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Changeset 3:02e3c674d917 (2019-06-19)

Previous changeset 2:07cf146e8964 (2018-06-05) Next changeset 4:a8d4be409446 (2019-06-23)

Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty

modified:
macros.xml
nanopolish_methylation.xml
test-data/methylation_calls.tsv
test-data/polished.fa
test-data/t2-polished.fa
test-data/t2-variants.vcf
test-data/variants.vcf

added:
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.sample
test-data/draft_single_seq.fa
test-data/enolase_reference.fas
test-data/fast5_files.tar
test-data/fast5_files.tar.bz2
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/t3_polished.fa
test-data/t3_variants.vcf
test-data/t4_polished.fa
test-data/t4_variants.vcf

diff -r 07cf146e8964 -r 02e3c674d917 macros.xml
--- a/macros.xml Tue Jun 05 18:25:34 2018 -0400
+++ b/macros.xml Wed Jun 19 03:45:24 2019 -0400

@@ -1,7 +1,7 @@
<macros>
     <xml name="requirements">
         <requirements>
-        <requirement type="package" version="0.9.2">nanopolish</requirement>
+        <requirement type="package" version="0.11.1">nanopolish</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -20,16 +20,8 @@

     <xml name="citations">
         <citations>
+            <citation type="doi">10.1038/nmeth.3444</citation>
             <citation type="doi">10.1038/nmeth.4184</citation>
-            <citation type="bibtex">
-@misc{githubnanopolish,
-  author = {LastTODO, FirstTODO},
-  year = {TODO},
-  title = {nanopolish},
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  url = {https://github.com/jts/nanopolish},
-}</citation>
             <yield />
         </citations>
     </xml>

diff -r 07cf146e8964 -r 02e3c674d917 nanopolish_methylation.xml
--- a/nanopolish_methylation.xml Tue Jun 05 18:25:34 2018 -0400
+++ b/nanopolish_methylation.xml Wed Jun 19 03:45:24 2019 -0400

@@ -9,12 +9,28 @@

         #if $input_reads_raw.extension == 'fast5':
             mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
-        #else
+
+        #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/ reads.fasta &&
+        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':
@@ -39,7 +55,7 @@
     <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" label="Flat archive file of raw fast5 files"/>
+        <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" />
@@ -59,6 +75,12 @@
             <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">
+            
+            <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="find variants in window of region chromsome:start-end" />
         <param name="batchsize" type="integer" optional="true" value="" label="Batch size" help="(-K)"/>

diff -r 07cf146e8964 -r 02e3c674d917 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 03:45:24 2019 -0400

@@ -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

diff -r 07cf146e8964 -r 02e3c674d917 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 03:45:24 2019 -0400

@@ -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

diff -r 07cf146e8964 -r 02e3c674d917 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 03:45:24 2019 -0400

@@ -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

diff -r 07cf146e8964 -r 02e3c674d917 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 03:45:24 2019 -0400

diff -r 07cf146e8964 -r 02e3c674d917 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 03:45:24 2019 -0400

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"

diff -r 07cf146e8964 -r 02e3c674d917 test-data/30xpolyA-small-subset.sorted.bam

Binary file test-data/30xpolyA-small-subset.sorted.bam has changed

diff -r 07cf146e8964 -r 02e3c674d917 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 03:45:24 2019 -0400

@@ -0,0 +1,1 @@
+draft draft draft ${__HERE__}/draft.fa
\ No newline at end of file

diff -r 07cf146e8964 -r 02e3c674d917 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 03:45:24 2019 -0400

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'

diff -r 07cf146e8964 -r 02e3c674d917 test-data/enolase_reference.fas
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/enolase_reference.fas Wed Jun 19 03:45:24 2019 -0400

@@ -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

diff -r 07cf146e8964 -r 02e3c674d917 test-data/fast5_files.tar

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diff -r 07cf146e8964 -r 02e3c674d917 test-data/fast5_files.tar.bz2

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diff -r 07cf146e8964 -r 02e3c674d917 test-data/fast5_files_30xpolyA-small-subset.tar

Binary file test-data/fast5_files_30xpolyA-small-subset.tar has changed

diff -r 07cf146e8964 -r 02e3c674d917 test-data/fast5_files_30xpolyA-small-subset.tar.bz2

Binary file test-data/fast5_files_30xpolyA-small-subset.tar.bz2 has changed

diff -r 07cf146e8964 -r 02e3c674d917 test-data/fast5_files_30xpolyA-small-subset.tar.gz

Binary file test-data/fast5_files_30xpolyA-small-subset.tar.gz has changed

diff -r 07cf146e8964 -r 02e3c674d917 test-data/methylation_calls.tsv
--- a/test-data/methylation_calls.tsv Tue Jun 05 18:25:34 2018 -0400
+++ b/test-data/methylation_calls.tsv Wed Jun 19 03:45:24 2019 -0400

