGCTCATCGTTAGCCGACTGTGCTTTCAAATCGTCCGGCGTGCCGCTGGCGATTAATTTCCCGCGGTACACCAGGCCGATGCGGTCGCAATATTCCGCTTCATCCATAAAGTGGGTGGTGACCATCACCGTGACGCCTTTCTCTACCATGCTGTTGATGTGCAGCCAAAATTCACGGCGGGTGAGGGGTCAACGCCGGAAGTCGGTTCGTCGAGAAACAGAATGTCCGGTTCATGCATCAGCGAACAGGCCAGCGCCAGCCGCTGTTTAAAACCTAATGGCAGTTCATCGGTGGCGTGGGAGGCGATACTTTTCAGGCCGAACGCCTCGCTCATGCGGGAGATTTTTCGTTCTGCGCCCGACCGCGTAAGCCATACACACCAGAGAAAAAGCGTAAATTCTGTTCGACCGTCAGGTTACCGTAGAGCGAAAATTTTTGCGCCATATAGCCGAGATGCTGGCGCGCTTTACCGGAACTCTCTTTCAGATCCATCCCCAGCACCAGCGCCTGGCCGGAAGTCGGCACCAGCAAACCGCACATCATCTTAAAGGTGGTCGATTTACCCGCGCCGTTTGGCCCCAGCAAACCAAAAATCTCCCCACGTTTAACGGCAAAGTTGACGTGATCGGTGGCGGCAAAATCCCCAAATTTCTTGGTCAGTTCTTTCGCTTCGATCACCGTCTCGCCGGGTGTGCCTTCTACCGTATGTAATATTGCGCCCAGCGGCGATTCCGAGGTTCCGGCACCGCCCAGCAAATCAATAAACGCATCTTCAAAACGCGGCGTAGTTTCGTTGATGTTGATTTCCGGCATCCCGTCGGCATGGCGAATATCGTCTGGTGTGGCCTCTTTTTGAGGATCAGACGTACCGATTTCCCCTGAATCATGCCGTCGCTGACCTGCGGCAGTTTCAAGGCGCGTTGCAACAGTTTGCGGTTGCCCTCGTGTGGACTGGTCATCAGAAAGCTGCGTCCGGCCATGGTTTGTGTCAGGGCTTTTGGTTCTCCCTGATACAGCAACTCGCCTTCGTTCATCAGTAACACGTCACGGCACTGCTCGGCTTCGTCGAGATACGAGGTACTCCAGAGGATTAACATCCCTTCGCCCGCCAGCTCATGCACCA\n' |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/reads-draft.eventalign.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads-draft.eventalign.sam Wed Jun 19 07:00:20 2019 -0400 |
| b |
| b'@@ -0,0 +1,148 @@\n+@HD\tVN:1.5\tSO:coordinate\n+@SQ\tSN:tig00000001\tLN:4376233\n+@SQ\tSN:tig00000005\tLN:10541\n+@SQ\tSN:tig00000118\tLN:234051\n+@PG\tID:minimap2\tPN:minimap2\tVN:2.10-r761\tCL:minimap2 -ax map-ont -t 8 draft.fa reads.fasta\n+0a238451-b9ed-446d-a152-badd074006c4.template\t0\ttig00000001\t16\t60\t10711S1M1I1M3I1M1I1M2I2M2I2M19I1M20I2D4M70I5M2I6D3M1I3D2M1I1M153I2M6I1M1I1M13I1M2I1M6I1M2I3M1I1M1I5M1I3M3I3M2I2M1I2M2I2M1I1M1I1M1I2M1I5M3I3M1I1M1D2M1I5M1I4D3M2I2M1I5M2I9M1I4M2I1M1I1D2M2I2M2I3M1I1M1I10M1I1M1I1D2M1I3M1I2M1I1M1I1M1I2M1I1M1I2M2I1M2I4M1I3M1I1M1I7M1I4M1I2M2I1M1I1M4I2M1I1M2I5M2I1M2I3D1M1I1M4I3M1I4M1I2M2I2M2I1M2I2M1I6M1I1D1M2I5M1I2M3I3M1I1M1I2M1I1D4M2I1M1I1D1M1I1M1I1M2I3M1I7M1I4M1I3M1I2D1M1I1M1I2M3I1M2I9M1I6M2I3M1I1M3I2M1I1M3I2M1I1M2I1M2I1M1I1M1I2M2I4M1I6M3I4M1I1M2I2M2I1M3I2M2I1M1I7M1I3M1I1M1I1D4M4I1M1I1M1I3M1I4M1I2M1I5M2I1M2I1M3I2M1I3M1I1M1I3M1I2D4M1I1M2I4M1I1M3I5M1I2M1I2M1I1M1I3M1I2M1I1M1I2D3M1I2M1I2M3I2M3I1M3I1M1I1M1I5M2I1M1I1M1I2M1I1M1I3M1I2M2I2M1I2M1I2M2I1M2I2M1I3M1I4M1I4M1I1D2M1I2M1I3M1I5M1I1M1I1D3M1I1M1I1D6M4I6M2I1M1I3M2I4M2I1M2I2M1I1M2I1M2I1M1I1D3M1I3M1I3M1I2M3I2M2I3M1I2M2I1M2I2M1I1D2M3I1M1I3D3M2I3M1I3M2I2M1I6M2I1M1I3M1I4M1I1D3M1I2M2I2M2I2M2I4M1I3M2I4M1I2M1I1D5M1I1M3I1M1I3M1I6M2I1M2I2M1I2D3M1I1M5I9M1I3D5M1I2M1I3M3I1M1I1M2I3M1I2M1I1D2M2I1M2I2M2I1M3I3M1I1D5M1I2M1I3M1I2M1I4M1I4M1I1M5I1M1I1M1I3M1I1M1I2M1I2M1I5M1I7M1I1D2M1I3M1I1D2M1D2M1I1M1I2M4I4M1I4M1D5M1I1M1I1M1I2D3M1I1D2M1I1M1I2M1I5M1I1M1I4M2I4M1I6M1I4M1I1M1I3M6I1M2I4M4I1M1I1M1I1M1I2M1I2M1I2M2I1M1I1M2I1M2I2M1I2M2I1M1I1M1I2D3M1I2M1I9M1I2M1I1M1I3M3I1M2I5M3I4M1I2M3I1M1I1M1I1M2I4M1I1M2I3M2I2M3I2M1I4M1I2M2I1D1M3I1M2I2M1I1M1I4M1I1M3I3M2I2M2I1M1I4M2I5M1I2M1I4M1I5M2I2M3I4M1I2M1I1M1I1M2I7M1I2D8M1I1M1I2D4M1I3M1I3M1I1D1M1I1M5I3M1I1M1I6M1I1M1I2M2I1M2I1M1I2M1I2M3I1M1I1M1I1M1I1M3I2M1D2M1I5M1I2M1I11M1I3M1I4M2I3M2I4M2I4M1I2M2I2M2I8M1I1M1I1M1I2M1I1M1I3M2I1M1I2M2I1M2I1D2M1I2M2I1M1I2M1I1M1I1M3I2M2I1M1D2M1I1M1I2M1I1D1M1I2M3I2M1I3M2I2M3I1M1I2M2I4M2I3M1I3M1I5M1I2M1I1M1I2M2I1M1I3M1I4M1I2D1M1I6M1I3M1I1M1I2M1I1M2I1M1I4M2I1M1I3M2I2M1I1M1I2M1I3M1I2M1I2M1I4M1I2M1I4M1I8M1I5M4I2M1I5M4I2M1I1M2I1M1I2M2I2M1I3M1I2M1I1M1I1M2I15M1I2M1I1D8M2I2M1I1M1I4M4I3D2M1I2M3I1M1I1M1I1M1I1D3M1I4M1I3M2I3M1D4M1I5M3I8M1I2M1I2M3I2M3I5M1I7M1I2M1I1M1I2M1I1M2I2M2I1M2I3M1I5M2I5M3I3M1I2M2I1M1I1M2I2M1D4M1I2M1I3M1I1M1I2D3M1I2M1I7M1I3M1I4M1I1M1I3M1I1M1I2M1I4M1I2M1I2M1I1M1I1M1I1M1I3M1I1M1I1M1I5M1I1M1I1M1I10M1I1M1I4M1I3M1I2M1I3D4M1I2M2I2M3I1M2I1M1I1D3M2I10M3I7M1I2M1I3M1I1M2I4M1I1M1I2M1I2M2I1D1M1I2M1I6M1I2D3M1I2M1I1D3M1I3M4I1M1I3D2M2I3M3I2M1I2M1I2M1I2M1I1M1I1M1I9M1I1M3I3M2I5M1I6M1I1M6I1M1I1M2I3M1I3M1I2M2I3M1I1M3I1M4I1M1I5M1I1D6M1I2M1I6M1I1M1I8M1I3M1I6M2I6M1I4M1I1M1I1M1I2M1I1M2I3M1I1M2I2M1I2M1I2M1I2D3M2I6M1I3M1I1M1I3M3I2D5M2I1M1I3D7M1I4D2M2I1M1I1M1I1M1I4M1I2D3M3I1M1I6M1I2M3I1M1I2M2I3M1I2M4I1M1I1M2I2M2I5M1I1M2I1M1I2M1I4M2I1M2I2M2I4M1I2M1I3M2I4M9I7M1I2M1I1M1I5M1I2M1I3M1I4M5I2M1I1M1I1D1M2I1M1I1M1I1M1I2M3I1M1I1M2I3M1I2D1M1I4M1I1M1I1M1I2M1I2M2I4M1I4M1I2M1I6M3I1M1I2D1M1I2M1I10M1I1D1M1I1M1I5M2I1M2I2M4I2M8I1M2I5M5I1M1I3M1I4M1I1D3M1I1D3M1I1D6M2I6M6I2M2I2M1D3M1I1M1I1M4I1D3M2I1M2I4M1I3M1I6M1I2M1I3M1I2M1I5M1I2D2M1I4M1I2D2M2I3M1I1M6I1M1I1M1I4M1I1M1I1M1I3M1I1D9M8I1M1I1M2I5M1I1M2I2M2I2M1I2M1I3M1I1M2I1M1I1D4M1I1M1I5M1I1M3I3M7I3M2I2M3I1M1I1M1I1M2I5M1I1D3M1I1M1I1M1I5M3I1M2I2M1I1D2M1I1M1I3M1I4M4I1D3M1I3M1I1M1I2M1I1M1I2M6I1M1I3M1I1M2I1M1I2M1I1M4I4M1I2M2I4M1I1M1I1M2I2M1I2M1I2M1I5M1I1M2I4M1I4M1I1M1I1M4I1M1I2M1I4M2I1M1I1M1I1M2I1M1I6M2I2M3I1M1I2D1M6I8M2I1M2I3D6M2I3M2I1M2I1M1I1M3I1M1I1M3I4M3I2M2I2M1I4M2I3M2I2M1I1M2I4M1I1M1I1M1I10M6I6M1I3M1I1M2I15M1I3M2I6M1I2M4I4M1I1M3I3M2I1M1I8M2I1M3I3M1I4M1I2M1I1M1I4M1I1M1I2D3M1I4M3I1M1I3M1I2M1I2M2I2D2M5I3M1I2M1I3M2I1M1I1M2I1M3I2M3I1M2I1M2I2M2I2D3M1I1D5M1I12D4M1I1M2I2D1M1I3M3I1D1M2I5M4I1M3I1M10I5M1I1M1I1D3M1I1M3I1M1I3M2I2M2I1M2I1M1I3D2M3I2M2I1M1I2M1I1M2I2M1I4M1I1D2M1I1M1I1M1I3M1I1M1I4M1I4M1I10M1I3M1I1M1I2M1I1M3I1M1I2M1I2M1I3M1I3M1I2M1I1M1I1M5I1M3I2M1I1M1I1M2I3M2I1M1I3M1I4M1I3M2I2M2I5M1I1M3I3M1I2M1I2M1I3M8I2M1I1M1I4M1I3M1I2M2I1M1I1M3I5M2I1M1I3M3I3M1I1M1I2M2I1M1I1M4I2M3I9M1I1M1I2M1I1D3M1I1M2I3M3I4M1I1M1I1M3I2M1I2M1I1M1I3M2I2M1I2M2'..b'4D2M1I1M11I1M2I2D1M4I6D1M1I2M1I4M1I1D3M9I1M1I13D4M1I1M3I1D1M2I3D1M1I1M3I7D1M1I1M1I2D1M1I3D1M1I2D1M2I2D3M1I3D2M2I1D4M2I2D2M3I1M1I1D1M2I4M4I4M4I6M1I5D6M1I1M1I2M2I2M2I16D2M2I1M1I3M1I1M1I1M1I2M1I1M2I1M3I8D1M4I2M1I1M1I4M3I2D2M2I3D1M3I2D2M1I2M2I1M2I2M1I2M7I1M2I1M3I1D1M5I1D3M2I2D4M1I1M1I4D2M1I1M1I1M1I1M3I3M1I1D1M2I3M1I1M5I1D2M1I3M1I1M3I1M1I1M6I1M6I2M3I2M1I1D4M1I2D1M2I2D1M3I2M1I1M1I1M4I2M1I3M3I3M1I3D2M2I4D3M1I3D3M3I1M2I2D1M4I1M3I1M1I1M1I1M3I3M2I5M1I10D3M2I1M2I1D3M3I1M1I2M1I1D3M2I1M2I1M6I2M3I1M1I2M2I2M3I1D2M4I1M4I1M1I2D3M4I1D2M2I1M1I2D2M1I2D2M1I9D2M1I2M1I2M5D3M1I1D3M1I1D6M1I3D1M6I1D2M2I4M1I1M5I1M4I1D1M1I3M1I1M1I1D3M2I2D1M5I3M2I2D1M4I1M4I1M2I1M1I2M1I3M1I4M4I1M2I1M8I1D2M4I1M2I3D1M2I1M1I1M2I1M1I1M1I1M11I1M1I1M4I1M1I2M5I1M1I1M2I1M1I1D