Repository 'nanocompore_sampcomp'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/nanocompore_sampcomp

Changeset 0:557cf45ff2c8 (2020-05-05)
Next changeset 1:c43f4b80f5a9 (2020-06-08)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
added:
macros.xml
sampcomp.xml
test-data/reference.fa
test-data/sample1.tsv
test-data/sample1.tsv.idx
test-data/sample2.tsv
test-data/sample2.tsv.idx
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diff -r 000000000000 -r 557cf45ff2c8 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue May 05 06:57:10 2020 -0400
[
@@ -0,0 +1,31 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">1.0.0rc3.post2</token>
+    <token name="@WRAPPER_VERSION@">galaxy0</token>
+    <token name="@DESCRIPTION@"></token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">nanocompore</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@online{Nanocompore,
+              author = {Adrien Leger, Tommaso Leonard},
+              title = {Nanocompore},
+              year = 2019,
+              url = {https://nanocompore.rna.rocks/},
+              urldate = {2020-04-30}
+            }</citation>
+        </citations>
+    </xml>
+    <token name="@WID@"><![CDATA[
+Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples
+
+Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.
+    ]]></token>
+
+    <token name="@REFERENCES@"><![CDATA[
+More information are available on the `project website <https://nanocompore.rna.rocks/>`_ and `github <https://github.com/tleonardi/nanocompore>`_.
+    ]]></token>
+</macros>
\ No newline at end of file
b
diff -r 000000000000 -r 557cf45ff2c8 sampcomp.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sampcomp.xml Tue May 05 06:57:10 2020 -0400
[
b'@@ -0,0 +1,220 @@\n+<?xml version="1.0"?>\n+<tool id="nanocompore_sampcomp" name="SampComp" version="@TOOL_VERSION@+@WRAPPER_VERSION@">\n+    <description>to compare Nanopolished datasets</description>\n+    <macros>\n+        <import>macros.xml</import>\n+    </macros>\n+    <expand macro="requirements"/>\n+    <version_command><![CDATA[nanocompore --version]]></version_command>\n+    <command detect_errors="exit_code"><![CDATA[\n+        ## initialize\n+        ## requires a minimum of 3 threads\n+        threads=\\$((3 > \\${GALAXY_SLOTS:-3} ? 3 : \\${GALAXY_SLOTS:-3})) &&\n+        ## same name pattern required\n+        #for $i, $current in enumerate($file1_rep)\n+            ln -s \'$current.file\' \'sample_1_${i}.tsv\' &&\n+            ln -s \'$current.index\' \'sample_1_${i}.tsv.idx\' &&\n+        #end for\n+        #for $i, $current in enumerate($file2_rep)\n+            ln -s \'$current.file\' \'sample_2_${i}.tsv\' &&\n+            ln -s \'$current.index\' \'sample_2_${i}.tsv.idx\' &&\n+        #end for\n+\n+        ## run\n+        nanocompore sampcomp\n+        ## required\n+        --label1 \'$label1\'\n+        #set files1 = \',\'.join([\'sample_1_\' + str(item) + \'.tsv\' for item in range(len($file1_rep))])\n+        --file_list1 \'$files1\'\n+        --label2 \'$label2\'\n+        #set files2 = \',\'.join([\'sample_2_\' + str(item) + \'.tsv\' for item in range(len($file2_rep))])\n+        --file_list2 \'$files2\'\n+        --fasta \'$fasta\'\n+        ## optional\n+        #if $ap.bed\n+            --bed \'$ap.bed\'\n+        #end if\n+        --max_invalid_kmers_freq $ap.max_invalid_kmers_freq\n+        --min_coverage $ap.min_coverage\n+        --min_ref_length $ap.min_ref_length\n+        --comparison_methods \'$ap.comparison_methods\'\n+        --sequence_context $ap.sequence_context\n+        --sequence_context_weights \'$ap.sequence_context_weights\'\n+        --pvalue_thr $ap.pvalue_thr\n+        $ap.logit\n+        $ap.allow_warnings\n+        --outpath \'results\'\n+        --nthreads \\$threads\n+        --log_level debug\n+\n+        && tar -cf \'results/db.tar\' \'results/out_SampComp.db.bak\' \'results/out_SampComp.db.dir\' \'results/out_SampComp.db.dat\'\n+        ]]></command>\n+    <inputs>\n+        <param argument="--label1" type="text" value="Condition 1" label="Set label of first condition"/>\n+        <repeat name="file1_rep" min="1" title="First condition files">\n+            <param name="file" type="data" format="tabular" label="Select NanopolishComp file" help="(--file_list1)"/>\n+            <param name="index" type="data" format="tabular" label="Select index file"/>\n+        </repeat>\n+        <param argument="--label2" type="text" value="Condition 2" label="Set label of second condition"/>\n+        <repeat name="file2_rep" min="1" title="Second condition