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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4 |
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scater-normalize.xml scater_macros.xml test-data/R_scater_cpm.rds test-data/R_scater_normalize.rds test-data/R_scater_qc.rds test-data/R_scater_serialized.rds test-data/barcodes.tsv test-data/extracted_metrics_file.txt test-data/genes.tsv test-data/matrix.mtx test-data/outliers_file.txt |
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| diff -r 000000000000 -r c01a342be892 scater-normalize.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scater-normalize.xml Wed Apr 03 11:38:57 2019 -0400 |
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| @@ -0,0 +1,53 @@ +<tool id="scater_normalize" name="Scater Normalise" version="@TOOL_VERSION@+galaxy0"> + <description>expression values by library size in log2 scale</description> + <macros> + <import>scater_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +scater-normalize.R -i '${R_scater_qc}' +#if $exprs_value: + --exprs-values '$exprs_value' +#end if +#if $log_exprs_offset: + --log-exprs-offset '$log_exprs_offset' +#end if + --return-log '$return_log' + --centre-size-factors '$centre_size_factors' + -o '$R_scater_normalize' + ]]></command> + + <inputs> + <param name="R_scater_qc" type="data" format="rdata" label="SingleCellExperiment object" + help="File name in which a serialized R SingleCellExperiment object where object matrix found."/> + + <param name="exprs_value" argument="--exprs-values" type="text" optional="True" value="counts" label="Name of expression values" + help="character string indicating which slot of the assayData from the SingleCellExperiment object should be used to compute log-transformed expression values. Valid options are counts, tpm, cpm and fpkm. Defaults to the first available value of the options in the order shown"/> + + <param name="return_log" argument="--return-log" type="boolean" checked="true" label="Save normalized values in log scale" + help="logical, should normalized values be returned on the log scale? Default is TRUE. If TRUE, output is stored as logcounts in the returned object; if FALSE output is stored as normcounts"/> + + <param name="log_exprs_offset" argument="--log-exprs-offset" type="integer" optional="True" value="1" label="Pseudo counts to add when doing log transformation" + help="scalar numeric value giving the offset to add when taking log2 of normalised values to return as expression values. If NULL, value is taken from log.exprs.offset if defined, otherwise 1."/> + + <param name="centre_size_factors" argument="--centre-size-factors" type="boolean" checked="true" label="Save centred size factors" + help="logical, should size factors centred at unity be stored in the returned object if exprs_values=counts, Defaults to TRUE. Regardless, centred size factors will always be used to calculate exprs from count data. This argument is ignored for other exprs_values, where no size factors are used or modified"/> + </inputs> + + <outputs> + <data name="R_scater_normalize" format="rdata" label="${tool.name} on ${on_string}: serialized SingleCellExperiment object containing normalised expression values"/> + </outputs> + + <tests> + <test> + <param name="R_scater_qc" value="R_scater_qc.rds"/> + <output name="R_scater_normalize" file="R_scater_normalize.rds"/> + </test> + </tests> + <help><![CDATA[ + @HELP@ + + @VERSION_HISTORY@ + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r c01a342be892 scater_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scater_macros.xml Wed Apr 03 11:38:57 2019 -0400 |
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| @@ -0,0 +1,50 @@ +<macros> + <token name="@TOOL_VERSION@">1.8.4</token> + <token name="@HELP@">More information can be found at https://bioconductor.org/packages/release/bioc/html/scater.html</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.0.4">bioconductor-scater-scripts</requirement> + <yield/> + </requirements> + </xml> + <xml name="version"> + <version_command><![CDATA[ + echo $(R --version | grep version | grep -v GNU)", scater version" $(R --vanilla --slave -e "library(scater); cat(sessionInfo()\$otherPkgs\$scater\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + </xml> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +1.8.4+galaxy0: Initial contribution. Suhaib Mohammed, Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ and and Teichmann Lab at Wellcome Sanger