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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-is-outlier.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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| @@ -0,0 +1,69 @@ +<tool id="scater_is_outlier" name="Scater DetectOutlier" version="@TOOL_VERSION@+galaxy0"> + <description>cells based on expression metrics</description> + <macros> + <import>scater_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +scater-extract-qc-metric.R -i '${R_scater_qc}' -m '$metrics' -o metrics.csv && + +scater-is-outlier.R -m metrics.csv +#if $nmads: + -n '$nmads' +#end if +#if $outlier_type: + -t '$outlier_type' +#end if +#if $outlier_log: + -l '$outlier_log' +#end if +#if $outlier_min_diff: + -d '$outlier_min_diff' +#end if + -o outliers.txt && + +cut -f1 -d',' outliers.txt > '$outliers_file' + ]]></command> + + <inputs> + <param name="R_scater_qc" type="data" format="rdata" label="Input serialized SingleCellExperiment RDS object" + help="A serialized SingleCellExperiment RDS object with pre-calculated QC metrics"/> + + <param name="metrics" type="text" label="Name of the QC metric used to detected outlier" + help ="character scalar, name of a numeric QC metric available in the input SingleCellExperiment object."/> + + <param name="outlier_type" argument="--type" type="select" value="both" label="Detect outlier from lower/higher/both ends of the distribution" + help="character scalar, choice indicate whether outliers should be looked for at both tails (default: both) or only at the lower end (lower) or the higher end (higher)."> + <option value="both">Both</option> + <option value="lower">Lower</option> + <option value="higher">Higher</option> + </param> + + <param name="outlier_log" argument="--log" type="boolean" checked="false" label="Transform to log10 scale" + help="logical, should the values of the metric be transformed to the log10 scale before computing median-absolute-deviation for outlier detection"/> + + <param name="nmads" argument="--nmads" type="integer" optional="true" value="5" label="Threshold in number of MAD away from the median" + help="scalar, number of median-absolute-deviations away from median required for a value to be called an outlier."/> + + <param name="outlier_min_diff" argument="--min-diff" type="integer" optional="true" label="Threshold in value difference from the median" + help="numeric scalar indicating the minimum difference from the median to consider as an outlier. The outlier threshold is defined from the larger of nmads MADs and min.diff, to avoid calling many outliers when the MAD is very small. If NA, it is ignored."/> + </inputs> + + <outputs> + <data name="outliers_file" format="csv" label="${tool.name} on ${on_string}: a one column csv of outliers"/> + </outputs> + + <tests> + <test> + <param name="extracted_metrics_file" value="extracted_metrics_file.txt"/> + <output name="outliers_file" file="outliers_file.txt"/> + </test> + </tests> + + <help><![CDATA[ +@HELP@ + +@VERSION_HISTORY@ + ]]></help> + <expand macro="citations"/> +</tool> |
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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+TGGTTA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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 add247843ef0 test-data/genes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes.tsv Wed Apr 03 11:42:39 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 add247843ef0 test-data/matrix.mtx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/matrix.mtx Wed Apr 03 11:42:39 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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2\n+12231 2700 1\n+12217 2700 1\n+12049 2700 3\n+11888 2700 10\n+11847 2700 1\n+11790 2700 1\n+11734 2700 1\n+11673 2700 1\n+11551 2700 1\n+11517 2700 1\n+11448 2700 19\n+11352 2700 1\n+11278 2700 2\n+11228 2700 1\n+11224 2700 1\n+11141 2700 1\n+11092 2700 1\n+11083 2700 25\n+10780 2700 2\n+10756 2700 12\n+10745 2700 1\n+10740 2700 20\n+10720 2700 1\n+10719 2700 1\n+10715 2700 1\n+10710 2700 29\n+10692 2700 2\n+10680 2700 1\n+10662 2700 1\n+10642 2700 3\n+10608 2700 4\n+10595 2700 3\n+10593 2700 4\n+10562 2700 1\n+10552 2700 3\n+10539 2700 1\n+10535 2700 3\n+10532 2700 2\n+10441 2700 1\n+10420 2700 1\n+10389 2700 1\n+10294 2700 1\n+10283 2700 1\n+10280 2700 1\n+10189 2700 1\n+10152 2700 8\n+10121 2700 1\n+10089 2700 1\n+10060 2700 1\n+10023 2700 1\n+9994 2700 1\n+9993 2700 1\n+9987 2700 8\n+9977 2700 1\n+9972 2700 11\n+9924 2700 1\n+9887 2700 1\n+9849 2700 1\n+9814 2700 1\n+9800 2700 12\n+9635 2700 1\n+9597 2700 1\n+9591 2700 1\n+9517 2700 1\n+9500 2700 1\n+9178 2700 1\n+9145 2700 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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 add247843ef0 test-data/outliers_file.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outliers_file.txt Wed Apr 03 11:42:39 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 |