b'@@ -1,16999 +1,16999 @@\n-chromosome\tstart\tend\tread_name\tlog_lik_ratio\tlog_lik_methylated\tlog_lik_unmethylated\tnum_calling_strands\tnum_cpgs\tsequence\n-tig00000001\t191153\t191157\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-6.31\t-130.59\t-124.28\t1\t2\tTATTACGACCGCTGA\n-tig00000001\t191181\t191181\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.75\t-101.63\t-100.88\t1\t1\tTTTGGCGTTGA\n-tig00000001\t191196\t191215\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-11.45\t-223.51\t-212.05\t1\t3\tCAGTGCGGCAAACAGCGGATAGAACGGGCT\n-tig00000001\t191229\t191229\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-5.42\t-101.51\t-96.09\t1\t1\tGGAGGCGTGCA\n-tig00000001\t191244\t191244\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.28\t-82.87\t-80.59\t1\t1\tAAAGGCGTTGT\n-tig00000001\t191255\t191273\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-9.25\t-167.61\t-158.35\t1\t3\tTCATGCGTTTGTGCGGTACATAACGCTGT\n-tig00000001\t191354\t191354\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-4.06\t-98.18\t-94.12\t1\t1\tGATTGCGTAAC\n-tig00000001\t191369\t191374\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-1.70\t-119.73\t-118.02\t1\t2\tATACCCGGATCGTTCT\n-tig00000001\t191399\t191420\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-14.84\t-212.15\t-197.31\t1\t4\tAACAGCGGCGAACAGTCCGCCATCATCGGAAT\n-tig00000001\t191440\t191440\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.39\t-97.48\t-95.10\t1\t1\tATAGCCGACCC\n-tig00000001\t191502\t191524\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-7.13\t-196.90\t-189.78\t1\t5\tCTTGGCGGGCGTTATAAATCGTACCGTCGTAGG\n-tig00000001\t191548\t191562\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t2.03\t-164.90\t-166.93\t1\t3\tCACAGCGAGGCGGAAAGGACGAGCC\n-tig00000001\t191576\t191595\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-16.47\t-198.51\t-182.04\t1\t5\tTTGCCCGCTGCGGTGCGACTTCCGCGATCA\n-tig00000001\t191606\t191606\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.43\t-106.24\t-105.81\t1\t1\tGCTCACGCAGG\n-tig00000001\t191632\t191632\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-5.03\t-101.77\t-96.74\t1\t1\tCAGTGCGCATC\n-tig00000001\t191646\t191646\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.52\t-102.26\t-101.75\t1\t1\tGCCACCGATAA\n-tig00000001\t191659\t191671\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-6.16\t-155.98\t-149.82\t1\t3\tCCATACGGGTTACGTGCCGTTTC\n-tig00000001\t191686\t191686\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-1.12\t-84.86\t-83.73\t1\t1\tTAAACCGGTGT\n-tig00000001\t191710\t191715\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-1.66\t-141.17\t-139.51\t1\t2\tAGCAACGCTCCGTGGT\n-tig00000001\t191741\t191741\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.49\t-76.49\t-74.01\t1\t1\tTATTGCGATCA\n-tig00000001\t191764\t191764\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.28\t-106.49\t-104.21\t1\t1\tTCACCCGGTGT\n-tig00000001\t191778\t191778\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-8.95\t-111.16\t-102.21\t1\t1\tCAGGGCGTTTA\n-tig00000001\t191820\t191820\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-1.97\t-129.21\t-127.24\t1\t1\tTAAAACGAAGT\n-tig00000001\t191835\t191835\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.83\t-101.24\t-100.41\t1\t1\tTTTATCGGCAT\n-tig00000001\t191854\t191854\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-3.07\t-94.72\t-91.65\t1\t1\tTTTGCCGCATG\n-tig00000001\t191878\t191886\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-11.48\t-176.19\t-164.71\t1\t3\tCATGGCGCGCCTTCGTGAA\n-tig00000001\t191901\t191919\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-5.54\t-179.90\t-174.37\t1\t5\tCAGATCGCCCATCGCTACGTCGGCGTTGC\n-tig00000001\t191931\t191944\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-19.26\t-177.78\t-158.53\t1\t3\tCAAGTCGGCACGGAACAGCGCCTC\n-tig00000001\t191977\t192002\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-8.41\t-244.04\t-235.63\t1\t6\tTTCCCCGCCGGATGGCGACGGAAAATTCGCCGCCCT\n-tig00000001\t192027\t192029\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.80\t-105.66\t-104.86\t1\t2\tTCAAACGCGCTGT\n-tig00000001\t192053\t192064\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.40\t-160.39\t-157.99\t1\t3\tATAATCGACCAGTGCGCGGAAG\n-tig00000001\t192079\t192079\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-7.16\t-99.97\t-92.81\t1\t1\tGTGGGCGCAGT\n-tig00000001\t192107\t192107\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.87\t-96.22\t-95.35\t1\t1\tGGCAGCGGTTT\n-tig00000001\t192121\t192121\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.94\t-100.94\t-100.00\t1\t1\tACTGGCGACCA\n-tig00000001\t192136\t192146\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-4.34\t-143.10\t-138.77\t1\t4\tATTCTCGTCGCGATTCGCAAT\n-tig00000001\t192165\t192172\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-7.29'..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'

diff -r 07cf146e8964 -r 02e3c674d917 test-data/polished.fa
--- a/test-data/polished.fa Tue Jun 05 18:25:34 2018 -0400
+++ b/test-data/polished.fa Wed Jun 19 03:45:24 2019 -0400