files">\n+            <param name="file" type="data" format="tabular" label="Select NanopolishComp file" help="(--file_list2)"/>\n+            <param name="index" type="data" format="tabular" label="Select index file"/>\n+        </repeat>\n+        <param argument="--fasta" type="data" format="fasta" label="Select mapping file"/>\n+\n+        <section name="ap" title="Advanced parameters">\n+            <param argument="--bed" type="data" format="bed" optional="true" label="Select mapping file with annotation of transcriptome"/>\n+            <param argument="--max_invalid_kmers_freq" type="float" value="0.1" min="0.0" max="1.0" label="Set max fequency of invalid kmers"/>\n+            <param argument="--min_coverage" type="integer" value="30" min="0" label="Set minimum coverage required in each condition to do the comparison"/>\n+            <param argument="--min_ref_length" type="integer" value="100" min="0" label="Set minimum length of a reference transcript to include it in the analysis"/>\n+            <param argument="--comparison_methods" type="select" multiple="true" label="Select comparison methods">\n+                <option value="GMM" selected="true">GMM</option>\n+                <option value="KS" selected="true">KS</option>\n+               '..b'\n+                <assert_contents>\n+                    <has_size value="5408256"/>\n+                </assert_contents>\n+            </output>\n+        </test>\n+        <!-- #2 -->\n+        <test expect_num_outputs="4">\n+            <param name="label1" value="C1"/>\n+            <repeat name="file1_rep">\n+                <param name="file" value="sample1.tsv"/>\n+                <param name="index" value="sample1.tsv.idx"/>\n+            </repeat>\n+            <param name="label2" value="C2"/>\n+            <repeat name="file2_rep">\n+                <param name="file" value="sample2.tsv"/>\n+                <param name="index" value="sample2.tsv.idx"/>\n+            </repeat>\n+            <param name="fasta" value="reference.fa"/>\n+            <section name="ap">\n+                <param name="max_invalid_kmers_freq" value="0.2"/>\n+                <param name="min_coverage" value="31"/>\n+                <param name="min_ref_length" value="101"/>\n+                <param name="comparison_methods" value="GMM,KS,TT,MW"/>\n+                <param name="sequence_context" value="1"/>\n+                <param name="sequence_context_weights" value="harmonic"/>\n+                <param name="pvalue_thr" value="0.06"/>\n+                <param name="logit" value="true"/>\n+                <param name="allow_warnings" value="true"/>\n+                <param name="out" value="results,shift,db,log"/>\n+            </section>\n+            <output name="out_results">\n+                <assert_contents>\n+                    <has_n_lines n="3"/>\n+                    <has_text_matching expression="pos&#09;chr.+"/>\n+                    <has_text_matching expression="22102&#09;NA.+"/>\n+                </assert_contents>\n+            </output>\n+            <output name="out_shift">\n+                <assert_contents>\n+                    <has_n_lines n="3"/>\n+                    <has_text_matching expression="ref\\_id&#09;pos.+"/>\n+                    <has_text_matching expression="chr&#09;22102.+"/>\n+                </assert_contents>\n+            </output>\n+            <output name="out_db">\n+                <assert_contents>\n+                    <has_size value="5410304"/>\n+                </assert_contents>\n+            </output>\n+            <output name="out_log">\n+                <assert_contents>\n+                    <has_n_lines n="31"/>\n+                    <has_text_matching expression=".+package\\_name.+"/>\n+                </assert_contents>\n+            </output>\n+        </test>\n+    </tests>\n+    <help><![CDATA[\n+.. class:: infomark\n+\n+**What it does**\n+\n+@WID@\n+\n+SampComp provides a very flexible analysis framework with a few mandatory options and many optional parameters.\n+\n+First, SampComp parses the sample eventalign collapse files and then the observed results are piled-up per reference at position level. In a second time, positions are compared using various statistical methods and the statistics are stored in a shelve DBM database containing the results for all positions with sufficient coverage.\n+\n+**Input**\n+\n+SampComp requires sample files obtained with NanopolishComp EventalignCollapse as explained before (see data preparation) for both the control and the experimental conditions. 