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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8 |
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circexplorer2.xml macros.xml test-data/STAR_chimeric.junction test-data/annotation_01.gtf test-data/annotation_02.txt test-data/assemble.tgz test-data/mapsplice_chimeric.junction test-data/reads_01.fastq test-data/reads_01.fastq.gz test-data/reads_02.fastq test-data/reads_02.fastq.gz test-data/reads_03.fastq test-data/reads_03.fastq.gz test-data/reference_01.fa test-data/reference_02.fa test-data/test_02.bigwig test-data/test_03.bed test-data/test_04.bed test-data/test_05.tabular test-data/test_06.tabular test-data/test_07_annotated.txt test-data/test_07_combined.txt test-data/test_07_full.txt test-data/test_07_novel.txt test-data/test_08_a3bs.txt test-data/test_08_a5bs.txt test-data/test_08_annotated.txt test-data/test_08_combined.txt test-data/test_08_full.txt test-data/test_08_novel.txt |
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| diff -r 000000000000 -r 465d6578b4d0 circexplorer2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circexplorer2.xml Fri Aug 26 22:43:38 2022 +0000 |
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| b'@@ -0,0 +1,408 @@\n+<tool id="circexplorer2" name="CIRCexplorer2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">\n+ <description>circular RNA analysis</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro=\'xrefs\'/>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $mode.selector == \'align\'\n+ mkdir -p reads &&\n+ #set file_paths = []\n+ #for $i,$input_file in enumerate($mode.fastq)\n+ #set $fname = \'file\' + str($i) + "." + $input_file.ext\n+ #set $file_path = \'reads/\' + $fname\n+ ln -s \'$input_file\' \'$file_path\' &&\n+ $file_paths.append($file_path)\n+ #end for\n+ CIRCexplorer2 align\n+ @threads@\n+ --gtf \'$mode.gtf\'\n+ -g \'$mode.genome\'\n+ --fastq #echo \',\'.join($file_paths)#\n+ $mode.bw\n+ $mode.scale\n+ $mode.skip_tophat\n+ $mode.skip_tophat_fusion\n+ && tar -zcvf alignment.tgz \'./alignment\'\n+ #else if $mode.selector == \'parse\'\n+ CIRCexplorer2 parse\n+ -t $mode.aligner.selector\n+ $mode.aligner.fusion_file\n+ #if $mode.aligner.selector == \'TopHat-Fusion\'\n+ $mode.aligner.pe\n+ #end if\n+ $mode.aligner.f\n+ #else if $mode.selector == \'annotate\'\n+ ln -s $mode.genome reference_genome.fa &&\n+ CIRCexplorer2 annotate\n+ -r $mode.ref\n+ -g reference_genome.fa\n+ -b $mode.bed\n+ $mode.no_fix\n+ $mode.low_confidence\n+ #else if $mode.selector == \'assemble\'\n+ tar -zxf $mode.tophat &&\n+ CIRCexplorer2 assemble\n+ @threads@\n+ -r $mode.ref\n+ -m ./alignment\n+ $mode.remove_rRNA\n+ && tar -zcvf assemble.tgz \'./assemble\'\n+ #else\n+ ln -s \'$mode.genome\' reference_genome.fa &&\n+ #if $mode.assemble_file.ext.endswith(".gz")\n+ tar -zxf $mode.assemble_file &&\n+ #else\n+ tar -xf $mode.assemble_file &&\n+ #end if\n+ #if $mode.as_option.selector == \'enabled\'\n+ tar -zxf $mode.as_option.tophat &&\n+ #end if\n+ CIRCexplorer2 denovo\n+ -d ./assemble\n+ -r $mode.ref\n+ -b $mode.bed\n+ -g reference_genome.fa\n+ #if $mode.abs\n+ --abs \'abs\'\n+ #end if\n+ #if $mode.as_option.selector == \'enabled\'\n+ --as \'as\'\n+ $mode.as_option.type_mapping \'./alignment\'\n+ #end if\n+ $mode.no_fix\n+ $mode.rpkm\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <conditional name="mode">\n+ <param name="selector" type="select" \n+ label="Tool module" help="CIRCexplorer2 contains 5 modules. Each module \n+ functions as an independent component owning its distinctive duty. \n+ Meanwhile, they inteact with each other, and different circular RNA \n+ analysis pipelines are derived from different combinations of several \n+ modules.">\n+ <option value="align">Align: Map circular RNA junction reads with TopHat2/TopHat-Fusion</option>\n+ <option value="parse">Parse: Parse fusion junction information from other aligners</option>\n+ <option value="annotate">Annotate: Annotate circular RNA junction reads with gene annotations</option>\n+ <option value="assemble">Assemble: Assemble transcriptome for circular RNAs</option>\n+ <option value="denovo">De novo: Fetch de novo circular RNA isoforms</option>\n+ </param>\n+ <when value="align">\n+ <param argument="--gtf" type="data" format="'..b'"test_04.bed"/>\n+ </conditional>\n+ <output name="annotate" value="test_05.tabular" ftype="tabular"/>\n+ </test>\n+ <test expect_num_outputs="2">\n+ <!--Test 06: Module annotate-->\n+ <conditional name="mode">\n+ <param name="selector" value="annotate"/>\n+ <param name="ref" value="annotation_02.txt"/>\n+ <param name="genome" value="reference_02.fa"/>\n+ <param name="bed" value="test_04.bed"/>\n+ <param name="no_fix" value="true"/>\n+ <param name="low_confidence" value="true"/>\n+ </conditional>\n+ <output name="annotate" value="test_06.tabular" ftype="tabular"/>\n+ </test>\n+ <test expect_num_outputs="4">\n+ <!--Test 07: Module de novo-->\n+ <conditional name="mode">\n+ <param name="selector" value="denovo"/>\n+ <param name="ref" value="annotation_02.txt"/>\n+ <param name="bed" value="test_04.bed"/>\n+ <param name="genome" value="reference_02.fa"/>\n+ <param name="assemble_file" value="assemble.tgz"/>\n+ </conditional>\n+ <output name="denovo_combined" value="test_07_combined.txt" ftype="tabular"/>\n+ <output name="denovo_circularRNA" value="test_07_full.txt" ftype="tabular"/>\n+ <output name="denovo_annotated" value="test_07_annotated.txt" ftype="tabular"/>\n+ <output name="denovo_novel" value="test_07_novel.txt" ftype="tabular"/>\n+ </test>\n+ <test expect_num_outputs="6">\n+ <!--Test 08: Module de novo additional options-->\n+ <conditional name="mode">\n+ <param name="selector" value="denovo"/>\n+ <param name="ref" value="annotation_02.txt"/>\n+ <param name="bed" value="test_04.bed"/>\n+ <param name="genome" value="reference_02.fa"/>\n+ <param name="assemble_file" value="assemble.tgz"/>\n+ <param name="abs" value="true"/>\n+ <param name="no_fix" value="true"/>\n+ <param name="rpkm" value="true"/>\n+ </conditional>\n+ <output name="denovo_combined" value="test_08_combined.txt" ftype="tabular"/>\n+ <output name="denovo_circularRNA" value="test_08_full.txt" ftype="tabular"/>\n+ <output name="denovo_annotated" value="test_08_annotated.txt" ftype="tabular"/>\n+ <output name="denovo_novel" value="test_08_novel.txt" ftype="tabular"/>\n+ <output name="denovo_abs5" value="test_08_a5bs.txt" ftype="tabular"/>\n+ <output name="denovo_abs3" value="test_08_a3bs.txt" ftype="tabular"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+**Purpose**\n+\n+CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. It is the successor \n+of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization.\n+\n+-------------------\n+\n+ .. class:: infomark\n+\n+**Features**\n+\n+ * Precisely annotate circular RNAs (Annotate)\n+ * Support multiple circular RNA aligners (TopHat2/TopHat-Fusion, STAR, MapSplice, BWA and segemehl) (Align and Parse)\n+ * De novo assemble novel circular RNA transcripts (Assemble)\n+ * Characterize various of alternative (back-)splicing events of circular RNAs (Denovo)\n+ * Fast identify circuar RNAs with STAR or BWA (Parse)\n+ * Support both single-read and paired-end sequencing.\n+\n+-------------------\n+\n+.. class:: infomark\n+\n+**Modules** \n+\n+CIRCexplorer2 contains 5 modules. Each module functions as an independent component owning its distinctive duty. \n+Meanwhile, they inteact with each other, and different circular RNA analysis pipelines are derived from different \n+combinations of several modules. Understanding the detailed mechanism of each module could facilitate your circular \n+RNA research.\n+\n+CIRCexplorer2 documentation is available from `here <http://circexplorer2.readthedocs.org/>`_, including installation instructions and tutorial.\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 465d6578b4d0 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Aug 26 22:43:38 2022 +0000 |
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| @@ -0,0 +1,42 @@ +<macros> + <token name="@TOOL_VERSION@">2.3.8</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">circexplorer2</requirement> + </requirements> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">circexplorer2</xref> + </xrefs> + </xml> + <xml name="parse_fusion" token_format="" token_label="" token_help=""> + <param name="fusion_file" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP@"/> + </xml> + <xml name="parse_statistics"> + <param argument="-f" type="boolean" truevalue="-f" falsevalue="" checked="false" + label="Statistics fragment numbers rather than read numbers"/> + </xml> + <xml name="genome_file"> + <param argument="--genome" type="data" format="fasta" label="Reference genome" help="In FASTA format"/> + </xml> + <xml name="annotation_file"> + <param argument="--ref" type="data" format="txt" label="Gene annotation" + help="The file is in the format of Gene Predictions and RefSeq Genes with Gene Names" /> + </xml> + <xml name="junction_file"> + <param argument="--bed" type="data" format="bed" label="Back spliced junction file" + help="This file can be created by CIRCexplorer2 parse or CIRCexplorer2 align" /> + </xml> + <xml name="tophat_file"> + <param argument="--tophat" type="data" format="tgz" label="TopHat alignment file" + help="Generated by the align module" /> + </xml> + <token name="@threads@"><![CDATA[--thread=\${GALAXY_SLOTS:-10}]]></token> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.202895.115</citation> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r 465d6578b4d0 test-data/STAR_chimeric.junction --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/STAR_chimeric.junction Fri Aug 26 22:43:38 2022 +0000 |