b'@@ -1,2 +1,2 @@\n->tig00000001:199960-202040\n-TCCTGAGAAGCTACAGGCCCCATGGGTAACAGCTGTTGCGCTCCTTCAACGGTATTCACAGCCTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCTCATGCTCTGGCGGGTAAACGCACGGATGAGGGCAAAAATCACCGCAATCCCGCTGGCGGCAGAAAGAAAGTTTTGCACCGTTAAGCCCGCCATCTGGCTGAAATAGCTCAACGTGGTTTCACCGCTATAAGATTGCCAGTTGGTATTGGTGACAAAGCTGACGGCGGTATTCAGCGCCAGATCCCACGACAGCCCTGGCAACTGCTGTGGATTAAGCGGCAGATAGTGCTGACCGAGCAACATAAAAACAGCACCGCCAGCCCCAGCATGTTCAGGCCGAGAATGGCACAAAGATATTGCTTCCAGTTCATCTCACGGTCAGAGACGCCAAGTGCGCGAAAAAGTACGCGCTCAACGCCCGTTGTACCGGGAAGAGGAATGTCATTAATCAGCCGCGCCAGCCCGCTGCCTAAAGGACGCGCCAGCACCATTAACACCAGTAAAAACGTGGCGATCAGTAAGAACCCTTGCGCAGCCATCAGAACGCCTCCGCATTGATCAGGGCATAAACCAGATAACCCAGTAATAAAAACACCAGCAATACGCCGGTTATCACGCCTGCACTCACAGTGCACCTCCAGTGGCCTAAAAGTGATACCGGAAGGGTAGAATTCTGGCTGCAAAGATTTCGCAAAAATCTGCGGGCGGGGTGTAAAAAAGTATAAAAATGGCAAAAGCCATGATTTAACTAATGTTTAGTATTAATTTAACTTTTGTGTAACTTAATTACAGGATGAATGTAAATAAACCATCAATAAGCAAAAATAAGTGGTCGGATGAGTAGTAAAATTACACAAAAGGCGGTACTATTTTCATCAGATAAACAAATTCATTTTTCCGGTGCCATTCACCGGGTAGATACAAAAGGGGGAGAAAAGTATGGAACTCTACAGAGAATATCCTGCATGGCTTATCTTTTTACGCCGTACTTATGCGGTTGCAGCGGGCGTTCTGGCGCTGCCTTTCATGCTTTTCTGGAAAGACCGCGCCCGCTTTTACAGCTACCTGCATCGCGTCTGGTCGAAAACCAGCGATAAACCGGTGTGGATGGATCAGGCCGAAAAGGCAACTGGTGATTTTTATTGATTGCTGAGTTTTGAATACATTGAAAACCGCCAGCGGAAACGCTGGCGGTTTTTTGTATCAGGAAGATGTTCAGAGGAATATTTAGACATCGTTATACCAATCGAAACATATATTCATGAAATATATATAAATATTTTCCTAATTGTTCTTATCTGACAGATATCTCACTTAAGGCTTTCTTATAAATCTGTAGGGTTTCGCCTGTCAGCAGACAAATAACCCGATAAAACAAGGATGAGCAGATGAGCGGAAAACCGGCGGCGCGTCAGGGCGACATGACGCAGTATGGCGGTAGCATTGTCCAGGGTTCAGCCGGGGTACGCATCGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGGGTGACGTCCGGCCATCCGGTCAATCCGCTGCTCGGTGCAAAGGTCCTTCCCGGTGAAACCGACATCGCCCTGCCCGGCCCGCTGCCGTTCATTCTCTCCCGCACCTACAGCAGTTACCGGACAAAAACGCCCGCGCCGGTGGGGAGCCTCGGCCCCGGCTGGAAAATGCCTGCGGATATCCGCTTACAGCTGCGCGATAACACACTGATACTCAGTGATAACGGCGGCAGAAGCCTGTATTTTGAGCACCTGTTTCCCGGTGAGGACGGTTACAGCCGCAGCGAGTCACTGTGGCTGGTGCGCGGCGGCGTGGCGAAACTGGATGAAGGTCACCGGCTGGCCGCACTCTGGCAGGCGCTGCCGGAAGAACTCCGCTTAAGTCCGCATCGTTATCTGGCGACAAACAGTCCGCAGGGGCCGTGGTGGCTGCTCGGCTGGTGTGAGCGGGTGCC\n+>tig00000001\n+AGATGCTTTGAAAGAAACGCAGAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTGAAAAGAAAATGTCCCACAGGTACAGATAGAGTTGCTGCTTATCATACTCACGGTGCAGATAGTCATGGCGATTATGTTGATGAATTTTTTCAAGTAGCGATAAAATCTTGTAAGAAGTAAAGATAATAATCTTGAAGCATTTTATCTCGCAACACCTGATGGACGATTTGAGGCGCTTAATAATAAAGGAGAATATATTTTATCAGAAATAGTGTCCCGGGATTGAGTTCAGTATGCATACCGTATCATGATTAATTTTAGTGCTTTTATTAGTGGGGCCTATAGGAGATTCAATGAAATATAGTTCAATATTTTCGATGCTTTCATTTTTATACTATTTGCCTGTAATGAGACAGCTGTTTACGGTTCTGATGAAAACATTATTTTTATGAGGTATGTGGAAAAATTACATTTAGATAAATACTCTGTTAAAAATACGGTAAAACTGAAACAATGGCGATACAATTAGCTGAAATATATGTTAGGTATCGCTATGGCGAACGGATTGCAGAAGAAAAACCATATTTAATTACGGAACTACCAGATAGTTGGGTTGTTGAGGGAGCAAAGTTACCTTATGAAGTTGCGGGTGGTGTATTTATTATAGAAATTAATAAGAAAAATGGATGTGTTTTGAATTTCCTACATAGTAAATAATGCTGGCGCTGATGGATGCGGATGGAAACATTGCGTGGAGCGGGGAGTATGATGAGTGGGGCAACCAGCTGAATGAAGAGAACCCGCATCACCTGCACCAGCCGTACCGGCTGCCGGGGCAGCAGTATGATAAGGAGTCGGGGCTGTACTACAACCGGAACCGGTACTACGATCCGTTGCAGGGCGGTATATCACCAGGACCCGATAGGGCTGAGGGGGATGGAGTCTGTATGCGTATCCGCTGAATCCGGTGAATGGTATTGATCCATTAGGTTAAGTCCCGCAGATGTAGCGCTAATAAGAAGAAAAGATCAACTAAACCATCAAAGAGCATGGGATATATTATCTGATACTTATGAAGATATGAAGAGATTAAATTTAGGTGGGACTGATCAATTTTTCCATTGTATGGCATTTTGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGTAAAGCTATCCCATTCTGAAATGATTGAAGATAATAAAAAGACTTGGCTGTAAATGACCATGGGTTGACATGTCCATCAACAACAGATTGCTCAGATAGATGTAGTGATTATATTAATCCAGCATAAAAAACGATAAAGGCTTTACAAGATGCTGGCTATCTCAAGTAATCTATCAAAGATGATAATATTTATTTTTGCTATTATAATCATTGTTGTTTTATGCGTAATTACTTATCTTTATTTATACAAAGATGAATCTCTTGTAAGTAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTCTTATTTTCCCTAACAAATGATGATGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAGTGTGGTGTAAAT'..b'GGTAAAGCCTTTGTGAATATTGATGGTGAGCACCTTGAACGAAAATTGTTGTGTTTGATCGGGCATAATTTTCCTGTCTTTGCCTCTTATCTCATTGAAATAGTGTAGTCGGCGTCACAAAAGGTGCGGTCTTACGGAATTTTCCGTAAAGTTCGGTACTCTGAGTAAGTAGAGATAAATTCTTCAGGAGAGAAGCCATGAAGTGGCAACAACGTGTTCGTGTCGCAACGGGTCTAAGTTGCTGGCAGATTATGTTGCATTTACTGGTAGTGGCGCTGCTGGTGGTGGGCTGGATGAGTAAGACTCTGGTTCACGTCGGCGTGGGATTATGCGCACTGTATTGTGTCACGGTAGTGATGATGCTGGTGTTTCAGCGCCACCCCGAGCAACGCTGGCGTGAGGTGGCAGACGTGCTGGAAGAGCTGACCACGACCTGGTATTTTGGCGCAGCGCTGATTGTGCTGTGGCTGTTGTCCCGCGTTCTGGAAAACAACTTTTGCTGGCAATTGCAGGGCTGGCAATCCTTGCCGGCCCGGCGGTAGTGTCTTTGCTGGCGAAAGATAAGAAGTTACATCACCTTACGTCTAAACATCGCGTACGCCGCTGACCCTGTCGTGGCCGTTATCACCAGTAGCGGCCACAAACTATTCCACACAATATCCAGACTCGCATCCTTCAAATAAATCTGCTTGGTAATGTCCGTAAAGTGGCGAATAGGGTTAATCCACGTCAGGTTTTGCAGCCATACCGGCATGTTTTCCACCGGAGAAACGTAACCGGAAAGGAGAATGGCGGGCATCATAAAGACAAACACGCCGATAAACGCCTGCTGTTGTGTTGAACAGAGTGATGAAATCAACAGACCGAATCCCACCAGCGATAAACCATAAATCACCATCGTAAAGTAGAACAGCGCCAGCGATCCGGCGAAGGGATTTGATACGCCCAGATACCAATCGCCAGCACAATGGTGGCCTGGAAGGTGGCGACAATTAACGCCGGTACGGCTTTGCCGATGAAGATCTGCCAGGTGGTGAGCGGCGAAACCAGTAGCTGATCGAGCGTACCTTGTTCACGTTCGCGGGCGACGGAAAGTGAAGTGACGATCATTACGCCGATAGTGGTGATCATGGCGATCAGTGACGGCACCACAAACCATTTGTAGTCGAGATTCGGGTTATACCAGTTGCGTACCACCAGCTCGCTGTTGTTAGGTTTCGGTTTTCCTTCCAGCAGCTCCTGCTGATAATTTTGACGATCTGTTGCAGGTAGTTGGCGGCAATTTGCGCACTGTTGGAGTTACGCCCGTCGAGGATCAACTGCAAAGGCGCGGTCTGGAAGGTATCCAGTTTGCGCGAGAAGTCAGCCGGGAAACGCACCAGTAGTAACGCCTTTGTGTGTCGATGGTTGGGCGGATCTCCTGTGGGCTTTTCAGCAGCAGCACATGAGTAAAGGCGCTGGCGCGGGCAAAACGTTGGGTCAGCTCCACCGAATGCTCGCCGTTATCTTCATCGTAGATGGCGATGGTGGCGTTAGTCACTTCCAGCGTGGCGGCGAACGGGAACAGGATCACCTGAATTAGCACGGGTAAAATCAGAATCGCGCGGGTTTGCGGTTCGCGCAGCAACGACTGCAACTCTTTGCGGATTAACGTCCATAAGCGATGAAACATGCTCTTCTCCTAATCCAGCCGACGTTTGGTTTTCAGCCACGTCAGGCCGATAAACATCACCGCCGAAGCGATCAAAAACAGCACGTTTACCACCAGCACCACTGGAATATTCCCGGCGAGGAACAGGCTTTGCAGGGTGCTGACGAAATAACGAGCGGGAATAATGTACGTCACCGCGCGGATCACCGCGGGCATACTGTCGATCTGAAAAATAAAGCCGGAAAGCATAATCGACGGCAGAAAAGCGGCGTTCAGGGCGACCTGAGCGGCATTGAACTGGTTGCGGGTAATCGTGGAAATCAGCAGCCCCATCCCCAGGGTACTGAGTAAAACAGGCTGGAGATAAAAACAGAATCAGCAGCGACCCGCGATACGGCACGCCGAGAATAAACACTGACACCAGCATACACAGCAACATCGCCAGCATCCCGAGAAAGTAATAAGGGATCAGCTTACACAGCAGCAGTTCCGTGCGGGTAATCTCCGTAGAGAGCAGAGCCTCCATGGTGCCGCGTTCCCATTCTCGCGCCACCACCAGCGAGGTGAGAATCGCGCCGATGACCGTCATGATAATGGTCACCGCACCGGGGATAATGAAGTGCTGGCTAATCGCCGCCGGGTTAAACCAGTAGCGGGTTTGTACATCAATAAGCGGTTCAAAAGTCTGCCCGTTGTCCTCCGCTCGCTGCATTTGCCAGATCTGCCAGATCCCTTCGACATACCCTGTACAAAGTTAGCGGTATTCGGCTCACTGCCGTCGGTGATCACCTGAATCGGTGCGGTGGCGTTGGCGCGCTCCATCTGTTCCGCAAAATCCACCGGAATAACCACCAGACCGCGAATTTTCCCCGCCTGCATTTTGGCGATCAGTTCCTGACGGTTATCGCTGATGGTGGCGTCGATGTAGGGCGAACCGGTCATGGTGTGGTGAAATCCAGCGCCGCTTCGCTACGCTGTTCCAGTAAAATCCCGACCCGCAGCTTGCTGGAGTCGAGGTTAATGCCGTAACCAAAATAAACAGCAGTAGCAGCGGGATCACTACCGCAATCAGCCAGCTACTCGGATCGCGAACGATCTGCCGCGTCTCTTTAACGCACAGCGCCCGTACGCGACGCCAGGACAGGATCGGGTTACTCATTGCTATGCTCCTTATCCCAGTCGTGGATCAACTGAATAAAGGCTTGCTCCATGGTGGGATCGGGTTGCTCATCGTTAGCCGACTGTGCTTTCAAATCGTCCGGCGTGCCGCTGGCGATTAATTTCCCGCGGTACACCAGGCCGATGCGGTCGCAATATTCCGCTTCATCCATAAAGTGGGTGGTGACCATCACCGTGACGCCTTTCTCTACCATGCTGTTGATGTGCAGCCAAAATTCACGGCGGGTGAGGGGTCAACGCCGGAAGTCGGTTCGTCGAGAAACAGAATGTCCGGTTCATGCATCAGCGAACAGGCCAGCGCCAGCCGCTGTTTAAAACCTAATGGCAGTTCATCGGTGGCGTGGGAGGCGATACTTTTCAGGCCGAACGCCTCGCTCATGCGGGAGATTTTTCGTTCTGCGCCCGACCGCGTAAGCCATACACACCAGAGAAAAAGCGTAAATTCTGTTCGACCGTCAGGTTACCGTAGAGCGAAAATTTTTGCGCCATATAGCCGAGATGCTGGCGCGCTTTACCGGAACTCTCTTTCAGATCCATCCCCAGCACCAGCGCCTGGCCGGAAGTCGGCACCAGCAAACCGCACATCATCTTAAAGGTGGTCGATTTACCCGCGCCGTTTGGCCCCAGCAAACCAAAAATCTCCCCACGTTTAACGGCAAAGTTGACGTGATCGGTGGCGGCAAAATCCCCAAATTTCTTGGTCAGTTCTTTCGCTTCGATCACCGTCTCGCCGGGTGTGCCTTCTACCGTATGTAATATTGCGCCCAGCGGCGATTCCGAGGTTCCGGCACCGCCCAGCAAATCAATAAACGCATCTTCAAAACGCGGCGTAGTTTCGTTGATGTTGATTTCCGGCATCCCGTCGGCATGGCGAATATCGTCTGGTGTGGCCTCTTTTTGAGGATCAGACGTACCGATTTCCCCTGAATCATGCCGTCGCTGACCTGCGGCAGTTTCAAGGCGCGTTGCAACAGTTTGCGGTTGCCCTCGTGTGGACTGGTCATCAGAAAGCTGCGTCCGGCCATGGTTTGTGTCAGGGCTTTTGGTTCTCCCTGATACAGCAACTCGCCTTCGTTCATCAGTAACACGTCACGGCACTGCTCGGCTTCGTCGAGATACGAGGTACTCCAGAGGATTAACATCCCTTCGCCCGCCAGCTCATGCACCA\n'