1M1I1D3M1I7D4M1I2D1M1I1D6M1I1M7I11D4M2I2D1M5I1M3I2M1I1M3I1M2I1M4I1M1I5D4M6I2D2M2I1M1I1M3I2D4M1I2M6I1M1I1M1I2M1I2D1M2I1D3M2I1M3I4D1M2I6M1I1D3M2I1M2I1D1M1I2M2I3M1I1M4I1D2M1I1M3I2M1I2M2I1M2I1D2M4I1M1I14D4M1I2D1M2I2M2I2D3M2I1M2I4M1I1M2I2D3M2I3M1I1D1M4I2M1I4D2M1I1D1M1I1M1I1M3I3D2M2I1M1I1D2M4I2D1M14I1M3I3M3I1M3I1M1I4D1M1I1M2I2D1M1I1M1I3M2I2D3M7I1M2I3M7I1M1I1M1I3D2M7I1M8I3M1I1M1I3M2I1M4I1D2M2I7D1M2I2M1I2D3M1I1M2I1M2I1M3I1M1I2D2M2I1M2I1D2M3I5D1M2I2D3M1I1M3I2M6I2M2I1M2I1M7I1D2M1I1M1I1M1I13D1M3I6M1I1M2I1M3I3D1M2I1D1M2I1M3I1M3I1M8I5M1I1M1I1D2M1I1M1I4D2M1I1D1M1I1M15D7M1I3D4M1I2M2I1M1I1M1I1M3I1D1M1I2M1I1M5I1M7I3D2M7I1D1M2I1D4M4I2M2I1M4I3D5M1I2D5M1I2D1M10I1M8I2D2M1I1M2I1D4M2I4D4M1I1D8M1I1M4I3D2M2I3M1I4M1I2D1M3I1M4I1M4I1D2M2I1M1I2M5I2D1M1I1D1M1I4M7I2M9I1D1M6I2M3I1D1M4I2M4I2M4I1M2I3M1I3M1I1M1I11D3M1I1M3I4M1I1D1M4I1D1M1I1M1I2D3M1I4D4M1I5D2M1I2M1I3D2M1I1M3I1M5I1M5I1M1I2D2M2I1M5I1D2M9I1D3M1I1M2I2M2I3M2I1M3I1D1M5I1M2I2M1I1D1M3I1M1I8D2M1I2M1I4D4M5I1M5I1M1I2M1I1M1I1D1M1I1M1I7D4M1I3M1I2D1M1I2M1I2D1M1I4D1M1I1M1I1M4I1M2I2D1M6I1D1M2I2M1I1M5I4M5I1M2I2D1M1I3D4M1I2D1M2I1M10I1D1M2I1D2M1I1M3I3M6I1M1I1M2I1M1I3M1I2D3M1I2D1M7I1M2I1M1I2M7I1D1M2I1M2I1M10I1D2M1I3D4M4I6D2M2I2D2M3I1M1I1M1I3D3M1I9D1M1I2D1M1I1M5I1D1M\t*\t0\t0\t*\t*\tES:i:-1\n+280af896-8e53-4427-89d3-a554c87269fd.template\t0\ttig00000118\t21\t60\t1587S1M1I4M1I1M1I1M1I2D1M2I3M1I2M2I1M2I1D1M6I2M2I4M1I2M1I1D4M3I5M1I3M6I4M1I2D4M2I1M1I3M1I1M1I1M3I2M3I4M4I5M1I1M3I3M1I3M1D3M1I6M1I4M2I2M1I1M2I1M1I1M3I1M1I1M1I1M1I1M1I1M2I2M1I2M3I5M2I1M1I1D1M1I1M3I1M1I2D3M2I1M1I1M1I1M1I1M6I2M2I1M1I6M1I1M1I4M1I1M2I1M1I6M2I1M1I1M1I2M1I3M2I11M1I1M2I1M4I3M3I2M1I1M2I6M1I3M1I2M1I1M2I2M1I5M2I1D4M3I12M2I1M1I2D1M1I2M2I2M4I1M1D7M2I1M1I1M2I3M3I1M4I1M1I3M4I3M1I1M2I1M1I1M5I2M1I2M2I5M1I2M2I1M10I5M3I3M1I2M1I13M2I1M2I2M1I4M2I2M1I4M4I2M2I2M1I1M1I1M1I2M1I1M1I1M2I1M1I3M2I2M1I1M1I5M2I2M1I5M1I3M1I2M1I3M1I2M2I3M1I1M1I1M1I3M1I2M2I1M1D3M1I1M3I1M1I2M5I2M1I2M2I5M1I3M4I1M1I2M1I4M4I1M1I4M4I2M1I1M6I2M2I5M1I2M2I4M1I2M1I4M1I3M1I1D1M1I3M1I1M1I2M1I6M1I1M3I1M4I3M2I1M2I5M1I1M1I2M1I2M1I4M1I1M1I1M1I2M3I1M3I2M3I3M3I2M1I2D2M1I3M2I1D3M2I1M1I1M1I2D8M2I2M1I2M5I2M1I2M1I2M1D2M2I4M1I2M1I1M1I6M2I3M1I2M1I3M1I2M3I1D3M1I2M2I1M2I3M2I2M1I2M5I1M2I1M1I1D5M2I7M3I2M6I1M1I1M3I1M1I4M1I3D1M1I2M1I2M3I1M2I1M2I6M3I1M2I1M1I1D2M3I4M3I2M3I5M1I1M1I5M1I2M1I2M1I1M1I1M1I1M1I6M2I4M1I3M2I1M2I1M1I1M2I1M1I2M1I3M1I1D5M1I2M1I1M1I1M3I2M1I1M1I1M1I2D2M1I1M1I1M1I1M2I1M3I1M1I1M4I1M4I3M1I2M1I2M1I6M1I4M1I2M12I1M1I3M1I2M2I1M1I2M1I1M2I3M1I8M1I1M2I3M1I2M2I1M2I2M1I2M1I4M1I2M1I3M1I2M1I2M2I5M1I2M1I2M2I2M1I2M2I1M1I1M1I2M1I1M3I1M1I1M2I3M1I1M1I3M1I2M1I1M1I5M1I3M7I1M1I2M1I1M1I1M1I1M2I3M1I2M1I1M1I1D3M3I2M1I1M2I1M1I2M3I1M1I2M3I1M2I6M1I1M1I1M1I3M3I1M2I4M2I3M1I2M3I2M1I1M1I2M3I2M7I\t*\t0\t0\t*\t*\tES:i:1\n+b1594985-30ce-4f59-9230-dff6ec966710.template\t16\ttig00000118\t4962\t60\t21118S1M1I1M1I6D1M9I1M5I1M1I1M1I3D1M1I1M1I1M1I2M1I1D1M1I2M1I2M1I1D2M1I2M6I2M2I2M3I1M1I1D2M5I2D1M1I3M1I3D5M1I1M1I3D1M1I1M1I2M1I2D2M2I3D3M2I1M1I5M1I2M1I3M1I7D1M1I2M5I1D3M14I1M1I2M3I3M2I2M2I1D1M1I2D1M1I2M2I1M14I1M5I1M1I1D3M1I2M2I1M2I3M1I1D3M11I2M6I1M2I1M1I1M1I1D4M2I1M1I1D1M1I1M2I2M1I1M2I2D1M2I1D1M4I2M2I1D6M3I1M3I1M2I1M9I1M3I1M1I2M5I1M4I1D2M3I7M1I1M1I1D2M3I1M3I2M9I1M1I2M4I3M2I1D1M2I1M1I3M3I1M2I2M5I2D1M1I1M2I1M1I1M2I1M1I1D1M10I5M1I1M1I1M3I1M1I1D2M3I2D1M4I1M2I2M2I1M3I1M6I2M5I1M1I2D1M6I6M1I4M1I7D1M1I2M3I2D3M1I5D2M4I1D2M1I5D4M7I1M1I1M1I2D1M1I\t*\t0\t0\t*\t*\tES:i:-1\n' |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/reads.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fasta Wed Jun 19 07:00:20 2019 -0400 |
| b |
| b'@@ -0,0 +1,224 @@\n+>fa9ad683-35c5-4dad-a3af-de7a86b1ffa8\n+TTGGTATGCTTCGTTCCAGTTACGTATTACTTTCTGTTGGTGCTGATGTTGCGTCTGCTGATTGTTTAACCTGGCTGGATCGCTGCTGAATAACTTCGCCGCATGGCCGCTGAAATCTTTCACCCTCTGCGCCTGGCGGTTAGCCGCCTGTTACGTCAGCCGTGGTCAACGTTAAGTCAGCTTTTCGGCATTTCGCTCCGCTATGCTGGCACTGCTGCGGTGTGCATAGCGATCTGCTCGACCGCTGGCAGCAGCATCTCAAGCGAACTACTTGCATTCATCGCCACAGAACAGGTAACCATCGAGGCGTTCCTCGGAACATCAGATAGTCAGAATCGTTTTGTATCCGAGTGGGTACAGGCGCGGCTGACGGCGATTAACGATAAGCAACAAAAGGTAAATAGAAGATGCGGCGCTTAACCGCGAGCTCAATCTTACCTGGCAAAATACGCGGCTTGATCATGATCGATTGTAATGCCCGGTAACTGGCCGCCAAAGCCGATGAAGTGTCGATGGAAGGGGCTGGCCGAAACGCTTAAACGATTGCCCTCGGTGATACCGTGGCTTTGCGGGGCGATGCGCAGGAGTTTCCGCGCTAAAGTAGCCAGCCTGCGCAAGTGGACTGGAAAGTCACGGCCTAATTTCTATTTTATTTTTCCCTGAAGGGCATTCGTTAAGGCAACCGCAGAGCAACCACCCAGTTTCCGCTGGGAGAATGGCAACGGCATGATGACACCGGCTCTTCGCCAGTTCCCGACCATCAGCCTGATAGATATTGGCGCGATTTTTAAAACCGTCGGTCAGGTGCTGGAGCAGATGGGGTCGGGCGCTGGAAGTGATAAATTGGTACTGGTCACCGCCTGCGGTATATTTGCTGTTGCTAGCACAGGGGTACGGGCGAGACATCCAGCGTCATCAAGGCTAATTGGGTGTGGCGCACTCGGTGCGGAAAAAGGCTTTGCTGCGTACCACGTTGGCAAGTGTAGAGTTCGCCATACTTGGGTTTTGTTTTGTACCAAGTGGCCGCAAAATTAGTGCACAGAAACAGCGCTGGCGGCGGTGTGCAGGCGAAAGTGAACGATTTTCAAAGTAGGAGCCAAGACTGGCGATTGTGGATTATTCTACCGTGCAGCGGGCGGCTGCTGCTGTCGCTTTCCGGCGGCTGGCTGGGTGCGGTTGGGTAGGCGCTGTTCGAGGCAGTTTGCAGAAATGCGCAAGGTAAATAGGGGGCGTTCTGGTTTAGAATGAACGCGCCCAGCAATTTCGATGAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTTATCTTTCTGTTGCTGTCGCTAATCACAAGATCGAGGTGGGTTTGTTGATTTTTAAATGTAGCCTACAATACTCCGTTCGTGAAATCATAAAAAGCCATATGCGTTGAATGGATGTCATCCTATGGTAATTTGTTGATGATGAATTCATCCTGTGTAAAAATGTTAGTTTAATAAAATATTAGTGACCTGTAACTAACGGTTTGTTTGTTGATTGAGAACCGTGGTTATATTGAAAAATATATAAATACATTGGCTGGTCTTGTATGTCGGTTTTATTTTTTGTTGCCTAAACACAGGGATATCGAACTAATAACTAAAGGGCACTTTATAGGCAGAAAAACCAACGCGTCGGGAGATATGAGCTCAAGTATGGCGGATCCCATTGTCCGGGGCTCGGCAGGTGTAAAATTGGCGCGCCCACCAGCGTGGCATGCTCGTTGTCGGGCGGGATGACTTCGGGCAACCCGGTAAATCCGCTGCTGGGGGCAGGTACGCTTGGCCGAGACGGACTTGCCGCTGCCCGTACGCTGCGTTCATTCTCTCCCGCACCTAAAAAGCCTTCTGGACGAAGACGCCTGCCGGTGGGCGTTTTCGGCCCCGGCACAAACGCTGATATCCGCTTACAACTGCGTGATGACGGACTGATACTCCAGCAACAACGGCAGACGAACATTCCGCTGAGCCGCTGCTGCCACATGAGGAGAGCGAAATTAATACAACCGCAGGGTACGAGTCAATGTGGCTGGTGCGGTAAGGCAGCGCAACTGGACGGCCATACTGCTAGCGCGCGGCTGTGGGGGCTATACCGCCGGATATCAGTTAAGCCCGCATCTTTACCTGGCGACCAACGCGCACAGGGGCCGTGGTGGATGCTGGGTGGTCTGAGCGGGTGCCGGGTGCTGAGGACGCTTGCTGCCAGCGCCGCTGCCGTACCAGGTGCCACCAGGATAGCGGACCGCTTCAGGCGGACGCTGACGCCTGCGGCGTAGAACATGGTGACCCTGGCCAGAAATCACCAGCGTGACGGACGGTGCCGGGCGGGGTTATTCTGATTTTGTCACGCAGGCGCGAGCGTTGCGGAAAAGGCCACTTACCTCTTCGCTATCTTAATACGACGTTCCCCGCCCTATATAGCCTCAGCGTTCCCCAACCTACCCAGTACCGAATACGGCCCCGTGGTGGCTGATCACGACCGGCATGCCAGAGAAACCCTGCCGCTGCGCCACTAGATTGCGGTACGTCTCTGGAAACCGAGTGAACTGCGGCGGTATATGAGCCGCAGCAATACGCAGGTGCGCTTTCATTATGACGCGCTTACCCGGGCAGATGTGGCGCACCGTTACACTTAGGAAAGGCCGGAGATGCGCTACCACTTCGACGATACAGGGCGGGTGGTGGAGCAACGACCAGCAGGGGTTAAGCTACACTATCTTTATAGGCAAGGACCATATCGTCACCGACGGCCTGAACCGGCGTGGGAGTGCTGCATACAGAAGGCAGGGCCGGGCTAAAACAAATTGGTGAAAAAGAACGAGCGGACGGCACAGAAGCGTTCCGCGCTGAAATTGCATCGACCGCGAAGCAGGAAGGCTCACGGCATGAACGGACGCGGCAGGGCAGGAGGATAAGTACGGTCTGAATGTGGTGTCCAGCGATATCGAATACCACCGGACGGGCGGGAGACGAAATTCCTATAACGACGGGAGCCAGCTGACGGCGGTGGTAATGCCGGACGAACTGGAGAAACCGCCAGGAATATGATGAACCGGGCAGGCTGGTGTCAGAACATCGCGCAGCGGGGACAGTACGCTACCGCTACGTGGCCGCCTGATAGTTACCGGCGACGACAACGGATGCGACGGGCGCTTACCAACAGATAATATAGACACGCTACGGGCGTTGCTGGCGTTCTGGCTTTTCGACACGGAGCCATTATGAATACGACCGCTTCGGCCAGATGACGGCGAAGTCCACCGCGAAGGCATCAAACGCTACCGCTATAATAACGTGGCGGTTAACCTCGATGAAAACCGCACAGGGCGATGAAACGCGACATGAGCCACAACGCCGCAGAGCAACCTATTTCGCCAATTATCTGCCCCGGACGCGGCCGGAGCGGAAGACACGAGGTACGATGCGTGGGGAAAGGCGGGTCAGCACCACACCAGGGCGGCTGACGCGCAGTATCATTACGGTGCTGCCGGATGTCATCGCCCTGACCAACGAGAACACGGCAGCCACGGCGTCTTCTGGTTACGATGCGCTGGACCGGCTGGTGGGACAAACACCAAGCAGACGCCGAAGATGAGAACGATGAGCAGTATACCCGTAATGACGCTTCCTC\n+>a403a23e-20e7-43f7-a5fa-dae8ebc59a01\n+TTGACTGTGCTTCGTTCGGTTACGTATTGCTTTTTCTGTTGGTGCTGATATTGCGGCGTCTGTAGGTGTTTAACCTGCCAGCATCACACGAGATTGGTCAAGTGCGGTTGGGTTTTTCAAACGGATGCGACAGCAGTTGGCATTAAAGAAGCCACCGCCGTTAGGCGCCGAGCATCTTGATGCTTCCACGAAGCTACGATACCGCCGGGTAACAGCTGTTGCGCTCCTTCAACGGTATTC'..b'CCGGGGCTGAGGCTCCCCACCGGCGCGGGCGTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGAATGAAAGACGGCAGCAGGCCGGGGCAGGGGGCGTCAGTTTCACCAGGAAGGACCTTTACCGAGCAGCGGATTGACCGGATGGCCGGACGTCACCCGCGGGGCACCGAACAGGCCACGCCGGTGGGGCACCGATGCGTACCCCGGCTGAACCCTGGACAATGCTGCCGCCATACCGTCATGTCGCCCTGACGCCGCCGGTTTTCCGCTCATCTGCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAACTAAGTGAGATATCTGTCAGATAAGAACAATTAGGAAAATATTTATATATATTTCCTTGAATATATGTTTCGATTGGTATAACGATGTCACAAATATTCCTCTGAACATCTTCCTGTTAAAAAACCGCCAGCGTTTCCCGCTGGCGGTTTCAATAATATTCAAACTCAGCAATCAATAAAATCACCAGTTGCCTTTTCGGCCTGATCCATCCGCACCGGTTTATCATGGTTTCGATGGAGCGCGATGCAAGGTAGCTGTAAAGCGGGCGCGGTCTTTCCAGAAAAGCATAAGAAAAGAGCCAGCGCCAGAACGCCCGCTGCAACCGCATAAGTACAGCGTAAAGATAAAGCCATGCAGGATATTCTCTGTAGAGTTCCATACTTTTCTCCCCTTTTATCTACCCGATTATGAATGGCACCGGAAAAATGAATTGTTTATCTGATGAAAATAGTACCGCCAGCACGTAGTTTTACTACTCATCCGACCACTTATTTTGCTTATTGATGGTTTATTTACATTCATCCGCAATTAAGTTACACAAAGTTAAATTAATACTAAACATTAGTTAAATCATGGCTTTTGCCATTTTTATACTTTACACCCCGCCCGCAGATTTTGCGAAATCTTTGCAGCCAGGTCTACCTTCGGTATCACTTTTAGGCCACTGGAGGTGCACTGTGAGTGCAGGCGTGATAACCGGCATTATTGCTGGTGTTTTATTACTGGGTTATCTGGTTTGTAACCTGATCCAAATGCGGAGCGTTCTGATGGCTGCGCAAAGGGTTCTTACTGATCGCCACGTTTTTACTGGTGTTATGGGTGCTGGCGCGTCCTTTAGGCAGCGGGCTGGCGCAGCTGATTAATGACATTCCCTTCCCGGTACAACGGGCGTTGAGCGCGTACTTTTTCCTTTGCCCAGCGTCTCTGACCGTGAGAGATGAACTGGAAGCAATATCTTTGTGCCATTCTCGGCCTGAACATGCTGGGGCTGGCGGTGCTGTTTTATGTTATCAGTCAGCACTATCTGCCGCCAATCCACAGCAGTTGCCAGGGCTGTCATTGGGATCTGGCGCTGAATACCGTCAGCTTTGTCACCAATACCAACTGGCAATCTTATAGCGGTGAAACCACGTTGACTTCTTCAGCCAGATGGCGGGCTTAACGGTGCAAACTTTCTTTCTGCCGCCAGCGGGATTGCGGTGATTTTGCCTCATCCGTGCAGTTTACCCGCCAGGTATGAGCACGCTCAAGAATGCCTGGGTCGATCTGCTACGCATCACGTTATGATTGCTAGTCCTGTGGCGTTGTTGATTGCGCTGTTTTTATTCAGCAAGGTGCGCTGCAAACTTTCTGCCTTATCGGGCTGTGAATACCGTTGAAGAGGCGCAACAGCTGTTACCATGGGGCCTGCTGCTTCTCAGGAAGCAGTCAAGATGCTCAGTACTAGCGAAGGCGGTGGCCTAACAATGCCAGCTCAAAATCGCATCCGTTTGAAAACAACCGCGCGGCAACTTCGTGCAGATGCTGGCGATCTTCTTGATCCCAACGGCGCTGGTAATACTTTGCCTTTGGTGAAGTGATGGGCGATCGCCGCCGAGAGCATGTTGCTTATGTGGGCGATGTCGGTAATTTTTTGTGTCATCTCTGCGTAGGCGTGGTGATGTGGGCAGAAGTTCAGGGTAATCCTCATCTGCTGGCACTGGGCACGGACGCTTGTATCAATATGGAAGGTAAAGAGAGCCGTTTCGGCGTGCTGGTCAGTAACCTGTTTGCGGTCGACGGCTGACGGCTTCCTGTGTTGCAGTGATTACGCGATGCATGATTCGTTTACCGCTCTCGGTGGCATGGTGCCGATGTGGCTGATGCTAAATTGGTGGTGGTAATTTCGGCGGTGTCGGTTCTGGTCTTTGGCATGATGCTGTTTGTCCTGCTGGCGGTGTTTTGTGCCGGGCTGATGATTGGGGTCGTACACCGGAATATCTGGGTAAAAAAATCGACGTACGCGAGATGAAGCTGACTGCGCACAGCAGTCTGGTTACCCCGACGCTGGTGCTGATGGGCGCGGCGTTGTGATATTGACCGACGCCGGACGTAGCGCCATGCTCAACCCCTGGCCCGCATGGTTTTAGCGAAGTGCTGCTACGCCATGTCATCACCGCCGCTAACAACAACGGCAGCGCCTTTGCCAGTTCGCGCCAACTCCGTTCTGGAACTGTTTACTGGCGTTCTGCATGTTTTGTCGGTCCTTCGGGGTGATTATCCCGGTGATGGCAGTGCCGGTTCGCTGGTGATAAAAAGAGCCAAACCGCCAGCTCGGCACGCTGCCAGCACACGGCCCGCTGTTTGTTGGCCTGTTAATCGCTGCTGTGTTGCTGGTTGGCACTGAAGCCTTTATCTGCTGGCGGTCAGTGGCGGGAATATCTCTCCTGATGATGTTGGTGAGCACTGGATATGAGTCGTAAACAAACTTCCGGCTATTCAAGACCAACACTTGTCGTTCAGGCGCTGAAAGAAGCGGTGAAAAATTAAACCCGCAGGCGCAATGGCGCAATCCGGTGATGTTATCGTCTGGATCGGCAGTCTGCTGACCACCTGTATTAGCATCGCGATGGCAAAAGCAGGTGCGATGCCCGGCAATGCTGTTTAGCGCGGCCATTAGCGGTTGGCTGTGGGATCACCGTACTGTTCCTTCAATTTCGCCGAGGCGCTGGCAGAAGGCCGCAGTAAGCCTGGGTAACAGTCTGAAGGTGAAAAAACTGCGCTTTGCCCACCAAGCTGCGTGAGCCGAAATATGGCGCTGCGGCAGACCAAAGTTCCTGCGACCAACTTCGTAAAGGCGATATCATGCTGGTAGAAGCTGGCGATATTATCCCCTGCGATGGTGAAGTTATTGAAGGAAATTGCATCGGTCGATAAACTATGCATCACTGCGAGAATCGGCACCGGTGATCCGTGAATCCGGCGGCGTTTTGCCTCGATCACCGGCGGCGCATATTCTTTCTGACTGGCTGGTGATTGGGTGTAGCGTTAACTTGGCAGACATTTCTGGATCGGATGATCGCGATGGTGGAAAGGCGCACAGCGGCGCAAAACGCCGAACGAAATTGCCCTGACCATTCTGCTGATTGCCCTGACTATCGTCACTGCTGGCAACCGCCGCACGCTGTAACCGTTTTCGCGTAGGGCGGTAATGCAGTCAGCGTAACGGTACTGGTGGCGCTGCTGGTCTGTCTGATCCCAAAAGCCACTATTGGCGGCCTGTTGTCAGCAGTCGTCGCCGGGATGAGCCGGATGCTAGGCGCCGAATGTGATTGCCACCAGCGGACGATGCAGTTGAAGCGGCAGGTGACGTTGACGTTCTGCTACTGGATAAAACCAGCACCATCACACTCGGTAACCGTCAGGCGTCGAGTTTATCCCACGCAGAGGGCGTGGATGAAAAAACGCTGGCTGACGCCGCTGGCAGCTTCGCTGGCTGATGAAACGCGGAAGGCCGCAGTATTGATCCTCGCCAAGCAGCGTTTTAACCTGCGCGAGCGCGATGTGCAGTCATCATGCCACCCTTTGTACCGTTTGCAAGCCGGATGAAGCCAGGATCAGCATCGACAACCGCAGGTTAAACACCCAAGCAGACGCCGAAGATGGGGAAACCGTA\n' |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/reads.fasta.index |
| b |
| Binary file test-data/reads.fasta.index has changed |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/reads.fasta.index.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fasta.index.fai Wed Jun 19 07:00:20 2019 -0400 |
| b |
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| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/reads.fasta.index.gzi |
| b |
| Binary file test-data/reads.fasta.index.gzi has changed |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/reads.fasta.index.readdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fasta.index.readdb Wed Jun 19 07:00:20 2019 -0400 |