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| b'@@ -0,0 +1,5901 @@\n+chr21\t40555792\t+\tchr21\t40555807\t+\t0\t0\t5\tHWI-ST1145:75:C102MACXX:8:1103:2916:85032\t40555724\t68M32S\t40555808\t68S32M\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:1103:6962:86588\t33478176\t75M25S\t42762453\t25M75S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:1103:13747:89413\t33478176\t75M25S\t42762453\t25M75S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:1103:13864:91736\t33478176\t75M25S\t42762453\t25M75S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:1103:9302:93440\t33478176\t75M25S\t42762453\t25M75S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:1103:21005:93508\t33478176\t75M25S\t42762453\t25M75S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:1103:16088:95780\t33478176\t75M25S\t42762453\t25M75S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:1103:3239:96377\t33478176\t75M25S\t42762453\t25M75S\n+chr21\t9827017\t-\tchr14\t20811404\t+\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:1103:9373:98764\t9827018\t23S77M\t20811405\t77S23M\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:1104:21120:2777\t33478176\t75M25S\t42762453\t25M75S\n+chr21\t15457410\t+\tchr4\t76807249\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:1104:8093:4207\t15457362\t48M52S\t76807197\t52M48S\n+chr21\t15457410\t+\tchr4\t76807249\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:1104:12723:4243\t15457362\t48M52S\t76807197\t52M48S\n+chr21\t16415896\t+\tchr21\t16386664\t+\t2\t1\t1\tHWI-ST1145:75:C102MACXX:8:1104:2211:5278\t16415835\t61M39S\t16386665\t61S39M\n+chr21\t15457410\t+\tchr4\t76807249\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:1104:8489:8368\t15457362\t48M52S\t76807197\t52M48S\n+chr21\t9827044\t-\tchr21\t9827580\t-\t0\t0\t2\tHWI-ST1145:75:C102MACXX:8:1104:7539:11189\t9827045\t78S22M\t9827502\t78M22S\n+chr21\t15457410\t+\tchr4\t76807249\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:1104:16766:12649\t15457362\t48M52S\t76807197\t52M48S\n+chr21\t38792600\t-\tchr21\t38798084\t-\t2\t0\t0\tHWI-ST1145:75:C102MACXX:8:1106:14631:41650\t38792601\t73S27M\t38798011\t73M27S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:1106:20825:43503\t33478176\t75M25S\t42762453\t25M75S\n+chr19\t24184156\t+\tchr21\t42762477\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:1106:15093:44244\t24184080\t76M24S\t42762453\t24M76S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:1106:6574:44839\t33478176\t75M25S\t42762453\t25M75S\n+chr19\t24184156\t+\tchr21\t42762477\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:1106:1468:46111\t24184080\t76M24S\t42762453\t24M76S\n+chr19\t24184156\t+\tchr21\t42762477\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:1106:8056:47212\t24184079\t77M23S\t42762454\t23M77S\n+chr21\t27228086\t-\tchr15\t65588475\t-\t0\t0\t1\tHWI-ST1145:75:C102MACXX:8:1106:11914:49309\t27228087\t43S57M\t65588432\t43M57S\n+chr21\t9827290\t-\tchr16\t33963108\t-\t0\t0\t2\tHWI-ST1145:75:C102MACXX:8:1106:20038:51678\t9827291\t36S64M\t33963072\t36M64S\n+chr21\t16415896\t+\tchr21\t16386664\t+\t2\t1\t1\tHWI-ST1145:75:C102MACXX:8:1106:10295:53707\t16415827\t69M31S\t16386665\t69S31M\n+chr21\t15457410\t+\tchr4\t76807249\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:1106:10428:55717\t15457362\t48M52S\t76807197\t52M48S\n+chr21\t9827360\t-\tchr2\t118847187\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:1106:7809:56221\t9827361\t24S76M\t118847164\t1S23M76S\n+chr21\t27327997\t+\tchr21\t27326960\t+\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:1106:13638:57873\t27327961\t36M64S\t27326961\t36S43M937N21M\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:1106:9775:58966\t33478176\t75M25S\t42762453\t25M75S\n+chr19\t24184156\t+\tchr21\t42762477\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:1106:18126:63071\t24184080\t76M24S\t42762453\t24M76S\n+chr21\t9827050\t-\tchr16\t33963128\t-\t0\t0\t3\tHWI-ST1145:75:C102MACXX:8:1106:2426:68714\t9827051\t61S39M\t33963067\t61M39S\n+chr21\t15457410\t+\tchr4\t76807249\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:1109:12744:13924\t15457362\t48M52S\t76807197\t52M48S\n+chr21\t34067593\t+\tchr21\t34066537\t+\t2\t1\t0\tHWI-ST1145:75:C102MACXX:8:1109:19265:15033\t34067567\t26M74S\t34066538\t26S74M\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:1109:18880:15951\t33478176\t75M25S\t42762453\t25M75S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX'..b'49\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2313:15648:54045\t15457362\t48M52S\t76807197\t52M48S\n+chr21\t9827030\t-\tchr10\t71390672\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:2313:8256:61125\t9827031\t27S73M\t71390646\t1S26M73S\n+chr21\t9827134\t-\tchr21\t9827313\t-\t0\t0\t1\tHWI-ST1145:75:C102MACXX:8:2313:18102:61303\t9827135\t65S35M\t9827248\t65M35S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:2313:11846:61549\t33478176\t75M25S\t42762453\t25M75S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:2313:17592:61851\t33478176\t75M25S\t42762453\t25M75S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:2313:14300:62064\t33478176\t75M25S\t42762453\t25M75S\n+chr21\t15457410\t+\tchr4\t76807249\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2313:4025:62573\t15457362\t48M52S\t76807197\t52M48S\n+chr21\t9827033\t-\tchr2\t118847187\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2313:17396:62829\t9827034\t23S77M\t118847164\t23M77S\n+chr21\t9827438\t-\tchr1\t7723413\t-\t0\t0\t2\tHWI-ST1145:75:C102MACXX:8:2313:19336:64989\t9827439\t33S67M\t7723389\t9S24M67S\n+chr21\t9827160\t-\tchr3\t32127282\t-\t0\t0\t1\tHWI-ST1145:75:C102MACXX:8:2313:15983:67189\t9827161\t23S77M\t32127260\t1S22M77S\n+chr21\t15457410\t+\tchr4\t76807249\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2313:12804:67659\t15457362\t48M52S\t76807197\t52M48S\n+chr19\t24184156\t+\tchr21\t42762477\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2313:14434:69896\t24184080\t76M24S\t42762453\t24M76S\n+chr21\t46548316\t-\tchr21\t46554748\t-\t2\t0\t3\tHWI-ST1145:75:C102MACXX:8:2313:4960:72975\t46548317\t79S21M\t46554671\t2S77M21S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:2313:10088:73763\t33478176\t75M25S\t42762453\t25M75S\n+chr21\t15457410\t+\tchr4\t76807249\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2313:14119:75715\t15457362\t48M52S\t76807197\t52M48S\n+chr21\t9827103\t-\tchr4\t976504\t+\t0\t0\t1\tHWI-ST1145:75:C102MACXX:8:2313:3892:77798\t9827104\t22S78M\t976505\t78S22M\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:2316:17828:30345\t33478176\t75M25S\t42762453\t25M75S\n+chr21\t15457410\t+\tchr4\t76807249\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2316:14137:32866\t15457362\t48M52S\t76807197\t52M48S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:2316:12960:33813\t33478176\t75M25S\t42762453\t25M75S\n+chr21\t47709817\t-\tchr21\t47709958\t-\t2\t17\t7\tHWI-ST1145:75:C102MACXX:8:2316:11394:36024\t47709818\t60S40M\t47709901\t3S57M40S\n+chr21\t38792600\t-\tchr21\t38794169\t-\t2\t0\t2\tHWI-ST1145:75:C102MACXX:8:2316:10325:38414\t38792601\t50S50M\t38794126\t7S43M50S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:2316:15016:40312\t33478176\t75M25S\t42762453\t25M75S\n+chr21\t9827012\t-\tchr21\t9827135\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2316:7880:40922\t9827013\t46S50M4S\t9827090\t1S45M54S\n+chr21\t9827012\t-\tchr21\t9827135\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2316:7882:40939\t9827013\t46S54M\t9827090\t1S45M54S\n+chr19\t24184156\t+\tchr21\t42762477\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2316:7058:41985\t24184080\t76M24S\t42762453\t24M76S\n+chr19\t24184156\t+\tchr21\t42762477\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2316:3499:42141\t24184080\t76M24S\t42762453\t24M76S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:2316:16185:43907\t33478176\t75M25S\t42762453\t25M75S\n+chr21\t15457410\t+\tchr4\t76807249\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2316:7570:44248\t15457362\t48M52S\t76807197\t52M48S\n+chr21\t16415896\t+\tchr21\t16386664\t+\t2\t1\t1\tHWI-ST1145:75:C102MACXX:8:2316:7492:44951\t16415843\t53M47S\t16386665\t53S47M\n+chr21\t9827098\t-\tchr2\t103455186\t-\t0\t0\t2\tHWI-ST1145:75:C102MACXX:8:2316:15779:47157\t9827099\t27S73M\t103455159\t27M73S\n+chr19\t24184156\t+\tchr21\t42762477\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2316:2679:50673\t24184080\t76M24S\t42762453\t24M76S\n+chr21\t15457410\t+\tchr4\t76807249\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2316:12287:51300\t15457362\t48M52S\t76807197\t52M48S\n+chr21\t38792600\t-\tchr21\t38794169\t-\t2\t0\t2\tHWI-ST1145:75:C102MACXX:8:2316:12272:54469\t38792601\t61S39M\t38794108\t61M39S\n+chr17\t33478251\t+\tchr21\t42762478\t-\t0\t0\t4\tHWI-ST1145:75:C102MACXX:8:2316:16891:58677\t33478176\t75M25S\t42762453\t25M75S\n+chr21\t15457410\t+\tchr4\t76807249\t-\t0\t0\t0\tHWI-ST1145:75:C102MACXX:8:2316:6401:59076\t15457362\t48M52S\t76807197\t52M48S\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/annotation_01.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotation_01.gtf Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,2801 @@\n+##gtf-version 3\n+#!gff-spec-version 1.21\n+#!processor NCBI annotwriter\n+#!genome-build ASM301845v1\n+#!genome-build-accession NCBI_Assembly:GCF_003018455.1\n+#!annotation-date 05/25/2022 04:54:31\n+#!annotation-source NCBI RefSeq \n+##sequence-region NZ_CP027599.1 1 5942969\n+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=562\n+NZ_CP027601.1\tRefSeq\tgene\t1\t542\t.\t-\t.\tgene_id "nbis-pseudogene-254"; ID "nbis-pseudogene-254"; Name "C7A06_RS33350"; gbkey "Gene"; gene_biotype "pseudogene"; locus_tag "C7A06_RS33350"; original_biotype "pseudogene"; partial "true"; pseudo "true"; start_range "." "1";\n+NZ_CP027601.1\tRefSeq\ttranscript\t1\t542\t.\t-\t.\tgene_id "nbis-pseudogene-254"; transcript_id "gene-C7A06_RS33350"; ID "gene-C7A06_RS33350"; Name "C7A06_RS33350"; Parent "nbis-pseudogene-254"; gbkey "Gene"; gene_biotype "pseudogene"; locus_tag "C7A06_RS33350"; original_biotype "mrna"; partial "true"; pseudo "true"; start_range "." "1";\n+NZ_CP027601.1\tProtein Homology\texon\t1\t542\t.\t-\t.\tgene_id "nbis-pseudogene-254"; transcript_id "gene-C7A06_RS33350"; ID "nbis-exon-5902"; Note "frameshifted; incomplete; missing C-terminus"; Parent "gene-C7A06_RS33350"; gbkey "CDS"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_001066419.1"; locus_tag "C7A06_RS33350"; partial "true"; product "IS66 family transposase zinc-finger binding domain-containing protein"; pseudo "true"; start_range "." "1"; transl_table "11";\n+NZ_CP027601.1\tProtein Homology\tCDS\t1\t542\t.\t-\t0\tgene_id "nbis-pseudogene-254"; transcript_id "gene-C7A06_RS33350"; ID "cds-C7A06_RS33350"; Note "frameshifted; incomplete; missing C-terminus"; Parent "gene-C7A06_RS33350"; gbkey "CDS"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_001066419.1"; locus_tag "C7A06_RS33350"; partial "true"; product "IS66 family transposase zinc-finger binding domain-containing protein"; pseudo "true"; start_range "." "1"; transl_table "11";\n+NZ_CP027601.1\tRefSeq\tgene\t562\t909\t.\t-\t.\tgene_id "nbis-gene-5648"; ID "nbis-gene-5648"; Name "tnpB"; gbkey "Gene"; gene "tnpB"; gene_biotype "protein_coding"; locus_tag "C7A06_RS33355";\n+NZ_CP027601.1\tRefSeq\ttranscript\t562\t909\t.\t-\t.\tgene_id "nbis-gene-5648"; transcript_id "gene-C7A06_RS33355"; ID "gene-C7A06_RS33355"; Name "tnpB"; Parent "nbis-gene-5648"; gbkey "Gene"; gene "tnpB"; gene_biotype "protein_coding"; locus_tag "C7A06_RS33355"; original_biotype "mrna";\n+NZ_CP027601.1\tProtein Homology\texon\t562\t909\t.\t-\t.\tgene_id "nbis-gene-5648"; transcript_id "gene-C7A06_RS33355"; Dbxref "Genbank:WP_000631725.1"; ID "nbis-exon-5903"; Name "WP_000631725.1"; Note "TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase."; Parent "gene-C7A06_RS33355"; gbkey "CDS"; gene "tnpB"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_858152.1"; locus_tag "C7A06_RS33355"; product "IS66 family insertion sequence element accessory protein TnpB"; protein_id "WP_000631725.1"; transl_table "11";\n+NZ_CP027601.1\tProtein Homology\tCDS\t562\t909\t.