diff -r 07cf146e8964 -r 02e3c674d917 test-data/t2-polished.fa
--- a/test-data/t2-polished.fa Tue Jun 05 18:25:34 2018 -0400
+++ b/test-data/t2-polished.fa Wed Jun 19 03:45:24 2019 -0400

b'@@ -0,0 +1,2 @@\n+>tig00000001\n+AGATGCTTTGAAAGAAACGCAGAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTGAAAAGAAAATGTCCCACAGGTACAGATAGAGTTGCTGCTTATCATACTCACGGTGCAGATAGTCATGGCGATTATGTTGATGAATTTTTTCAAGTAGCGATAAAATCTTGTAAGAAGTAAAGATAATAATCTTGAAGCATTTTATCTCGCAACACCTGATGGACGATTTGAGGCGCTTAATAATAAAGGAGAATATATTTTATCAGAAATAGTGTCCCGGGATTGAGTTCAGTATGCATACCGTATCATGATTAATTTTAGTGCTTTTATTAGTGGGGCCTATAGGAGATTCAATGAAATATAGTTCAATATTTTCGATGCTTTCATTTTTATACTATTTGCCTGTAATGAGACAGCTGTTTACGGTTCTGATGAAAACATTATTTTTATGAGGTATGTGGAAAAATTACATTTAGATAAATACTCTGTTAAAAATACGGTAAAACTGAAACAATGGCGATACAATTAGCTGAAATATATGTTAGGTATCGCTATGGCGAACGGATTGCAGAAGAAAAACCATATTTAATTACGGAACTACCAGATAGTTGGGTTGTTGAGGGAGCAAAGTTACCTTATGAAGTTGCGGGTGGTGTATTTATTATAGAAATTAATAAGAAAAATGGATGTGTTTTGAATTTCCTACATAGTAAATAATGCTGGCGCTGATGGATGCGGATGGAAACATTGCGTGGAGCGGGGAGTATGATGAGTGGGGCAACCAGCTGAATGAAGAGAACCCGCATCACCTGCACCAGCCGTACCGGCTGCCGGGGCAGCAGTATGATAAGGAGTCGGGGCTGTACTACAACCGGAACCGGTACTACGATCCGTTGCAGGGCGGTATATCACCAGGACCCGATAGGGCTGAGGGGGATGGAGTCTGTATGCGTATCCGCTGAATCCGGTGAATGGTATTGATCCATTAGGTTAAGTCCCGCAGATGTAGCGCTAATAAGAAGAAAAGATCAACTAAACCATCAAAGAGCATGGGATATATTATCTGATACTTATGAAGATATGAAGAGATTAAATTTAGGTGGGACTGATCAATTTTTCCATTGTATGGCATTTTGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGTAAAGCTATCCCATTCTGAAATGATTGAAGATAATAAAAAGACTTGGCTGTAAATGACCATGGGTTGACATGTCCATCAACAACAGATTGCTCAGATAGATGTAGTGATTATATTAATCCAGCATAAAAAACGATAAAGGCTTTACAAGATGCTGGCTATCTCAAGTAATCTATCAAAGATGATAATATTTATTTTTGCTATTATAATCATTGTTGTTTTATGCGTAATTACTTATCTTTATTTATACAAAGATGAATCTCTTGTAAGTAAACATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAATGTAGAAGATGATTATTTTTTCTTATTTTCCCTAACAAATGATGATGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATACAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGGCAAGGGATGGTGTAAACCTTTTTTGTTGGTGAAATTAATGTTACGCATTATTTTATAACAAATATTGGAGCTGGATTGCCTGATGCTTGTGCAGAGTAATTGCTTGAATTAAGAGTCTATCCCATATCGAAGTCGTCAACTTCGTAGTGAGGAAAAGTAAAATTCCTGACTGAGAAAAGACATGTCGGCTATTGTGTAAAGCCATATAGCTCAGACGATGAATATCTACTCGTATTCAGTTGTTTATTGAGGGTGAGTTCCGACCCTGAAACAACAAATAAAATGAACAGTCAGAGAGTTTACATAGAATTGCACTGGTCTTTTACGATATCTGACATTGTGTAATACATATTCAGCCATGCATTAATTAAAATGTTACGTGTTTAATGTGAGTCCCTATCTGAAAATAAATAATCCTTCCGGATTAAAATAAATTCTTGCCGGGAAAGAAAGAGGAAATAAACCATTAGCGGAAAACCAGCGGCACGCCAGGGTGACATGCCCCAGTACGGCGGCCCGATAGTCCAGGGTTCAGCGGGGTACTGATAGTCGCGCCGACTGCATCGAGAACTCCATACAACTTTTACGGAACGTCACCTGATAAAATTTGTTCAGTATCGTCTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAACCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATAAAACGTATCACGCGAAACGCCCATGATTTTACAGGCTTTTGATACGTTGCTGAGTTCTTCAGCCAGATTGAGCAAACCGGCTTTGTGTTTGATGACGGGATTGGCAGTATGAAGCATGAGAGTTACCTCTTGTTTTGGATAAGGATTCGACACTCATATCAAAACCGGTAACTCTCAACCTTTCAAGGCCATGTGTCAGATCAAGTCGCGACTAATACAAATACGTCCCTCATTACCGCGCCTTAACCCATTCCGCCACTTCCGCCCACTCACCGCGAAAGACAACTTTTTCCGCTTTTTCTCAAGCTGATAGCGATACATCGGGTCGTAATATTCTTCAAGTAACGGCACCAGCCAGGCCAGATGACCGTCGGTGCTGCCGGTGGTGAGTTGCGTTGTCAGTGCTGCATCCAGCCTTGCAGCCAGTTCGTTATAGCGCTGTAGCCCCAGCCGACGCTTAATCGCCGAAAGTCCGTGATGCAGGTATTCGCAATACTCCTGCCAGCCCTGTTCGTCGCCGTACGCGTGGGTAAAATCATGATGCATACGCAAGAAATACTCTTCGTTCAGGCGCTCAAGACGGATCTCAAACGGATCTTCTACCACCGCAATCGCCGCCTGAGTCATTCGCTCGCGCAGGCATTCCGGCAGGTGATTCGAACCGATCATCCGGCTTTCGTCTTCCAGCACCCACAGGCGCAAATTCTGACGGGCGTCGGTTTTAGCATTTCGGCAGCCAGCAGGTTTTCAAAACTCGCCTGGCTAAGTTGTGGTTGTAACGTGCGACCAAACGCCGAACCGCGATGACGCGCCAACCCTTCCAGATCAACACCGTTCGGCTGTTGCTGCACTAACAGCGTTTTACCGCTGCCGGTACAACCGCCAATCAGCACTATCGGTTTTGTGCCAGTTCAATAGTCGCCTGAATCGCGGTCTGGCGCAGTGCCTTATAACCGCCTTCCACCAGCGGATAATCAATCCCCGCTGCATGCAACCAGCTTTGCACAATATGTGAGCGCTGACCGCCACGGGCGCAGCAGAGAATACCTTGCGGATTTTGCAGGCACGCTGCCCGCCAGGCGTCCATGCGCTGCTGACGAATTTCACCCGCCACCAGTTTATGTCCCAGCGCCAGCGCTGCGTCTGAGCCTTGCTGTTTATAGCAGGTGCCAACGGCGGCGCGTTCATCGTTATTCATTAACGGCAGATTGATAGCGGCGGGCATTGCGCCGTGCTCAAACTCG'..b'GGTAAAGCCTTTGTGAATATTGATGGTGAGCACCTTGAACGAAAATTGTTGTGTTTGATCGGGCATAATTTTCCTGTCTTTGCCTCTTATCTCATTGAAATAGTGTAGTCGGCGTCACAAAAGGTGCGGTCTTACGGAATTTTCCGTAAAGTTCGGTACTCTGAGTAAGTAGAGATAAATTCTTCAGGAGAGAAGCCATGAAGTGGCAACAACGTGTTCGTGTCGCAACGGGTCTAAGTTGCTGGCAGATTATGTTGCATTTACTGGTAGTGGCGCTGCTGGTGGTGGGCTGGATGAGTAAGACTCTGGTTCACGTCGGCGTGGGATTATGCGCACTGTATTGTGTCACGGTAGTGATGATGCTGGTGTTTCAGCGCCACCCCGAGCAACGCTGGCGTGAGGTGGCAGACGTGCTGGAAGAGCTGACCACGACCTGGTATTTTGGCGCAGCGCTGATTGTGCTGTGGCTGTTGTCCCGCGTTCTGGAAAACAACTTTTGCTGGCAATTGCAGGGCTGGCAATCCTTGCCGGCCCGGCGGTAGTGTCTTTGCTGGCGAAAGATAAGAAGTTACATCACCTTACGTCTAAACATCGCGTACGCCGCTGACCCTGTCGTGGCCGTTATCACCAGTAGCGGCCACAAACTATTCCACACAATATCCAGACTCGCATCCTTCAAATAAATCTGCTTGGTAATGTCCGTAAAGTGGCGAATAGGGTTAATCCACGTCAGGTTTTGCAGCCATACCGGCATGTTTTCCACCGGAGAAACGTAACCGGAAAGGAGAATGGCGGGCATCATAAAGACAAACACGCCGATAAACGCCTGCTGTTGTGTTGAACAGAGTGATGAAATCAACAGACCGAATCCCACCAGCGATAAACCATAAATCACCATCGTAAAGTAGAACAGCGCCAGCGATCCGGCGAAGGGATTTGATACGCCCAGATACCAATCGCCAGCACAATGGTGGCCTGGAAGGTGGCGACAATTAACGCCGGTACGGCTTTGCCGATGAAGATCTGCCAGGTGGTGAGCGGCGAAACCAGTAGCTGATCGAGCGTACCTTGTTCACGTTCGCGGGCGACGGAAAGTGAAGTGACGATCATTACGCCGATAGTGGTGATCATGGCGATCAGTGACGGCACCACAAACCATTTGTAGTCGAGATTCGGGTTATACCAGTTGCGTACCACCAGCTCGCTGTTGTTAGGTTTCGGTTTTCCTTCCAGCAGCTCCTGCTGATAATTTTGACGATCTGTTGCAGGTAGTTGGCGGCAATTTGCGCACTGTTGGAGTTACGCCCGTCGAGGATCAACTGCAAAGGCGCGGTCTGGAAGGTATCCAGTTTGCGCGAGAAGTCAGCCGGGAAACGCACCAGTAGTAACGCCTTTGTGTGTCGATGGTTGGGCGGATCTCCTGTGGGCTTTTCAGCAGCAGCACATGAGTAAAGGCGCTGGCGCGGGCAAAACGTTGGGTCAGCTCCACCGAATGCTCGCCGTTATCTTCATCGTAGATGGCGATGGTGGCGTTAGTCACTTCCAGCGTGGCGGCGAACGGGAACAGGATCACCTGAATTAGCACGGGTAAAATCAGAATCGCGCGGGTTTGCGGTTCGCGCAGCAACGACTGCAACTCTTTGCGGATTAACGTCCATAAGCGATGAAACATGCTCTTCTCCTAATCCAGCCGACGTTTGGTTTTCAGCCACGTCAGGCCGATAAACATCACCGCCGAAGCGATCAAAAACAGCACGTTTACCACCAGCACCACTGGAATATTCCCGGCGAGGAACAGGCTTTGCAGGGTGCTGACGAAATAACGAGCGGGAATAATGTACGTCACCGCGCGGATCACCGCGGGCATACTGTCGATCTGAAAAATAAAGCCGGAAAGCATAATCGACGGCAGAAAAGCGGCGTTCAGGGCGACCTGAGCGGCATTGAACTGGTTGCGGGTAATCGTGGAAATCAGCAGCCCCATCCCCAGGGTACTGAGTAAAACAGGCTGGAGATAAAAACAGAATCAGCAGCGACCCGCGATACGGCACGCCGAGAATAAACACTGACACCAGCATACACAGCAACATCGCCAGCATCCCGAGAAAGTAATAAGGGATCAGCTTACACAGCAGCAGTTCCGTGCGGGTAATCTCCGTAGAGAGCAGAGCCTCCATGGTGCCGCGTTCCCATTCTCGCGCCACCACCAGCGAGGTGAGAATCGCGCCGATGACCGTCATGATAATGGTCACCGCACCGGGGATAATGAAGTGCTGGCTAATCGCCGCCGGGTTAAACCAGTAGCGGGTTTGTACATCAATAAGCGGTTCAAAAGTCTGCCCGTTGTCCTCCGCTCGCTGCATTTGCCAGATCTGCCAGATCCCTTCGACATACCCTGTACAAAGTTAGCGGTATTCGGCTCACTGCCGTCGGTGATCACCTGAATCGGTGCGGTGGCGTTGGCGCGCTCCATCTGTTCCGCAAAATCCACCGGAATAACCACCAGACCGCGAATTTTCCCCGCCTGCATTTTGGCGATCAGTTCCTGACGGTTATCGCTGATGGTGGCGTCGATGTAGGGCGAACCGGTCATGGTGTGGTGAAATCCAGCGCCGCTTCGCTACGCTGTTCCAGTAAAATCCCGACCCGCAGCTTGCTGGAGTCGAGGTTAATGCCGTAACCAAAATAAACAGCAGTAGCAGCGGGATCACTACCGCAATCAGCCAGCTACTCGGATCGCGAACGATCTGCCGCGTCTCTTTAACGCACAGCGCCCGTACGCGACGCCAGGACAGGATCGGGTTACTCATTGCTATGCTCCTTATCCCAGTCGTGGATCAACTGAATAAAGGCTTGCTCCATGGTGGGATCGGGTTGCTCATCGTTAGCCGACTGTGCTTTCAAATCGTCCGGCGTGCCGCTGGCGATTAATTTCCCGCGGTACACCAGGCCGATGCGGTCGCAATATTCCGCTTCATCCATAAAGTGGGTGGTGACCATCACCGTGACGCCTTTCTCTACCATGCTGTTGATGTGCAGCCAAAATTCACGGCGGGTGAGGGGTCAACGCCGGAAGTCGGTTCGTCGAGAAACAGAATGTCCGGTTCATGCATCAGCGAACAGGCCAGCGCCAGCCGCTGTTTAAAACCTAATGGCAGTTCATCGGTGGCGTGGGAGGCGATACTTTTCAGGCCGAACGCCTCGCTCATGCGGGAGATTTTTCGTTCTGCGCCCGACCGCGTAAGCCATACACACCAGAGAAAAAGCGTAAATTCTGTTCGACCGTCAGGTTACCGTAGAGCGAAAATTTTTGCGCCATATAGCCGAGATGCTGGCGCGCTTTACCGGAACTCTCTTTCAGATCCATCCCCAGCACCAGCGCCTGGCCGGAAGTCGGCACCAGCAAACCGCACATCATCTTAAAGGTGGTCGATTTACCCGCGCCGTTTGGCCCCAGCAAACCAAAAATCTCCCCACGTTTAACGGCAAAGTTGACGTGATCGGTGGCGGCAAAATCCCCAAATTTCTTGGTCAGTTCTTTCGCTTCGATCACCGTCTCGCCGGGTGTGCCTTCTACCGTATGTAATATTGCGCCCAGCGGCGATTCCGAGGTTCCGGCACCGCCCAGCAAATCAATAAACGCATCTTCAAAACGCGGCGTAGTTTCGTTGATGTTGATTTCCGGCATCCCGTCGGCATGGCGAATATCGTCTGGTGTGGCCTCTTTTTGAGGATCAGACGTACCGATTTCCCCTGAATCATGCCGTCGCTGACCTGCGGCAGTTTCAAGGCGCGTTGCAACAGTTTGCGGTTGCCCTCGTGTGGACTGGTCATCAGAAAGCTGCGTCCGGCCATGGTTTGTGTCAGGGCTTTTGGTTCTCCCTGATACAGCAACTCGCCTTCGTTCATCAGTAACACGTCACGGCACTGCTCGGCTTCGTCGAGATACGAGGTACTCCAGAGGATTAACATCCCTTCGCCCGCCAGCTCATGCACCA\n'