Institute. + ]]></token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @article{doi:10.1093/bioinformatics/btw777, + author = {McCarthy, Davis J and Campbell, Kieran R and Lun, Aaron T L and Wills, Quin F}, + title = {Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R}, + journal = {Bioinformatics}, + volume = {33}, + number = {8}, + pages = {1179-1186}, + year = {2017}, + doi = {10.1093/bioinformatics/btw777}, + URL = {http://dx.doi.org/10.1093/bioinformatics/btw777}, + eprint = {/oup/backfile/content_public/journal/bioinformatics/33/8/10.1093_bioinformatics_btw777/2/btw777.pdf} + } + </citation> + <citation type="bibtex"> + @misc{githubbioconductor-scater-scripts.git, + author = {Jonathan Manning, Ni Huang, Suhaib Mohammed, EBI Gene Expression Team}, + year = {2018}, + title = {Scater-scripts: command line interface for Scater}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts.git}, + } + </citation> + <yield /> + </citations> + </xml> +</macros> |
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| b'@@ -0,0 +1,2700 @@\n+AAACATACAACCAC-1\n+AAACATTGAGCTAC-1\n+AAACATTGATCAGC-1\n+AAACCGTGCTTCCG-1\n+AAACCGTGTATGCG-1\n+AAACGCACTGGTAC-1\n+AAACGCTGACCAGT-1\n+AAACGCTGGTTCTT-1\n+AAACGCTGTAGCCA-1\n+AAACGCTGTTTCTG-1\n+AAACTTGAAAAACG-1\n+AAACTTGATCCAGA-1\n+AAAGAGACGAGATA-1\n+AAAGAGACGCGAGA-1\n+AAAGAGACGGACTT-1\n+AAAGAGACGGCATT-1\n+AAAGATCTGGGCAA-1\n+AAAGCAGAAGCCAT-1\n+AAAGCAGATATCGG-1\n+AAAGCCTGTATGCG-1\n+AAAGGCCTGTCTAG-1\n+AAAGTTTGATCACG-1\n+AAAGTTTGGGGTGA-1\n+AAAGTTTGTAGAGA-1\n+AAAGTTTGTAGCGT-1\n+AAATCAACAATGCC-1\n+AAATCAACACCAGT-1\n+AAATCAACCAGGAG-1\n+AAATCAACCCTATT-1\n+AAATCAACGGAAGC-1\n+AAATCAACTCGCAA-1\n+AAATCATGACCACA-1\n+AAATCCCTCCACAA-1\n+AAATCCCTGCTATG-1\n+AAATGTTGAACGAA-1\n+AAATGTTGCCACAA-1\n+AAATGTTGTGGCAT-1\n+AAATTCGAAGGTTC-1\n+AAATTCGAATCACG-1\n+AAATTCGAGCTGAT-1\n+AAATTCGAGGAGTG-1\n+AAATTCGATTCTCA-1\n+AAATTGACACGACT-1\n+AAATTGACTCGCTC-1\n+AACAAACTCATTTC-1\n+AACAAACTTTCGTT-1\n+AACAATACGACGAG-1\n+AACACGTGCAGAGG-1\n+AACACGTGGAAAGT-1\n+AACACGTGGAACCT-1\n+AACACGTGGCTACA-1\n+AACACGTGTACGAC-1\n+AACAGCACAAGAGT-1\n+AACATTGATGGGAG-1\n+AACCAGTGATACCG-1\n+AACCCAGATCGCTC-1\n+AACCGATGCTCCCA-1\n+AACCGATGGTCATG-1\n+AACCGATGTTCTAC-1\n+AACCGCCTAGCGTT-1\n+AACCGCCTCTACGA-1\n+AACCTACTGTGAGG-1\n+AACCTACTGTGTTG-1\n+AACCTTACGAGACG-1\n+AACCTTACGCGAGA-1\n+AACCTTACTAACGC-1\n+AACCTTTGGACGGA-1\n+AACCTTTGTACGCA-1\n+AACGCAACAAGTAG-1\n+AACGCATGACCCAA-1\n+AACGCATGCCTTCG-1\n+AACGCATGTACTTC-1\n+AACGCCCTCGGGAA-1\n+AACGCCCTCGTACA-1\n+AACGCCCTGCTTAG-1\n+AACGCCCTGGCATT-1\n+AACGTCGAGTATCG-1\n+AACGTGTGAAAGCA-1\n+AACGTGTGGCGGAA-1\n+AACGTGTGTCCAAG-1\n+AACGTGTGTGCTTT-1\n+AACTACCTTAGAGA-1\n+AACTCACTCAAGCT-1\n+AACTCACTTGGAGG-1\n+AACTCGGAAAGTGA-1\n+AACTCGGAAGGTCT-1\n+AACTCTTGCAGGAG-1\n+AACTGTCTCCCTTG-1\n+AACTTGCTACGCTA-1\n+AACTTGCTGGGACA-1\n+AAGAACGAGTGTTG-1\n+AAGAAGACGTAGGG-1\n+AAGACAGAAGTCTG-1\n+AAGACAGAGGATCT-1\n+AAGACAGATTACCT-1\n+AAGAGATGGGTAGG-1\n+AAGATGGAAAACAG-1\n+AAGATGGAGAACTC-1\n+AAGATGGAGATAAG-1\n+AAGATTACAACCTG-1\n+AAGATTACAGATCC-1\n+AAGATTACCCGTTC-1\n+AAGATTACCGCCTT-1\n+AAGATTACCTCAAG-1\n+AAGATTACTCCTCG-1\n+AAGCAAGAGCGAGA-1\n+AAGCAAGAGCTTAG-1\n+AAGCAAGAGGTGTT-1\n+AAGCACTGAGCAAA-1\n+AAGCACTGCATACG-1\n+AAGCACTGGTTCTT-1\n+AAGCCAACGTGTTG-1\n+AAGCCATGAACTGC-1\n+AAGCCATGACACGT-1\n+AAGCCATGCGTGAT-1\n+AAGCCATGTCTCGC-1\n+AAGCCTGACATGCA-1\n+AAGCCTGACCGAAT-1\n+AAGCGACTCCTCAC-1\n+AAGCGACTGTGTCA-1\n+AAGCGACTTACAGC-1\n+AAGCGACTTTGACG-1\n+AAGCGTACGTCTTT-1\n+AAGGCTTGCGAACT-1\n+AAGGTCACGGTTAC-1\n+AAGGTCACTGTTTC-1\n+AAGGTCACTTCCCG-1\n+AAGGTCTGACAGTC-1\n+AAGGTCTGCAGATC-1\n+AAGGTCTGGTATGC-1\n+AAGTAACTCTGAAC-1\n+AAGTAACTGAGATA-1\n+AAGTAGGATACAGC-1\n+AAGTATACCGAACT-1\n+AAGTCCGACTTGTT-1\n+AAGTCCGATAGAAG-1\n+AAGTCTCTAGTCGT-1\n+AAGTCTCTCGGAGA-1\n+AAGTGGCTTGGAGG-1\n+AAGTTCCTCATTCT-1\n+AAGTTCCTTCTTAC-1\n+AATAAGCTCGAATC-1\n+AATAAGCTCGTTGA-1\n+AATACCCTGGACGA-1\n+AATACCCTGGCATT-1\n+AATACTGAAAGGGC-1\n+AATACTGAATTGGC-1\n+AATAGGGAACCCTC-1\n+AATAGGGAGAATGA-1\n+AATCAAACTATCGG-1\n+AATCCGGAATGCTG-1\n+AATCCTACCGGTAT-1\n+AATCCTTGACGGGA-1\n+AATCCTTGGTGAGG-1\n+AATCGGTGGAACTC-1\n+AATCGGTGTGCTTT-1\n+AATCTAGAAAAGTG-1\n+AATCTAGAATCGGT-1\n+AATCTCACAGCCTA-1\n+AATCTCACTCTAGG-1\n+AATCTCTGAACAGA-1\n+AATCTCTGCTTTAC-1\n+AATGATACACCAAC-1\n+AATGATACGGTCAT-1\n+AATGCGTGACACCA-1\n+AATGCGTGGACGGA-1\n+AATGCGTGGCTATG-1\n+AATGGAGAATCGTG-1\n+AATGGAGATCCTTA-1\n+AATGGCTGACACCA-1\n+AATGGCTGCGTGAT-1\n+AATGGCTGTAAAGG-1\n+AATGGCTGTACTCT-1\n+AATGGCTGTGAAGA-1\n+AATGTAACGGTGGA-1\n+AATGTAACGTTTGG-1\n+AATGTCCTCTTCTA-1\n+AATGTTGACAGTCA-1\n+AATGTTGAGTTGAC-1\n+AATGTTGATCTACT-1\n+AATTACGAATTCCT-1\n+