\t-\t0\tgene_id "nbis-gene-5648"; transcript_id "gene-C7A06_RS33355"; Dbxref "Genbank:WP_000631725.1"; ID "cds-WP_000631725.1"; Name "WP_000631725.1"; Note "TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase."; Parent "gene-C7A06_RS33355"; gbkey "CDS"; gene "tnpB"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_858152.1"; locus_tag "C7A06_RS33355"; product "IS66 family insertion sequence element accessory protein TnpB"; protein_id "WP_000631725.1"; transl_table "11";\n+NZ_CP027601.1\tRefSeq\tgene\t906\t1580\t.\t-\t.\tgene_id "nbis-gene-5649"; ID "nbis-gene-5649"; Name "tnpA"; gbkey "Gene"; gene "tnpA"; gene_biotype "protein_coding"; locus_tag "C7A06_RS33360";\n+NZ_CP027601.1\tRefSeq\ttranscript\t906\t1580\t.\t-\t.\tgene_id "nbis-gene-5649"; transcript_id '..b'NA modification|0006400||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_312074.1"; locus_tag "C7A06_RS03295"; product "tRNA pseudouridine(55) synthase TruB"; protein_id "WP_000089719.1"; transl_table "11";\n+NZ_CP027599.1\tProtein Homology\tCDS\t624137\t625081\t.\t+\t0\tgene_id "nbis-gene-564"; transcript_id "gene-C7A06_RS03295"; Dbxref "Genbank:WP_000089719.1"; ID "cds-WP_000089719.1"; Name "WP_000089719.1"; Ontology_term "GO:0006400" "GO:0004730"; Parent "gene-C7A06_RS03295"; gbkey "CDS"; gene "truB"; go_function "pseudouridylate synthase activity|0004730||IEA"; go_process "tRNA modification|0006400||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_312074.1"; locus_tag "C7A06_RS03295"; product "tRNA pseudouridine(55) synthase TruB"; protein_id "WP_000089719.1"; transl_table "11";\n+NZ_CP027599.1\tRefSeq\tgene\t625230\t625499\t.\t+\t.\tgene_id "nbis-gene-565"; ID "nbis-gene-565"; Name "rpsO"; gbkey "Gene"; gene "rpsO"; gene_biotype "protein_coding"; locus_tag "C7A06_RS03300";\n+NZ_CP027599.1\tRefSeq\ttranscript\t625230\t625499\t.\t+\t.\tgene_id "nbis-gene-565"; transcript_id "gene-C7A06_RS03300"; ID "gene-C7A06_RS03300"; Name "rpsO"; Parent "nbis-gene-565"; gbkey "Gene"; gene "rpsO"; gene_biotype "protein_coding"; locus_tag "C7A06_RS03300"; original_biotype "mrna";\n+NZ_CP027599.1\tProtein Homology\texon\t625230\t625499\t.\t+\t.\tgene_id "nbis-gene-565"; transcript_id "gene-C7A06_RS03300"; Dbxref "Genbank:WP_000059466.1"; ID "nbis-exon-579"; Name "WP_000059466.1"; Ontology_term "GO:0006412" "GO:0003735" "GO:0000314" "GO:0022627"; Parent "gene-C7A06_RS03300"; gbkey "CDS"; gene "rpsO"; go_component "organellar small ribosomal subunit|0000314||IEA" "cytosolic small ribosomal subunit|0022627||IEA"; go_function "structural constituent of ribosome|0003735||IEA"; go_process "translation|0006412||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_004933502.1"; locus_tag "C7A06_RS03300"; product "30S ribosomal protein S15"; protein_id "WP_000059466.1"; transl_table "11";\n+NZ_CP027599.1\tProtein Homology\tCDS\t625230\t625499\t.\t+\t0\tgene_id "nbis-gene-565"; transcript_id "gene-C7A06_RS03300"; Dbxref "Genbank:WP_000059466.1"; ID "cds-WP_000059466.1"; Name "WP_000059466.1"; Ontology_term "GO:0006412" "GO:0003735" "GO:0000314" "GO:0022627"; Parent "gene-C7A06_RS03300"; gbkey "CDS"; gene "rpsO"; go_component "organellar small ribosomal subunit|0000314||IEA" "cytosolic small ribosomal subunit|0022627||IEA"; go_function "structural constituent of ribosome|0003735||IEA"; go_process "translation|0006412||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_004933502.1"; locus_tag "C7A06_RS03300"; product "30S ribosomal protein S15"; protein_id "WP_000059466.1"; transl_table "11";\n+NZ_CP027599.1\tRefSeq\tgene\t625746\t627881\t.\t+\t.\tgene_id "nbis-gene-566"; ID "nbis-gene-566"; Name "pnp"; gbkey "Gene"; gene "pnp"; gene_biotype "protein_coding"; locus_tag "C7A06_RS03305";\n+NZ_CP027599.1\tRefSeq\ttranscript\t625746\t627881\t.\t+\t.\tgene_id "nbis-gene-566"; transcript_id "gene-C7A06_RS03305"; ID "gene-C7A06_RS03305"; Name "pnp"; Parent "nbis-gene-566"; gbkey "Gene"; gene "pnp"; gene_biotype "protein_coding"; locus_tag "C7A06_RS03305"; original_biotype "mrna";\n+NZ_CP027599.1\tProtein Homology\texon\t625746\t627881\t.\t+\t.\tgene_id "nbis-gene-566"; transcript_id "gene-C7A06_RS03305"; Dbxref "Genbank:WP_001297425.1"; ID "nbis-exon-580"; Name "WP_001297425.1"; Ontology_term "GO:0006402" "GO:0004654"; Parent "gene-C7A06_RS03305"; gbkey "CDS"; gene "pnp"; go_function "polyribonucleotide nucleotidyltransferase activity|0004654||IEA"; go_process "mRNA catabolic process|0006402||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_312072.2"; locus_tag "C7A06_RS03305"; product "polyribonucleotide nucleotidyltransferase"; protein_id "WP_001297425.1"; transl_table "11";\n+NZ_CP027599.1\tProtein Homology\tCDS\t625746\t627881\t.\t+\t0\tgene_id "nbis-gene-566"; transcript_id "gene-C7A06_RS03305"; Dbxref "Genbank:WP_001297425.1"; ID "cds-WP_0\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/annotation_02.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotation_02.txt Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,945 @@\n+ADARB1\tNM_001112\tchr21\t+\t46494494\t46646475\t46591571\t46642112\t11\t46494494,46548316,46591524,46595644,46600244,46602499,46603276,46604837,46624469,46640750,46641932,\t46494708,46548488,46591599,46596579,46600359,46602668,46603425,46605006,46624651,46640929,46646475,\n+DIP2A\tNM_001146116\tchr21\t+\t47878861\t47989926\t47879044\t47987535\t38\t47878861,47904669,47910512,47916900,47918494,47924273,47929169,47931341,47949004,47952039,47953436,47953916,47954497,47957136,47957358,47958395,47959789,47961668,47965049,47965793,47966827,47969683,47970455,47971546,47971736,47974081,47974487,47974734,47975894,47976851,47977497,47978135,47980634,47981660,47983770,47985625,47986472,47987282,\t47879135,47904741,47910632,47917020,47918746,47924402,47929289,47931527,47949096,47952150,47953560,47954026,47954600,47957201,47957452,47958515,47959904,47961808,47965186,47965874,47966955,47969798,47970657,47971656,47971817,47974205,47974609,47974846,47976004,47976982,47977666,47978306,47980696,47981718,47983845,47985800,47986596,47989926,\n+NCAM2\tNM_004540\tchr21\t+\t22370726\t22915650\t22370881\t22910278\t18\t22370726,22652897,22656513,22658588,22664423,22696702,22707824,22710708,22746182,22782593,22790792,22804427,22838926,22840982,22849611,22881171,22906857,22910166,\t22370936,22652972,22656720,22658732,22664561,22696820,22707985,22710854,22746333,22782781,22790889,22804601,22839046,22841104,22849792,22881376,22906977,22915650,\n+LINC00313\tNR_026863\tchr21\t-\t44881973\t44898103\t44898103\t44898103\t4\t44881973,44891391,44895851,44897943,\t44882141,44891574,44895919,44898103,\n+RUNX1-IT1\tNR_026812\tchr21\t-\t36410229\t36411723\t36411723\t36411723\t1\t36410229,\t36411723,\n+N6AMT1\tNR_047510\tchr21\t-\t30244512\t30257695\t30257695\t30257695\t7\t30244512,30248633,30250513,30252191,30254481,30255306,30257533,\t30245061,30248813,30250655,30252275,30254572,30255393,30257695,\n+LCA5L\tNM_001384287\tchr21\t-\t40777653\t40817704\t40777807\t40800419\t10\t40777653,40781904,40782189,40783643,40792631,40794901,40800097,40801056,40807345,40817650,\t40778538,40782022,40782293,40783728,40792769,40795416,40800429,40801137,40807468,40817704,\n+IFNAR1\tNM_001384500\tchr21\t+\t34697274\t34732170\t34717640\t34727855\t11\t34697274,34707829,34713304,34715573,34715816,34717551,34721396,34721694,34725063,34725943,34727621,\t34697436,34707953,34713480,34715728,34715982,34717666,34721596,34721849,34725214,34726089,34732170,\n+PCBP3-AS1\tNR_038876\tchr21\t-\t47247754\t47256333\t47256333\t47256333\t3\t47247754,47252521,47256199,\t47251155,47252572,47256333,\n+TPTE\tNM_199261\tchr21\t-\t10906742\t10990874\t10906904\t10973733\t24\t10906742,10908824,10910306,10914362,10916369,10920083,10921933,10933851,10934038,10934936,10941907,10942710,10942920,10944667,10951265,10952912,10959740,10969074,10970008,10971291,10973722,10985044,10987768,10990762,\t10907040,10908895,10910399,10914442,10916475,10920164,10921995,10933940,10934120,10934997,10941972,10942774,10943020,10944787,10951427,10952963,10959800,10969128,10970062,10971345,10973776,10985102,10987877,10990874,\n+ABCG1\tNM_004915\tchr21\t+\t43639266\t43717354\t43639372\t43716502\t15\t43639266,43645780,43691179,43693412,43697004,43702383,43704669,43705989,43707998,43708320,43710159,43711201,43711607,43714651,43716273,\t43639414,43646024,43691297,43693545,43697055,43702529,43704793,43706104,43708183,43708422,43710328,43711302,43711766,43714770,43717354,\n+MAP3K7CL\tNM_001371376\tchr21\t+\t30494310\t30548208\t30532294\t30547213\t4\t30494310,30521509,30532261,30547032,\t30494534,30521571,30532377,30548208,\n+PDXK\tNM_003681\tchr21\t+\t45139009\t45182180\t45139175\t45175944\t11\t45139009,45153949,45161547,45163604,45165959,45168875,45170380,45172398,45173463,45175578,45175831,\t45139262,45154004,45161652,45163688,45166006,45168961,45170426,45172510,45173600,45175645,45182180,\n+CFAP298-TCP10L\tNM_001350338\tchr21\t-\t33946031\t33984687\t33949083\t33984553\t8\t33946031,33951003,33954509,33975470,33976434,33979958,33982147,33984414,\t33949233,33951141,33954725,33975602,33976593,33980026,33982315,33984687,\n+CFAP298\tNM_001350337\tchr21\t-\t33973978\t33984687\t33974'..b'7362364\t47269999\t47361620\t18\t47063638,47088787,47155305,47175330,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359943,47361583,\t47063782,47088866,47155343,47175366,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNR_145492\tchr21\t+\t47063638\t47362364\t47362364\t47362364\t18\t47063638,47088787,47155305,47175330,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359950,47361583,\t47063782,47088866,47155343,47175366,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_001348243\tchr21\t+\t47167927\t47362364\t47269999\t47361620\t16\t47167927,47169294,47175330,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349833,47355166,47359943,47361583,\t47168053,47169389,47175366,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47355219,47360113,47362364,\n+PCBP3\tNM_001382277\tchr21\t+\t47167927\t47362364\t47269999\t47361620\t16\t47167927,47169294,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359943,47361583,\t47168053,47169389,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_001130141\tchr21\t+\t47268063\t47362364\t47269999\t47361620\t14\t47268063,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47337501,47349833,47350699,47355166,47359943,47361583,\t47268315,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_001382278\tchr21\t+\t47268063\t47362364\t47269999\t47361620\t15\t47268063,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349833,47350699,47355166,47359943,47361583,\t47268315,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_001382279\tchr21\t+\t47268063\t47362364\t47269999\t47361620\t15\t47268063,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359943,47361583,\t47268315,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47334008,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_020528\tchr21\t+\t47268063\t47362364\t47269999\t47361620\t15\t47268063,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359943,47361583,\t47268315,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+IFNAR2\tNM_001385054\tchr21\t+\t34602242\t34637968\t34614227\t34634882\t8\t34602242,34614190,34615977,34617255,34619022,34621013,34624966,34634865,\t34602521,34614282,34616019,34617379,34619195,34621159,34625135,34637968,\n+IFNAR2\tNM_001385055\tchr21\t+\t34602242\t34637968\t34614227\t34637276\t10\t34602242,34614190,34615977,34617255,34619022,34621013,34624966,34632901,34635097,34637238,\t34602521,34614282,34616019,34617379,34619195,34621159,34625135,34633032,34635575,34637968,\n+SH3BGR\tNM_001317740\tchr21\t+\t40823895\t40887428\t40824022\t40883702\t6\t40823895,40834300,40847060,40880924,40883606,40887014,\t40824067,40834486,40847141,40880954,40883736,40887428,\n+SH3BGR\tNM_007341\tchr21\t+\t40823895\t40887428\t40824022\t40883702\t7\t40823895,40834300,40847060,40871748,40880924,40883606,40887014,\t40824067,40834486,40847141,40871841,40880954,40883736,40887428,\n+APP\tNM_001385253\tchr21\t-\t27252860\t27543088\t27253980\t27542938\t17\t27252860,27264033,27269884,27277335,27284052,27326903,27327940,27347382,27348266,27354656,27369674,27394155,27423315,27425551,27462258,27484295,27542881,\t27254082,27264180,27269985,27277389,27284274,27327003,27328069,27347541,27348341,27354790,27369731,27394358,27423509,27425664,27462388,27484463,27543088,\n' |