| b |
| b'@@ -0,0 +1,112 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|
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/reads.sorted.bam |
| b |
| Binary file test-data/reads.sorted.bam has changed |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/t2-polished.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t2-polished.fa Wed Jun 19 07:00:20 2019 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>tig00000001\n+AGATGCTTTGAAAGAAACGCAGAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTGAAAAGAAAATGTCCCACAGGTACAGATAGAGTTGCTGCTTATCATACTCACGGTGCAGATAGTCATGGCGATTATGTTGATGAATTTTTTCAAGTAGCGATAAAATCTTGTAAGAAGTAAAGATAATAATCTTGAAGCATTTTATCTCGCAACACCTGATGGACGATTTGAGGCGCTTAATAATAAAGGAGAATATATTTTATCAGAAATAGTGTCCCGGGATTGAGTTCAGTATGCATACCGTATCATGATTAATTTTAGTGCTTTTATTAGTGGGGCCTATAGGAGATTCAATGAAATATAGTTCAATATTTTCGATGCTTTCATTTTTATACTATTTGCCTGTAATGAGACAGCTGTTTACGGTTCTGATGAAAACATTATTTTTATGAGGTATGTGGAAAAATTACATTTAGATAAATACTCTGTTAAAAATACGGTAAAACTGAAACAATGGCGATACAATTAGCTGAAATATATGTTAGGTATCGCTATGGCGAACGGATTGCAGAAGAAAAACCATATTTAATTACGGAACTACCAGATAGTTGGGTTGTTGAGGGAGCAAAGTTACCTTATGAAGTTGCGGGTGGTGTATTTATTATAGAAATTAATAAGAAAAATGGATGTGTTTTGAATTTCCTACATAGTAAATAATGCTGGCGCTGATGGATGCGGATGGAAACATTGCGTGGAGCGGGGAGTATGATGAGTGGGGCAACCAGCTGAATGAAGAGAACCCGCATCACCTGCACCAGCCGTACCGGCTGCCGGGGCAGCAGTATGATAAGGAGTCGGGGCTGTACTACAACCGGAACCGGTACTACGATCCGTTGCAGGGCGGTATATCACCAGGACCCGATAGGGCTGAGGGGGATGGAGTCTGTATGCGTATCCGCTGAATCCGGTGAATGGTATTGATCCATTAGGTTAAGTCCCGCAGATGTAGCGCTAATAAGAAGAAAAGATCAACTAAACCATCAAAGAGCATGGGATATATTATCTGATACTTATGAAGATATGAAGAGATTAAATTTAGGTGGGACTGATCAATTTTTCCATTGTATGGCATTTTGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGTAAAGCTATCCCATTCTGAAATGATTGAAGATAATAAAAAGACTTGGCTGTAAATGACCATGGGTTGACATGTCCATCAACAACAGATTGCTCAGATAGATGTAGTGATTATATTAATCCAGCATAAAAAACGATAAAGGCTTTACAAGATGCTGGCTATCTCAAGTAATCTATCAAAGATGATAATATTTATTTTTGCTATTATAATCATTGTTGTTTTATGCGTAATTACTTATCTTTATTTATACAAAGATGAATCTCTTGTAAGTAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTCTTATTTTCCCTAACAAATGATGATGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGGCAAGGGATGGTGTAAACCTTTTTTGTTGGTGAAATTAATGTTACGCATTATTTTATAACAAATATTGGAGCTGGATTGCCTGATGCTTGTGCAGAGTAATTGCTTGAATTAAGAGTCTATCCCATATCGAAGTCGTCAACTTCGTAGTGAGGAAAAGTAAAATTCCTGACTGAGAAAAGACATGTCGGCTATTGTGTAAAGCCATATAGCTCAGACGATGAATATCTACTCGTATTCAGTTGTTTATTGAGGGTGAGTTCCGACCCTGAAACAACAAATAAAATGAACAGTCAGAGAGTTTACATAGAATTGCACTGGTCTTTTACGATATCTGACATTGTGTAATACATATTCAGCCATGCATTAATTAAAATGTTACGTGTTTAATGTGAGTCCCTATCTGAAAATAAATAATCCTTCCGGATTAAAATAAATTCTTGCCGGGAAAGAAAGAGGAAATAAACCATTAGCGGAAAACCAGCGGCACGCCAGGGTGACATGCCCCAGTACGGCGGCCCGATAGTCCAGGGTTCAGCGGGGTACTGATAGTCGCGCCGACTGCATCGAGAACTCCATACAACTTTTACGGAACGTCACCTGATAAAATTTGTTCAGTATCGTCTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAACCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATAAAACGTATCACGCGAAACGCCCATGATTTTACAGGCTTTTGATACGTTGCTGAGTTCTTCAGCCAGATTGAGCAAACCGGCTTTGTGTTTGATGACGGGATTGGCAGTATGAAGCATGAGAGTTACCTCTTGTTTTGGATAAGGATTCGACACTCATATCAAAACCGGTAACTCTCAACCTTTCAAGGCCATGTGTCAGATCAAGTCGCGACTAATACAAATACGTCCCTCATTACCGCGCCTTAACCCATTCCGCCACTTCCGCCCACTCACCGCGAAAGACAACTTTTTCCGCTTTTTCTCAAGCTGATAGCGATACATCGGGTCGTAATATTCTTCAAGTAACGGCACCAGCCAGGCCAGATGACCGTCGGTGCTGCCGGTGGTGAGTTGCGTTGTCAGTGCTGCATCCAGCCTTGCAGCCAGTTCGTTATAGCGCTGTAGCCCCAGCCGACGCTTAATCGCCGAAAGTCCGTGATGCAGGTATTCGCAATACTCCTGCCAGCCCTGTTCGTCGCCGTACGCGTGGGTAAAATCATGATGCATACGCAAGAAATACTCTTCGTTCAGGCGCTCAAGACGGATCTCAAACGGATCTTCTACCACCGCAATCGCCGCCTGAGTCATTCGCTCGCGCAGGCATTCCGGCAGGTGATTCGAACCGATCATCCGGCTTTCGTCTTCCAGCACCCACAGGCGCAAATTCTGACGGGCGTCGGTTTTAGCATTTCGGCAGCCAGCAGGTTTTCAAAACTCGCCTGGCTAAGTTGTGGTTGTAACGTGCGACCAAACGCCGAACCGCGATGACGCGCCAACCCTTCCAGATCAACACCGTTCGGCTGTTGCTGCACTAACAGCGTTTTACCGCTGCCGGTACAACCGCCAATCAGCACTATCGGTTTTGTGCCAGTTCAATAGTCGCCTGAATCGCGGTCTGGCGCAGTGCCTTATAACCGCCTTCCACCAGCGGATAATCAATCCCCGCTGCATGCAACCAGCTTTGCACAATATGTGAGCGCTGACCGCCACGGGCGCAGCAGAGAATACCTTGCGGATTTTGCAGGCACGCTGCCCGCCAGGCGTCCATGCGCTGCTGACGAATTTCACCCGCCACCAGTTTATGTCCCAGCGCCAGCGCTGCGTCTGAGCCTTGCTGTTTATAGCAGGTGCCAACGGCGGCGCGTTCATCGTTATTCATTAACGGCAGATTGATAGCGGCGGGCATTGCGCCGTGCTCAAACTCG'..b'GGTAAAGCCTTTGTGAATATTGATGGTGAGCACCTTGAACGAAAATTGTTGTGTTTGATCGGGCATAATTTTCCTGTCTTTGCCTCTTATCTCATTGAAATAGTGTAGTCGGCGTCACAAAAGGTGCGGTCTTACGGAATTTTCCGTAAAGTTCGGTACTCTGAGTAAGTAGAGATAAATTCTTCAGGAGAGAAGCCATGAAGTGGCAACAACGTGTTCGTGTCGCAACGGGTCTAAGTTGCTGGCAGATTATGTTGCATTTACTGGTAGTGGCGCTGCTGGTGGTGGGCTGGATGAGTAAGACTCTGGTTCACGTCGGCGTGGGATTATGCGCACTGTATTGTGTCACGGTAGTGATGATGCTGGTGTTTCAGCGCCACCCCGAGCAACGCTGGCGTGAGGTGGCAGACGTGCTGGAAGAGCTGACCACGACCTGGTATTTTGGCGCAGCGCTGATTGTGCTGTGGCTGTTGTCCCGCGTTCTGGAAAACAACTTTTGCTGGCAATTGCAGGGCTGGCAATCCTTGCCGGCCCGGCGGTAGTGTCTTTGCTGGCGAAAGATAAGAAGTTACATCACCTTACGTCTAAACATCGCGTACGCCGCTGACCCTGTCGTGGCCGTTATCACCAGTAGCGGCCACAAACTATTCCACACAATATCCAGACTCGCATCCTTCAAATAAATCTGCTTGGTAATGTCCGTAAAGTGGCGAATAGGGTTAATCCACGTCAGGTTTTGCAGCCATACCGGCATGTTTTCCACCGGAGAAACGTAACCGGAAAGGAGAATGGCGGGCATCATAAAGACAAACACGCCGATAAACGCCTGCTGTTGTGTTGAACAGAGTGATGAAATCAACAGACCGAATCCCACCAGCGATAAACCATAAATCACCATCGTAAAGTAGAACAGCGCCAGCGATCCGGCGAAGGGATTTGATACGCCCAGATACCAATCGCCAGCACAATGGTGGCCTGGAAGGTGGCGACAATTAACGCCGGTACGGCTTTGCCGATGAAGATCTGCCAGGTGGTGAGCGGCGAAACCAGTAGCTGATCGAGCGTACCTTGTTCACGTTCGCGGGCGACGGAAAGTGAAGTGACGATCATTACGCCGATAGTGGTGATCATGGCGATCAGTGACGGCACCACAAACCATTTGTAGTCGAGATTCGGGTTATACCAGTTGCGTACCACCAGCTCGCTGTTGTTAGGTTTCGGTTTTCCTTCCAGCAGCTCCTGCTGATAATTTTGACGATCTGTTGCAGGTAGTTGGCGGCAATTTGCGCACTGTTGGAGTTACGCCCGTCGAGGATCAACTGCAAAGGCGCGGTCTGGAAGGTATCCAGTTTGCGCGAGAAGTCAGCCGGGAAACGCACCAGTAGTAACGCCTTTGTGTGTCGATGGTTGGGCGGATCTCCTGTGGGCTTTTCAGCAGCAGCACATGAGTAAAGGCGCTGGCGCGGGCAAAACGTTGGGTCAGCTCCACCGAATGCTCGCCGTTATCTTCATCGTAGATGGCGATGGTGGCGTTAGTCACTTCCAGCGTGGCGGCGAACGGGAACAGGATCACCTGAATTAGCACGGGTAAAATCAGAATCGCGCGGGTTTGCGGTTCGCGCAGCAACGACTGCAACTCTTTGCGGATTAACGTCCATAAGCGATGAAACATGCTCTTCTCCTAATCCAGCCGACGTTTGGTTTTCAGCCACGTCAGGCCGATAAACATCACCGCCGAAGCGATCAAAAACAGCACGTTTACCACCAGCACCACTGGAATATTCCCGGCGAGGAACAGGCTTTGCAGGGTGCTGACGAAATAACGAGCGGGAATAATGTACGTCACCGCGCGGATCACCGCGGGCATACTGTCGATCTGAAAAATAAAGCCGGAAAGCATAATCGACGGCAGAAAAGCGGCGTTCAGGGCGACCTGAGCGGCATTGAACTGGTTGCGGGTAATCGTGGAAATCAGCAGCCCCATCCCCAGGGTACTGAGTAAAACAGGCTGGAGATAAAAACAGAATCAGCAGCGACCCGCGATACGGCACGCCGAGAATAAACACTGACACCAGCATACACAGCAACATCGCCAGCATCCCGAGAAAGTAATAAGGGATCAGCTTACACAGCAGCAGTTCCGTGCGGGTAATCTCCGTAGAGAGCAGAGCCTCCATGGTGCCGCGTTCCCATTCTCGCGCCACCACCAGCGAGGTGAGAATCGCGCCGATGACCGTCATGATAATGGTCACCGCACCGGGGATAATGAAGTGCTGGCTAATCGCCGCCGGGTTAAACCAGTAGCGGGTTTGTACATCAATAAGCGGTTCAAAAGTCTGCCCGTTGTCCTCCGCTCGCTGCATTTGCCAGATCTGCCAGATCCCTTCGACATACCCTGTACAAAGTTAGCGGTATTCGGCTCACTGCCGTCGGTGATCACCTGAATCGGTGCGGTGGCGTTGGCGCGCTCCATCTGTTCCGCAAAATCCACCGGAATAACCACCAGACCGCGAATTTTCCCCGCCTGCATTTTGGCGATCAGTTCCTGACGGTTATCGCTGATGGTGGCGTCGATGTAGGGCGAACCGGTCATGGTGTGGTGAAATCCAGCGCCGCTTCGCTACGCTGTTCCAGTAAAATCCCGACCCGCAGCTTGCTGGAGTCGAGGTTAATGCCGTAACCAAAATAAACAGCAGTAGCAGCGGGATCACTACCGCAATCAGCCAGCTACTCGGATCGCGAACGATCTGCCGCGTCTCTTTAACGCACAGCGCCCGTACGCGACGCCAGGACAGGATCGGGTTACTCATTGCTATGCTCCTTATCCCAGTCGTGGATCAACTGAATAAAGGCTTGCTCCATGGTGGGATCGGGTTGCTCATCGTTAGCCGACTGTGCTTTCAAATCGTCCGGCGTGCCGCTGGCGATTAATTTCCCGCGGTACACCAGGCCGATGCGGTCGCAATATTCCGCTTCATCCATAAAGTGGGTGGTGACCATCACCGTGACGCCTTTCTCTACCATGCTGTTGATGTGCAGCCAAAATTCACGGCGGGTGAGGGGTCAACGCCGGAAGTCGGTTCGTCGAGAAACAGAATGTCCGGTTCATGCATCAGCGAACAGGCCAGCGCCAGCCGCTGTTTAAAACCTAATGGCAGTTCATCGGTGGCGTGGGAGGCGATACTTTTCAGGCCGAACGCCTCGCTCATGCGGGAGATTTTTCGTTCTGCGCCCGACCGCGTAAGCCATACACACCAGAGAAAAAGCGTAAATTCTGTTCGACCGTCAGGTTACCGTAGAGCGAAAATTTTTGCGCCATATAGCCGAGATGCTGGCGCGCTTTACCGGAACTCTCTTTCAGATCCATCCCCAGCACCAGCGCCTGGCCGGAAGTCGGCACCAGCAAACCGCACATCATCTTAAAGGTGGTCGATTTACCCGCGCCGTTTGGCCCCAGCAAACCAAAAATCTCCCCACGTTTAACGGCAAAGTTGACGTGATCGGTGGCGGCAAAATCCCCAAATTTCTTGGTCAGTTCTTTCGCTTCGATCACCGTCTCGCCGGGTGTGCCTTCTACCGTATGTAATATTGCGCCCAGCGGCGATTCCGAGGTTCCGGCACCGCCCAGCAAATCAATAAACGCATCTTCAAAACGCGGCGTAGTTTCGTTGATGTTGATTTCCGGCATCCCGTCGGCATGGCGAATATCGTCTGGTGTGGCCTCTTTTTGAGGATCAGACGTACCGATTTCCCCTGAATCATGCCGTCGCTGACCTGCGGCAGTTTCAAGGCGCGTTGCAACAGTTTGCGGTTGCCCTCGTGTGGACTGGTCATCAGAAAGCTGCGTCCGGCCATGGTTTGTGTCAGGGCTTTTGGTTCTCCCTGATACAGCAACTCGCCTTCGTTCATCAGTAACACGTCACGGCACTGCTCGGCTTCGTCGAGATACGAGGTACTCCAGAGGATTAACATCCCTTCGCCCGCCAGCTCATGCACCA\n' |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/t2-variants.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t2-variants.vcf Wed Jun 19 07:00:20 2019 -0400 |
| b |
| @@ -0,0 +1,11 @@ +##fileformat=VCFv4.2 +##nanopolish_window=tig00000001:198000-202000 +##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant"> +##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant"> +##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant"> +##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant"> +##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele"> +##INFO=<ID=SupportFractionByBase,Number=4,Type=Integer,Description="The fraction of reads supporting A,C,G,T at this position"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample +tig00000001 198435 . G A 22.3 PASS BaseCalledReadsWithVariant=10;BaseCalledFraction=0.238095;TotalReads=42;AlleleCount=1;SupportFraction=0.388965;SupportFractionByBase=0.210,0.030,0.718,0.041 GT 0/1 |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/t3_polished.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t3_polished.fa Wed Jun 19 07:00:20 2019 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>tig00000001\n+AGATGCTTTGAAAGAAACGCAGAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTGAAAAGAAAATGTCCCACAGGTACAGATAGAGTTGCTGCTTATCATACTCACGGTGCAGATAGTCATGGCGATTATGTTGATGAATTTTTTCAAGTAGCGATAAAATCTTGTAAGAAGTAAAGATAATAATCTTGAAGCATTTTATCTCGCAACACCTGATGGACGATTTGAGGCGCTTAATAATAAAGGAGAATATATTTTATCAGAAATAGTGTCCCGGGATTGAGTTCAGTATGCATACCGTATCATGATTAATTTTAGTGCTTTTATTAGTGGGGCCTATAGGAGATTCAATGAAATATAGTTCAATATTTTCGATGCTTTCATTTTTATACTATTTGCCTGTAATGAGACAGCTGTTTACGGTTCTGATGAAAACATTATTTTTATGAGGTATGTGGAAAAATTACATTTAGATAAATACTCTGTTAAAAATACGGTAAAACTGAAACAATGGCGATACAATTAGCTGAAATATATGTTAGGTATCGCTATGGCGAACGGATTGCAGAAGAAAAACCATATTTAATTACGGAACTACCAGATAGTTGGGTTGTTGAGGGAGCAAAGTTACCTTATGAAGTTGCGGGTGGTGTATTTATTATAGAAATTAATAAGAAAAATGGATGTGTTTTGAATTTCCTACATAGTAAATAATGCTGGCGCTGATGGATGCGGATGGAAACATTGCGTGGAGCGGGGAGTATGATGAGTGGGGCAACCAGCTGAATGAAGAGAACCCGCATCACCTGCACCAGCCGTACCGGCTGCCGGGGCAGCAGTATGATAAGGAGTCGGGGCTGTACTACAACCGGAACCGGTACTACGATCCGTTGCAGGGCGGTATATCACCAGGACCCGATAGGGCTGAGGGGGATGGAGTCTGTATGCGTATCCGCTGAATCCGGTGAATGGTATTGATCCATTAGGTTAAGTCCCGCAGATGTAGCGCTAATAAGAAGAAAAGATCAACTAAACCATCAAAGAGCATGGGATATATTATCTGATACTTATGAAGATATGAAGAGATTAAATTTAGGTGGGACTGATCAATTTTTCCATTGTATGGCATTTTGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGTAAAGCTATCCCATTCTGAAATGATTGAAGATAATAAAAAGACTTGGCTGTAAATGACCATGGGTTGACATGTCCATCAACAACAGATTGCTCAGATAGATGTAGTGATTATATTAATCCAGCATAAAAAACGATAAAGGCTTTACAAGATGCTGGCTATCTCAAGTAATCTATCAAAGATGATAATATTTATTTTTGCTATTATAATCATTGTTGTTTTATGCGTAATTACTTATCTTTATTTATACAAAGATGAATCTCTTGTAAGTAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTCTTATTTTCCCTAACAAATGATGATGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGGCAAGGGATGGTGTAAACCTTTTTTGTTGGTGAAATTAATGTTACGCATTATTTTATAACAAATATTGGAGCTGGATTGCCTGATGCTTGTGCAGAGTAATTGCTTGAATTAAGAGTCTATCCCATATCGAAGTCGTCAACTTCGTAGTGAGGAAAAGTAAAATTCCTGACTGAGAAAAGACATGTCGGCTATTGTGTAAAGCCATATAGCTCAGACGATGAATATCTACTCGTATTCAGTTGTTTATTGAGGGTGAGTTCCGACCCTGAAACAACAAATAAAATGAACAGTCAGAGAGTTTACATAGAATTGCACTGGTCTTTTACGATATCTGACATTGTGTAATACATATTCAGCCATGCATTAATTAAAATGTTACGTGTTTAATGTGAGTCCCTATCTGAAAATAAATAATCCTTCCGGATTAAAATAAATTCTTGCCGGGAAAGAAAGAGGAAATAAACCATTAGCGGAAAACCAGCGGCACGCCAGGGTGACATGCCCCAGTACGGCGGCCCGATAGTCCAGGGTTCAGCGGGGTACTGATAGTCGCGCCGACTGCATCGAGAACTCCATACAACTTTTACGGAACGTCACCTGATAAAATTTGTTCAGTATCGTCTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAACCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATAAAACGTATCACGCGAAACGCCCATGATTTTACAGGCTTTTGATACGTTGCTGAGTTCTTCAGCCAGATTGAGCAAACCGGCTTTGTGTTTGATGACGGGATTGGCAGTATGAAGCATGAGAGTTACCTCTTGTTTTGGATAAGGATTCGACACTCATATCAAAACCGGTAACTCTCAACCTTTCAAGGCCATGTGTCAGATCAAGTCGCGACTAATACAAATACGTCCCTCATTACCGCGCCTTAACCCATTCCGCCACTTCCGCCCACTCACCGCGAAAGACAACTTTTTCCGCTTTTTCTCAAGCTGATAGCGATACATCGGGTCGTAATATTCTTCAAGTAACGGCACCAGCCAGGCCAGATGACCGTCGGTGCTGCCGGTGGTGAGTTGCGTTGTCAGTGCTGCATCCAGCCTTGCAGCCAGTTCGTTATAGCGCTGTAGCCCCAGCCGACGCTTAATCGCCGAAAGTCCGTGATGCAGGTATTCGCAATACTCCTGCCAGCCCTGTTCGTCGCCGTACGCGTGGGTAAAATCATGATGCATACGCAAGAAATACTCTTCGTTCAGGCGCTCAAGACGGATCTCAAACGGATCTTCTACCACCGCAATCGCCGCCTGAGTCATTCGCTCGCGCAGGCATTCCGGCAGGTGATTCGAACCGATCATCCGGCTTTCGTCTTCCAGCACCCACAGGCGCAAATTCTGACGGGCGTCGGTTTTAGCATTTCGGCAGCCAGCAGGTTTTCAAAACTCGCCTGGCTAAGTTGTGGTTGTAACGTGCGACCAAACGCCGAACCGCGATGACGCGCCAACCCTTCCAGATCAACACCGTTCGGCTGTTGCTGCACTAACAGCGTTTTACCGCTGCCGGTACAACCGCCAATCAGCACTATCGGTTTTGTGCCAGTTCAATAGTCGCCTGAATCGCGGTCTGGCGCAGTGCCTTATAACCGCCTTCCACCAGCGGATAATCAATCCCCGCTGCATGCAACCAGCTTTGCACAATATGTGAGCGCTGACCGCCACGGGCGCAGCAGAGAATACCTTGCGGATTTTGCAGGCACGCTGCCCGCCAGGCGTCCATGCGCTGCTGACGAATTTCACCCGCCACCAGTTTATGTCCCAGCGCCAGCGCTGCGTCTGAGCCTTGCTGTTTATAGCAGGTGCCAACGGCGGCGCGTTCATCGTTATTCATTAACGGCAGATTGATAGCGGCGGGCATTGCGCCGTGCTCAAACTCG'..b'GGTAAAGCCTTTGTGAATATTGATGGTGAGCACCTTGAACGAAAATTGTTGTGTTTGATCGGGCATAATTTTCCTGTCTTTGCCTCTTATCTCATTGAAATAGTGTAGTCGGCGTCACAAAAGGTGCGGTCTTACGGAATTTTCCGTAAAGTTCGGTACTCTGAGTAAGTAGAGATAAATTCTTCAGGAGAGAAGCCATGAAGTGGCAACAACGTGTTCGTGTCGCAACGGGTCTAAGTTGCTGGCAGATTATGTTGCATTTACTGGTAGTGGCGCTGCTGGTGGTGGGCTGGATGAGTAAGACTCTGGTTCACGTCGGCGTGGGATTATGCGCACTGTATTGTGTCACGGTAGTGATGATGCTGGTGTTTCAGCGCCACCCCGAGCAACGCTGGCGTGAGGTGGCAGACGTGCTGGAAGAGCTGACCACGACCTGGTATTTTGGCGCAGCGCTGATTGTGCTGTGGCTGTTGTCCCGCGTTCTGGAAAACAACTTTTGCTGGCAATTGCAGGGCTGGCAATCCTTGCCGGCCCGGCGGTAGTGTCTTTGCTGGCGAAAGATAAGAAGTTACATCACCTTACGTCTAAACATCGCGTACGCCGCTGACCCTGTCGTGGCCGTTATCACCAGTAGCGGCCACAAACTATTCCACACAATATCCAGACTCGCATCCTTCAAATAAATCTGCTTGGTAATGTCCGTAAAGTGGCGAATAGGGTTAATCCACGTCAGGTTTTGCAGCCATACCGGCATGTTTTCCACCGGAGAAACGTAACCGGAAAGGAGAATGGCGGGCATCATAAAGACAAACACGCCGATAAACGCCTGCTGTTGTGTTGAACAGAGTGATGAAATCAACAGACCGAATCCCACCAGCGATAAACCATAAATCACCATCGTAAAGTAGAACAGCGCCAGCGATCCGGCGAAGGGATTTGATACGCCCAGATACCAATCGCCAGCACAATGGTGGCCTGGAAGGTGGCGACAATTAACGCCGGTACGGCTTTGCCGATGAAGATCTGCCAGGTGGTGAGCGGCGAAACCAGTAGCTGATCGAGCGTACCTTGTTCACGTTCGCGGGCGACGGAAAGTGAAGTGACGATCATTACGCCGATAGTGGTGATCATGGCGATCAGTGACGGCACCACAAACCATTTGTAGTCGAGATTCGGGTTATACCAGTTGCGTACCACCAGCTCGCTGTTGTTAGGTTTCGGTTTTCCTTCCAGCAGCTCCTGCTGATAATTTTGACGATCTGTTGCAGGTAGTTGGCGGCAATTTGCGCACTGTTGGAGTTACGCCCGTCGAGGATCAACTGCAAAGGCGCGGTCTGGAAGGTATCCAGTTTGCGCGAGAAGTCAGCCGGGAAACGCACCAGTAGTAACGCCTTTGTGTGTCGATGGTTGGGCGGATCTCCTGTGGGCTTTTCAGCAGCAGCACATGAGTAAAGGCGCTGGCGCGGGCAAAACGTTGGGTCAGCTCCACCGAATGCTCGCCGTTATCTTCATCGTAGATGGCGATGGTGGCGTTAGTCACTTCCAGCGTGGCGGCGAACGGGAACAGGATCACCTGAATTAGCACGGGTAAAATCAGAATCGCGCGGGTTTGCGGTTCGCGCAGCAACGACTGCAACTCTTTGCGGATTAACGTCCATAAGCGATGAAACATGCTCTTCTCCTAATCCAGCCGACGTTTGGTTTTCAGCCACGTCAGGCCGATAAACATCACCGCCGAAGCGATCAAAAACAGCACGTTTACCACCAGCACCACTGGAATATTCCCGGCGAGGAACAGGCTTTGCAGGGTGCTGACGAAATAACGAGCGGGAATAATGTACGTCACCGCGCGGATCACCGCGGGCATACTGTCGATCTGAAAAATAAAGCCGGAAAGCATAATCGACGGCAGAAAAGCGGCGTTCAGGGCGACCTGAGCGGCATTGAACTGGTTGCGGGTAATCGTGGAAATCAGCAGCCCCATCCCCAGGGTACTGAGTAAAACAGGCTGGAGATAAAAACAGAATCAGCAGCGACCCGCGATACGGCACGCCGAGAATAAACACTGACACCAGCATACACAGCAACATCGCCAGCATCCCGAGAAAGTAATAAGGGATCAGCTTACACAGCAGCAGTTCCGTGCGGGTAATCTCCGTAGAGAGCAGAGCCTCCATGGTGCCGCGTTCCCATTCTCGCGCCACCACCAGCGAGGTGAGAATCGCGCCGATGACCGTCATGATAATGGTCACCGCACCGGGGATAATGAAGTGCTGGCTAATCGCCGCCGGGTTAAACCAGTAGCGGGTTTGTACATCAATAAGCGGTTCAAAAGTCTGCCCGTTGTCCTCCGCTCGCTGCATTTGCCAGATCTGCCAGATCCCTTCGACATACCCTGTACAAAGTTAGCGGTATTCGGCTCACTGCCGTCGGTGATCACCTGAATCGGTGCGGTGGCGTTGGCGCGCTCCATCTGTTCCGCAAAATCCACCGGAATAACCACCAGACCGCGAATTTTCCCCGCCTGCATTTTGGCGATCAGTTCCTGACGGTTATCGCTGATGGTGGCGTCGATGTAGGGCGAACCGGTCATGGTGTGGTGAAATCCAGCGCCGCTTCGCTACGCTGTTCCAGTAAAATCCCGACCCGCAGCTTGCTGGAGTCGAGGTTAATGCCGTAACCAAAATAAACAGCAGTAGCAGCGGGATCACTACCGCAATCAGCCAGCTACTCGGATCGCGAACGATCTGCCGCGTCTCTTTAACGCACAGCGCCCGTACGCGACGCCAGGACAGGATCGGGTTACTCATTGCTATGCTCCTTATCCCAGTCGTGGATCAACTGAATAAAGGCTTGCTCCATGGTGGGATCGGGTTGCTCATCGTTAGCCGACTGTGCTTTCAAATCGTCCGGCGTGCCGCTGGCGATTAATTTCCCGCGGTACACCAGGCCGATGCGGTCGCAATATTCCGCTTCATCCATAAAGTGGGTGGTGACCATCACCGTGACGCCTTTCTCTACCATGCTGTTGATGTGCAGCCAAAATTCACGGCGGGTGAGGGGTCAACGCCGGAAGTCGGTTCGTCGAGAAACAGAATGTCCGGTTCATGCATCAGCGAACAGGCCAGCGCCAGCCGCTGTTTAAAACCTAATGGCAGTTCATCGGTGGCGTGGGAGGCGATACTTTTCAGGCCGAACGCCTCGCTCATGCGGGAGATTTTTCGTTCTGCGCCCGACCGCGTAAGCCATACACACCAGAGAAAAAGCGTAAATTCTGTTCGACCGTCAGGTTACCGTAGAGCGAAAATTTTTGCGCCATATAGCCGAGATGCTGGCGCGCTTTACCGGAACTCTCTTTCAGATCCATCCCCAGCACCAGCGCCTGGCCGGAAGTCGGCACCAGCAAACCGCACATCATCTTAAAGGTGGTCGATTTACCCGCGCCGTTTGGCCCCAGCAAACCAAAAATCTCCCCACGTTTAACGGCAAAGTTGACGTGATCGGTGGCGGCAAAATCCCCAAATTTCTTGGTCAGTTCTTTCGCTTCGATCACCGTCTCGCCGGGTGTGCCTTCTACCGTATGTAATATTGCGCCCAGCGGCGATTCCGAGGTTCCGGCACCGCCCAGCAAATCAATAAACGCATCTTCAAAACGCGGCGTAGTTTCGTTGATGTTGATTTCCGGCATCCCGTCGGCATGGCGAATATCGTCTGGTGTGGCCTCTTTTTGAGGATCAGACGTACCGATTTCCCCTGAATCATGCCGTCGCTGACCTGCGGCAGTTTCAAGGCGCGTTGCAACAGTTTGCGGTTGCCCTCGTGTGGACTGGTCATCAGAAAGCTGCGTCCGGCCATGGTTTGTGTCAGGGCTTTTGGTTCTCCCTGATACAGCAACTCGCCTTCGTTCATCAGTAACACGTCACGGCACTGCTCGGCTTCGTCGAGATACGAGGTACTCCAGAGGATTAACATCCCTTCGCCCGCCAGCTCATGCACCA\n' |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/t3_variants.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t3_variants.vcf Wed Jun 19 07:00:20 2019 -0400 |
| b |
| @@ -0,0 +1,21 @@ +##fileformat=VCFv4.2 +##nanopolish_window=tig00000001:200000-202000 +##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant"> +##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant"> +##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant"> +##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant"> +##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample +tig00000001 200061 . T TA 22.4 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.583757 GT 1 +tig00000001 200180 . C CA 30.6 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.596279 GT 1 +tig00000001 200484 . G GA 25.3 PASS TotalReads=63;AlleleCount=1;SupportFraction=0.569915 GT 1 +tig00000001 200672 . T TA 94.1 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.431464 GT 1 +tig00000001 200776 . C CA 82.3 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.362655 GT 1 +tig00000001 200796 . T TAA 117.1 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.268565 GT 1 +tig00000001 201007 . A AG 31.0 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.604821 GT 1 +tig00000001 201216 . A AT 85.8 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.457699 GT 1 +tig00000001 201273 . G GT 25.2 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.588877 GT 1 +tig00000001 201554 . G GC 49.9 PASS TotalReads=76;AlleleCount=1;SupportFraction=0.632029 GT 1 +tig00000001 201588 . C CG 125.4 PASS TotalReads=75;AlleleCount=1;SupportFraction=0.387616 GT 1 +tig00000001 201712 . C CA 21.1 PASS TotalReads=74;AlleleCount=1;SupportFraction=0.57415 GT 1 |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/t4_polished.