AATTACGACTTCTA-1\n+AATTACGAGTAGCT-1\n+AATTACGAGTGAGG-1\n+AATTACGATTGGCA-1\n+AATTCCTGCTCAGA-1\n+AATTGATGTCGCAA-1\n+AATTGTGACTTGGA-1\n+ACAAAGGAGGGTGA-1\n+ACAAATTGATTCTC-1\n+ACAAATTGCTCAGA-1\n+ACAAATTGTTGCGA-1\n+ACAACCGAGGGATG-1\n+ACAACCGAGTTACG-1\n+ACAAGAGAAGTCGT-1\n+ACAAGAGACTTATC-1\n+ACAAGAGAGTTGAC-1\n+ACAATCCTAACCGT-1\n+ACAATCCTTAGCGT-1\n+ACAATTGACTGACA-1\n+ACAATTGATGACTG-1\n+ACACAGACACCTGA-1\n+ACACAGACCATACG-1\n+ACACCAGAGGGCAA-1\n+ACACCCTGGTGTTG-1\n+ACACGAACAGTTCG-1\n+ACACGATGACGCAT-1\n+ACACGATGATGTGC-1\n+ACACGATGTCGTAG-1\n+ACACGATGTGGTCA-1\n+ACAGACACGGCATT-1\n+ACAGACACGTTGTG-1\n+ACAGCAACACCTAG-1\n+ACAGCAACCTCAAG-1\n+ACAGGTACCCCACT-1\n+ACAGGTACGCTGTA-1\n+ACAGGTACTGGTGT-1\n+ACAGTCGACCCAAA-1\n+ACAGTCGACCGATA-1\n+ACAGTGACTCACCC-1\n+ACAGTGACTCTATC-1\n+A'..b'-1\n+TGCTATACTGCTGA-1\n+TGCTGAGAGAGCAG-1\n+TGCTGAGATTATCC-1\n+TGGAAAGACTCTCG-1\n+TGGAAAGAGCGATT-1\n+TGGAAAGAGGTCAT-1\n+TGGAAAGATATGGC-1\n+TGGAACACAAACAG-1\n+TGGAACACGCTAAC-1\n+TGGAAGCTCAGATC-1\n+TGGACCCTACACTG-1\n+TGGACCCTCATGGT-1\n+TGGACCCTGGTACT-1\n+TGGACTGAGTATGC-1\n+TGGAGACTATCAGC-1\n+TGGAGACTGAAACA-1\n+TGGAGACTTCAAGC-1\n+TGGAGACTTGACCA-1\n+TGGAGGGACGGAGA-1\n+TGGAGGGAGCTATG-1\n+TGGATCGATAAAGG-1\n+TGGATGTGACCTAG-1\n+TGGATGTGATGTCG-1\n+TGGATGTGTGAAGA-1\n+TGGATTCTCATACG-1\n+TGGCAATGCTTGTT-1\n+TGGCAATGGAGGGT-1\n+TGGCACCTTCACGA-1\n+TGGCACCTTCAGTG-1\n+TGGGTATGAAGAGT-1\n+TGGGTATGCACAAC-1\n+TGGGTATGGTACGT-1\n+TGGGTATGTTTGGG-1\n+TGGTAGACATGCCA-1\n+TGGTAGACCCTCAC-1\n+TGGTAGACCTGATG-1\n+TGGTAGTGCACTGA-1\n+TGGTATCTAAACAG-1\n+TGGTATCTCTTCCG-1\n+TGGTCAGACCCAAA-1\n+TGGTCAGACCGTTC-1\n+TGGTTACTGACGTT-1\n+TGGTTACTGTTCTT-1\n+TGTAACCTAGAGGC-1\n+TGTAACCTTGCCTC-1\n+TGTAATGACACAAC-1\n+TGTAATGAGGTAAA-1\n+TGTACTTGCTCTAT-1\n+TGTAGGTGCGAGAG-1\n+TGTAGGTGCTATGG-1\n+TGTAGGTGCTCTAT-1\n+TGTAGGTGTGCTGA-1\n+TGTAGTCTTCCAGA-1\n+TGTAGTCTTGCACA-1\n+TGTATCTGTTAGGC-1\n+TGTATGCTCATGGT-1\n+TGTATGCTGTAGGG-1\n+TGTATGCTTTCATC-1\n+TGTCAGGAATACCG-1\n+TGTCAGGAGATGAA-1\n+TGTCTAACCCCTTG-1\n+TGTGACGATTCTCA-1\n+TGTGAGACTGTCAG-1\n+TGTGAGACTTGAGC-1\n+TGTGAGTGACCACA-1\n+TGTGAGTGAGTGCT-1\n+TGTGAGTGGAGATA-1\n+TGTGATCTCTCTAT-1\n+TGTGATCTGACACT-1\n+TGTGGATGGCCAAT-1\n+TGTTAAGACAAAGA-1\n+TGTTAAGATAAGGA-1\n+TGTTAAGATTGGCA-1\n+TGTTACACCGCATA-1\n+TGTTACACGACTAC-1\n+TGTTACTGGCTACA-1\n+TGTTACTGTAGTCG-1\n+TTAACCACCGTAAC-1\n+TTAACCACTAAGGA-1\n+TTAACCACTCAGAC-1\n+TTACACACGTGTTG-1\n+TTACACACTCCTAT-1\n+TTACCATGAATCGC-1\n+TTACCATGGTTGAC-1\n+TTACCATGTGTCTT-1\n+TTACCATGTTGTGG-1\n+TTACGACTGAGAGC-1\n+TTACGACTTGACAC-1\n+TTACGTACGTTCAG-1\n+TTACTCGAACGTTG-1\n+TTACTCGAAGAATG-1\n+TTACTCGACGCAAT-1\n+TTACTCGAGGGTGA-1\n+TTACTCGATCTACT-1\n+TTAGAATGTGGTGT-1\n+TTAGAATGTGTAGC-1\n+TTAGACCTCCTACC-1\n+TTAGACCTCCTTTA-1\n+TTAGCTACAACCGT-1\n+TTAGCTACTGTCCC-1\n+TTAGCTACTTTCGT-1\n+TTAGGGACGCGAAG-1\n+TTAGGGTGCTGGAT-1\n+TTAGGGTGTCCTGC-1\n+TTAGGTCTACTTTC-1\n+TTAGTCACCAGTTG-1\n+TTAGTCTGAAAGCA-1\n+TTAGTCTGCCAACA-1\n+TTAGTCTGTGCACA-1\n+TTATCCGACTAGTG-1\n+TTATCCGAGAAAGT-1\n+TTATGAGAGATAAG-1\n+TTATGCACGTCACA-1\n+TTATGGCTTATGGC-1\n+TTATTCCTATGCTG-1\n+TTATTCCTGGACAG-1\n+TTATTCCTGGTACT-1\n+TTATTCCTTCGTGA-1\n+TTCAAAGATAAAGG-1\n+TTCAACACAACAGA-1\n+TTCAACACCCCAAA-1\n+TTCAACACGGACGA-1\n+TTCAAGCTAAGAAC-1\n+TTCAAGCTAGATGA-1\n+TTCAAGCTGTTGAC-1\n+TTCAAGCTTCCAAG-1\n+TTCAAGCTTGATGC-1\n+TTCAAGCTTTCGCC-1\n+TTCACAACCCGTTC-1\n+TTCACAACGTCTGA-1\n+TTCAGACTACCCAA-1\n+TTCAGACTCTCGAA-1\n+TTCAGTACCGACTA-1\n+TTCAGTACTCAAGC-1\n+TTCAGTACTCCTAT-1\n+TTCAGTTGCCAAGT-1\n+TTCAGTTGTCCTTA-1\n+TTCAGTTGTCTAGG-1\n+TTCAGTTGTCTCGC-1\n+TTCATCGAGGTGGA-1\n+TTCATGTGTGGTGT-1\n+TTCATTCTATGTCG-1\n+TTCATTCTTCTCTA-1\n+TTCCAAACCTATGG-1\n+TTCCAAACCTCCCA-1\n+TTCCAAACTCCCAC-1\n+TTCCAAACTTGACG-1\n+TTCCATGACGAGAG-1\n+TTCCATGACTGTCC-1\n+TTCCCACTTGAGGG-1\n+TTCCCACTTGTCTT-1\n+TTCCTAGAAAGTGA-1\n+TTCCTAGACTAGTG-1\n+TTCGAGGACTCTAT-1\n+TTCGAGGAGGGCAA-1\n+TTCGAGGATAGAAG-1\n+TTCGATTGAGCATC-1\n+TTCGGAGAATGCCA-1\n+TTCGGAGATGTGCA-1\n+TTCGTATGAAAAGC-1\n+TTCGTATGGATAGA-1\n+TTCGTATGGTCTGA-1\n+TTCGTATGTCCTTA-1\n+TTCTACGAACGTAC-1\n+TTCTACGAGTTGGT-1\n+TTCTAGTGACACGT-1\n+TTCTAGTGCATGAC-1\n+TTCTAGTGGAGAGC-1\n+TTCTAGTGGTCACA-1\n+TTCTCAGAAGAGAT-1\n+TTCTCAGAAGCATC-1\n+TTCTCAGATGGAGG-1\n+TTCTGATGGAGACG-1\n+TTCTTACTCTGGAT-1\n+TTGAACCTCCTTGC-1\n+TTGAATGAACTACG-1\n+TTGAATGACTTACT-1\n+TTGAATGATCTCAT-1\n+TTGACACTCTGTAG-1\n+TTGACACTGATAAG-1\n+TTGAGGACAGAACA-1\n+TTGAGGACTACGCA-1\n+TTGAGGTGGACGGA-1\n+TTGCATTGAGCTAC-1\n+TTGCATTGCTAAGC-1\n+TTGCATTGTGACTG-1\n+TTGCTAACACCAAC-1\n+TTGCTAACACGCTA-1\n+TTGCTAACCACTCC-1\n+TTGCTATGGTACGT-1\n+TTGCTATGGTAGGG-1\n+TTGGAGACCAATCG-1\n+TTGGAGACGCTATG-1\n+TTGGAGACTATGGC-1\n+TTGGGAACTGAACC-1\n+TTGGTACTACTGGT-1\n+TTGGTACTCTTAGG-1\n+TTGGTACTGAATCC-1\n+TTGGTACTGGATTC-1\n+TTGTACACGTTGTG-1\n+TTGTACACTTGCAG-1\n+TTGTAGCTAGCTCA-1\n+TTGTAGCTCTCTTA-1\n+TTGTCATGGACGGA-1\n+TTTAGAGATCCTCG-1\n+TTTAGCTGATACCG-1\n+TTTAGCTGGATACC-1\n+TTTAGCTGTACTCT-1\n+TTTAGGCTCCTTTA-1\n+TTTATCCTGTTGTG-1\n+TTTCACGAGGTTCA-1\n+TTTCAGTGGAAGGC-1\n+TTTCAGTGTCACGA-1\n+TTTCAGTGTCTATC-1\n+TTTCAGTGTGCAGT-1\n+TTTCCAGAGGTGAG-1\n+TTTCGAACACCTGA-1\n+TTTCGAACTCTCAT-1\n+TTTCTACTGAGGCA-1\n+TTTCTACTTCCTCG-1\n+TTTGCATGAGAGGC-1\n+TTTGCATGCCTCAC-1\n' 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| b |