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| diff -r 000000000000 -r 465d6578b4d0 test-data/assemble.tgz |
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| Binary file test-data/assemble.tgz has changed |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/mapsplice_chimeric.junction --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapsplice_chimeric.junction Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,97 @@\n+chr14~chr21\t50053492\t9827236\tFUSIONJUNC_1235\t5\t--\t255,0,0\t2\t76,28,76,28,\t0,18446744073669325389,\t0.500402\t0\tCCGG\t0\t1\t0.400000\t0\t28\t44\t0\t5\t0\t0\t0\t0\t0\t5\t0\t50053568\t9827208\t50053492,76M|\t9827209,28M|\t0\t0\t100000\t100000\t76\t76\t28\t28\t0\t0.004\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr14~chr21\t50053493\t9827094\tFUSIONJUNC_1236\t2\t--\t255,0,0\t2\t75,30,75,30,\t0,18446744073669325248,\t0.693147\t0\tACTT\t1\t1\t1.000000\t0\t30\t40\t0\t2\t0\t0\t0\t0\t0\t2\t0\t50053568\t9827064\t50053493,75M|\t9827065,30M|\t0\t0\t100000\t100000\t75\t75\t30\t30\t0\t0.01\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr14~chr21\t50053493\t9827185\tFUSIONJUNC_1237\t2\t--\t255,0,0\t2\t75,50,75,50,\t0,18446744073669325359,\t0.693147\t0\tACCG\t0\t2\t1.000000\t50\t50\t0\t0\t2\t0\t0\t0\t0\t0\t2\t0\t50053568\t9827135\t50053493,75M|\t9827136,50M|\t0\t0\t100000\t100000\t75\t75\t50\t50\t0\t0.01\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr14~chr21\t50329372\t9827094\tFUSIONJUNC_1238\t2\t+-\t255,0,0\t2\t75,30,75,30,\t0,18446744073669049369,\t0.693147\t0\tACTT\t1\t1\t1.000000\t0\t30\t40\t0\t2\t0\t0\t0\t0\t0\t2\t0\t50329297\t9827064\t50283377,6M45920N70M|\t9827065,30M|\t0\t0\t100000\t100000\t76\t76\t30\t30\t0\t0.01\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr14~chr21\t50329372\t9827185\tFUSIONJUNC_1239\t2\t+-\t255,0,0\t2\t75,50,75,50,\t0,18446744073669049480,\t0.693147\t0\tACCG\t0\t2\t1.000000\t50\t50\t0\t0\t2\t0\t0\t0\t0\t0\t2\t0\t50329297\t9827135\t50283377,6M45921N69M|\t9827136,50M|\t0\t0\t100000\t100000\t75\t75\t50\t50\t0\t0.01\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr14~chr21\t50329373\t9827236\tFUSIONJUNC_1240\t5\t+-\t255,0,0\t2\t76,28,76,28,\t0,18446744073669049508,\t0.500402\t0\tCCGG\t0\t1\t0.400000\t0\t28\t44\t0\t5\t0\t0\t0\t0\t0\t5\t0\t50329297\t9827208\t50283377,6M45919N72M|\t9827209,28M|\t0\t0\t100000\t100000\t78\t78\t28\t28\t0\t0.004\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr15~chr21\t65597049\t9827236\tFUSIONJUNC_1576\t2\t--\t255,0,0\t2\t72,40,72,40,\t0,18446744073653781844,\t0.693147\t0\tAAGG\t0\t0\t0.000000\t0\t40\t20\t0\t2\t0\t0\t0\t0\t0\t2\t0\t65597121\t9827196\t65597049,72M|\t9827197,40M|\t0\t0\t100000\t100000\t72\t72\t40\t40\t0\t0\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr16~chr21\t33962574\t9827005\tFUSIONJUNC_1888\t2\t-+\t255,0,0\t2\t31,72,31,72,\t0,18446744073685416120,\t0.693147\t0\tTACC\t0\t0\t0.000000\t31\t0\t38\t0\t2\t0\t0\t0\t0\t0\t2\t0\t33962605\t9827077\t33962574,31M|\t9827005,72M|\t0\t0\t100000\t100000\t31\t31\t72\t72\t0\t0\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chr21\t9827041\t9827486\tFUSIONJUNC_3283\t7\t--\t255,0,0\t2\t54,74,54,74,\t0,520,\t1.004242\t0\tAGTG\t0\t1\t0.142857\t27\t46\t8\t0\t7\t0\t0\t0\t0\t0\t7\t0\t9827095\t9827412\t9827041,54M|\t9827413,74M|\t0\t0\t100000\t100000\t54\t54\t74\t74\t0\t0.00142857\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chr21\t16386665\t16387546\tFUSIONJUNC_3284\t5\t--\t255,0,0\t2\t89,42,89,42,\t0,924,\t1.332179\t5\tGTAG\t0\t1\t0.200000\t0\t42\t16\t5\t0\t0\t0\t0\t0\t0\t5\t0\t16386754\t16387504\t16386665,89M|\t16387505,42M|\t0\t0\t100000\t100000\t89\t89\t42\t42\t0\t0.002\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chr21\t16386665\t16415895\tFUSIONJUNC_3285\t71\t--\t255,0,0\t2\t94,95,94,95,\t0,29326,\t3.069150\t5\tGTAG\t0\t3\t0.197183\t50\t50\t0\t71\t0\t0\t0\t0\t0\t0\t71\t0\t16386759\t16415800\t16386665,94M|\t16386773,15M29028N80M|16387536,11M28269N80M|\t0\t0\t100000\t100000\t94\t94\t95\t91\t0\t0.00197183\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chr21\t17138460\t17135210\tFUSIONJUNC_3286\t27\t++\t255,0,0\t2\t82,90,82,90,\t0,3333,\t2.176285\t6\tGTAG\t0\t3\t0.259259\t39\t49\t2\t27\t0\t0\t0\t0\t0\t0\t27\t0\t17138378\t17135300\t17135210,78M1269N4M|17135210,78M1836N12M|17135210,78M3028N7M|\t17138379,82M|\t0\t0\t100000\t100000\t90\t82\t82\t82\t0\t0.00259259\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chr21\t17172162\t17135210\tFUSIONJUNC_3287\t2\t++\t255,0,0\t2\t60,64,60,64,\t0,37013,\t0.693147\t6\tGTAG\t0\t0\t0.000000\t36\t40\t20\t2\t0\t0\t0\t0\t0\t0\t2\t0\t17172102\t17135274\t17135210,64M|\t17172103,60M|\t0\t0\t100000\t100000\t64\t64\t60\t60\t0\t0\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chr21\t27269885\t27284274\tFUSIONJUNC_3288\t2\t--\t255,0,0\t2\t62,77,62,77,\t0,14467,\t0.693147\t5\tGTAG\t0\t0\t0.000000\t23\t38\t24\t2\t0\t0\t0\t0\t0\t0\t2\t0\t27269947\t27284197\t27269885,62M|\t27284198,77M|\t0\t0\t100000\t100000\t62\t62\t77\t77\t0\t0\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chr21\t27326904\t27328069\tFUSIONJUNC_3289\t6\t--\t255,0,0\t2\t75,63,75,63,\t0,1229,\t1.791759\t5\tGTAG\t0\t0\t0.000000\t50\t50\t0\t6\t0\t0\t0\t0\t0\t0\t6\t0\t27326979\t27328006\t27326904,75M|\t27328007,63M|\t0\t0\t100000\t100000\t75\t75\t63\t63\t0\t0\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chr21\t27326904\t27354790\tFUSIONJUNC_3290\t2\t--\t255,0,0\t2\t62,72,62,72,\t0,27959,\t0.69314'..b'571\t50\t50\t0\t0\t7\t0\t0\t0\t0\t0\t7\t0\t9827066\t109301\t9827067,51M|\t109207,94M|\t0\t0\t100000\t100000\t51\t51\t94\t94\t0\t0.00428571\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chrUn_gl000220\t9827117\t153179\tFUSIONJUNC_3357\t7\t++\t255,0,0\t2\t51,94,51,94,\t0,18446744073699877773,\t1.277034\t0\tGTTC\t0\t2\t0.428571\t50\t50\t0\t0\t7\t0\t0\t0\t0\t0\t7\t0\t9827066\t153273\t9827067,51M|\t153179,94M|\t0\t0\t100000\t100000\t51\t51\t94\t94\t0\t0.00428571\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chrUn_gl000220\t9827134\t109190\tFUSIONJUNC_3358\t7\t--\t255,0,0\t2\t94,51,94,51,\t0,18446744073699833724,\t1.277034\t0\tGAAC\t0\t2\t0.428571\t50\t50\t0\t0\t7\t0\t0\t0\t0\t0\t7\t0\t9827228\t109139\t9827134,94M|\t109140,51M|\t0\t0\t100000\t100000\t94\t94\t51\t51\t0\t0.00428571\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chrUn_gl000220\t9827134\t153162\tFUSIONJUNC_3359\t7\t--\t255,0,0\t2\t94,51,94,51,\t0,18446744073699877696,\t1.277034\t0\tGAAC\t0\t2\t0.428571\t50\t50\t0\t0\t7\t0\t0\t0\t0\t0\t7\t0\t9827228\t153111\t9827134,94M|\t153112,51M|\t0\t0\t100000\t100000\t94\t94\t51\t51\t0\t0.00428571\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chrUn_gl000220\t9827144\t109357\tFUSIONJUNC_3360\t2\t--\t255,0,0\t2\t26,76,26,76,\t0,18446744073699833906,\t0.693147\t0\tGGCG\t0\t0\t0.000000\t26\t0\t48\t0\t2\t0\t0\t0\t0\t0\t2\t0\t9827170\t109281\t9827144,26M|\t109282,76M|\t0\t0\t100000\t100000\t26\t26\t76\t76\t0\t0\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chrUn_gl000220\t9827144\t153329\tFUSIONJUNC_3361\t2\t--\t255,0,0\t2\t26,76,26,76,\t0,18446744073699877878,\t0.693147\t0\tGGCG\t0\t0\t0.000000\t26\t0\t48\t0\t2\t0\t0\t0\t0\t0\t2\t0\t9827170\t153253\t9827144,26M|\t153254,76M|\t0\t0\t100000\t100000\t26\t26\t76\t76\t0\t0\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chrUn_gl000220\t9827149\t109375\tFUSIONJUNC_3362\t2\t++\t255,0,0\t2\t76,29,76,29,\t0,18446744073699833872,\t0.693147\t0\tGATA\t1\t1\t1.000000\t0\t29\t42\t0\t2\t0\t0\t0\t0\t0\t2\t0\t9827073\t109404\t9827074,76M|\t109375,29M|\t0\t0\t100000\t100000\t76\t76\t29\t29\t0\t0.01\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chrUn_gl000220\t9827149\t153347\tFUSIONJUNC_3363\t2\t++\t255,0,0\t2\t76,29,76,29,\t0,18446744073699877844,\t0.693147\t0\tGATA\t1\t1\t1.000000\t0\t29\t42\t0\t2\t0\t0\t0\t0\t0\t2\t0\t9827073\t153376\t9827074,76M|\t153347,29M|\t0\t0\t100000\t100000\t76\t76\t29\t29\t0\t0.01\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chrUn_gl000220\t9827284\t109217\tFUSIONJUNC_3364\t2\t++\t255,0,0\t2\t76,26,76,26,\t0,18446744073699833576,\t0.693147\t0\tCGCC\t0\t0\t0.000000\t0\t26\t48\t0\t2\t0\t0\t0\t0\t0\t2\t0\t9827208\t109243\t9827209,76M|\t109217,26M|\t0\t0\t100000\t100000\t76\t76\t26\t26\t0\t0\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chrUn_gl000220\t9827284\t153189\tFUSIONJUNC_3365\t2\t++\t255,0,0\t2\t76,26,76,26,\t0,18446744073699877548,\t0.693147\t0\tCGCC\t0\t0\t0.000000\t0\t26\t48\t0\t2\t0\t0\t0\t0\t0\t2\t0\t9827208\t153215\t9827209,76M|\t153189,26M|\t0\t0\t100000\t100000\t76\t76\t26\t26\t0\t0\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chrUn_gl000229\t9827005\t18248\tFUSIONJUNC_3366\t2\t-+\t255,0,0\t2\t72,31,72,31,\t0,18446744073699742891,\t0.693147\t0\tGGTA\t0\t0\t0.000000\t0\t31\t38\t0\t2\t0\t0\t0\t0\t0\t2\t0\t9827077\t18279\t9827005,72M|\t18248,31M|\t0\t0\t100000\t100000\t72\t72\t31\t31\t0\t0\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr2~chr21\t32117061\t37502930\tFUSIONJUNC_3988\t3\t-+\t255,0,0\t2\t57,89,57,89,\t0,5385959,\t1.098612\t0\tGTCC\t0\t0\t0.000000\t47\t43\t6\t0\t3\t0\t0\t0\t0\t0\t3\t0\t32117118\t37503019\t32117061,57M|\t37502930,89M|\t0\t0\t100000\t100000\t57\t57\t89\t89\t0\t0\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr2~chr21\t32117061\t37502999\tFUSIONJUNC_3989\t7\t-+\t255,0,0\t2\t89,65,89,65,\t0,5386004,\t1.945910\t0\tGTAC\t0\t1\t0.285714\t39\t27\t22\t0\t7\t0\t0\t0\t0\t0\t7\t0\t32117150\t37503064\t32117061,89M|\t37502999,65M|\t0\t0\t100000\t100000\t89\t89\t65\t65\t0\t0.00285714\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr2~chr21\t32142995\t37502848\tFUSIONJUNC_3990\t4\t-+\t255,0,0\t2\t82,78,82,78,\t0,5359932,\t1.386294\t5\tGTAG\t0\t0\t0.000000\t42\t39\t16\t0\t4\t0\t0\t0\t0\t0\t4\t0\t32143077\t37502926\t32142995,82M|\t37502848,78M|\t0\t0\t100000\t100000\t82\t82\t78\t78\t0\t0\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr2~chr21\t32142995\t37502930\tFUSIONJUNC_3991\t79\t-+\t255,0,0\t2\t87,92,87,92,\t0,5360028,\t2.730105\t0\tGTCC\t0\t3\t0.278481\t50\t50\t0\t79\t0\t0\t0\t0\t0\t0\t79\t0\t32143082\t37503022\t32142995,87M|\t37502930,92M|\t0\t0\t100000\t100000\t87\t87\t92\t92\t0\t0.00278481\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n+chr21~chr2\t37503360\t32157204\tFUSIONJUNC_3992\t3\t+-\t255,0,0\t2\t57,89,57,89,\t0,5346214,\t1.098612\t6\tGTAG\t0\t0\t0.000000\t47\t43\t6\t0\t3\t0\t0\t0\t0\t0\t3\t0\t37503303\t32157115\t32145960,20M11156N69M|\t37503304,57M|\t0\t0\t100000\t100000\t89\t89\t57\t57\t0\t0\t0\t0\t0\t0\t1e+06\t0\t0\t0\t0\t0\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/reads_01.