2 conditions are expected and at least 2 replicates per conditions are highly recommended.\n+\n+A transcriptome FASTA reference file is required to extract kmer sequences during the analyses. The reference has to be the same as the one used at the mapping step.\n+\n+Optionally, a BED file containing the genome annotations corresponding to the transcriptome fasta file can be provided. In that case Nanocompore will also convert the transcript coordinates into the genome space.\n+\n+**Output**\n+\n+The database object returned by Sampcomp is a Python GDBM object database indexed by reference id and can be be used with SampCompDB.\n+\n+.. class:: infomark\n+\n+**References**\n+\n+@REFERENCES@\n+    ]]></help>\n+    <expand macro="citations"/>\n+</tool>\n\\ No newline at end of file\n'
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diff -r 000000000000 -r 557cf45ff2c8 test-data/reference.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.fa Tue May 05 06:57:10 2020 -0400
b
b'@@ -0,0 +1,417 @@\n+>chr\n+ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACG\n+AACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAAT\n+TACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAG\n+CCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTT\n+CAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGG\n+AGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGT\n+TGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACC\n+TCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACT\n+TGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAA\n+TAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGA\n+TCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGA\n+GCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTG\n+CATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGACAC\n+TAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAG\n+CTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAA\n+TTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTT\n+TATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCT\n+CATGAAGTGTGATCATTGTGGTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTG\n+TGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAAT\n+TTATTGTCCAGCATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGG\n+CTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTG\n+CCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGG\n+AGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGT\n+TGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGT\n+GGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTAC\n+AAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATT\n+TGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCG\n+TGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTAT\n+GATGTTCACATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTT\n+GACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGA\n+AGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGC\n+TTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAA\n+GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAA\n+TTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGG\n+CCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT\n+AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGC\n+TCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGTACTG\n+TGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTAC\n+TTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAG\n+GATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGC\n+CTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGA\n+TTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATAT\n+GTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAGAAGAGTTTGAGCCATC\n+AACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATTTGGTGCCACTTCTGCTGC\n+TCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGA\n+CGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATTAGAGATGGAACT\n+TACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTTAAAACTTACTGACAATGTATACAT\n+TAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACAGTGGTTGTTAATGCAGCCAATGTTTA\n+CCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTACTAACAATGCCATGCAAGTTGAATCTGA\n+TGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTTTAAGCGGACACAATCTTGCTAA\n+ACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGTGAAGACATTCAACTTCTTAAGAGTGCTTATGA\n+AAATTTTAATCAGCACGAAGTTCTACTTGCACCATTATTATCAGCTGGTATTTTTGGTGCTGACCCTATACA\n+TTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAATGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGA\n+CAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGTGAAAAGCAAGTTGAACAA'..b'ACTTCAGACTATTACCAGCTGTACTCAACTCAATTGAGTACAGACACTGGT\n+GTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGCCTGAAGAACATGTCCAAATTCACACA\n+ATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGC\n+GTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTA\n+ATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCG\n+CTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCT\n+CGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTCTGGTCTAAACGAACTAAATATTATATTAGTTT\n+TTCTGTTTGGAACTTTAATTTTAGCCATGGCAGATTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGC\n+TCCTTGAACAATGGAACCTAGTAATAGGTTTCCTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATG\n+CCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTT\n+GTTTTGTGCTTGCTGCTGTTTACAGAATAAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTG\n+TAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCAT\n+TCAATCCAGAAACTAACATTCTTCTCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAA\n+GTGAACTCGTAATCGGAGCTGTGATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTG\n+ACATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTT\n+CGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACA\n+CAGACCATTCCAGTAGCAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTT\n+GACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTT\n+GATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGAT\n+GAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCT\n+ACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCT\n+GGAACATACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACT\n+CAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAA\n+CTGTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT\n+ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTGCT\n+TTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAAGATC\n+ATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTG\n+CATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTA\n+TTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGG\n+ATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCTGTTCACCTTTTA\n+CAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGAAGACTTTTTAGAGT\n+ATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTGATAATGGACCCCAAAA\n+TCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGAATGGAGAACG\n+CAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACTGCGTCTTGGTTCACCGCTCT\n+CACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACACCAATAGCAGTCC\n+AGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCT\n+CAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGA\n+CGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAAAAGATCACATTGGCACCCGCAATCCTGC\n+TAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAACATTGCCAAAAGGCTTCTACGCAGAAGGGAG\n+CAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGTAGTCGCAACAGTTCAAGAAATTCAACTCCAGG\n+CAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCT\n+TGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTAA\n+GAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGGCAAAAACGTACTGCCACTAAAGCATACAATGTAACACA\n+AGCTTTCGGCAGACGTGGTCCAGAACAAACCCAAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAAC\n+TGATTACAAACATTGGCCGCAAATTGCACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCAT\n+TGGCATGGAAGTCACACCTTCGGGAACGTGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCC\n+AAATTTCAAAGATCAAGTCATTTTGCTGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCC\n+TAAAAAGGACAAAAAGAAGAAGGCTGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGT\n+GACTCTTCTTCCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTC\n+AACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTAC\n+GATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAA\n+TCTCACATAGCAATCTTTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAG\n+GCCACGCGGAGTACGATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATG\n+TGTAAAATTAATTTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAA\n'
b
diff -r 000000000000 -r 557cf45ff2c8 test-data/sample1.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample1.tsv Tue May 05 06:57:10 2020 -0400
b