| b'@@ -0,0 +1,2700 @@\n+AAACATACAACCAC-1,2421\n+AAACATTGAGCTAC-1,4903\n+AAACATTGATCAGC-1,3149\n+AAACCGTGCTTCCG-1,2639\n+AAACCGTGTATGCG-1,981\n+AAACGCACTGGTAC-1,2164\n+AAACGCTGACCAGT-1,2176\n+AAACGCTGGTTCTT-1,2260\n+AAACGCTGTAGCCA-1,1276\n+AAACGCTGTTTCTG-1,1103\n+AAACTTGAAAAACG-1,3918\n+AAACTTGATCCAGA-1,2392\n+AAAGAGACGAGATA-1,2412\n+AAAGAGACGCGAGA-1,3034\n+AAAGAGACGGACTT-1,1152\n+AAAGAGACGGCATT-1,792\n+AAAGATCTGGGCAA-1,1348\n+AAAGCAGAAGCCAT-1,1158\n+AAAGCAGATATCGG-1,4586\n+AAAGCCTGTATGCG-1,2929\n+AAAGGCCTGTCTAG-1,4974\n+AAAGTTTGATCACG-1,1270\n+AAAGTTTGGGGTGA-1,3286\n+AAAGTTTGTAGAGA-1,1102\n+AAAGTTTGTAGCGT-1,2684\n+AAATCAACAATGCC-1,2321\n+AAATCAACACCAGT-1,1414\n+AAATCAACCAGGAG-1,2801\n+AAATCAACCCTATT-1,5680\n+AAATCAACGGAAGC-1,3473\n+AAATCAACTCGCAA-1,2812\n+AAATCATGACCACA-1,4128\n+AAATCCCTCCACAA-1,956\n+AAATCCCTGCTATG-1,822\n+AAATGTTGAACGAA-1,3211\n+AAATGTTGCCACAA-1,1761\n+AAATGTTGTGGCAT-1,2763\n+AAATTCGAAGGTTC-1,2741\n+AAATTCGAATCACG-1,2567\n+AAATTCGAGCTGAT-1,2971\n+AAATTCGAGGAGTG-1,2981\n+AAATTCGATTCTCA-1,2643\n+AAATTGACACGACT-1,2359\n+AAATTGACTCGCTC-1,3412\n+AACAAACTCATTTC-1,2179\n+AACAAACTTTCGTT-1,2688\n+AACAATACGACGAG-1,2104\n+AACACGTGCAGAGG-1,1801\n+AACACGTGGAAAGT-1,2632\n+AACACGTGGAACCT-1,2280\n+AACACGTGGCTACA-1,2653\n+AACACGTGTACGAC-1,3571\n+AACAGCACAAGAGT-1,689\n+AACATTGATGGGAG-1,4713\n+AACCAGTGATACCG-1,3841\n+AACCCAGATCGCTC-1,2343\n+AACCGATGCTCCCA-1,2295\n+AACCGATGGTCATG-1,2633\n+AACCGATGTTCTAC-1,2296\n+AACCGCCTAGCGTT-1,3391\n+AACCGCCTCTACGA-1,3998\n+AACCTACTGTGAGG-1,5687\n+AACCTACTGTGTTG-1,2675\n+AACCTTACGAGACG-1,2771\n+AACCTTACGCGAGA-1,1248\n+AACCTTACTAACGC-1,1947\n+AACCTTTGGACGGA-1,2078\n+AACCTTTGTACGCA-1,4621\n+AACGCAACAAGTAG-1,2049\n+AACGCATGACCCAA-1,2778\n+AACGCATGCCTTCG-1,2866\n+AACGCATGTACTTC-1,2915\n+AACGCCCTCGGGAA-1,2503\n+AACGCCCTCGTACA-1,1915\n+AACGCCCTGCTTAG-1,1074\n+AACGCCCTGGCATT-1,1442\n+AACGTCGAGTATCG-1,2149\n+AACGTGTGAAAGCA-1,2820\n+AACGTGTGGCGGAA-1,2071\n+AACGTGTGTCCAAG-1,1665\n+AACGTGTGTGCTTT-1,1933\n+AACTACCTTAGAGA-1,2876\n+AACTCACTCAAGCT-1,2607\n+AACTCACTTGGAGG-1,2124\n+AACTCGGAAAGTGA-1,1840\n+AACTCGGAAGGTCT-1,1290\n+AACTCTTGCAGGAG-1,2103\n+AACTGTCTCCCTTG-1,2331\n+AACTTGCTACGCTA-1,2336\n+AACTTGCTGGGACA-1,1864\n+AAGAACGAGTGTTG-1,780\n+AAGAAGACGTAGGG-1,1440\n+AAGACAGAAGTCTG-1,1125\n+AAGACAGAGGATCT-1,2315\n+AAGACAGATTACCT-1,2309\n+AAGAGATGGGTAGG-1,1346\n+AAGATGGAAAACAG-1,878\n+AAGATGGAGAACTC-1,3117\n+AAGATGGAGATAAG-1,4023\n+AAGATTACAACCTG-1,2119\n+AAGATTACAGATCC-1,4065\n+AAGATTACCCGTTC-1,2763\n+AAGATTACCGCCTT-1,3063\n+AAGATTACCTCAAG-1,2280\n+AAGATTACTCCTCG-1,642\n+AAGCAAGAGCGAGA-1,2480\n+AAGCAAGAGCTTAG-1,2171\n+AAGCAAGAGGTGTT-1,1698\n+AAGCACTGAGCAAA-1,3239\n+AAGCACTGCATACG-1,803\n+AAGCACTGGTTCTT-1,6157\n+AAGCCAACGTGTTG-1,2764\n+AAGCCATGAACTGC-1,7070\n+AAGCCATGACACGT-1,1538\n+AAGCCATGCGTGAT-1,2111\n+AAGCCATGTCTCGC-1,909\n+AAGCCTGACATGCA-1,1790\n+AAGCCTGACCGAAT-1,1048\n+AAGCGACTCCTCAC-1,2103\n+AAGCGACTGTGTCA-1,3131\n+AAGCGACTTACAGC-1,1494\n+AAGCGACTTTGACG-1,3668\n+AAGCGTACGTCTTT-1,2048\n+AAGGCTTGCGAACT-1,2076\n+AAGGTCACGGTTAC-1,1870\n+AAGGTCACTGTTTC-1,1775\n+AAGGTCACTTCCCG-1,2387\n+AAGGTCTGACAGTC-1,2589\n+AAGGTCTGCAGATC-1,968\n+AAGGTCTGGTATGC-1,715\n+AAGTAACTCTGAAC-1,1874\n+AAGTAACTGAGATA-1,659\n+AAGTAGGATACAGC-1,1725\n+AAGTATACCGAACT-1,3253\n+AAGTCCGACTTGTT-1,1523\n+AAGTCCGATAGAAG-1,3369\n+AAGTCTCTAGTCGT-1,3287\n+AAGTCTCTCGGAGA-1,1838\n+AAGTGGCTTGGAGG-1,1572\n+AAGTTCCTCATTCT-1,2336\n+AAGTTCCTTCTTAC-1,3265\n+AATAAGCTCGAATC-1,2760\n+AATAAGCTCGTTGA-1,1606\n+AATACCCTGGACGA-1,1501\n+AATACCCTGGCATT-1,3310\n+AATACTGAAAGGGC-1,1747\n+AATACTGAATTGGC-1,1816\n+AATAGGGAACCCTC-1,2877\n+AATAGGGAGAATGA-1,1864\n+AATCAAACTATCGG-1,1457\n+AATCCGGAATGCTG-1,2805\n+AATCCTACCGGTAT-1,2440\n+AATCCTTGACGGGA-1,2533\n+AATCCTTGGTGAGG-1,1754\n+AATCGGTGGAACTC-1,1955\n+AATCGGTGTGCTTT-1,1896\n+AATCTAGAAAAGTG-1,2582\n+AATCTAGAATCGGT-1,3168\n+AATCTCACAGCCTA-1,3553\n+AATCTCACTCTAGG-1,2149\n+AATCTCTGAACAGA-1,2183\n+AATCTCTGCTTTAC-1,1710\n+AATGATACACCAAC-1,1918\n+AATGATACGGTCAT-1,3095\n+AATGCGTGACACCA-1,2866\n+AATGCGTGGACGGA-1,4439\n+AATGCGTGGCTATG-1,2225\n+AATGGAGAATCGTG-1,2381\n+AATGGAGATCCTTA-1,1959\n+AATGGCTGACACCA-1,3038\n+AATGGCTGCGTGAT-1,2211\n+AATGGCTGTAAAGG-1,1286\n+AATGGCTGTACTCT-1,1208\n+AATGGCTGTGAAG'..b',4907\n+TGTAGGTGCGAGAG-1,1144\n+TGTAGGTGCTATGG-1,4234\n+TGTAGGTGCTCTAT-1,6287\n+TGTAGGTGTGCTGA-1,2544\n+TGTAGTCTTCCAGA-1,4154\n+TGTAGTCTTGCACA-1,2177\n+TGTATCTGTTAGGC-1,1996\n+TGTATGCTCATGGT-1,1479\n+TGTATGCTGTAGGG-1,1455\n+TGTATGCTTTCATC-1,1968\n+TGTCAGGAATACCG-1,2767\n+TGTCAGGAGATGAA-1,4083\n+TGTCTAACCCCTTG-1,1978\n+TGTGACGATTCTCA-1,3098\n+TGTGAGACTGTCAG-1,2666\n+TGTGAGACTTGAGC-1,2447\n+TGTGAGTGACCACA-1,1583\n+TGTGAGTGAGTGCT-1,4110\n+TGTGAGTGGAGATA-1,969\n+TGTGATCTCTCTAT-1,1690\n+TGTGATCTGACACT-1,1108\n+TGTGGATGGCCAAT-1,1945\n+TGTTAAGACAAAGA-1,848\n+TGTTAAGATAAGGA-1,2173\n+TGTTAAGATTGGCA-1,598\n+TGTTACACCGCATA-1,3410\n+TGTTACACGACTAC-1,1953\n+TGTTACTGGCTACA-1,2483\n+TGTTACTGTAGTCG-1,1772\n+TTAACCACCGTAAC-1,2192\n+TTAACCACTAAGGA-1,1198\n+TTAACCACTCAGAC-1,1828\n+TTACACACGTGTTG-1,2613\n+TTACACACTCCTAT-1,2508\n+TTACCATGAATCGC-1,2421\n+TTACCATGGTTGAC-1,4142\n+TTACCATGTGTCTT-1,1123\n+TTACCATGTTGTGG-1,1548\n+TTACGACTGAGAGC-1,3288\n+TTACGACTTGACAC-1,1902\n+TTACGTACGTTCAG-1,947\n+TTACTCGAACGTTG-1,15301\n+TTACTCGAAGAATG-1,3863\n+TTACTCGACGCAAT-1,5031\n+TTACTCGAGGGTGA-1,2549\n+TTACTCGATCTACT-1,2551\n+TTAGAATGTGGTGT-1,1740\n+TTAGAATGTGTAGC-1,627\n+TTAGACCTCCTACC-1,2485\n+TTAGACCTCCTTTA-1,2311\n+TTAGCTACAACCGT-1,2101\n+TTAGCTACTGTCCC-1,3703\n+TTAGCTACTTTCGT-1,2921\n+TTAGGGACGCGAAG-1,2200\n+TTAGGGTGCTGGAT-1,2846\n+TTAGGGTGTCCTGC-1,2734\n+TTAGGTCTACTTTC-1,1106\n+TTAGTCACCAGTTG-1,2674\n+TTAGTCTGAAAGCA-1,2747\n+TTAGTCTGCCAACA-1,1735\n+TTAGTCTGTGCACA-1,1692\n+TTATCCGACTAGTG-1,1903\n+TTATCCGAGAAAGT-1,4231\n+TTATGAGAGATAAG-1,1293\n+TTATGCACGTCACA-1,1590\n+TTATGGCTTATGGC-1,6165\n+TTATTCCTATGCTG-1,3963\n+TTATTCCTGGACAG-1,2514\n+TTATTCCTGGTACT-1,2496\n+TTATTCCTTCGTGA-1,3207\n+TTCAAAGATAAAGG-1,2385\n+TTCAACACAACAGA-1,2430\n+TTCAACACCCCAAA-1,2094\n+TTCAACACGGACGA-1,2584\n+TTCAAGCTAAGAAC-1,2641\n+TTCAAGCTAGATGA-1,2974\n+TTCAAGCTGTTGAC-1,2375\n+TTCAAGCTTCCAAG-1,740\n+TTCAAGCTTGATGC-1,2404\n+TTCAAGCTTTCGCC-1,2878\n+TTCACAACCCGTTC-1,2526\n+TTCACAACGTCTGA-1,678\n+TTCAGACTACCCAA-1,789\n+TTCAGACTCTCGAA-1,2264\n+TTCAGTACCGACTA-1,2769\n+TTCAGTACTCAAGC-1,5220\n+TTCAGTACTCCTAT-1,1850\n+TTCAGTTGCCAAGT-1,2003\n+TTCAGTTGTCCTTA-1,1975\n+TTCAGTTGTCTAGG-1,1031\n+TTCAGTTGTCTCGC-1,1865\n+TTCATCGAGGTGGA-1,1914\n+TTCATGTGTGGTGT-1,3025\n+TTCATTCTATGTCG-1,2625\n+TTCATTCTTCTCTA-1,1986\n+TTCCAAACCTATGG-1,1057\n+TTCCAAACCTCCCA-1,2726\n+TTCCAAACTCCCAC-1,793\n+TTCCAAACTTGACG-1,1647\n+TTCCATGACGAGAG-1,1840\n+TTCCATGACTGTCC-1,1050\n+TTCCCACTTGAGGG-1,1520\n+TTCCCACTTGTCTT-1,3163\n+TTCCTAGAAAGTGA-1,1552\n+TTCCTAGACTAGTG-1,1943\n+TTCGAGGACTCTAT-1,2746\n+TTCGAGGAGGGCAA-1,1816\n+TTCGAGGATAGAAG-1,2749\n+TTCGATTGAGCATC-1,1910\n+TTCGGAGAATGCCA-1,1191\n+TTCGGAGATGTGCA-1,2412\n+TTCGTATGAAAAGC-1,1991\n+TTCGTATGGATAGA-1,1983\n+TTCGTATGGTCTGA-1,2258\n+TTCGTATGTCCTTA-1,4348\n+TTCTACGAACGTAC-1,2494\n+TTCTACGAGTTGGT-1,2589\n+TTCTAGTGACACGT-1,3018\n+TTCTAGTGCATGAC-1,2073\n+TTCTAGTGGAGAGC-1,1586\n+TTCTAGTGGTCACA-1,2832\n+TTCTCAGAAGAGAT-1,2189\n+TTCTCAGAAGCATC-1,2497\n+TTCTCAGATGGAGG-1,2643\n+TTCTGATGGAGACG-1,2434\n+TTCTTACTCTGGAT-1,1741\n+TTGAACCTCCTTGC-1,1746\n+TTGAATGAACTACG-1,2289\n+TTGAATGACTTACT-1,2102\n+TTGAATGATCTCAT-1,2015\n+TTGACACTCTGTAG-1,1943\n+TTGACACTGATAAG-1,1315\n+TTGAGGACAGAACA-1,2956\n+TTGAGGACTACGCA-1,6344\n+TTGAGGTGGACGGA-1,2011\n+TTGCATTGAGCTAC-1,1991\n+TTGCATTGCTAAGC-1,3248\n+TTGCATTGTGACTG-1,2441\n+TTGCTAACACCAAC-1,1921\n+TTGCTAACACGCTA-1,2576\n+TTGCTAACCACTCC-1,1943\n+TTGCTATGGTACGT-1,3109\n+TTGCTATGGTAGGG-1,3406\n+TTGGAGACCAATCG-1,4166\n+TTGGAGACGCTATG-1,2662\n+TTGGAGACTATGGC-1,1779\n+TTGGGAACTGAACC-1,2652\n+TTGGTACTACTGGT-1,3268\n+TTGGTACTCTTAGG-1,2928\n+TTGGTACTGAATCC-1,1855\n+TTGGTACTGGATTC-1,1883\n+TTGTACACGTTGTG-1,1537\n+TTGTACACTTGCAG-1,2260\n+TTGTAGCTAGCTCA-1,2519\n+TTGTAGCTCTCTTA-1,2136\n+TTGTCATGGACGGA-1,2178\n+TTTAGAGATCCTCG-1,2362\n+TTTAGCTGATACCG-1,2756\n+TTTAGCTGGATACC-1,2454\n+TTTAGCTGTACTCT-1,5678\n+TTTAGGCTCCTTTA-1,1984\n+TTTATCCTGTTGTG-1,3680\n+TTTCACGAGGTTCA-1,2037\n+TTTCAGTGGAAGGC-1,1781\n+TTTCAGTGTCACGA-1,1634\n+TTTCAGTGTCTATC-1,937\n+TTTCAGTGTGCAGT-1,1322\n+TTTCCAGAGGTGAG-1,2187\n+TTTCGAACACCTGA-1,4460\n+TTTCGAACTCTCAT-1,3461\n+TTTCTACTGAGGCA-1,3447\n+TTTCTACTTCCTCG-1,1684\n+TTTGCATGAGAGGC-1,1024\n+TTTGCATGCCTCAC-1,1985\n' |
| b |