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads_01.fastq Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,2224 @@\n+@A00270:331:HYHKLDSX2:3:1101:9209:1000 1:N:0:NTGGACGA+NGCCTAGT\n+TGCCGCCCGGTCGGGTTCAGACCGATTCGACCCGTGGCACTAATAATCCCCTGGGTAATGGTCTGCCCGAGGTTGTACGGGTTACCGATCGCCAGTACTACGTCGCCAATGTGCGGTACGCGACGTGCATTGATCGGAATGGTAGGTAAA\n++\n+FFFFFFFFFFF:FFF,FFFFFFFFFFF::FFFFFFFFF,:F:F:F,FFFFFFF,FFF:F,FFFF::FFFFFF,FFF:F:FFFFFFFFFFFFFFFFFFFFFFF:F:FFF,FFFFFFF,FFFFFFFF:FFF,FFF:FFFFFFFF,FFFFFF:\n+@A00270:331:HYHKLDSX2:3:1101:17761:1000 1:N:0:NTGGACGA+NGCCTAGT\n+GTCAGAAAACTGATTTTGCCTAACTGAGATGCGTTATGCAGACGGGCAACCGCGCTCAGAATAGAGGCGAAGACTAACGGCATAACGATCATTTGCAGCAGTTGAACATAGCCGTTACCAACGATGTTAAACCACTGTACAGAATCTTTA\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFF:FFFFFFFF,FF,FF\n+@A00270:331:HYHKLDSX2:3:1101:18810:1000 1:N:0:NTGGACGA+NGCCTAGT\n+CCACAGTTCTTTGTCACGCTGCCAGAGGCGCAGGTTTTCATCCCAGTTTAAGCCAACACCTGCAGTCGCCTGACGAATTTGTCCAGCTTCGCGATCTTTCACCGGGCTGAACGGAAAATTACCGACTTTGTATTTGGGGGCGGGTAAGGC\n++\n+FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFF::FFFFFFF,::FFFFFFFFFFF:FFF,FFFFFFFF:,,FFFF:FFF:FFFFFFFFF,FF:FFFFFFFF:F:FFFFF:F:,F:,FFFFFFFFF:FFFFFFFFFFFF,F\n+@A00270:331:HYHKLDSX2:3:1101:19488:1016 1:N:0:NTGGACGA+NGCCTAGT\n+CGACAATCGATAACGCCTTCATCAACCAGGGCGCAATGATCAATAACCCTTTACCTAATGCCTGCATCAGCGCGCTGGATTTTTCCGCCAGCCAATACCCCAGGTCATCAATCTTAACGATAACCCCTACCAGACCGTAGACGCCCACGG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FFFFFFFFFFFFFFFF,FFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:19524:1016 1:N:0:NTGGACGA+NGCCTAGT\n+CCATGACAGTCTCCAGTTTGTTTCAGTTAAAACGTAGTAGTGTTGGTAAATTAATGTTCTTCAGACGCCATCGACAGATAGACGATCGTCAGAACCATGAAGATGAAGGCTTGCAGCGTAATGATCAGGATGTGGAAAATGGCCCACGGC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:19560:1016 1:N:0:NTGGACGA+NGCCTAGT\n+CATGTGCAGCGGCCCGGACATCGTCTCGCCCTGCTGGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGTACGGTACGCGCCTGATCTACCAGCAGCATTCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACAT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:20591:1016 1:N:0:NTGGACGA+NGCCTAGT\n+GCCCAGACCAGCGCCACGCTGGCGGCCTACGGCGTCGATTTCATCGATAAAGATGATGCACGGTGCCGCTTTCTTCGCCTGTTCGAACATGTCACGAACACGGGATGCACCCACACCGACGAACATTTCTACGAAGTCAGAACCGGAGAT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:,,F,FFF,:,FFFFF:FFFFFFFF,FF,FFFFFF::FF,F:FF,FF::F:FFF:FF,FF,F,,FFFF:F:FFFFF:::F,,FF,F:FFFF,F:,F:F,F:F:F,F\n+@A00270:331:HYHKLDSX2:3:1101:24840:1016 1:N:0:NTGGACGA+NGCCTAGT\n+GTGCTGCATGACCCCATTACCGGCGGAACATCAATACCACCCGCGACCGCCAGATAACTGCGCATCCCGTGCTGCGGGCGTTTAAGCGGTAAACGCTGGCCTGCTTTCATCGGCAATCGCCAGCCGGTCCAGACGGCATTATCATCCAGC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF,F:F,FF,::FFF,F,:FFFFF::FF:FFFFFF,::::FF,:FFFF,FFFF:F:FFF,FF:,,,:,:FF\n+@A00270:331:HYHKLDSX2:3:1101:13548:1031 1:N:0:NTGGACGA+NGCCTAGT\n+GTGATGATGGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACGAGCGAGCTACCTTTATCGCGCAACTCACCGTCCAGTGCTTTGAGGAATGGTTGCTGATTAATTTCCAGATCGGTTATCGCC\n++\n+FFFFFFFFFF:FFFFFFFFF:FFFFF:F:FFFFFFFFF:FFFFFFF::::FFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFF:F::FFFF:FFFF:FFFFF:FFFF:FFF:F\n+@A00270:331:HYHKLDSX2:3:1101:15103:1031 1:N:0:NTGGACGA+NGCCTAGT\n+CCTTCACCAAATTCAGCAACACAGTCTTCACGGGTGGCGTATTTCGGCGCAGTACGTTCGGCTTCTTTCAGCGCATTGTTGTACGCGGTGGTACATTCGGCGCTTTTGCCTGGGTTTGCAGCTGAACAGTCGTCAGCATTTTGATAGAGA\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF:,FFFFF\n+@A00270:331:HYHKLDSX2:3:1101:18557:1031 1:N:0:NTGGACGA+NGCCTAGT\n+GCACCGATTGCCGGATGCAGCGTAAACGCCTTATCCGGCCTACGATTCCCATTATTTCAACAGATTACATTAAAGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCAGTTGCACTGAATGGCAGATGCGGCCAAAACACCTTATCC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF'..b'TTTGATGGACTGACGAACGGTTTTCCAGTTAGTCAGCATACCGCCCAGCCAGCGATGGTTCACGAAGAACTGGTCGCAGCTCAGAGCAGCGTCTTTC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:15429:4100 1:N:0:TTGGACGA+TGCCTAGT\n+TGCTACCTTCGAACACTTCTGCCGCCAGGCCCACAGACTCGTGCAGAGTCGGGTGCGCGTGGATGGTCAGTGCGATGTCTTCAGCATCACAACCCATTTCGATTGCCAGGCCGATTTCACCCAGCAGCTCGCCGCCGTTGGTACCGACAA\n++\n+FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFF:FFFF:FFF:F:FFFF::FFFFFFF:FFFF::FFFFFF,FFFFF:FFFFFFFFF,FFFFFFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:24126:4100 1:N:0:TTGGACGA+TGCCTAGT\n+GGGTAGAAGCGCTTACCTGCCCAGATGGTGGAACCTGGCAGCCATTCGATCAGGTTTTTACCCTGCACGTTTGCTTCACGGAAGGCCGGATCGGTAGCTTCCCAGTCATTCTGTTGCGCGACGGAATAGGCCACGTTAGTGTCGAAATAG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF:FFFF::FFFF\n+@A00270:331:HYHKLDSX2:3:1101:3179:4116 1:N:0:TTGGACGA+TGCCTAGT\n+CTCCGCTTTCCACCGCTTTCTCTACCTTCTTCAGCAAGTGCAGGTCAATAAAAGGACCTTTCTTGAGAGAACGTGGCATGGCGTATCCTCTCAAATTATTTGCTACGGCGACGTACGATGAATTTATCAGTACGCTTGTTGCTGCGGGTC\n++\n+FFFFFF,F:FFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFF,FFF:FFFFFF,FFF:FFF,FFF,FF,FF:FF,FFF,FFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFF:FFFF::FFFFFF,F\n+@A00270:331:HYHKLDSX2:3:1101:15176:4131 1:N:0:TTGGACGA+TGCCTAGT\n+CCGGGTTCTGTCGTGGACAGTCATTCATCTAGGCCAGCAATCGCTCACTGGCTCAAGCAGCCTACCCGGGTTCAGTACGGGCCGTACCTTATGAACCCCTATTTGGCCTTGCTCCGGGTGGAGTTTACCGTGCAACGGACTGTTACCAGC\n++\n+FF:FFFFFFF:FFFFFFFF:FFFFFFFFFFF,FFFFFFFFFF::FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFF:FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFF,FFFFFFF:F\n+@A00270:331:HYHKLDSX2:3:1101:20618:4131 1:N:0:TTGGACGA+TGCCTAGT\n+GCTGGAACAGCTTTACCCTGCGGTACCAGGAAGTTACGAGCATAGCCCGCTTTAACGTTTACCTGATCACCCAGGCTACCCAGGTTTGCTACTTTATCAAGCAGAATAACTTGCATTACCTTATCCTCTCAAAGTCGTATTAATGGACCG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FF:F:FFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:14299:4147 1:N:0:TTGGACGA+TGCCTAGT\n+GGAGGTTCCTTCAGTTTTCTGATGAAGCGCGAATATAGAGAAATATCCCGAATGTGCAGTTAACGAATTCTTGCGGTTTCTTTTAGCGCCGCCAATACCGCCAGCCCGTCGCGCAAGGGGCGCGGCTCGTGTGTGCGGATGAAGTCAGCT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:F\n+@A00270:331:HYHKLDSX2:3:1101:4490:4163 1:N:0:TTGGACGA+TGCCTAGT\n+TCCGCCATTCCCGCTTTGCAGTCCACGCTGACCTGGTAATGAATATCGGCACTTTTACCACGCACGGTTAGCGGTACTGACCATTTATCATCTTTACCCTGAATGTCCTGCAAACTGACCCAAGCCACGGGATCGGCCTGACCGACAATT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFF:\n+@A00270:331:HYHKLDSX2:3:1101:12210:4163 1:N:0:TTGGACGA+TGCCTAGT\n+CACCGTATAAGAGAATTGGCTTAAGTCCTCAGTGTTGGGGTTATGCGGGTAATCGTCTGACTGATGGCGAACAAATTTGTGGTAATTATCCCAGAATGGAATATTTTCCTCGTCAAACCAGTGAGAATAAGAGGTTATCCAGGTCAGATT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:17454:4163 1:N:0:TTGGACGA+TGCCTAGT\n+CGTCGGACCAGACATGCATGTTATTGGCCTGCGTTCCCAGCTTACCGCTCTGGTCGGTCATATCCGCTGGCAGCGAGAAACTTAACTTGCCATCAAGCAGGTTGACGGGATTCCCGGTAGCGTTACTTTCCGCGACCGAACCCTGCGCCG\n++\n+FFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFF,F:FFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFF:FFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:21142:4163 1:N:0:TTGGACGA+TGCCTAGT\n+ACCAGGTTGCTGACGATATAGTACAGCACCAGACCTGACGGGAACCACAGGAAGAACACGGTGAAGATGACCGGCATAAAGGTCATGATCTTCTGCTGCATCGGGTCGGTCACTGTGGTCGGCGACATCTTCTGAATGAAGAACATCGTT\n++\n+FFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/reads_01.fastq.gz |
| b |
| Binary file test-data/reads_01.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/reads_02.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads_02.fastq Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,2224 @@\n+@A00270:331:HYHKLDSX2:3:1101:16613:4178 1:N:0:TTGGACGA+TGCCTAGT\n+AGCGGAGAACAGCATTACTTCGTCTTCGCCGCTGGTCAGGTCAACGCCGATCAGCTCATCGCCGTCAACCAGTTTGATCGCCACTTTACCGGCGGTACGCAGACGGTTGAACTCGGTGAGGACAGTTTTCTTCACGGTACCGTTAGCGGT\n++\n+FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFF\n+@A00270:331:HYHKLDSX2:3:1101:7166:4194 1:N:0:TTGGACGA+TGCCTAGT\n+TCCGCATTCATCCCTAACGTCATAAGCATCCTGCTGTCTTTTTCTCCTTCAAAACGTTTCTCGCCGGAAGCATCACGCAAGACCGTTTCTCCGTTCGCCAGCAGGTCAAACTGGTAACCCAGCCCGGCGCGCGCTGTGATTTTCCAGTCA\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,\n+@A00270:331:HYHKLDSX2:3:1101:17418:4194 1:N:0:TTGGACGA+TGCCTAGT\n+GCGGTGGGCGACGTGATTGGTTATCCGAGCCTGGCATCAGCGGCCTATGACCAGGGGCGCATTGCCGCGCAGGCGCTGGTAAAAGGCGAAGCCACCGCGCATCTGATTGAAGATATCCCTACCGGCATTTACACCATCCCGGAAATCAGC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFF:F:F,FFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:30725:4194 1:N:0:TTGGACGA+TGCCTAGT\n+CCTGGATGTTTGCCAGAGAAAATCTCTGGAACTCACTTCACTCCTCCAAACGGAGAGAGCGTCTTAATTACGGTGAGCAGAAACAAGCCAGAATATAAAAGAATAATCTTAGCGTTCTGTCACCGTCTACGCAGGGGATTAAGTTTCTTG\n++\n+F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFF:FFFFF:,FFFFFFFFFFFFFF:\n+@A00270:331:HYHKLDSX2:3:1101:8838:4210 1:N:0:TTGGACGA+TGCCTAGT\n+GGCACGGGTGATGGAGAGTTTTCCTGCACCGGACTCTGTCGCCAGTCCGCACTCAATGGCCAGTGTGGTGATGGAGCACTGGACGCGGTTGGCCAGCGGGTCATAGTGGAAACACAGCCCCTGCAGCAGCGCATCAATTGCCCGTCGACG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:15040:4210 1:N:0:TTGGACGA+TGCCTAGT\n+GACTTGACCTGATAGTTTGGCTGTGAGCAATTATGTGCTTAGTGCATCTAACGCCGCCATAAACGGCGACAGGGTGGCGGGCCGCATTGGCAGAAAAAAGCGACGCCCATCGCCACCCGCGCGGGCAGACTGGGGGCCGGGGTGTTTGGT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,F,,,,,,,,,:,,,:FF:,,,,,,,,F,,,,,,,,:,,,:,,,,,,,,,,,,,,F,,,,,,F,,,,,F,,\n+@A00270:331:HYHKLDSX2:3:1101:17246:4210 1:N:0:TTGGACGA+TGCCTAGT\n+AGTCGGTTCGTCGAGCAGCAGCAAGTCTGAACGGCAAATCAGCGCCTGGGCAAGGTTAAGACGCATACGCCAGCCCCCGGAAAAATCACTTACCGGGCGCTCCAGTTGTTCATTGCTGAAACCGAGGCCGTGCAGCAGGCTGGCAGCACG\n++\n+FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFF:FFFFFFFFFFF::F:FFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:17427:4210 1:N:0:TTGGACGA+TGCCTAGT\n+GCGGTGGGCGACGTGATTGGTTATCCGAGCCTGGCATCAGCGGCCTATGACCAGGGGCGCATTGCCGCGCAGGCGCTGGTAAAAGGCGAAGCCACCGCGCATCTGATTGAAGATATCCCTACCGGCATTTACACCATCCCGGAAATCAGC\n++\n+F:FFFFFFFFFFF,FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFF:F:F,FFFFF\n+@A00270:331:HYHKLDSX2:3:1101:15194:4225 1:N:0:TTGGACGA+TGCCTAGT\n+CTGCAGCTAATAACCACTTTTTCACAATAAACTCCTTACCATCCCATTTGCACCGGAGGGTGCAGTTCTTTGCGTGGCCCGGCGATCTTATATTGATCGCCTAAAGTCATCGCTACACTACCACTACATTCCTTTGTGGAGAACACTTAC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FF\n+@A00270:331:HYHKLDSX2:3:1101:24035:4225 1:N:0:TTGGACGA+TGCCTAGT\n+GGATGTGAGTCGCGACGGAAAGCGTGGAACAGACGGGTAATCTGCTCGTGGATCATGGTATGACGGGTCACCGTAGTTTTAAATTCGTCATACTGTTCCTGAGTCGGTTTTTGAACATTCAGCAGGAAGTAACAAACTAACACGGAGTTA\n++\n+FFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FF,FFFFFFFF:FF::FFFFFFF,F,FF,F,FF,:,FFF,,F,,FF:F,FFF:,,FFF,F,FF,F,\n+@A00270:331:HYHKLDSX2:3:1101:31268:4225 1:N:0:TTGGACGA+TGCCTAGT\n+GCCTGGTCTATAAGGGCTCTCCCCCTTCATATTTCGCGCCGCAGATGCGTTATCTTCGCTCGCTCATCCCGGTCACTTACTGATGTAAGCTCCCGGGAATTCTCGAGCTTGCCGCCTTTCTGCAACTCGAACTATTTTGGGGGAGTTATC\n++\n+FFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF'..b'GTTATCAAAGAACGAACGGAAGACTTTGGCGCTAATCGGGTAGATATCACGGCCGGGGATCAACACGGTCGCATTCACCGTCATGATCATCTGATACTCTG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:7627:7435 