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t4_polished.fa Wed Jun 19 07:00:20 2019 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>tig00000001\n+AGATGCTTTGAAAGAAACGCAGAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTGAAAAGAAAATGTCCCACAGGTACAGATAGAGTTGCTGCTTATCATACTCACGGTGCAGATAGTCATGGCGATTATGTTGATGAATTTTTTCAAGTAGCGATAAAATCTTGTAAGAAGTAAAGATAATAATCTTGAAGCATTTTATCTCGCAACACCTGATGGACGATTTGAGGCGCTTAATAATAAAGGAGAATATATTTTATCAGAAATAGTGTCCCGGGATTGAGTTCAGTATGCATACCGTATCATGATTAATTTTAGTGCTTTTATTAGTGGGGCCTATAGGAGATTCAATGAAATATAGTTCAATATTTTCGATGCTTTCATTTTTATACTATTTGCCTGTAATGAGACAGCTGTTTACGGTTCTGATGAAAACATTATTTTTATGAGGTATGTGGAAAAATTACATTTAGATAAATACTCTGTTAAAAATACGGTAAAACTGAAACAATGGCGATACAATTAGCTGAAATATATGTTAGGTATCGCTATGGCGAACGGATTGCAGAAGAAAAACCATATTTAATTACGGAACTACCAGATAGTTGGGTTGTTGAGGGAGCAAAGTTACCTTATGAAGTTGCGGGTGGTGTATTTATTATAGAAATTAATAAGAAAAATGGATGTGTTTTGAATTTCCTACATAGTAAATAATGCTGGCGCTGATGGATGCGGATGGAAACATTGCGTGGAGCGGGGAGTATGATGAGTGGGGCAACCAGCTGAATGAAGAGAACCCGCATCACCTGCACCAGCCGTACCGGCTGCCGGGGCAGCAGTATGATAAGGAGTCGGGGCTGTACTACAACCGGAACCGGTACTACGATCCGTTGCAGGGCGGTATATCACCAGGACCCGATAGGGCTGAGGGGGATGGAGTCTGTATGCGTATCCGCTGAATCCGGTGAATGGTATTGATCCATTAGGTTAAGTCCCGCAGATGTAGCGCTAATAAGAAGAAAAGATCAACTAAACCATCAAAGAGCATGGGATATATTATCTGATACTTATGAAGATATGAAGAGATTAAATTTAGGTGGGACTGATCAATTTTTCCATTGTATGGCATTTTGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGTAAAGCTATCCCATTCTGAAATGATTGAAGATAATAAAAAGACTTGGCTGTAAATGACCATGGGTTGACATGTCCATCAACAACAGATTGCTCAGATAGATGTAGTGATTATATTAATCCAGCATAAAAAACGATAAAGGCTTTACAAGATGCTGGCTATCTCAAGTAATCTATCAAAGATGATAATATTTATTTTTGCTATTATAATCATTGTTGTTTTATGCGTAATTACTTATCTTTATTTATACAAAGATGAATCTCTTGTAAGTAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTCTTATTTTCCCTAACAAATGATGATGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGGCAAGGGATGGTGTAAACCTTTTTTGTTGGTGAAATTAATGTTACGCATTATTTTATAACAAATATTGGAGCTGGATTGCCTGATGCTTGTGCAGAGTAATTGCTTGAATTAAGAGTCTATCCCATATCGAAGTCGTCAACTTCGTAGTGAGGAAAAGTAAAATTCCTGACTGAGAAAAGACATGTCGGCTATTGTGTAAAGCCATATAGCTCAGACGATGAATATCTACTCGTATTCAGTTGTTTATTGAGGGTGAGTTCCGACCCTGAAACAACAAATAAAATGAACAGTCAGAGAGTTTACATAGAATTGCACTGGTCTTTTACGATATCTGACATTGTGTAATACATATTCAGCCATGCATTAATTAAAATGTTACGTGTTTAATGTGAGTCCCTATCTGAAAATAAATAATCCTTCCGGATTAAAATAAATTCTTGCCGGGAAAGAAAGAGGAAATAAACCATTAGCGGAAAACCAGCGGCACGCCAGGGTGACATGCCCCAGTACGGCGGCCCGATAGTCCAGGGTTCAGCGGGGTACTGATAGTCGCGCCGACTGCATCGAGAACTCCATACAACTTTTACGGAACGTCACCTGATAAAATTTGTTCAGTATCGTCTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAACCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATAAAACGTATCACGCGAAACGCCCATGATTTTACAGGCTTTTGATACGTTGCTGAGTTCTTCAGCCAGATTGAGCAAACCGGCTTTGTGTTTGATGACGGGATTGGCAGTATGAAGCATGAGAGTTACCTCTTGTTTTGGATAAGGATTCGACACTCATATCAAAACCGGTAACTCTCAACCTTTCAAGGCCATGTGTCAGATCAAGTCGCGACTAATACAAATACGTCCCTCATTACCGCGCCTTAACCCATTCCGCCACTTCCGCCCACTCACCGCGAAAGACAACTTTTTCCGCTTTTTCTCAAGCTGATAGCGATACATCGGGTCGTAATATTCTTCAAGTAACGGCACCAGCCAGGCCAGATGACCGTCGGTGCTGCCGGTGGTGAGTTGCGTTGTCAGTGCTGCATCCAGCCTTGCAGCCAGTTCGTTATAGCGCTGTAGCCCCAGCCGACGCTTAATCGCCGAAAGTCCGTGATGCAGGTATTCGCAATACTCCTGCCAGCCCTGTTCGTCGCCGTACGCGTGGGTAAAATCATGATGCATACGCAAGAAATACTCTTCGTTCAGGCGCTCAAGACGGATCTCAAACGGATCTTCTACCACCGCAATCGCCGCCTGAGTCATTCGCTCGCGCAGGCATTCCGGCAGGTGATTCGAACCGATCATCCGGCTTTCGTCTTCCAGCACCCACAGGCGCAAATTCTGACGGGCGTCGGTTTTAGCATTTCGGCAGCCAGCAGGTTTTCAAAACTCGCCTGGCTAAGTTGTGGTTGTAACGTGCGACCAAACGCCGAACCGCGATGACGCGCCAACCCTTCCAGATCAACACCGTTCGGCTGTTGCTGCACTAACAGCGTTTTACCGCTGCCGGTACAACCGCCAATCAGCACTATCGGTTTTGTGCCAGTTCAATAGTCGCCTGAATCGCGGTCTGGCGCAGTGCCTTATAACCGCCTTCCACCAGCGGATAATCAATCCCCGCTGCATGCAACCAGCTTTGCACAATATGTGAGCGCTGACCGCCACGGGCGCAGCAGAGAATACCTTGCGGATTTTGCAGGCACGCTGCCCGCCAGGCGTCCATGCGCTGCTGACGAATTTCACCCGCCACCAGTTTATGTCCCAGCGCCAGCGCTGCGTCTGAGCCTTGCTGTTTATAGCAGGTGCCAACGGCGGCGCGTTCATCGTTATTCATTAACGGCAGATTGATAGCGGCGGGCATTGCGCCGTGCTCAAACTCG'..b'GGTAAAGCCTTTGTGAATATTGATGGTGAGCACCTTGAACGAAAATTGTTGTGTTTGATCGGGCATAATTTTCCTGTCTTTGCCTCTTATCTCATTGAAATAGTGTAGTCGGCGTCACAAAAGGTGCGGTCTTACGGAATTTTCCGTAAAGTTCGGTACTCTGAGTAAGTAGAGATAAATTCTTCAGGAGAGAAGCCATGAAGTGGCAACAACGTGTTCGTGTCGCAACGGGTCTAAGTTGCTGGCAGATTATGTTGCATTTACTGGTAGTGGCGCTGCTGGTGGTGGGCTGGATGAGTAAGACTCTGGTTCACGTCGGCGTGGGATTATGCGCACTGTATTGTGTCACGGTAGTGATGATGCTGGTGTTTCAGCGCCACCCCGAGCAACGCTGGCGTGAGGTGGCAGACGTGCTGGAAGAGCTGACCACGACCTGGTATTTTGGCGCAGCGCTGATTGTGCTGTGGCTGTTGTCCCGCGTTCTGGAAAACAACTTTTGCTGGCAATTGCAGGGCTGGCAATCCTTGCCGGCCCGGCGGTAGTGTCTTTGCTGGCGAAAGATAAGAAGTTACATCACCTTACGTCTAAACATCGCGTACGCCGCTGACCCTGTCGTGGCCGTTATCACCAGTAGCGGCCACAAACTATTCCACACAATATCCAGACTCGCATCCTTCAAATAAATCTGCTTGGTAATGTCCGTAAAGTGGCGAATAGGGTTAATCCACGTCAGGTTTTGCAGCCATACCGGCATGTTTTCCACCGGAGAAACGTAACCGGAAAGGAGAATGGCGGGCATCATAAAGACAAACACGCCGATAAACGCCTGCTGTTGTGTTGAACAGAGTGATGAAATCAACAGACCGAATCCCACCAGCGATAAACCATAAATCACCATCGTAAAGTAGAACAGCGCCAGCGATCCGGCGAAGGGATTTGATACGCCCAGATACCAATCGCCAGCACAATGGTGGCCTGGAAGGTGGCGACAATTAACGCCGGTACGGCTTTGCCGATGAAGATCTGCCAGGTGGTGAGCGGCGAAACCAGTAGCTGATCGAGCGTACCTTGTTCACGTTCGCGGGCGACGGAAAGTGAAGTGACGATCATTACGCCGATAGTGGTGATCATGGCGATCAGTGACGGCACCACAAACCATTTGTAGTCGAGATTCGGGTTATACCAGTTGCGTACCACCAGCTCGCTGTTGTTAGGTTTCGGTTTTCCTTCCAGCAGCTCCTGCTGATAATTTTGACGATCTGTTGCAGGTAGTTGGCGGCAATTTGCGCACTGTTGGAGTTACGCCCGTCGAGGATCAACTGCAAAGGCGCGGTCTGGAAGGTATCCAGTTTGCGCGAGAAGTCAGCCGGGAAACGCACCAGTAGTAACGCCTTTGTGTGTCGATGGTTGGGCGGATCTCCTGTGGGCTTTTCAGCAGCAGCACATGAGTAAAGGCGCTGGCGCGGGCAAAACGTTGGGTCAGCTCCACCGAATGCTCGCCGTTATCTTCATCGTAGATGGCGATGGTGGCGTTAGTCACTTCCAGCGTGGCGGCGAACGGGAACAGGATCACCTGAATTAGCACGGGTAAAATCAGAATCGCGCGGGTTTGCGGTTCGCGCAGCAACGACTGCAACTCTTTGCGGATTAACGTCCATAAGCGATGAAACATGCTCTTCTCCTAATCCAGCCGACGTTTGGTTTTCAGCCACGTCAGGCCGATAAACATCACCGCCGAAGCGATCAAAAACAGCACGTTTACCACCAGCACCACTGGAATATTCCCGGCGAGGAACAGGCTTTGCAGGGTGCTGACGAAATAACGAGCGGGAATAATGTACGTCACCGCGCGGATCACCGCGGGCATACTGTCGATCTGAAAAATAAAGCCGGAAAGCATAATCGACGGCAGAAAAGCGGCGTTCAGGGCGACCTGAGCGGCATTGAACTGGTTGCGGGTAATCGTGGAAATCAGCAGCCCCATCCCCAGGGTACTGAGTAAAACAGGCTGGAGATAAAAACAGAATCAGCAGCGACCCGCGATACGGCACGCCGAGAATAAACACTGACACCAGCATACACAGCAACATCGCCAGCATCCCGAGAAAGTAATAAGGGATCAGCTTACACAGCAGCAGTTCCGTGCGGGTAATCTCCGTAGAGAGCAGAGCCTCCATGGTGCCGCGTTCCCATTCTCGCGCCACCACCAGCGAGGTGAGAATCGCGCCGATGACCGTCATGATAATGGTCACCGCACCGGGGATAATGAAGTGCTGGCTAATCGCCGCCGGGTTAAACCAGTAGCGGGTTTGTACATCAATAAGCGGTTCAAAAGTCTGCCCGTTGTCCTCCGCTCGCTGCATTTGCCAGATCTGCCAGATCCCTTCGACATACCCTGTACAAAGTTAGCGGTATTCGGCTCACTGCCGTCGGTGATCACCTGAATCGGTGCGGTGGCGTTGGCGCGCTCCATCTGTTCCGCAAAATCCACCGGAATAACCACCAGACCGCGAATTTTCCCCGCCTGCATTTTGGCGATCAGTTCCTGACGGTTATCGCTGATGGTGGCGTCGATGTAGGGCGAACCGGTCATGGTGTGGTGAAATCCAGCGCCGCTTCGCTACGCTGTTCCAGTAAAATCCCGACCCGCAGCTTGCTGGAGTCGAGGTTAATGCCGTAACCAAAATAAACAGCAGTAGCAGCGGGATCACTACCGCAATCAGCCAGCTACTCGGATCGCGAACGATCTGCCGCGTCTCTTTAACGCACAGCGCCCGTACGCGACGCCAGGACAGGATCGGGTTACTCATTGCTATGCTCCTTATCCCAGTCGTGGATCAACTGAATAAAGGCTTGCTCCATGGTGGGATCGGGTTGCTCATCGTTAGCCGACTGTGCTTTCAAATCGTCCGGCGTGCCGCTGGCGATTAATTTCCCGCGGTACACCAGGCCGATGCGGTCGCAATATTCCGCTTCATCCATAAAGTGGGTGGTGACCATCACCGTGACGCCTTTCTCTACCATGCTGTTGATGTGCAGCCAAAATTCACGGCGGGTGAGGGGTCAACGCCGGAAGTCGGTTCGTCGAGAAACAGAATGTCCGGTTCATGCATCAGCGAACAGGCCAGCGCCAGCCGCTGTTTAAAACCTAATGGCAGTTCATCGGTGGCGTGGGAGGCGATACTTTTCAGGCCGAACGCCTCGCTCATGCGGGAGATTTTTCGTTCTGCGCCCGACCGCGTAAGCCATACACACCAGAGAAAAAGCGTAAATTCTGTTCGACCGTCAGGTTACCGTAGAGCGAAAATTTTTGCGCCATATAGCCGAGATGCTGGCGCGCTTTACCGGAACTCTCTTTCAGATCCATCCCCAGCACCAGCGCCTGGCCGGAAGTCGGCACCAGCAAACCGCACATCATCTTAAAGGTGGTCGATTTACCCGCGCCGTTTGGCCCCAGCAAACCAAAAATCTCCCCACGTTTAACGGCAAAGTTGACGTGATCGGTGGCGGCAAAATCCCCAAATTTCTTGGTCAGTTCTTTCGCTTCGATCACCGTCTCGCCGGGTGTGCCTTCTACCGTATGTAATATTGCGCCCAGCGGCGATTCCGAGGTTCCGGCACCGCCCAGCAAATCAATAAACGCATCTTCAAAACGCGGCGTAGTTTCGTTGATGTTGATTTCCGGCATCCCGTCGGCATGGCGAATATCGTCTGGTGTGGCCTCTTTTTGAGGATCAGACGTACCGATTTCCCCTGAATCATGCCGTCGCTGACCTGCGGCAGTTTCAAGGCGCGTTGCAACAGTTTGCGGTTGCCCTCGTGTGGACTGGTCATCAGAAAGCTGCGTCCGGCCATGGTTTGTGTCAGGGCTTTTGGTTCTCCCTGATACAGCAACTCGCCTTCGTTCATCAGTAACACGTCACGGCACTGCTCGGCTTCGTCGAGATACGAGGTACTCCAGAGGATTAACATCCCTTCGCCCGCCAGCTCATGCACCA\n' |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/t4_variants.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t4_variants.vcf Wed Jun 19 07:00:20 2019 -0400 |
| b |
| @@ -0,0 +1,21 @@ +##fileformat=VCFv4.2 +##nanopolish_window=tig00000001:200000-202000 +##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant"> +##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant"> +##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant"> +##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant"> +##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample +tig00000001 200061 . T TA 22.4 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.583757 GT 1 +tig00000001 200180 . C CA 30.6 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.596279 GT 1 +tig00000001 200484 . G GA 25.3 PASS TotalReads=63;AlleleCount=1;SupportFraction=0.569915 GT 1 +tig00000001 200672 . T TA 94.1 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.431464 GT 1 +tig00000001 200776 . C CA 82.3 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.362655 GT 1 +tig00000001 200796 . T TAA 117.1 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.268565 GT 1 +tig00000001 201007 . A AG 31.0 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.604821 GT 1 +tig00000001 201216 . A AT 85.8 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.457699 GT 1 +tig00000001 201273 . G GT 25.2 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.588877 GT 1 +tig00000001 201554 . G GC 49.9 PASS TotalReads=76;AlleleCount=1;SupportFraction=0.632029 GT 1 +tig00000001 201588 . C CG 125.4 PASS TotalReads=75;AlleleCount=1;SupportFraction=0.387616 GT 1 +tig00000001 201712 . C CA 21.1 PASS TotalReads=74;AlleleCount=1;SupportFraction=0.57415 GT 1 |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 test-data/variants.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/variants.vcf Wed Jun 19 07:00:20 2019 -0400 |
| b |
| @@ -0,0 +1,21 @@ +##fileformat=VCFv4.2 +##nanopolish_window=tig00000001:200000-202000 +##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant"> +##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant"> +##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant"> +##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant"> +##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample +tig00000001 200061 . T TA 22.4 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.583757 GT 1 +tig00000001 200180 . C CA 30.6 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.596279 GT 1 +tig00000001 200484 . G GA 25.3 PASS TotalReads=63;AlleleCount=1;SupportFraction=0.569915 GT 1 +tig00000001 200672 . T TA 94.1 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.431464 GT 1 +tig00000001 200776 . C CA 82.3 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.362655 GT 1 +tig00000001 200796 . T TAA 117.1 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.268565 GT 1 +tig00000001 201007 . A AG 31.0 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.604821 GT 1 +tig00000001 201216 . A AT 85.8 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.457699 GT 1 +tig00000001 201273 . G GT 25.2 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.588877 GT 1 +tig00000001 201554 . G GC 49.9 PASS TotalReads=76;AlleleCount=1;SupportFraction=0.632029 GT 1 +tig00000001 201588 . C CG 125.4 PASS TotalReads=75;AlleleCount=1;SupportFraction=0.387616 GT 1 +tig00000001 201712 . C CA 21.1 PASS TotalReads=74;AlleleCount=1;SupportFraction=0.57415 GT 1 |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Wed Jun 19 07:00:20 2019 -0400 |
| b |
| @@ -0,0 +1,19 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# + |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Jun 19 07:00:20 2019 -0400 |
| b |
| @@ -0,0 +1,9 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables> + |
| b |
| diff -r 000000000000 -r 7739a9b0dd83 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Jun 19 07:00:20 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables> |