b'@@ -0,0 +1,236 @@\n+#f30a0489-ec1e-4f6e-829e-fa6d16dbee2e\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00664\t0.0\t0.0\t124.18560791015625\t122.90550231933594\t20\n+22102\tGGAAA\t2\t0.00564\t0.0\t0.0\t127.36959838867188\t130.8000030517578\t17\n+#e924b30f-22dc-4156-8e5c-ba664abbe7a7\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.0073\t0.0\t0.0\t118.83446502685547\t119.46699523925781\t22\n+22102\tGGAAA\t2\t0.0249\t0.0\t0.0\t124.0261459350586\t123.86900329589844\t75\n+#d4988330-6f34-498a-b1e3-6574d8b3dae2\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t2\t0.020249999999999997\t0.0\t0.0\t118.07210540771484\t119.5469970703125\t61\n+22102\tGGAAA\t1\t0.00531\t0.0\t0.0\t125.96463012695312\t129.28799438476562\t16\n+#0f8c0aae-a5ce-47ae-af66-a762f44a9d3a\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t4\t0.02025\t0.0\t0.0\t115.89058685302734\t116.44599914550781\t61\n+22102\tGGAAA\t5\t0.032529999999999996\t0.0\t0.0\t123.7591552734375\t123.37649536132812\t98\n+#43000cf1-c697-4e0b-8414-5aed3db85976\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00863\t0.0\t0.0\t115.45061492919922\t115.2125015258789\t26\n+22102\tGGAAA\t5\t0.03153\t0.0\t0.0\t123.54806518554688\t124.41400146484375\t95\n+#1a0779f0-4d51-4400-8b0e-29363ea9aa91\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00332\t0.0\t0.0\t121.51219177246094\t122.51849365234375\t10\n+22102\tGGAAA\t1\t0.00664\t0.0\t0.0\t127.57340240478516\t126.875\t20\n+#85462d40-9227-4f0a-ad25-c4c5abb6b7e6\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00232\t0.0\t0.0\t118.0605697631836\t117.97699737548828\t7\n+22102\tGGAAA\t3\t0.01792\t0.0\t0.0\t125.30520629882812\t124.95249938964844\t54\n+#5bf2cef1-ec1f-4b1f-bf9f-e79dccb33836\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.01129\t0.0\t0.0\t123.4063491821289\t123.86349487304688\t34\n+22102\tGGAAA\t6\t0.03785\t0.0\t0.0\t127.39415740966797\t127.95649719238281\t114\n+#db70549e-4650-4e64-904d-7929f4701b4d\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00896\t0.0\t0.0\t113.59844970703125\t113.57099914550781\t27\n+22102\tGGAAA\t2\t0.02922\t0.0\t0.0\t123.96391296386719\t123.3489990234375\t88\n+#34c8247e-6fbd-4a8c-a17e-8c740d3bfb08\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t3\t0.02623\t0.0\t0.0\t116.989013671875\t117.33599853515625\t79\n+22102\tGGAAA\t4\t0.05378\t0.0\t0.0\t128.04013061523438\t128.47850036621094\t162\n+#0eb8f174-1680-41ca-a098-b762e6ee7b76\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t2\t0.017589999999999998\t0.0\t0.0\t121.86357879638672\t121.02200317382812\t53\n+22102\tGGAAA\t5\t0.030549999999999997\t0.0\t0.0\t120.92530059814453\t122.95249938964844\t92\n+#77489463-5e96-43b5-ba97-aad51f918336\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t3\t0.01726\t0.0\t0.0\t115.67981719970703\t115.3905029296875\t52\n+22102\tGGAAA\t7\t0.04051\t0.0\t0.0\t125.22063446044922\t126.13650512695312\t122\n+#4e6ece57-2cb1-4f12-8410-ae9696be4e43\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t2\t0.01494\t0.0\t0.0\t118.05428314208984\t119.79900360107422\t45\n+22102\tGGAAA\t3\t0.01594\t0.00299\t0.0\t122.89998626708984\t121.07949829101562\t48\n+#578c1cbf-e9c0-47b0-b5ad-eeeec8cacaa2\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00232\t0.0\t0.0\t112.2434310913086\t111.820999'..b'.07249450683594\t50\n+#7e6a64b0-7d43-4f78-a72c-d053eaac2b71\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t3\t0.01693\t0.0\t0.0\t114.24336242675781\t113.62000274658203\t51\n+22102\tGGAAA\t4\t0.01129\t0.0\t0.0\t124.12264251708984\t124.63099670410156\t34\n+#8b682e72-00ee-4a1a-98bf-362841494e57\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.01494\t0.0\t0.0\t121.48255920410156\t120.88600158691406\t45\n+22102\tGGAAA\t8\t0.05246\t0.0\t0.0\t124.7437973022461\t125.19549560546875\t158\n+#be2461c2-1165-47fc-ba73-2aadcfa12b5f\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00896\t0.0\t0.0\t119.70619201660156\t120.0780029296875\t27\n+22102\tGGAAA\t1\t0.00232\t0.0\t0.0\t129.27142333984375\t128.3769989013672\t7\n+#c395d12e-07b3-4a1d-88cc-d3f7a8603d64\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t3\t0.00863\t0.0\t0.0\t119.27664947509766\t119.33699798583984\t26\n+22102\tGGAAA\t3\t0.011290000000000001\t0.0\t0.0\t122.20012664794922\t121.69549560546875\t34\n+#af037c78-1908-4828-8e39-481c69de7afc\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t3\t0.02357\t0.0\t0.0\t115.24366760253906\t115.1719970703125\t71\n+22102\tGGAAA\t3\t0.01328\t0.0\t0.0\t124.0596923828125\t124.27850341796875\t40\n+#d1262e2d-f7d5-4afc-8e66-98c77bdf21b7\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t4\t0.023239999999999997\t0.0\t0.0\t114.12039947509766\t113.22699737548828\t70\n+22102\tGGAAA\t4\t0.05013\t0.0\t0.0\t123.6082763671875\t123.87899780273438\t151\n+#6b779e7d-26fb-4863-9082-04068823a29d\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00863\t0.0\t0.0\t125.01396179199219\t124.99749755859375\t26\n+22102\tGGAAA\t1\t0.00232\t0.0\t0.0\t133.4332733154297\t134.6649932861328\t7\n+#e8da2741-03f5-416a-a7f0-96250a49ddd6\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t3\t0.02358\t0.0\t0.0\t122.79644775390625\t122.7229995727539