1:N:0:TTGGACGA+TGCCTAGT\n+CCGCATTTCACCAGAACGCAGACGCAGGGTGACATAAGCACCATCACGAGCAACGATCTGAACGTAAGTACCAGCGGAACGTGCCAGCTGACCGCCTTTACCTGGTTTCATTTCTACGTTATGAACAGTAGAACCAACCGGGATGTTGCG\n++\n+:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:9977:7435 1:N:0:TTGGACGA+TGCCTAGT\n+CAACGTCATGGTAAGAACCGAAGTGCAGACGAATACCCATGTCTACTACCGGGTAGCCTGCCAGCGGACCTGCTTTCAGCTGTTCCTGGATACCTTTATCAACGGCCGGGATGTATTCGCCAGGGATTACACCACCTTTAATGTCGTTGA\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F\n+@A00270:331:HYHKLDSX2:3:1101:21947:7435 1:N:0:TTGGACGA+TGCCTAGT\n+CAGCCCGGCCAGCCGCCGCCAGTAGCCGTTACAGTCGCGGTTCGCCGTCAAAGGCCGTGGGGCAGCGCCATTTTCATTAGCGCGGAAGGCGTCGAGCCTCGCGAAAGTGTCAGTACCCTGCGGTGACAGGCGGACCACATCAACCAGGCC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:,F,,:F:,,FF,,FF,FF:F,FFF:FFFFF:FFF,:,,,FF:FFFF,FFFFF:FF,F,,,FFFFFF:FFF:FFFF:FF,,FFFFF,FF,FFFF,FF,FF,FF:,FF:FFF\n+@A00270:331:HYHKLDSX2:3:1101:26250:7435 1:N:0:TTGGACGA+TGCCTAGT\n+CTCTGATTGTAATAAGCGCGGCGCAAGCAGGGTTCGTCCGCCCATCGCTTCCAGTTGCTGCCAGGCAGTAACCACCTGCTGTGCGGCCTGTTCAGAAATCAGCCCGCCAATAAACGGCTGCGGTTCGTCATCCCAGTTGCCCGGCGTTAA\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFF\n+@A00270:331:HYHKLDSX2:3:1101:27082:7435 1:N:0:TTGGACGA+TGCCTAGT\n+CCAGCGCCGCAGAACCGGTACGACGGAAGTCTGCACATTCGTTGAACAGTTTGCCGACGATGTTGATGTAGGTAGTGGCGTACTGTTTTGCTTTGAACGGGAAGCCGGTCGCCAGAATAGTACCGTCGAGATCGCGAGCGGTGCTGCCGC\n++\n+FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F,FFFFFFF,FF,FFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFF:F:F,F,FFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:4634:7451 1:N:0:TTGGACGA+TGCCTAGT\n+GATCTGGATATCGAAGGGATCGTGCTGAAACAAGGTGCACCGACCGATCTGCCGAAAGATCTCGCCGCGCTGCAGAAAGGGAAGAAATTTACCCCGGAAAGCGTTTCTCGCCTGTTGGAAAAAATCAGTGCTGGTGGTTACGGTGACAAG\n++\n+FFFFFF,FFFF,FFFFFF,F,:FFFFFFFF:FF:FF,FFF,FF,::FF:FFF:FFFFF,F:FFF,:,FF:FFFF,FF:FFFF,,FFFFFFF:F:F,FFFFF,:FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:,:FFFFF:F,\n+@A00270:331:HYHKLDSX2:3:1101:4815:7451 1:N:0:TTGGACGA+TGCCTAGT\n+CGGCGGATAGGAGGCTTCGGTAGCAAAACGAATGGTTTCGGCAGCTGTGGCGGAAAGACTAAAACCTGCAATTAACGCGGCAATCAGAACTTTTTTCATTGTTGTTATCCCGAATCTTAGTGAGAGAGATAGTTTTTAAATGCTTCGGTT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:F,:FFFFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFF:FFFFFF:F:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFF:FFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:5990:7451 1:N:0:TTGGACGA+TGCCTAGT\n+CGCAGAAGTAACAAAGCTTATGGCAGAACGGGATATGTACGTAGAGAGATAATGGACGCTCAGGATAGCGCGCCACGGCTTGTAAAAACGCCTGTTCGCCGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCC\n++\n+FFFF,FFFFF:FFFFFFFFFFFFFFFFFF:F:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:F:FFF:FFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFF:FFF:FFFFFF:FFFF:FFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:7148:7451 1:N:0:TTGGACGA+TGCCTAGT\n+TGACCGTCGTCCATCGCGATCGGGTGGATCAGGGTAACAACCATTTTGATGTTGTCGCCCGGCATTACCATCTCTACGCCTTCCGGCAGTTCGATGGTACCAGTCATGTCAGTAGTACGGACGTAGAACTGCGGACGGTAGCCTTTGAAG\n++\n+FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFFFFFFFF:FFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:32515:7451 1:N:0:TTGGACGA+TGCCTAGT\n+CACCGGCAGCATCGCGTTACGCAGCGCATGGACGATAATCACCCGCATGCGGGTTAGCCCTTTGGCGCGCGCGGTGCGGATGTAATCCTCGCCCAGCACTTCCAGCATCGAGGAGCGTGTCATACGCACAATGACCGCCAGCGGAATAGT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/reads_02.fastq.gz |
| b |
| Binary file test-data/reads_02.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/reads_03.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads_03.fastq Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,2224 @@\n+@A00270:331:HYHKLDSX2:3:1101:17716:7467 1:N:0:TTGGACGA+TGCCTAGT\n+TTATCCGAAAAATCGAGCGACAGATTGCTCACTCAGGTGCCTCTACTTACGTTGATCATCTACCGTGACGCCTTGCGGCGGGGTGAAGGTAAATTTTGCTGCATCCACAGCCCCATTTTGCTGGGATTTCAGTTGATAACTGCTGCGCTG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:21459:7467 1:N:0:TTGGACGA+TGCCTAGT\n+CTCTTCGAGAAAGCGAATCAGGCTGCGGAGTTTTACCTGATAGTCGCCTTCATCTGTACCAGGACGGAATTTAATTTCCTTAACCTGGATAACTTTTTGCTTTTTCTTCTGTTCCTTAGAAGACTTGCTCTTTTCATAGAGGAATTTGCC\n++\n+FFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:2844:7482 1:N:0:TTGGACGA+TGCCTAGT\n+CCGTCAGAGTGGGCCAGCAGGTCGGCAAAATTACCCGCGCTGGCCTCTTTCGTGTCGACGAAATAGTTGCGCGCGGCGGGAGTAGAAAACTCATCAAATGCCGATTTGGCAAAACGCGGCAACAGCAGTGTGTTGGCGTAGCCATTGACC\n++\n+FFFFF:FFFFFFFFFFFFFFF,FFFFF,F,FF:FF:FFFF,FFFF:F:,FF,:F,FF:FFF:::,,::FFFFFFFFFFFF,F,:FF::FF,F:,F,FFFF:FFF:,FFFF,,FFFFFFFF,,FFFF,F,,,F,,FFFFF:FFF,:FF:FF\n+@A00270:331:HYHKLDSX2:3:1101:15230:7482 1:N:0:TTGGACGA+TGCCTAGT\n+CAATAATATTCAGGCCGCTGTCAGCCAGTTTCTTCGCGCCGAGTTCGGCGTTGTTACCTTCCAGACGTACCACGACCGGTACGTTAACACCCACTTCTGCTACCGCGCCGATGATACCGTCAGCGATCAGGTCGCAACGAACGATACCGC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:16333:7482 1:N:0:TTGGACGA+TGCCTAGT\n+CCTTAACTTTGCCGTTGATAACACCGGTAACAGTTTCAGCATCTTCGTAAGCTTTTTCCAGCGTGATCCAGGCTTCGTGACGTTTAGCTTTCTCACGGGACAGCAGAGTTTCACCGAAGCCGTCTTCTACTGCGTCCAGAGCAACGTCAA\n++\n+FFFFFFF:FFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:29767:7482 1:N:0:TTGGACGA+TGCCTAGT\n+TGTACGGCAGCAGGGACAGGTAGCGAGCGCGTTTGATAGCGCGAGCCAGCTGACGCTGGTATTTTGCACGGGTACCGGTGATACGGCTTGGGACAATCTTACCGCTTTCGGTGATGTAGTTTTTCAGCGTAGCGATATCTTTATAGTCGA\n++\n+FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:12002:7498 1:N:0:TTGGACGA+TGCCTAGT\n+GTCACGACCTTCGTCACGGAATTTCTCAGCCATGGTCAGACCGGTCAGAGCAACGCGCAGACGGTTTCCCGGCGGCTCGTTCATCTGGCCATACACCAGGGATACTTTGTCGATAACGTTGGAGTCGGTCATATAGTTGTAGAAGACGTT\n++\n+FFFFFFFFFFFFFFF,FFFFFF,FF:FFF,F:FFFFFFFF:FFFF:FFFFFFFFFFFFF:FFFFF:FF:F,FFFFFFFF:FF:FF,FFFFF:FFFF:,F:FF,:::::FFF:FFFFF:,FFFFFFFF:F:F:,F,,:,:FF,,F:,F:FF\n+@A00270:331:HYHKLDSX2:3:1101:16685:7498 1:N:0:TTGGACGA+TGCCTAGT\n+GAGCAGCTTCAACGATCCAACGCATTGCCAGAGCATTACGACGAACCGGACGGACTTCAACTGGTACCTGATAAGTAGAACCACCAACGCGGCGAGACTTAACTTCTACAGTCGGGCGCACGTTTTCGAGAGCTACTTCGAATGCTTCCA\n++\n+FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFF:FFFFFFF:FFFFF,FF:FFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:9118:7513 1:N:0:TTGGACGA+TGCCTAGT\n+TGCGGCATACGACCTAACCAGTCGTAACCCATTTCAAAACCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGGTTTTCGTGGGTCGGACCATTGTTAGGAATAAAACCAGTGTCATGGTACTGGGACCAGCCC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFF\n+@A00270:331:HYHKLDSX2:3:1101:24704:7513 1:N:0:TTGGACGA+TGCCTAGT\n+GGAGAGGGTGATAACGTTGTTCAGACCTTCTGCGCCGCAGAAACGAGACTGGGCGAACGGCAGATCGGCAGAGATACACAGCACAACGGTGTTGTCGATCTCAGTTGCCAGTTGGTTAAACTTACGTACTGATGCGGCGCAAACACCGGT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,FFFFFFFFFFFFFFFF:FFFFFF:,FFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:15619:7529 1:N:0:TTGGACGA+TGCCTAGT\n+ACCTGGTATCTGAAGGCTGCCGCTCAGGGGAGCGTCGGCGCTTACGTCAACATCGGTTATATGTATAAACACGGACAAGGCGTTGAGAAAGATTATCAGGCTGCCTTTGAATGGTTTACGAAAGCCGCTGAATGCAATGACGCCACTGCC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF'..b'ACGGTCAGCGCCCAGCGGCTGCGCCAGCACCTGATCGCCATGAATGCAGGTTTTCATCTGCTCGCTGGAGAGATACAAATCATCTTTAC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:14470:10770 1:N:0:TTGGACGA+TGCCTAGT\n+ACCGATGAACTCCATAAATGTGGAGACCGAGGTGCGGATCACACTCCCGCCTTTGGCGATACGCTGACGCGCCTGGCGCATGAGTTGGCGTAGCATTAAACCGCTCTCATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF\n+@A00270:331:HYHKLDSX2:3:1101:16315:10770 1:N:0:TTGGACGA+TGCCTAGT\n+GTTCCAGTGCGGTAACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCGATGA\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:9218:10786 1:N:0:TTGGACGA+TGCCTAGT\n+CTGGTGTTGCGGCGACGGACGAGCAGCCTCATGCTCCTGAGCGTTAGCCGGGGCATGATTCACGCGGTGAACACGAACCTCACCAACGCCCTCATCATCTTCGACATCCTCGTCATAAGAATCGTCGTCACGTTTTGACTTCATTCGTTT\n++\n+F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:30499:10786 1:N:0:TTGGACGA+TGCCTAGT\n+CGGACGATAGCCCTGTATAAAATCCTCATAGCTATAAGATTGATGGAACTGAACCATATTGACGCGTTGCGGAGCCTTTTCTCCTGTCAGCAGGTAAGCCAGACGGCGTGCAACAAAGGTTTTTCCAACGCCGGGCGGCCCCTGGAGGAT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:\n+@A00270:331:HYHKLDSX2:3:1101:2790:10802 1:N:0:TTGGACGA+TGCCTAGT\n+CTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGACCATCACGTACAGACCCAGACCTACAGCGATCCTCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAG\n++\n+F,FF:,:F:FFF:,:FF:FFFFF,FF,:FFF,,::F:,,F:F:F:FF:F,,FFFFF:FF:,F:FF,:,F,FFF:FF:FF:F:FFFF:F,F,F:FFF:,F:F:F,:,F:FF::FFFFFFF::,,,,FF:F,FFF,,FF,:F:,FF:FF::F\n+@A00270:331:HYHKLDSX2:3:1101:4164:10802 1:N:0:TTGGACGA+TGCCTAGT\n+CCACAATGTCGCCTTTCTTCGCGGTGCTTAATGCCTGGGCGAAGATCCCGGGCAACTCCTGAATACGGCCCCAGCCCATCTGGCCGCCGTTCAGCGCCTGCTGGTCGGCAGAATGAGCAATCGCCAGCTTACCGAAATCAGCGCCGTTAC\n++\n+F,F:FFFFFF,FFFFF,:FF:FFFFF:FFFFF,:FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFF:FFFFFFFF::FFFFFFFFF:FFFFF:F:,:FFF:FFF:FFFFFFFFFFFF:FF,FF:::FFFFFFFFFFFFFFF:FF:FF,FF,\n+@A00270:331:HYHKLDSX2:3:1101:11288:10802 1:N:0:TTGGACGA+TGCCTAGT\n+GCCTTCCCAGGTTGCCCATTGGGTATCGGTATCGATGTTCATTTTCACTACGCCGTAGCTTACGGAATCTTTGATTTCCTGAGCAGTAGAACCGGAGCCACCGTGGAATACGAAGTTCAGGCTGTTGTGCGGCAGGTTGTGTTTCTTAGA\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FF\n+@A00270:331:HYHKLDSX2:3:1101:18105:10802 1:N:0:TTGGACGA+TGCCTAGT\n+TCCGGGATCAGGAACAGTTTCCAGCGTTTGGTGCGCAGACCAACGGTGGCACGGCTGGAAATCACCGAAACAAACGGTGACAGGATCAACGAGAAGACAATCGGTGCCAGCCAGAACAGGAAACGCAGATCCAACCACGCCATACCAACA\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FF\n+@A00270:331:HYHKLDSX2:3:1101:19840:10802 1:N:0:TTGGACGA+TGCCTAGT\n+AGCTGAAGTTTGTCATCCGGCAACGCCTTAGCGAAAAGGGCGTCATCCATATCTTCTGTGCTGGCACTGTCGATGGTGACAAAATCCAGCGCGGTCAGATCTTCACGAACCAGACCTTCATCGAGCATTTCGGTAGCGACGCCGTCTGGT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF\n+@A00270:331:HYHKLDSX2:3:1101:3920:10817 1:N:0:TTGGACGA+TGCCTAGT\n+CTTGGCAAGAGTAATCAGCGGCTCAACTACGCGGCGCAGCTCTTTCGCTTTAGGCAGAGTCGTCTTGATGATTTCATGACGAACCAGTGAACCAGCCATATTGCGGAACAAAGCCTGGCGATGGCTGCTGTTGCGGTTCAGTTGACGACC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFF,,::,,F:FFF,,::,F,,F,F,,,:FF:F,FFF,,,:F,::F,FF:,:,:F,FFF:,,FFFF:F,,,FF,:F::FF,FF,:,FF:F\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/reads_03.fastq.gz |
| b |