diff -r 07cf146e8964 -r 02e3c674d917 test-data/t2-variants.vcf
--- a/test-data/t2-variants.vcf Tue Jun 05 18:25:34 2018 -0400
+++ b/test-data/t2-variants.vcf Wed Jun 19 03:45:24 2019 -0400

@@ -1,4 +1,5 @@
##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">
@@ -7,13 +8,4 @@
##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 200180 . C CA 30.6 PASS BaseCalledReadsWithVariant=18;BaseCalledFraction=0.268657;TotalReads=66;AlleleCount=2;SupportFraction=0.596279;SupportFractionByBase=0.042,0.831,0.008,0.119 GT 1/1
-tig00000001 200208 . GA G 28.2 PASS BaseCalledReadsWithVariant=15;BaseCalledFraction=0.223881;TotalReads=66;AlleleCount=1;SupportFraction=0.392611;SupportFractionByBase=0.180,0.007,0.780,0.034 GT 0/1
-tig00000001 200484 . G GA 37.7 PASS BaseCalledReadsWithVariant=17;BaseCalledFraction=0.261538;TotalReads=63;AlleleCount=1;SupportFraction=0.569915;SupportFractionByBase=0.049,0.009,0.928,0.014 GT 0/1
-tig00000001 200776 . C CA 82.3 PASS BaseCalledReadsWithVariant=24;BaseCalledFraction=0.358209;TotalReads=67;AlleleCount=2;SupportFraction=0.71125;SupportFractionByBase=0.039,0.883,0.046,0.032 GT 1/1
-tig00000001 200796 . T TA 82.1 PASS BaseCalledReadsWithVariant=17;BaseCalledFraction=0.253731;TotalReads=66;AlleleCount=2;SupportFraction=0.697381;SupportFractionByBase=0.037,0.148,0.018,0.797 GT 1/1
-tig00000001 200804 . TA T 82.1 PASS BaseCalledReadsWithVariant=20;BaseCalledFraction=0.298507;TotalReads=66;AlleleCount=1;SupportFraction=0.405017;SupportFractionByBase=0.100,0.185,0.006,0.709 GT 0/1
-tig00000001 200966 . CA C 45.5 PASS BaseCalledReadsWithVariant=16;BaseCalledFraction=0.242424;TotalReads=64;AlleleCount=1;SupportFraction=0.383448;SupportFractionByBase=0.039,0.740,0.061,0.159 GT 0/1
-tig00000001 201216 . A AT 85.8 PASS BaseCalledReadsWithVariant=24;BaseCalledFraction=0.352941;TotalReads=67;AlleleCount=2;SupportFraction=0.715932;SupportFractionByBase=0.908,0.004,0.026,0.061 GT 1/1
-tig00000001 201554 . G GC 50.2 PASS BaseCalledReadsWithVariant=20;BaseCalledFraction=0.263158;TotalReads=76;AlleleCount=2;SupportFraction=0.632478;SupportFractionByBase=0.090,0.047,0.821,0.042 GT 1/1
-tig00000001 201712 . C CA 29.7 PASS BaseCalledReadsWithVariant=21;BaseCalledFraction=0.272727;TotalReads=74;AlleleCount=1;SupportFraction=0.57415;SupportFractionByBase=0.046,0.747,0.074,0.133 GT 0/1
+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