\t71\n+22102\tGGAAA\t9\t0.04183\t0.0\t0.0\t123.63143920898438\t124.23600006103516\t126\n+#484f63e8-a501-4edd-8c0e-fba261ed96e1\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00764\t0.0\t0.0\t118.35243225097656\t120.302001953125\t23\n+22102\tGGAAA\t2\t0.01095\t0.0\t0.0\t126.8102035522461\t126.19499969482422\t33\n+#0f18df3d-e006-4d83-9c00-d2b6e2b668af\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00896\t0.0\t0.0\t123.11996459960938\t123.06900024414062\t27\n+22102\tGGAAA\t1\t0.00631\t0.0\t0.0\t129.66537475585938\t131.13299560546875\t19\n+#a7b0744a-4f4a-4d45-907d-b0eed99d2e98\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00598\t0.0\t0.0\t118.61209869384766\t117.44599914550781\t18\n+22102\tGGAAA\t2\t0.01726\t0.0\t0.0\t124.54773712158203\t125.95449829101562\t52\n+#30f0513c-dc44-44d4-ac18-1bfd7a9a28bb\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00996\t0.0\t0.0\t115.39576721191406\t114.21499633789062\t30\n+22102\tGGAAA\t6\t0.03054\t0.0\t0.0\t124.31990051269531\t125.22949981689453\t92\n+#6057e4db-745d-407d-98bb-83a8e9a5f0ce\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t2\t0.04349\t0.0\t0.0\t113.60332489013672\t113.35299682617188\t131\n+22102\tGGAAA\t5\t0.05743\t0.0\t0.0\t120.23699188232422\t121.44599914550781\t173\n+#55fb9fbe-c25a-486b-9fed-b50328c70e5a\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22102\tGGAAA\t1\t0.00631\t0.0\t0.0\t127.09893798828125\t128.00999450683594\t19\n+#\n'
b
diff -r 000000000000 -r 557cf45ff2c8 test-data/sample1.tsv.idx
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample1.tsv.idx Tue May 05 06:57:10 2020 -0400
b
@@ -0,0 +1,60 @@
+ref_id ref_start ref_end read_id kmers dwell_time NNNNN_kmers mismatch_kmers missing_kmers byte_offset byte_len
+chr 22101 22103 f30a0489-ec1e-4f6e-829e-fa6d16dbee2e 2 0.01228 0 0 0 0 282
+chr 22101 22103 e924b30f-22dc-4156-8e5c-ba664abbe7a7 2 0.0322 0 0 0 283 280
+chr 22101 22103 d4988330-6f34-498a-b1e3-6574d8b3dae2 2 0.025559999999999996 0 0 0 564 295
+chr 22101 22103 0f8c0aae-a5ce-47ae-af66-a762f44a9d3a 2 0.052779999999999994 0 0 0 860 295
+chr 22101 22103 43000cf1-c697-4e0b-8414-5aed3db85976 2 0.04016 0 0 0 1156 282
+chr 22101 22103 1a0779f0-4d51-4400-8b0e-29363ea9aa91 2 0.00996 0 0 0 1439 272
+chr 22101 22103 85462d40-9227-4f0a-ad25-c4c5abb6b7e6 2 0.020239999999999998 0 0 0 1712 281
+chr 22101 22103 5bf2cef1-ec1f-4b1f-bf9f-e79dccb33836 2 0.04914 0 0 0 1994 283
+chr 22101 22103 db70549e-4650-4e64-904d-7929f4701b4d 2 0.03818 0 0 0 2278 282
+chr 22101 22103 34c8247e-6fbd-4a8c-a17e-8c740d3bfb08 2 0.08001 0 0 0 2561 282
+chr 22101 22103 0eb8f174-1680-41ca-a098-b762e6ee7b76 2 0.048139999999999995 0 0 0 2844 309
+chr 22101 22103 77489463-5e96-43b5-ba97-aad51f918336 2 0.05777 0 0 0 3154 283
+chr 22101 22103 4e6ece57-2cb1-4f12-8410-ae9696be4e43 2 0.030879999999999998 1 0 0 3438 287
+chr 22101 22103 578c1cbf-e9c0-47b0-b5ad-eeeec8cacaa2 2 0.02555 0 0 0 3726 281
+chr 22101 22103 ff72f771-8174-4950-9ede-40ffb052d044 2 0.027889999999999998 0 0 0 4008 280
+chr 22101 22103 97b0f9b2-48c6-4928-b366-b1e7b8721271 2 0.02656 0 0 0 4289 282
+chr 22101 22103 136f4584-fa85-47b5-965d-2bc88fa15e4a 2 0.033190000000000004 0 0 0 4572 293
+chr 22101 22103 8a7c1cbe-453b-44a4-82aa-ad2305025760 2 0.02889 0 0 0 4866 283
+chr 22101 22103 a77db53e-9553-4045-858a-9953b6a42523 2 0.02391 0 0 0 5150 282
+chr 22101 22103 085929b9-c69c-4245-99dc-de3e01b24557 2 0.053099999999999994 0 0 0 5433 295
+chr 22101 22103 b03e37d7-1199-43e4-ad8e-90d5f65484ba 2 0.04017 0 0 0 5729 283
+chr 22101 22103 66e23a5c-4fde-4b66-9b25-ff5bade5ebf6 2 0.03719 0 0 0 6013 295
+chr 22101 22103 7931a9dc-02fd-4dfd-a8e1-92d6fe1a2e9a 2 0.00996 0 0 0 6309 281
+chr 22101 22103 679e2499-ffd9-4d91-bd03-5fa5228fb2b0 2 0.01294 0 0 0 6591 280
+chr 22101 22103 d6e01353-c2f7-4051-b49d-b77f23df84db 2 0.057769999999999995 0 0 0 6872 281
+chr 22101 22103 593e8df7-d17f-45dc-97e9-7dd9f17eccc5 2 0.07436000000000001 0 0 0 7154 284
+chr 22101 22103 6781c476-1d7d-424f-be2f-7272f2293816 2 0.01593 0 0 0 7439 282
+chr 22101 22103 24561b20-06f9-4395-bb5d-06df8c7af304 2 0.01593 0 0 0 7722 282
+chr 22101 22103 dc6b006e-8002-4f07-8ec5-e5256be95278 2 0.00896 0 0 0 8005 282
+chr 22101 22103 79f6a527-ae56-4f0c-9374-80ec5312d014 2 0.02324 0 0 0 8288 281
+chr 22101 22103 da09104c-079f-4258-8c19-7c9d5cc89538 2 0.02556 0 0 0 8570 283
+chr 22101 22103 39db71ed-6c5a-4ede-a358-e81f0e6bf313 2 0.02557 0 0 0 8854 296
+chr 22101 22103 36e065cf-3fd1-4960-a8fb-e49eab5350c1 2 0.04317 0 0 0 9151 282
+chr 22101 22103 4f330c34-6e05-41aa-b867-90bbd125e829 2 0.08267000000000001 1 0 0 9434 283