| diff -r 000000000000 -r c01a342be892 test-data/genes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes.tsv Wed Apr 03 11:38:57 2019 -0400 |
| b |
| b'@@ -0,0 +1,32738 @@\n+ENSG00000243485\tMIR1302-10\n+ENSG00000237613\tFAM138A\n+ENSG00000186092\tOR4F5\n+ENSG00000238009\tRP11-34P13.7\n+ENSG00000239945\tRP11-34P13.8\n+ENSG00000237683\tAL627309.1\n+ENSG00000239906\tRP11-34P13.14\n+ENSG00000241599\tRP11-34P13.9\n+ENSG00000228463\tAP006222.2\n+ENSG00000237094\tRP4-669L17.10\n+ENSG00000235249\tOR4F29\n+ENSG00000236601\tRP4-669L17.2\n+ENSG00000236743\tRP5-857K21.15\n+ENSG00000231709\tRP5-857K21.1\n+ENSG00000235146\tRP5-857K21.2\n+ENSG00000239664\tRP5-857K21.3\n+ENSG00000230021\tRP5-857K21.4\n+ENSG00000223659\tRP5-857K21.5\n+ENSG00000185097\tOR4F16\n+ENSG00000235373\tRP11-206L10.3\n+ENSG00000240618\tRP11-206L10.5\n+ENSG00000229905\tRP11-206L10.4\n+ENSG00000228327\tRP11-206L10.2\n+ENSG00000237491\tRP11-206L10.9\n+ENSG00000269831\tAL669831.1\n+ENSG00000177757\tFAM87B\n+ENSG00000225880\tLINC00115\n+ENSG00000230368\tFAM41C\n+ENSG00000269308\tAL645608.2\n+ENSG00000272438\tRP11-54O7.16\n+ENSG00000230699\tRP11-54O7.1\n+ENSG00000241180\tRP11-54O7.2\n+ENSG00000223764\tRP11-54O7.3\n+ENSG00000187634\tSAMD11\n+ENSG00000268179\tAL645608.1\n+ENSG00000188976\tNOC2L\n+ENSG00000187961\tKLHL17\n+ENSG00000187583\tPLEKHN1\n+ENSG00000187642\tC1orf170\n+ENSG00000272512\tRP11-54O7.17\n+ENSG00000188290\tHES4\n+ENSG00000224969\tRP11-54O7.11\n+ENSG00000187608\tISG15\n+ENSG00000188157\tAGRN\n+ENSG00000273443\tRP11-54O7.18\n+ENSG00000237330\tRNF223\n+ENSG00000131591\tC1orf159\n+ENSG00000223823\tRP11-465B22.5\n+ENSG00000272141\tRP11-465B22.8\n+ENSG00000205231\tTTLL10-AS1\n+ENSG00000162571\tTTLL10\n+ENSG00000186891\tTNFRSF18\n+ENSG00000186827\tTNFRSF4\n+ENSG00000078808\tSDF4\n+ENSG00000176022\tB3GALT6\n+ENSG00000184163\tFAM132A\n+ENSG00000260179\tRP5-902P8.12\n+ENSG00000160087\tUBE2J2\n+ENSG00000230415\tRP5-902P8.10\n+ENSG00000162572\tSCNN1D\n+ENSG00000131584\tACAP3\n+ENSG00000169972\tPUSL1\n+ENSG00000127054\tCPSF3L\n+ENSG00000224051\tGLTPD1\n+ENSG00000169962\tTAS1R3\n+ENSG00000107404\tDVL1\n+ENSG00000162576\tMXRA8\n+ENSG00000175756\tAURKAIP1\n+ENSG00000221978\tCCNL2\n+ENSG00000224870\tRP4-758J18.2\n+ENSG00000242485\tMRPL20\n+ENSG00000272455\tRP4-758J18.13\n+ENSG00000235098\tANKRD65\n+ENSG00000225905\tRP4-758J18.7\n+ENSG00000205116\tTMEM88B\n+ENSG00000225285\tRP4-758J18.10\n+ENSG00000179403\tVWA1\n+ENSG00000215915\tATAD3C\n+ENSG00000160072\tATAD3B\n+ENSG00000197785\tATAD3A\n+ENSG00000205090\tTMEM240\n+ENSG00000160075\tSSU72\n+ENSG00000215014\tAL645728.1\n+ENSG00000228594\tC1orf233\n+ENSG00000272106\tRP11-345P4.9\n+ENSG00000197530\tMIB2\n+ENSG00000189409\tMMP23B\n+ENSG00000248333\tCDK11B\n+ENSG00000272004\tRP11-345P4.10\n+ENSG00000189339\tSLC35E2B\n+ENSG00000269737\tRP11-345P4.7\n+ENSG00000008128\tCDK11A\n+ENSG00000215790\tSLC35E2\n+ENSG00000008130\tNADK\n+ENSG00000078369\tGNB1\n+ENSG00000231050\tRP1-140A9.1\n+ENSG00000169885\tCALML6\n+ENSG00000178821\tTMEM52\n+ENSG00000142609\tC1orf222\n+ENSG00000233542\tRP11-547D24.1\n+ENSG00000187730\tGABRD\n+ENSG00000226969\tRP11-547D24.3\n+ENSG00000067606\tPRKCZ\n+ENSG00000271806\tRP5-892K4.1\n+ENSG00000182873\tRP11-181G12.2\n+ENSG00000162585\tC1orf86\n+ENSG00000269554\tAL590822.2\n+ENSG00000203301\tAL590822.1\n+ENSG00000243558\tRP11-181G12.5\n+ENSG00000234396\tRP11-181G12.4\n+ENSG00000157933\tSKI\n+ENSG00000116151\tMORN1\n+ENSG00000269753\tAL589739.1\n+ENSG00000157916\tRER1\n+ENSG00000157911\tPEX10\n+ENSG00000149527\tPLCH2\n+ENSG00000224387\tRP3-395M20.2\n+ENSG00000229393\tRP3-395M20.3\n+ENSG00000157881\tPANK4\n+ENSG00000197921\tHES5\n+ENSG00000272449\tRP3-395M20.12\n+ENSG00000157873\tTNFRSF14\n+ENSG00000225931\tRP3-395M20.7\n+ENSG00000228037\tRP3-395M20.9\n+ENSG00000157870\tFAM213B\n+ENSG00000142606\tMMEL1\n+ENSG00000237058\tRP13-436F16.1\n+ENSG00000215912\tTTC34\n+ENSG00000233234\tRP11-740P5.2\n+ENSG00000231630\tRP11-740P5.3\n+ENSG00000169717\tACTRT2\n+ENSG00000177133\tLINC00982\n+ENSG00000142611\tPRDM16\n+ENSG00000226286\tRP1-163G9.2\n+ENSG00000272235\tRP11-22L13.1\n+ENSG00000130762\tARHGEF16\n+ENSG00000272088\tRP11-168F9.2\n+ENSG00000162591\tMEGF6\n+ENSG00000238260\tRP11-46F15.2\n+ENSG00000158109\tTPRG1L\n+ENSG00000116213\tWRAP73\n+ENSG00000078900\tTP73\n+ENSG00000227589\tRP5-1092A11.5\n+ENSG00000235131\tRP5-1092A11.2\n+ENSG00000227372\tTP73-AS1\n+ENSG00000162592\tCCDC27\n+ENSG00000235169\tSMIM1\n+ENSG00000130764\tLRRC47\n+ENSG00000272153\tRP1-286D6.5\n+ENSG000'..b'G00000160202\tCRYAA\n+ENSG00000237864\tLINC00322\n+ENSG00000237989\tAP001046.5\n+ENSG00000225637\tAP001046.6\n+ENSG00000142178\tSIK1\n+ENSG00000188660\tLINC00319\n+ENSG00000185186\tLINC00313\n+ENSG00000223975\tAP001048.4\n+ENSG00000160207\tHSF2BP\n+ENSG00000160208\tRRP1B\n+ENSG00000160209\tPDXK\n+ENSG00000160213\tCSTB\n+ENSG00000160214\tRRP1\n+ENSG00000215458\tAP001053.11\n+ENSG00000160216\tAGPAT3\n+ENSG00000160218\tTRAPPC10\n+ENSG00000241945\tPWP2\n+ENSG00000160221\tC21orf33\n+ENSG00000225331\tAP001055.6\n+ENSG00000267913\tAP001055.1\n+ENSG00000237604\tAP001056.1\n+ENSG00000232124\tAP001057.1\n+ENSG00000232698\tAP001058.3\n+ENSG00000160223\tICOSLG\n+ENSG00000142182\tDNMT3L\n+ENSG00000232010\tAP001059.5\n+ENSG00000160224\tAIRE\n+ENSG00000141959\tPFKL\n+ENSG00000160226\tC21orf2\n+ENSG00000184441\tAP001062.7\n+ENSG00000232969\tAP001062.9\n+ENSG00000260256\tAP001063.1\n+ENSG00000142185\tTRPM2\n+ENSG00000230061\tAP001065.2\n+ENSG00000229356\tLRRC3-AS1\n+ENSG00000160233\tLRRC3\n+ENSG00000269430\tLRRC3DN\n+ENSG00000228709\tAP001065.15\n+ENSG00000175894\tTSPEAR\n+ENSG00000235890\tTSPEAR-AS1\n+ENSG00000182912\tC21orf90\n+ENSG00000215455\tKRTAP10-1\n+ENSG00000205445\tKRTAP10-2\n+ENSG00000212935\tKRTAP10-3\n+ENSG00000215454\tKRTAP10-4\n+ENSG00000241123\tKRTAP10-5\n+ENSG00000188155\tKRTAP10-6\n+ENSG00000205441\tKRTAP10-7\n+ENSG00000187766\tKRTAP10-8\n+ENSG00000221837\tKRTAP10-9\n+ENSG00000221859\tKRTAP10-10\n+ENSG00000243489\tKRTAP10-11\n+ENSG00000212933\tKRTAP12-4\n+ENSG00000205439\tKRTAP12-3\n+ENSG00000221864\tKRTAP12-2\n+ENSG00000187175\tKRTAP12-1\n+ENSG00000189169\tKRTAP10-12\n+ENSG00000184787\tUBE2G2\n+ENSG00000236519\tAL773604.8\n+ENSG00000184900\tSUMO3\n+ENSG00000183255\tPTTG1IP\n+ENSG00000160255\tITGB2\n+ENSG00000227039\tITGB2-AS1\n+ENSG00000183250\tC21orf67\n+ENSG00000272825\tLL21NC02-1C16.2\n+ENSG00000160256\tFAM207A\n+ENSG00000234880\tLINC00163\n+ENSG00000261706\tAP001505.9\n+ENSG00000224930\tLINC00162\n+ENSG00000268856\tAP001579.1\n+ENSG00000197381\tADARB1\n+ENSG00000268805\tPRED57\n+ENSG00000267857\tPRED58\n+ENSG00000182586\tLINC00334\n+ENSG00000186866\tPOFUT2\n+ENSG00000223768\tLINC00205\n+ENSG00000184274\tLINC00315\n+ENSG00000229382\tBX322557.13\n+ENSG00000237664\tLINC00316\n+ENSG00000228355\tBX322559.3\n+ENSG00000182871\tCOL18A1\n+ENSG00000224574\tCOL18A1-AS2\n+ENSG00000183535\tCOL18A1-AS1\n+ENSG00000173638\tSLC19A1\n+ENSG00000233922\tAL133493.2\n+ENSG00000183570\tPCBP3\n+ENSG00000267883\tPRED60\n+ENSG00000205424\tAL592528.1\n+ENSG00000268040\tPRED62\n+ENSG00000142156\tCOL6A1\n+ENSG00000224413\tAP001476.2\n+ENSG00000228235\tAP001476.4\n+ENSG00000226115\tAP001476.3\n+ENSG00000227438\tAP001471.1\n+ENSG00000142173\tCOL6A2\n+ENSG00000160282\tFTCD\n+ENSG00000237338\tFTCD-AS1\n+ENSG00000160284\tSPATC1L\n+ENSG00000228404\tAP001468.58\n+ENSG00000160285\tLSS\n+ENSG00000235878\tAP001468.1\n+ENSG00000223901\tAP001469.5\n+ENSG00000215424\tMCM3AP-AS1\n+ENSG00000160294\tMCM3AP\n+ENSG00000228137\tAP001469.7\n+ENSG00000239415\tAP001469.9\n+ENSG00000182362\tYBEY\n+ENSG00000160298\tC21orf58\n+ENSG00000160299\tPCNT\n+ENSG00000160305\tDIP2A\n+ENSG00000160307\tS100B\n+ENSG00000160310\tPRMT2\n+ENSG00000198888\tMT-ND1\n+ENSG00000198763\tMT-ND2\n+ENSG00000198804\tMT-CO1\n+ENSG00000198712\tMT-CO2\n+ENSG00000228253\tMT-ATP8\n+ENSG00000198899\tMT-ATP6\n+ENSG00000198938\tMT-CO3\n+ENSG00000198840\tMT-ND3\n+ENSG00000212907\tMT-ND4L\n+ENSG00000198886\tMT-ND4\n+ENSG00000198786\tMT-ND5\n+ENSG00000198695\tMT-ND6\n+ENSG00000198727\tMT-CYB\n+ENSG00000215642\tAL360154.1\n+ENSG00000234295\tAC109135.1\n+ENSG00000215750\tAC145212.1\n+ENSG00000215689\tMGC39584\n+ENSG00000229510\tAC018692.2\n+ENSG00000220903\tFRG2C\n+ENSG00000233094\tAL592170.1\n+ENSG00000212857\tAL356585.1\n+ENSG00000215781\tAC011043.1\n+ENSG00000218497\tZNF84\n+ENSG00000236575\tZNF26\n+ENSG00000229631\tAL603926.1\n+ENSG00000220023\tAL592183.1\n+ENSG00000212884\tAC011841.1\n+ENSG00000268851\tAL162851.1\n+ENSG00000269725\tBX072566.2\n+ENSG00000237375\tBX072566.1\n+ENSG00000215615\tAL354822.1\n+ENSG00000215764\tKIR2DL2\n+ENSG00000217792\tKIR3DL2\n+ENSG00000268276\tAL590523.1\n+ENSG00000148828\tCT476828.1\n+ENSG00000215700\tPNRC2\n+ENSG00000215699\tSRSF10\n+ENSG00000215635\tAC145205.1\n+ENSG00000268590\tBAGE5\n+ENSG00000251180\tCU459201.1\n+ENSG00000215616\tAC002321.2\n+ENSG00000215611\tAC002321.1\n' |
| b |
| diff -r 000000000000 -r c01a342be892 test-data/matrix.mtx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/matrix.mtx Wed Apr 03 11:38:57 2019 -0400 |
| b |