diff -r 07cf146e8964 -r 02e3c674d917 test-data/t3_polished.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/t3_polished.fa Wed Jun 19 03:45:24 2019 -0400

diff -r 07cf146e8964 -r 02e3c674d917 test-data/t3_variants.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/t3_variants.vcf Wed Jun 19 03:45:24 2019 -0400

@@ -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

diff -r 07cf146e8964 -r 02e3c674d917 test-data/t4_polished.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/t4_polished.fa Wed Jun 19 03:45:24 2019 -0400

diff -r 07cf146e8964 -r 02e3c674d917 test-data/t4_variants.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/t4_variants.vcf Wed Jun 19 03:45:24 2019 -0400

diff -r 07cf146e8964 -r 02e3c674d917 test-data/variants.vcf
--- a/test-data/variants.vcf Tue Jun 05 18:25:34 2018 -0400
+++ b/test-data/variants.vcf Wed Jun 19 03:45:24 2019 -0400

@@ -1,4 +1,5 @@
##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">
@@ -9,30 +10,6 @@
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=0.720712 GT 1
-tig00000001 200776 . C CA 82.3 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.71125 GT 1
-tig00000001 200796 . T TA 75.4 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.698132 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=0.715932 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=0.660079 GT 1
-tig00000001 201712 . C CA 21.1 PASS TotalReads=74;AlleleCount=1;SupportFraction=0.57415 GT 1
-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=0.544883 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
-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