+chr 22101 22103 5454e135-40bd-416c-836f-78c02e508a3c 2 0.0385 0 0 0 9718 283
+chr 22101 22103 539baf2c-e615-463f-950e-938f9370f66d 2 0.013940000000000001 0 0 0 10002 295
+chr 22101 22103 082d338f-2d9d-48da-9308-9031ffc98e33 2 0.01959 0 0 0 10298 282
+chr 22101 22103 905dc486-7e27-423d-bd9e-1ef91f051f5e 2 0.027229999999999997 1 0 0 10581 299
+chr 22101 22103 2e0984c3-ab2e-4f67-bcdf-2f83731e9b33 2 0.01394 1 0 0 10881 285
+chr 22101 22103 ca36cae0-9b99-4bc7-b542-5ceafd7fe08e 2 0.01759 0 0 0 11167 281
+chr 22101 22103 20efbede-e82d-497d-837a-a504f23daa7a 2 0.0069700000000000005 0 0 0 11449 282
+chr 22101 22103 e33453d3-70da-4985-b718-581993fffe54 2 0.03221 0 0 0 11732 283
+chr 22101 22103 3bcf4483-16f3-4ad3-9109-67138290cca3 2 0.0176 0 0 0 12016 282
+chr 22101 22103 7bb71d53-9b4a-4571-83f3-2aebd1fcbac1 2 0.03253 0 0 0 12299 282
+chr 22101 22103 501e4486-c0c2-4d1f-938b-af2449132fb0 2 0.021580000000000002 0 0 0 12582 279
+chr 22101 22103 7e6a64b0-7d43-4f78-a72c-d053eaac2b71 2 0.028220000000000002 0 0 0 12862 283
+chr 22101 22103 8b682e72-00ee-4a1a-98bf-362841494e57 2 0.0674 0 0 0 13146 283
+chr 22101 22103 be2461c2-1165-47fc-ba73-2aadcfa12b5f 2 0.011279999999999998 0 0 0 13430 280
+chr 22101 22103 c395d12e-07b3-4a1d-88cc-d3f7a8603d64 2 0.01992 0 0 0 13711 296
+chr 22101 22103 af037c78-1908-4828-8e39-481c69de7afc 2 0.03685 0 0 0 14008 281
+chr 22101 22103 d1262e2d-f7d5-4afc-8e66-98c77bdf21b7 2 0.07336999999999999 0 0 0 14290 296
+chr 22101 22103 6b779e7d-26fb-4863-9082-04068823a29d 2 0.010950000000000001 0 0 0 14587 280
+chr 22101 22103 e8da2741-03f5-416a-a7f0-96250a49ddd6 2 0.06541 0 0 0 14868 283
+chr 22101 22103 484f63e8-a501-4edd-8c0e-fba261ed96e1 2 0.01859 0 0 0 15152 280
+chr 22101 22103 0f18df3d-e006-4d83-9c00-d2b6e2b668af 2 0.015269999999999999 0 0 0 15433 283
+chr 22101 22103 a7b0744a-4f4a-4d45-907d-b0eed99d2e98 2 0.02324 0 0 0 15717 283
+chr 22101 22103 30f0513c-dc44-44d4-ac18-1bfd7a9a28bb 2 0.0405 0 0 0 16001 283
+chr 22101 22103 6057e4db-745d-407d-98bb-83a8e9a5f0ce 2 0.10092000000000001 0 0 0 16285 285
+chr 22102 22103 55fb9fbe-c25a-486b-9fed-b50328c70e5a 1 0.00631 0 0 0 16571 212
b
diff -r 000000000000 -r 557cf45ff2c8 test-data/sample2.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample2.tsv Tue May 05 06:57:10 2020 -0400
b
b'@@ -0,0 +1,401 @@\n+#7f1aeec8-0acc-4a78-8ff2-12116de7906f\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00531\t0.0\t0.0\t121.67037963867188\t121.23699951171875\t16\n+22102\tGGAAA\t4\t0.01892\t0.0\t0.0\t124.56398010253906\t124.41100311279297\t57\n+#3fb36f87-41a9-4053-bba0-e9c99c0f3af4\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00764\t0.0\t0.0\t117.99856567382812\t118.55400085449219\t23\n+22102\tGGAAA\t4\t0.01693\t0.0\t0.0\t124.62902069091797\t125.23799896240234\t51\n+#d6da51fb-29a9-4f08-a538-ad7a52d6e1e2\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.01228\t0.0\t0.0\t123.177734375\t123.62699890136719\t37\n+22102\tGGAAA\t5\t0.02124\t0.0\t0.0\t120.51213836669922\t123.08799743652344\t64\n+#833fd518-978e-4044-8640-a9d7c95c4783\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.0073\t0.0\t0.0\t123.09036254882812\t123.49099731445312\t22\n+22102\tGGAAA\t2\t0.00697\t0.0\t0.0\t124.90296173095703\t125.5459976196289\t21\n+#1c883a73-b331-4419-b280-d153eb932ba5\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t4\t0.034870000000000005\t0.0\t0.0\t122.48480987548828\t122.57599639892578\t105\n+22102\tGGAAA\t3\t0.022899999999999997\t0.0\t0.0\t125.73690795898438\t125.30000305175781\t69\n+#4b24388e-8804-421d-a416-6e84f24b437d\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00797\t0.0\t0.0\t113.0198745727539\t112.69200134277344\t24\n+22102\tGGAAA\t1\t0.01195\t0.0\t0.0\t123.59333038330078\t123.98100280761719\t36\n+#0a1578b4-b82c-48c3-934b-803f4bc9cb7e\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00664\t0.0\t0.0\t120.83223724365234\t121.28500366210938\t20\n+22102\tGGAAA\t1\t0.00365\t0.0\t0.0\t125.82282257080078\t124.02899932861328\t11\n+#27085b2d-47a1-4eb2-a6fe-d56385977a83\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t2\t0.01959\t0.0\t0.0\t117.96282196044922\t119.27300262451172\t59\n+22102\tGGAAA\t2\t0.00796\t0.0\t0.0\t122.18533325195312\t123.54949951171875\t24\n+#480de004-a586-4af7-b622-a805c27d079f\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t2\t0.00597\t0.0\t0.0\t122.96639251708984\t122.85050201416016\t18\n+22102\tGGAAA\t1\t0.02092\t0.0\t0.0\t124.03636169433594\t125.01100158691406\t63\n+#2e873328-dcad-4a50-a7bf-d1df635ea4ae\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00863\t0.0\t0.0\t121.93891906738281\t121.90950012207031\t26\n+22102\tGGAAA\t1\t0.01