| b'@@ -0,0 +1,2286887 @@\n+%%MatrixMarket matrix coordinate real general\n+%\n+32738 2700 2286884\n+32709 1 4\n+32707 1 1\n+32706 1 10\n+32704 1 1\n+32703 1 5\n+32702 1 6\n+32700 1 10\n+32699 1 25\n+32698 1 3\n+32697 1 8\n+32527 1 1\n+32496 1 1\n+32399 1 1\n+32346 1 1\n+32324 1 1\n+32209 1 1\n+32129 1 1\n+32106 1 1\n+32093 1 1\n+32068 1 1\n+32045 1 1\n+32023 1 25\n+32017 1 1\n+31998 1 1\n+31992 1 2\n+31971 1 2\n+31965 1 1\n+31964 1 1\n+31955 1 1\n+31929 1 1\n+31927 1 1\n+31886 1 1\n+31856 1 1\n+31785 1 1\n+31760 1 1\n+31666 1 1\n+31600 1 2\n+31591 1 1\n+31421 1 5\n+31399 1 10\n+31258 1 28\n+31189 1 7\n+31178 1 1\n+31169 1 1\n+31128 1 1\n+30984 1 1\n+30972 1 1\n+30971 1 37\n+30970 1 1\n+30958 1 2\n+30934 1 12\n+30927 1 1\n+30912 1 4\n+30895 1 1\n+30872 1 2\n+30849 1 1\n+30795 1 1\n+30792 1 1\n+30658 1 1\n+30656 1 22\n+30586 1 1\n+30570 1 5\n+30529 1 2\n+30406 1 1\n+30404 1 1\n+30379 1 2\n+30343 1 1\n+30314 1 1\n+30248 1 5\n+30170 1 1\n+30161 1 1\n+30147 1 1\n+30136 1 5\n+30126 1 1\n+30105 1 18\n+30038 1 1\n+30037 1 5\n+29959 1 1\n+29949 1 4\n+29943 1 19\n+29915 1 10\n+29910 1 3\n+29842 1 1\n+29831 1 1\n+29824 1 2\n+29795 1 1\n+29789 1 1\n+29782 1 1\n+29744 1 1\n+29734 1 4\n+29652 1 1\n+29634 1 1\n+29621 1 1\n+29620 1 8\n+29601 1 1\n+29569 1 1\n+29568 1 1\n+29515 1 1\n+29506 1 5\n+29498 1 1\n+29463 1 22\n+29454 1 1\n+29452 1 1\n+29450 1 1\n+29435 1 1\n+29431 1 1\n+29408 1 1\n+29378 1 1\n+29303 1 3\n+29210 1 1\n+29176 1 1\n+29167 1 1\n+29141 1 1\n+29073 1 1\n+29041 1 1\n+29035 1 1\n+28984 1 1\n+28966 1 1\n+28934 1 1\n+28924 1 1\n+28736 1 1\n+28676 1 1\n+28622 1 1\n+28593 1 2\n+28496 1 1\n+28313 1 1\n+28309 1 14\n+28290 1 1\n+28273 1 1\n+28165 1 1\n+28050 1 1\n+27960 1 2\n+27884 1 2\n+27867 1 1\n+27842 1 1\n+27838 1 1\n+27833 1 1\n+27827 1 1\n+27768 1 1\n+27724 1 1\n+27683 1 1\n+27682 1 4\n+27677 1 1\n+27663 1 1\n+27659 1 3\n+27639 1 1\n+27634 1 1\n+27617 1 4\n+27556 1 1\n+27548 1 1\n+27547 1 1\n+27519 1 1\n+27514 1 1\n+27501 1 1\n+27495 1 2\n+27334 1 1\n+27287 1 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1\n+5522 2700 16\n+5500 2700 1\n+5492 2700 1\n+5357 2700 1\n+5238 2700 7\n+5234 2700 2\n+5215 2700 1\n+5199 2700 1\n+5183 2700 1\n+5135 2700 1\n+5098 2700 1\n+5090 2700 2\n+5069 2700 2\n+5038 2700 1\n+4979 2700 6\n+4959 2700 1\n+4897 2700 1\n+4892 2700 2\n+4889 2700 1\n+4882 2700 1\n+4848 2700 1\n+4837 2700 1\n+4757 2700 1\n+4700 2700 1\n+4682 2700 1\n+4664 2700 1\n+4623 2700 1\n+4607 2700 1\n+4582 2700 1\n+4566 2700 1\n+4493 2700 1\n+4434 2700 1\n+4400 2700 1\n+4335 2700 2\n+4322 2700 1\n+4256 2700 1\n+4172 2700 12\n+4060 2700 1\n+4050 2700 1\n+4040 2700 1\n+4028 2700 18\n+3997 2700 1\n+3964 2700 1\n+3949 2700 1\n+3888 2700 1\n+3865 2700 1\n+3816 2700 1\n+3762 2700 12\n+3714 2700 1\n+3700 2700 1\n+3668 2700 2\n+3634 2700 1\n+3579 2700 1\n+3560 2700 1\n+3518 2700 1\n+3498 2700 2\n+3458 2700 1\n+3447 2700 1\n+3403 2700 1\n+3327 2700 1\n+3326 2700 1\n+3279 2700 1\n+3256 2700 5\n+3206 2700 1\n+2940 2700 1\n+2916 2700 1\n+2906 2700 2\n+2813 2700 1\n+2727 2700 1\n+2663 2700 1\n+2655 2700 1\n+2574 2700 1\n+2485 2700 1\n+2374 2700 1\n+2334 2700 1\n+2301 2700 2\n+2208 2700 1\n+2198 2700 4\n+2074 2700 1\n+2062 2700 1\n+1990 2700 20\n+1984 2700 1\n+1965 2700 4\n+1963 2700 1\n+1956 2700 1\n+1901 2700 2\n+1846 2700 2\n+1842 2700 1\n+1724 2700 1\n+1723 2700 4\n+1612 2700 1\n+1563 2700 1\n+1547 2700 1\n+1363 2700 9\n+1314 2700 1\n+1288 2700 1\n+1202 2700 1\n+1185 2700 1\n+1110 2700 7\n+1011 2700 1\n+925 2700 2\n+909 2700 9\n+860 2700 2\n+757 2700 1\n+710 2700 1\n+688 2700 1\n+687 2700 1\n+679 2700 2\n+589 2700 1\n+559 2700 3\n+518 2700 1\n+493 2700 19\n+465 2700 1\n+458 2700 1\n+416 2700 2\n+413 2700 2\n+179 2700 2\n+167 2700 4\n+122 2700 1\n+121 2700 1\n+82 2700 1\n' |
| b |
| diff -r 000000000000 -r c01a342be892 test-data/outliers_file.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outliers_file.txt Wed Apr 03 11:38:57 2019 -0400 |
| b |
| @@ -0,0 +1,28 @@ +AAGCACTGGTTCTT-1,6157 +AAGCCATGAACTGC-1,7070 +ACCCGTTGCTTCTA-1,6092 +ACGAACTGGCTATG-1,8931 +ACGAAGCTCTGAGT-1,7067 +ACGAGGGACAGGAG-1,7935 +AGAGGTCTACAGCT-1,10783 +ATACCGGAATGCTG-1,6582 +CAGGTTGAGGATCT-1,8015 +CATACTTGGGTTAC-1,7171 +CCAGTCTGCGGAGA-1,15844 +CGATACGACAGGAG-1,6733 +CGATCAGATGTGAC-1,6916 +GAAAGTGAAAGTGA-1,6177 +GACATTCTCCACCT-1,6193 +GAGCATACTTTGCT-1,6694 +GCCTCAACTCTTTG-1,5990 +GCGAAGGAGAGCTT-1,10282 +GCGTAAACACGGTT-1,5928 +GGCACGTGTGAGAA-1,10359 +GGGCCAACCTTGGA-1,8424 +GTGATGACAAGTGA-1,6333 +GTTAACCTTGCTTT-1,6102 +TGCAATCTTCAGGT-1,6317 +TGTAGGTGCTCTAT-1,6287 +TTACTCGAACGTTG-1,15301 +TTATGGCTTATGGC-1,6165 +TTGAGGACTACGCA-1,6344 |