062\t0.0\t0.0\t125.28668212890625\t123.88850402832031\t32\n+#f15e9f80-aeba-4e3f-af6e-af9844913cd5\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t2\t0.00963\t0.0\t0.0\t120.74498748779297\t120.75499725341797\t29\n+22102\tGGAAA\t6\t0.05378\t0.0\t0.0\t122.99015045166016\t124.61299896240234\t162\n+#30636390-aa9f-44d3-a266-93e4e2678473\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t4\t0.030539999999999998\t0.0\t0.0\t120.44935607910156\t121.31599426269531\t92\n+22102\tGGAAA\t1\t0.00299\t0.0\t0.0\t126.57222747802734\t126.14600372314453\t9\n+#d21823f1-8123-4a8c-80d9-405da871be9a\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.01494\t0.0\t0.0\t113.35908508300781\t113.60199737548828\t45\n+22102\tGGAAA\t2\t0.00963\t0.00631\t0.0\t123.0432357788086\t123.51599884033203\t29\n+#61978e0e-8af4-4cdd-bada-4cf5388a769a\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00498\t0.0\t0.0\t117.7689437866211\t118.45099'..b'tch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00465\t0.0\t0.0\t118.911865234375\t119.05000305175781\t14\n+22102\tGGAAA\t4\t0.042499999999999996\t0.0\t0.0\t124.17623901367188\t124.5510025024414\t128\n+#11a7069d-f176-41a3-a1af-799a2115de20\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t2\t0.0166\t0.0\t0.0\t118.78388977050781\t118.46099853515625\t50\n+22102\tGGAAA\t1\t0.01627\t0.0\t0.0\t123.67282104492188\t124.55000305175781\t49\n+#ccf05612-40af-4cdb-a7dd-940c9129d4f3\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t3\t0.01859\t0.0\t0.0\t114.39768981933594\t114.64700317382812\t56\n+22102\tGGAAA\t6\t0.06108\t0.0\t0.0\t122.79985046386719\t122.40299987792969\t184\n+#46b7c4ff-9ab5-40c8-9792-d7523178afbc\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00564\t0.0\t0.0\t121.00617218017578\t120.33799743652344\t17\n+22102\tGGAAA\t2\t0.015279999999999998\t0.0\t0.0\t125.62187957763672\t124.88099670410156\t46\n+#cabb84ef-c6c0-4e07-beff-e5eed05198d5\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00398\t0.0\t0.0\t121.41592407226562\t121.20050048828125\t12\n+22102\tGGAAA\t2\t0.01826\t0.0\t0.0\t118.0160903930664\t121.2760009765625\t55\n+#caeb4080-a076-4b28-87ff-71c109ccfc8e\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.01793\t0.0\t0.0\t118.19371795654297\t118.68350219726562\t54\n+22102\tGGAAA\t2\t0.010620000000000001\t0.0\t0.0\t126.31681823730469\t126.3699951171875\t32\n+#c2d50882-3d64-4dd0-895e-017e2c40782e\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00465\t0.0\t0.0\t116.38756561279297\t116.92999267578125\t14\n+22102\tGGAAA\t6\t0.03087\t0.0\t0.0\t125.23326873779297\t125.06199645996094\t93\n+#7e834f65-217d-4f76-9294-99bcb7319211\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.01062\t0.0\t0.0\t113.27202606201172\t114.08000183105469\t32\n+22102\tGGAAA\t1\t0.00199\t0.0\t0.0\t108.19467163085938\t108.24749755859375\t6\n+#ee04c7b7-669f-4d84-a589-63e8195cd11d\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00232\t0.0\t0.0\t119.85729217529297\t119.68800354003906\t7\n+22102\tGGAAA\t6\t0.06506999999999999\t0.0\t0.0\t123.23933410644531\t124.06050109863281\t196\n+#df7fde92-d62a-480d-a573-5568a21baf4a\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t2\t0.0069700000000000005\t0.0\t0.0\t115.64581298828125\t114.62200164794922\t21\n+22102\tGGAAA\t1\t0.04615\t0.0\t0.0\t120.60552215576172\t122.14099884033203\t139\n+#7e7c3159-d7ba-415c-aafd-5b6101cce083\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t4\t0.02457\t0.0\t0.0\t117.3227310180664\t116.90249633789062\t74\n+22102\tGGAAA\t5\t0.024239999999999998\t0.0\t0.0\t127.60884094238281\t128.68699645996094\t73\n+#2ead04b2-a520-4623-bed1-c58b2de4ad13\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t2\t0.00996\t0.0\t0.0\t123.75735473632812\t123.76800537109375\t30\n+22102\tGGAAA\t1\t0.0073\t0.0\t0.0\t124.35718536376953\t125.03250122070312\t22\n+#1b7e8d9c-dbc7-4131-87da-76ab5c31cef5\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t2\t0.02922\t0.0\t0.0\t121.81069946289062\t120.7969970703125\t88\n+22102\tGGAAA\t1\t0.00365\t0.0\t0.0\t128.2813720703125\t129.61500549316406\t11\n+#44f13b68-e386-4e9c-ba0d-eb9b8afe07a4\tchr\n+ref_pos\tref_kmer\tnum_events\tdwell_time\tNNNNN_dwell_time\tmismatch_dwell_time\tmean\tmedian\tnum_signals\n+22101\tAGGAA\t1\t0.00498\t0.0\t0.0\t115.5508041381836\t115.84200286865234\t15\n+22102\tGGAAA\t3\t0.04747\t0.0\t0.0\t123.99502563476562\t124.28800201416016\t143\n+#\n'
b
diff -r 000000000000 -r 557cf45ff2c8 test-data/sample2.tsv.idx
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample2.tsv.idx Tue May 05 06:57:10 2020 -0400
b
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