| Binary file test-data/reads_03.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/reference_01.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference_01.fa Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,12946 @@\n+>NZ_CP027599.1 Escherichia coli strain 97-3250 chromosome, complete genome\n+ATCCCGGCCCCGGCAGAACCGACCTATCGTTCTAACGTAAACGTCAAACACACGTTTGATAACTTCGTTGAAGGTAAATC\n+TAACCAACTGGCGCGCGCGGCGGCTCGCCAGGTGGCGGATAACCCTGGCGGTGCCTATAACCCGTTGTTCCTTTATGGCG\n+GCACGGGTCTGGGTAAAACTCACCTGCTGCATGCGGTGGGTAACGGCATTATGGCGCGCAAGCCGAATGCCAAAGTGGTT\n+TATATGCACTCCGAGCGCTTTGTTCAGGACATGGTTAAAGCCCTGCAAAACAACGCGATCGAAGAGTTTAAACGCTACTA\n+CCGTTCCGTAGATGCACTGCTGATCGACGATATTCAGTTTTTTGCTAATAAAGAACGATCTCAGGAAGAGTTTTTCCATA\n+CCTTCAACGCCCTGCTGGAAGGTAATCAACAGATCATTCTCACCTCGGATCGCTATCCGAAAGAGATCAACGGCGTTGAG\n+GATCGTTTGAAATCCCGCTTCGGTTGGGGACTGACTGTGGCAATCGAACCGCCAGAGCTGGAAACCCGTGTGGCGATCCT\n+GATGAAAAAGGCCGACGAAAACGACATTCGTTTGCCGGGCGAAGTGGCGTTCTTTATCGCCAAGCGTCTACGATCTAACG\n+TACGTGAGCTGGAAGGGGCGCTGAACCGCGTCATTGCCAATGCCAACTTTACCGGACGGGCGATCACCATCGACTTCGTG\n+CGTGAGGCGCTGCGCGACTTGCTGGCATTGCAGGAAAAACTGGTCACCATCGACAATATTCAGAAGACGGTGGCGGAGTA\n+CTACAAGATCAAAGTCGCGGATCTCCTTTCCAAGCGTCGATCCCGCTCGGTGGCGCGTCCGCGCCAGATGGCGATGGCGC\n+TGGCGAAAGAGCTGACTAACCACAGTCTGCCGGAGATTGGCGATGCGTTTGGTGGTCGTGACCACACGACGGTGCTTCAT\n+GCCTGCCGTAAGATCGAGCAGTTGCGTGAAGAGAGCCACGATATCAAAGAAGATTTTTCAAATTTAATCAGAACATTGTC\n+ATCGTAAACCTATGAAATTTACCGTAGAACGTGAGCATTTATTAAAACCGCTACAACAGGTGAGCGGTCCGTTAGGTGGT\n+CGTCCTACGCTACCGATTCTCGGTAATCTGCTGTTACAGGTTGCTGACGGTACGTTGTCGCTGACCGGTACTGATCTCGA\n+GATGGAAATGGTGGCACGTGTTGCGCTGGTTCAGCCACACGAGCCAGGAGCGACGACCGTTCCGGCGCGCAAATTCTTTG\n+ATATCTGCCGTGGTCTGCCTGAAGGCGCGGAAATTGCCGTGCAGCTGGAAGGTGAACGGATGCTGGTACGCTCCGGGCGT\n+AGCCGTTTTTCGCTGTCTACCCTGCCAGCGGCGGATTTCCCGAACCTCGATGACTGGCAGAGTGAAGTCGAATTTACCCT\n+GCCGCAGGCAACGATGAAGCGTCTGATTGAAGCGACCCAGTTTTCGATGGCGCATCAGGACGTTCGCTATTACTTAAATG\n+GTATGCTGTTTGAAACCGAAGGTGAAGAACTGCGCACCGTGGCAACCGACGGCCACCGTCTGGCGGTCTGTTCAATGCCA\n+ATTGGTCAATCTTTGCCAAGCCATTCGGTGATCGTACCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGG\n+CGACAATCCGCTGCGCGTGCAGATTGGCAGCAACAATATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGG\n+TGGATGGTCGCTTCCCGGATTACCGCCGCGTTCTGCCGAAGAATCCGGACAAACATCTGGAAGCTGGCTGCGATCTGCTC\n+AAGCAGGCGTTTGCCCGTGCGGCAATTCTCTCTAACGAGAAATTCCGCGGCGTGCGCCTGTATGTCAGCGAAAACCAGCT\n+GAAAATCACCGCCAACAACCCGGAACAGGAAGAAGCGGAAGAGATCCTCGACGTTACCTATAGCGGTGCGGAGATGGAAA\n+TCGGCTTCAACGTCAGCTATGTGCTGGATGTTCTGAACGCGCTGAAATGCGAAAACGTCCGCATGATGCTGACCGATTCG\n+GTTTCCAGCGTGCAGATTGAAGATGCCGCATCACAGTCGGCTGCCTATGTTGTCATGCCAATGAGACTGTAATGTCCCTC\n+ACCCGCTTGTTGATCCGCGATTTCCGCAACATTGAAACCGCGGATCTCGCTTTATCTCCCGGCTTTAACTTTCTGGTAGG\n+TGCCAACGGCAGTGGCAAAACCAGCGTGCTGGAAGCCATCTATACGCTCGGCCATGGTCGGGCGTTTCGCAGTTTGCAGA\n+TTGGTCGCGTCATTCGCCATGAGCAGGAGGCATTTGTTCTCCATGGGCGATTACAGGGCGAAGAGCGCGAGACGGCGATT\n+GGCTTAACCAAGGACAAACAGGGCGACAGCAAAGTCCGCATCGACGGTACTGACGGGCATAAAGTCGCGGAACTGGCGCA\n+CCTGATGCCAATGCAGCTGATAACGCCAGAAGGGTTTACTTTACTCAACGGCGGCCCCAAATACAGAAGAGCATTCCTCG\n+ACTGGGGATGCTTTCACAACGAACCCGGATTTTTCACCGCCTGGAGCAATCTCAAGCGATTGCTCAAGCAGCGCAATGCG\n+GCGCTGCGCCAGGTGACACGTTACGAACAGCTACGCCCGTGGGATAAAGAACTGATCCCGCTGGCGGAGCAAATCAGCAC\n+CTGGCGCGCGGAGTATAGCGCCGGTATCGCGGCCGATATGGCCGATACCTGTAAGCAATTTCTCCCTGAGTTTTCTCTGA\n+CTTTCTCTTTCCAGCGCGGCTGGGAGAAAGAGACAGAATATGCTGAGGTGCTGGAACGTAATTTTGAACGCGATCGCCAG\n+CTAACCTACACCGCGCATGGCCCGCATAAAGCGGACTTACGCATTCGCGCCGACGGTGCGCCGGTGGAAGATACCTTATC\n+GCGTGGGCAGCTTAAGCTGTTGATGTGCGCCTTACGTCTGGCGCAAGGAGAGTTCCTCACCCGTGAAAGCGGGCGGCGGT\n+GTCTCTACCTGATAGATGATTTTGCCTCTGAGCTTGATGATGAGCGTCGTGGGTTGCTTGCCAGCCGCTTAAAAGCGACG\n+CAATCACAGGTCTTTGTCAGCGCGATCAGTGCTGAACACGTTATAGACATGTCGGACGAAAATTCGAAGATGTTTACCGT\n+GGAAAAGGGTAAAATAACGGATTAACCCAAGTATAAATGAGCGAGAAACGTTGATGTCGAATTCTTATGACTCCTCCAGT\n+ATCAAAGTCCTGAAAGGGCTGGATGCGGTGCGTAAGCGCCCGGGTATGTATATCGGCGACACGGATGACGGCACCGGTCT\n+GCACCACATGGTATTCGAGGTGGTAGATAACGCTATCGACGAAGCGCTCGCGGGTCACTGTAAAGAAATTATCGTCACCA\n+TTCACGCCGACAACTCTGTCTCTGTACAGGATGACGGGCGCGGCATTCCGACCGGTATTCACCCGGAAGAGGGCGTATCG\n+GCGGCGGAAGTGATCATGACCGTTCTGCACGCAGGCGGTAAATTCGACGATAACTCCTATAAAGTGTCCGGCGGTCTGCA\n+CGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTTATCCAGCGCGAGGGTAAAATTCACCGTC\n+AGATCTACGAACACGGTGTACCGCAGGCCCCGCTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTC\n+TGGCCTAGCCTCGAAACTTTCACCAATGTGACCGAGTTCGAATATGAA'..b'AATAGTCGTTTGATGATTTCCAACCCTACTCACATTGCAATAGGGATATACTTTAAGCCACATCTTTCACCTATTCC\n+ATTGATTTCTGTAAGAGTAACTAATGAGGTGGCCTTAGGCGTAAGGAAATATGCAAAGGAAATCGGAATACCAATTATCA\n+CAGATAAAAAATTAGCACGAAAAAATTATGCTACCCATCGTCGCTACGATTATGTTAGCTTCGAAAATATAGATGAAATA\n+TTACGTCTTCTGCTGTGGCTTGAAGATGTGGAGAATGCTGGGCAACCTGTTCAAGATGAACAGCTCTCTTCAGAAGATAA\n+ATTCATTGAGGGTGAAGACACAAAAATCGAGAATAAAGACGATAATTTAAAAAATTAAACATCTGTCGTAGTCAGAAATT\n+TATAAGGATCTACACGCAAAAAGCGTGTAGATCCTTATTTAATGAGTTAAACGATCTTGTGAAATGATAAGCAATTGATA\n+CATACTCATCTCTTTATAAGCTGGAACTGTAGTAACCTGTGCAAATTCGCGATATAGCTTTTGCTCCAGTTCTGCTGATG\n+ATATATATTCCGGGTGTTCGCTAAAGAACTGTCTTGCATCTACTATCGCTTGGGATTCGCCACTTCTTTTATTTTGATTC\n+TCCTTTAATGAATTTTCTCTGGTGCATGCAGAGAGCAACGATATCAGCGCGATGGTTATTATGATGTTACTATTATATCC\n+TACTAATGACATATCAACTTTCTCTTACGCAAGATTGGAGTTTAAAATAATGTTTATCCCATTCACAGAGTGCTATAAAC\n+AACTAAACAGTACCTTTTATGTTAAGTTTATTTAGGGCTCTTATTTTGTGATATGATATTGTTTTATAATCAATTCCTTT\n+AATAATGGCTATTTGTTTTAACGAGTAAGAAACACATAACCGCAGGATATCTATCTCATCATGGGTAAGTGGTTCTTGTG\n+TGGAATACACATTTTGTGTATGAAGATTTGAAACCAGGAAATGCGTTAAATCAGATAATGTAATATTCTTATTGATCCTG\n+ATGAAATTGTTGCTCAAAAGGATGTTTACAGGTTCTGTATTTGGTTTGAGATTTCGATGTTGATGCTCATCAATAACAAC\n+GAACGAATGTCCAAGATCAACCAACGCAACTAAATCGCTGTAATATTCTTTTTGGGATGCTAATAATGCATTAGTGCCTA\n+CAGTGAAGTAGACATCACTGGAAAAGACTTGCATATGCCCACCTGTACTCTAAAATCATTTAGGGTAAATATTACGTGTA\n+AAATTTAAAATAAGAGTAATTGTTATATTTGCTTAACATTGAGGGAATAGGGTTTATACCTTAAATTGTAAATAAAGTTA\n+TGCATAGAGGCATTTAAAATAGTTCTCGGAATTATAATTTTTTTATTCTGTGTCATCATAATTTGGTCATGAAATTTCCG\n+TCTTGTTACACTACTCTAAACTAGAGCTTATGGAATTAGCGGGTGGTATTCATGGAAAATAATGATAAATTCTTATCACA\n+AGACTTATTGGAATCTTATGCCATTCGTTTGTTGAGCGGACCATTGAATGGATGCGAGTATGAAATACTTAATGGGCGTC\n+TACTTGTTATCATTGGTAATGATGTTTCGTTAGGAAGAAGTGATGCTTTTTCTGAGTTACCAGAAAACACAATAGTCGTT\n+CCTTATGGCGAGCTTACAGGTAGTTTTGAGATAATAATTACTACCGACCCTGATCTGGTAGTAACATTCAGAGAATTAAC\n+AGCACAAAAACCTGAAGATAGAACGTTAACATTGAATCAGCAAATAGAAGTTTTAGGTCTCAAATTTGCTGTAAAAGAAA\n+AAAATGAAGTTTGGCAGTATTCATTGCCAGGCATTATTGAAAATAACATTATTTCTACAAAACAACATTTCTTTAGCAGT\n+AAGCTGTTTAAGTATGTAATGCTTTTTTTTCTTTTTGCTATCATTTTCATTGCTTTTTATATTGTTAATGCCAGTAATGA\n+TCCGCAGCTGAGACATATCGATAAAATTCTTGTAAACAAAAACAGGAATTATGAAGTTTTATATGGTAGAGATCATGTTA\n+TCTATATTAATACCAATATTTTGGATGAAGCAGTCTGGGTCAAACAAGCACTGGAAAAAAATCAACCAGGAAAGCCAGTA\n+CGGGTGATAAATCCTGATGATGAATCGATACGAATTTTTTCATGGCTTGCTGATAATTTCCCTGATTTACAATATTTTAA\n+ACTTCAACTATTAGATGCCAGTAATCTAAGATTGACAGTGAGTAAGCAACGGAACGCTATCACACAGCAACTAATCGATA\n+ATCTTATTAAAGGATTACTGCAAACTATGCCATATGCCAGCAATATAAGTATTGCGGTATTAGATGATAATGTATTGGAA\n+AGTCAGGCTATTGAAACGTTGTCAGCGATAGGTCTTTCTTATGAAAAATATAAAACAGCTAACAATGTGTATTTCAATAT\n+CATTGGTACGTTAAGTGACAGTGAATTAAATAAAATTAATAACTATGTTGACGAATATTATAAACAATGGGGTAAACAAT\n+ATGTAAGATTTAATGTGAATTTGAAAAATCAGGACACAAATAATAGTTCATTTAGCTACGGAGATAACCGATTCGAGAAG\n+TCTCAAGGTAGCAACTGGACATTTCAGGAATAATTGAGGAGGACTTATGGCAGATTGGAATGGTTATATTATGGATATCA\n+GCAATCAATTTGATCAGGGCGTTGATGATCTGAACCAGCAAGTTGAAAAAGCGTTGGAGGATTTAGCCAACCAATCCCTC\n+CGACACGAAATTTCTTGCCGAATATCAAAGTGCATTAGCTGAGTATACATTATATCGAAATGCGCAATCTAACGTTGTAA\n+AAGCGTATAAAGATCTTGATTCAGCAATCATACAAAACTTCCGCTAAACTAGATAAGGATTTTATTATGTTAGTAAGCAA\n+TATGCCACCTATTGATAGAGCTGAGCAATCAACTGCTCATGAAATACAGCAAGCGAAAGTGATTGATTTAAATGACCGGG\n+TTCTCAATCTTGACAACCCGGATGATAAAATGATCTCCGCTTTTGCCAACTATGCTGTACAAACTGAAAATTGGCAGCAA\n+AATGCGTTACAAGCATTAAGGTCTGATAAAGAGGGGTTAACTCCTGAAAAATTATTAGTCTTGCAGGATCATGTGCTTAA\n+TTATAATGTCGAGGTTTCATTGGTGGAACATTAGCAAGAAAGATTGTCGCTGCAGTTGAGACGTTGACCCGCTCATGAAA\n+TATATATCATTATTATTGTTTATCCTGCTGTTGTGCGGCTGCAAGCAGCAGGAATTATTGAACCATCTTGATCAACAGCA\n+AGCTAATGATGTCCTTGCTGTTTTACAAAGACATAATATTAATGCTGAAAAGAAGGATCAAGGCAAAACAGGATTTTCAA\n+TATTTGTCGAACCAACGGATTTTGCTTCTGCGGTGGATTGGCTAAAAATCTACAATCTACCGGGTAAGCCTGATATTCAA\n+ATATCGCAGATGTTCCCTGCAGATGCACTCGTTTCATCTCCACGAGCGGAAAAAGCAAGGCTATATTCTGCTATTGAGCA\n+GCGGTTAGAGCAATCTCTCAAAATTATGGATGGCATTATTTCTTCGAGAGTACATGTTAGTTACGATGTTGATAATGGCG\n+ATAGTGGTAAAACTGCTTTACCAATTCATATTTCTGTACTTGCAGTATATGAAAAAGATATCAACCCAGAAATAAAAATA\n+AATGATATCAAGAGATTTATTGTTAATAGCTCTGCAAGCGTACAATATGAAAATATTTCTGTTGTATTGTCAAAACGAAG\n+AGACATTATTGAGCAAGCACCAACATATGAAATTAGC\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/reference_02.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference_02.fa Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,20562 @@\n+>chr21\n+ctccaaagaaattgtagttttcttctggcttagaggtagatcatcttggt\n+ccaatcagactgaaatgccttgaggctagatttcagtctttgtggcagct\n+ggtgaatttctagtttgccttttcagctagggattagctttttaggggtc\n+ccaatgcctagggagatttctaggtcctctgttccttgctgacctccaat\n+tttgtctatccttttgctgagaggtctgcttaacttccttttagtcaggt\n+agctccattttatgctaagcttcttagttgctcaccttctgcagctaaag\n+aatcagaaaatgctgtgaaggaaaaacaaaatgaaattgcattgtttcta\n+ccggccctttatcaagccctggccaccatgatagtcatgaattccaattg\n+ttgtctatgcaggcctaccagatttctaacatctctgagctaccattttc\n+ttcttagctatctgctcagcaaatgtatccaaatgaaaggctgtggagaa\n+tgttgaaatcacttcaatgtgtttctcttctttctgggagcttacacact\n+caagttctggatgctttgattgctatcagaagccgttaaatagctactta\n+tttttaattaattttacccagctttcataattgttcttgccaggtgggat\n+ggcctgatacaaattaacttgtcatagctagaattagaagAGGAAAACTT\n+TAAATAGCATTGAGTTATCAGTACTTTCATGTCTTGATACATTTCTTCTT\n+GAAAATGTTCATGCTTGCTGATTTGTCTGTTTGTTGAGAGGAGAATGTTC\n+AGAATTTTATATCTTCAACATCTTTTTCTTCATTAATAAGATACTGAGAT\n+TTTATAACTCTTGTCATTTTGGTCACTTATATTTTCATATGGAAATATCG\n+TATAATCCAGGGTTTCCAATATATTTGTGTAAAATTAAGAAAATTATCTT\n+ATCTAATAACTTGATCAATATCTGTGATTATATTTTCATTGCCTTCCAAT\n+TTTAATATTTGTTCTCTATTCCTTCTTAATCTGGATTGAAGTTCTGATTA\n+ATTATTTTAATGTTGCAAATTGTTTTCACTTTTTCCATAAAATGAGTTCT\n+AGAGTTTATTTCTTTACTGCATCATTCTATTTTCAAGTCATGAACTTCTG\n+CTTCAACTAAAAAAAAAAAACTCACCGTTTGTATGAAATTGTTGTGTTCa\n+tattttattttttatttactgtataattcagtattgaatatataatatta\n+taaaatatgtaataaaaGGATAAAAAATAAGATACAAAAAGTAAGGGGTG\n+TGCGTTTGGAAAATTATACTTGCTGATATGGTGAAATAACTCTGACCAAA\n+CTAACCTTCCAGCAATAAAAACAAATTTGGAAAACTGGAAAAAATATACA\n+TGGCAACATGTTAGGTCATCTTTGTCTGCCTTCAAACAACTATAAATATT\n+GTTCTACCCAAACAACTATAAATTTTGTAATACCTAGAACAATATAAATA\n+TTGTTCTACATTGTAAATTGTTCTACAATTTACAATGGTGTAAACTGTTA\n+TACACCATTTATTTGAGTAAATTTTGAAAATATCTATTCTTCATTTTTGC\n+TGTTTCTCGTGTGGTATATATTTCTCAGATAAAAGATATTTTCCCTTTTA\n+TCTTTCCCTAAGCTCACACTACATATATTGCATTTATCTTATATCTGCTT\n+TAAAACCTATTTATGTCTTTTTAGGTCACTTACATCAGAGGAGTTGTATT\n+GGTGCAGGAAGGGGAGTTTGATTTAATGAAACAATGCATTAAAAATTTGT\n+ATTCACTTTGTGATTCAATGATAGTCAATGTGGCATGTAATTTTTTTCTG\n+TCTTTTAATATTATATTGTCTTTGTTGCTTTTCTCTAACATGAAATATAT\n+GTTACACAGGCACAGTGCTGGTATCTTTTCTATTATTATCTTTGAATGGG\n+ACTCATTATTTTCTGAGCTATTTATTAAAATGGTGAAGGAAAAGATCAGT\n+AAAGTAAATTATGTCAATAGGCAGTATCAATTTAGGTCTATTTTCCATGA\n+ATATTTTCTCAGCAACtgtggtgttatgatatatattggttttcatccac\n+agttcctggcttataactcccctagcacttgttacagtcttttgttataa\n+tattgggtgtattaggcctcaggagcaggcctctcaccttctcatggcct\n+tttttcatttttatgttcctgcctttctggttgtgggtcttaagaccatc\n+tcaagagagagtcccaccctataccctggagggaggaatgctgatatcat\n+gaaacttccataaaaatccaggaggacagggttcagtgagcttctgggta\n+gttgaacacatggatgttcctgtagggtggcccgcccagggatggcatgg\n+aagctctgctcccttcccctatgaattgctctaagtgtccttcatctata\n+tcctttgcaatgtcctttataaaacaccaggaaatgtaagtgtttccctg\n+agttctgtgagccactccaacaaattaatcaaacccaaagagggggtcct\n+gagaagccaactcgaagccagcaggtcagaagttcagaggcctggacttc\n+tggctggtagtttgagggtgggcagtcttggggactgacctgtgagacct\n+gacactatctccaggtagatagtgtagtgtcagaactgaattagaggaca\n+ctcagctggtgtccactccttggtgtatgtatggaggaaaaaactcacac\n+atttggtcacagaagtcttttctgttgctgattgatctttgtggcatgag\n+actagaggaaaaacagagagagttttctctacacaGCAACTATATAATCT\n+GTGGGAATATCTCCTTTTACACCTAGCCCTACTTCTGTCTGGCTACAGTC\n+ATTTATCTGGCTTTGGGAAATGTGACCACAGAATCAGATATATACATGAG\n+ATTAAATAATACATGTGTATGTCATTTAAATATCTAGAAAAGTTATGACT\n+TCACCAGGTATGAAAAATATAAAAAGAACTCTGTCAAGAATCATACAGTA\n+AATAGATTTTTGAATTTAATCTAGTACCTAAATAATCAGAGTAGGGAGGT\n+TAGATATTAAAATCAGGCTAAAGATATAGGCAACATGGATCTAGAAAACA\n+TGGATTGCATGGCCATTTCACTTAGAGTTCATGGGCTTGGAATCTCTATT\n+AACATAACTTTTACAATGTTAGAATTTGTTCCCATATTAATGAGGGAAAA\n+ACAAACAATTACCCTGAGTATCTGAAGCTCCAGATCTCATTTTCCAGTCA\n+AAATCTCTGATAGGTAAACAACCTGAAAAAGTAGCCACAACTCACTGAGG\n+TGATAACCTCATTTGCTTAAGAGAATGTAATTGTTTTTATGATTTTTTTT\n+ATCCCAGGAAAACATTGAAAAAAAGTTTAGAGATGATGAAGTATATGAAA\n+ACTATAATATTTATACTTTAGAGATGTGatatttatttataattgtatta\n+gtatttaaatataGATTAGCATTTTACATTCCAATTTTCAATGTGTAACA\n+GAATATTTTAGATATTGGGGTTGTTTTTTAGTTGAAATAATAAGCGGTTT\n+TACCGAGTTGCCAGTAGTGGTTTAACATTGAAGATAATTTAACATTCATG\n+ATTTTGTGAGTTTAATTTATTAGCTCTATAAGGGTTGTTTAAGTACTCTG\n+AAGGCTTTATTTGTTAGTCCGATAATTAAAATGTTCATAAAGATAATTCA\n+ACATATTAAATTTGTAAATGTAGTTTAAAATCTTTAAGGGAGTTTAATTA\n+ACTAAGTTGTAAATGGAC'..b'aacggga\n+gggaatggaatcggaaggaagagaatggaatggagtggaatggagtggag\n+tggaatgcaacggaatggaatggaatggattggagtggagttgtgtggag\n+tggaatggaatggagcggaatggaatacaatggaatggaaataaaagcag\n+tggagtggagtggagcggaatggagtggaatggaatggaattgaatggga\n+aggaatggaattgaatggagtggagggcaatggaatggaatggaatgaag\n+tggaggggcttggagtggagtgcaatggaatggagaggagtggagtagat\n+tgcattttagtggagcggagtttaatggaatggaatggagtggaatggaa\n+tggaatggttttgaatggaacttaatcgaatggtatggaatcaaatggga\n+tgtaatcaaatacaagggaatagaatggaatgtaatcgaatgtaatgtaa\n+tcgaatggaatggaatcaaatggaattgaattaaatgaaatggaatcaaa\n+tgaaatggacacgaaaggaatggaatggaatggaatggacgtgaatggaa\n+tggactagaatggattggactggaatggaatggactcggattcaatggaa\n+tagaatggaatggaatcgaatggcattgaatggaatcgaatggaatgcgg\n+tgaagttgagtggagtggagtgaaatgcaatggaatggaatgggatagaa\n+tggtattgaatggagtggagaggagtggagtggaaagcaatggaatggaa\n+tggaatggcatggattggattggagggtagtggactgtagtggagtggaa\n+tggagtggaatggattggagtggaaaggagtggagaggactggagtggaa\n+tggagtggagaagagtggagaggagtggagttgaatgacattaaatggaa\n+tggagttgagtggaatcgattggaatagagtagaggagagtgtaatggag\n+tgcaatgtaatggaatggaatggaatggaatttaacggagtgaagtggag\n+tggagtggaatgcaatggaatggaattgaatggagtggagtggagtcgaa\n+tggaatgcaatggaatggaatggaatggaatggaatctaatggaatggat\n+ttgaatggaatggaatcaaatggaagggaatgggatggaattaatagaat\n+ggaatggatttgaaaggaacggaattgaatgggatcaaatggaatcgaat\n+ggaatgtggtgaagtggagtggagtggaattgagtgtaatggaatttggc\n+ggaatgcaattgaatggagtggagtggttttgaatggacaggaaaggaat\n+ggaatgggaatgaatgtaattgaatggagtggaggcgagtggagcggaat\n+gcaaaagaatggaatggaatggagtgtaggggagtggagtaaattctagt\n+ggagtggagaggaatggagtggaatggtatggaatggaaaggaatggagt\n+gcaattgaatcgaatggaatggaatggaatggaatgcagtggagtagagt\n+ggagtggactgcagttaaatggaatggaatggaatggaatgcagtggagt\n+agagtggagtggacagcagttaaatggaatggaatggaatggaatggaat\n+ggaatggaatggaatggagtgtagggaattggaatgcaatggaatggaat\n+ggaaaggaatggaatggattccaatggaatggaatggactgtaatggaat\n+cgactggaatggaatggattcgaatggaaagaaatcaaatggaatggaaa\n+cgaatggaatggattcgagtggaatggactggtatggaatggactagaat\n+ggactggacacgaatggaatggaattgaatgtaatggaatggaatggaaa\n+ggttatggaatggaatgaattagaatggattggactggaatttaatggac\n+tggaatggaatggagtggagtgtaatggactcgaatggaatggaattgaa\n+tggaatggattcgagcagaatggaattgaatggaatggattcgaaaggaa\n+tggaatcaaatggaatggaatcgaattgaatggataccaatggaattgac\n+tggaatggaagggatgcaaaatggaatggactcgaatggatttgactgga\n+atggaatggaatcgtatggaatggaattgaatgcaatggaatcgaatggc\n+atcaaatggaatcgaatggaatgcggtgaagtggagtggagtgaaatgca\n+gtggaatggaatggggtggaatggaattgaattgagtggggcagagtgga\n+gtggaatggagtggaattgaatggaggggaaggaatggaattgaacagac\n+ttgagtggagaggagtggattggaatgcaatagaatgaaatggaatggaa\n+tggagtggagtggagtggattggagtggaattaaatagaatggaatggaa\n+tggaatggaatggaatggaatggaatgaactcaaacggaatggactgcaa\n+gggaatggactggaatggaatggacccgaatggaatggactggaatggaa\n+tggactcaaaaggaatgaactcgaatgtaatggagtagaatggaaaggaa\n+tcgtactgaatggaatcgaatggaatggaatcaaatgaaataatatggaa\n+aggcgtcgaatggaatccagtgttatgcagtgaagtggagtggagaggag\n+tgtaattgagtggattggaatggggtggaatggaaaggaatgcagtggag\n+tgcactggagtgcaatagagtgggatggaatggaatgggaaggaatggaa\n+ttgaactgagtggagttgagtggagcggagaggagtggaatgcaaaggaa\n+tggtaaggagtgcaaaggaatggaatggaatggactggaatggaaaggac\n+tcgaatggaacggaattgaatggaatggacgcgaatggtatggactcgaa\n+tgcaatgtaatcaaacggagtggaatcaaatggcactgaattgaataaaa\n+tggaatcaaatggaaaggaatcggaaggcaacgagtggaagggaatggaa\n+tgtggttaattggagtgcaatgaattggaatgcagtggaatggaatgagg\n+tggaatggaattgattggagtggagtggagtggagcagaatgcaatggaa\n+tggaatggaccagcatggattggagttgagtggagtagagtggagtggag\n+agtagtggaatggagtgtagtgtagtggagtggagtggagtagagtggag\n+tggaatggaatgcacaggaaaggaatggactagaatggaacggacatcaa\n+tggaatggactcgaatggaatggactcgaatgcaatggaatcaaatggaa\n+tggaatagaatggaacggaattgaatgaaatggaatcaaatggaaaggaa\n+tcaaatggcatcaaacagaatggaatggaatgtggttaattggagtgcag\n+tgcattggaatggaatggtgtgcaatggaattgaatggagtggagtggag\n+tggagcagaatgcaatggaatggaagggaacagcatggattggagttgag\n+tgtagtagagtggagtggagtggaagggagtggagtggagtggagtggag\n+tggagtggaaaggaatggagtctagtggaatgtaatggaatagaatggaa\n+tggaatgtagtggaatggaatggaatggagttgaaataaatggaatggaa\n+tgcaatggaatggaatggaatggaatggattggaatgggatggaatggaa\n+aggagtggaatggaatgtaacgtagtggaatggaaagtattggaggggaa\n+tggaatggagtggaaaggaatggaatttaacagagtggagtggagtgtag\n+gggagtgga\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_02.bigwig |
| b |
| Binary file test-data/test_02.bigwig has changed |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_03.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03.bed Fri Aug 26 22:43:38 2022 +0000 |
| b |
| @@ -0,0 +1,65 @@ +chr21 9827040 9827486 FUSIONJUNC_8/7 0 + +chr21 16386664 16387546 FUSIONJUNC_9/5 0 + +chr21 16386664 16415895 FUSIONJUNC_10/71 0 + +chr21 17135209 17138460 FUSIONJUNC_11/27 0 + +chr21 17135209 17172162 FUSIONJUNC_12/2 0 + +chr21 27269884 27284274 FUSIONJUNC_13/2 0 + +chr21 27326903 27328069 FUSIONJUNC_14/6 0 + +chr21 27326903 27354790 FUSIONJUNC_15/2 0 + +chr21 27326903 27484463 FUSIONJUNC_16/2 0 + +chr21 27347382 27369731 FUSIONJUNC_17/4 0 + +chr21 27347382 27372497 FUSIONJUNC_18/4 0 + +chr21 27394155 27484463 FUSIONJUNC_19/2 0 + +chr21 27423315 27425664 FUSIONJUNC_20/9 0 + +chr21 30677524 30702014 FUSIONJUNC_21/2 0 + +chr21 30698379 30702014 FUSIONJUNC_22/3 0 + +chr21 32537278 32567621 FUSIONJUNC_23/4 0 + +chr21 32537278 32575328 FUSIONJUNC_24/3 0 + +chr21 33750753 33756773 FUSIONJUNC_25/2 0 + +chr21 34804483 34805178 FUSIONJUNC_26/15 0 + +chr21 34906884 34907626 FUSIONJUNC_27/6 0 + +chr21 34906884 34911662 FUSIONJUNC_28/3 0 + +chr21 35091101 35094956 FUSIONJUNC_29/37 0 + +chr21 35091101 35107509 FUSIONJUNC_30/9 0 + +chr21 35138178 35140132 FUSIONJUNC_31/3 0 + +chr21 35279644 35281515 FUSIONJUNC_32/2 0 + +chr21 35475133 35497780 FUSIONJUNC_33/4 0 + +chr21 35475133 35515007 FUSIONJUNC_34/2 0 + +chr21 37502929 37503360 FUSIONJUNC_35/3 0 + +chr21 37711069 37717005 FUSIONJUNC_36/10 0 + +chr21 37775055 37781763 FUSIONJUNC_37/2 0 + +chr21 37775055 37783902 FUSIONJUNC_38/23 0 + +chr21 38747352 38794168 FUSIONJUNC_39/4 0 + +chr21 38792600 38794168 FUSIONJUNC_40/121 0 + +chr21 38792600 38798083 FUSIONJUNC_41/9 0 + +chr21 38792600 38802702 FUSIONJUNC_42/21 0 + +chr21 38792600 38828610 FUSIONJUNC_43/8 0 + +chr21 38792600 38845182 FUSIONJUNC_44/14 0 + +chr21 40590077 40590586 FUSIONJUNC_45/6 0 + +chr21 40596333 40601362 FUSIONJUNC_46/2 0 + +chr21 40600425 40601362 FUSIONJUNC_47/15 0 + +chr21 40619626 40622815 FUSIONJUNC_48/3 0 + +chr21 40619626 40630598 FUSIONJUNC_49/8 0 + +chr21 40641824 40646398 FUSIONJUNC_50/6 0 + +chr21 44270150 44279832 FUSIONJUNC_51/3 0 + +chr21 44272364 44296877 FUSIONJUNC_52/5 0 + +chr21 44279771 44283706 FUSIONJUNC_53/3 0 + +chr21 44293660 44296877 FUSIONJUNC_54/2 0 + +chr21 44424435 44430334 FUSIONJUNC_55/4 0 + +chr21 44424435 44448984 FUSIONJUNC_56/4 0 + +chr21 44477019 44478255 FUSIONJUNC_57/2 0 + +chr21 44492094 44493451 FUSIONJUNC_58/3 0 + +chr21 45089764 45093836 FUSIONJUNC_59/2 0 + +chr21 45153949 45163688 FUSIONJUNC_60/5 0 + +chr21 45499444 45500008 FUSIONJUNC_61/3 0 + +chr21 46275124 46281186 FUSIONJUNC_62/12 0 + +chr21 46548316 46554747 FUSIONJUNC_63/37 0 + +chr21 46730370 46731344 FUSIONJUNC_64/2 0 + +chr21 46916482 46916936 FUSIONJUNC_65/2 0 + +chr21 47155305 47175366 FUSIONJUNC_66/4 0 + +chr21 47685469 47685839 FUSIONJUNC_67/2 0 + +chr21 47693301 47697631 FUSIONJUNC_68/3 0 + +chr21 47746290 47754682 FUSIONJUNC_69/2 0 + +chr21 47754310 47754682 FUSIONJUNC_70/3 0 + +chr21 47768925 47769734 FUSIONJUNC_71/5 0 + +chr21 47801608 47805898 FUSIONJUNC_72/8 0 + |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_04.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04.bed Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,661 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|
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_05.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_05.tabular Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,138 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500\t4,5,6,7,8,9,10,11,12,13,14,15\tchr21:46888700-46893808|chr21:46902735-46906774\n+chr21\t46897401\t46897635\tcircular_RNA/2\t0\t+\t46897401\t46897401\t0,0,0\t1\t234\t0\t2\tciRNA\tCOL18A1\tNM_001379500\t7\tchr21:46897401-46897663\n+chr21\t46901939\t46902675\tcircular_RNA/1\t1\t+\t46901939\t46901939\t0,0,0\t1\t736\t0\t1\tciRNA\tCOL18A1\tNM_001379500\t14\tchr21:46901939-46902708\n+chr21\t46916482\t46916936\tcircular_RNA/2\t1\t+\t46916482\t46916482\t0,0,0\t1\t454\t0\t2\tciRNA\tCOL18A1\tNM_001379500\t30\tchr21:46916482-46916963\n+chr21\t47155305\t47175366\tcircular_RNA/3\t0\t+\t47155305\t47155305\t0,0,0\t2\t38,36\t0,20025\t3\tcircRNA\tPCBP3\tNM_001348239\t3,4\tchr21:47088866-47155305|chr21:47175366-47269874\n+chr21\t47320504\t47321027\tcircular_RNA/1\t0\t+\t47320504\t47320504\t0,0,0\t2\t33,117\t0,406\t1\tcircRNA\tPCBP3\tNM_001348238\t7,8\tchr21:47319536-47320504|chr21:47321027-47329268\n+chr21\t47412724\t47414062\tcircular_RNA/2\t1\t+\t47412724\t47412724\t0,0,0\t1\t1338\t0\t2\tciRNA\tCOL6A1\tNM_001848\t19\tchr21:47412724-47414080\n+chr21\t47538590\t47538919\tcircular_RNA/1\t0\t+\t47538590\t47538590\t0,0,0\t1\t329\t0\t1\tciRNA\tCOL6A2\tNM_058174\t13\tchr21:47538590-47538943\n+chr21\t47641767\t47642652\tcircular_RNA/1\t0\t-\t47641767\t47641767\t0,0,0\t2\t122,76\t0,809\t1\tcircRNA\tLSS\tNM_001145436\t5,4\tchr21:47639486-47641767|chr21:47642652-47647465\n+chr21\t47693301\t47697631\tcircular_RNA/2\t0\t-\t47693301\t47693301\t0,0,0\t3\t198,140,191\t0,1798,4139\t2\tcircRNA\tMCM3AP\tNM_003906\t7,6,5\tchr21:47692743-47693301|chr21:47697631-47699906\n+chr21\t47699906\t47700489\tcircular_RNA/1\t0\t-\t47699906\t47699906\t0,0,0\t2\t145,79\t0,504\t1\tcircRNA\tMCM3AP\tNM_003906\t4,3\tchr21:47697631-47699906|chr21:47700489-47703528\n+chr21\t47746290\t47754682\tcircular_RNA/1\t0\t+\t47746290\t47746290\t0,0,0\t2\t213,372\t0,8020\t1\tcircRNA\tPCNT\tNM_006031\t2,3\tchr21:47744196-47746290|chr21:47754682-47766041\n+chr21\t47754310\t47754682\tcircular_RNA/3\t0\t+\t47754310\t47754310\t0,0,0\t1\t372\t0\t3\tcircRNA\tPCNT\tNM_006031\t3\tchr21:47746503-47754310|chr21:47754682-47766041\n+chr21\t47768925\t47769734\tcircular_RNA/1\t0\t+\t47768925\t47768925\t0,0,0\t2\t175,137\t0,672\t1\tcircRNA\tPCNT\tNM_006031\t7,8\tchr21:47767426-47768925|chr21:47769734-47771342\n+chr21\t47783394\t47787054\tcircular_RNA/1\t0\t+\t47783394\t47783394\t0,0,0\t2\t455,556\t0,3104\t1\tcircRNA\tPCNT\tNM_006031\t14,15\tchr21:47777106-47783394|chr21:47787054-47801608\n+chr21\t47801608\t47805898\tcircular_RNA/6\t0\t+\t47801608\t47801608\t0,0,0\t2\t147,152\t0,4138\t6\tcircRNA\tPCNT\tNM_006031\t16,17\tchr21:47787054-47801608|chr21:47805898-47808656\n+chr21\t47904669\t47917020\tcircular_RNA/1\t0\t+\t47904669\t47904669\t0,0,0\t3\t72,120,120\t0,5843,12231\t1\tcircRNA\tDIP2A\tNM_206891\t2,3,4\tchr21:47879135-47904669|chr21:47917020-47918494\n+chr21\t47904669\t47918746\tcircular_RNA/1\t0\t+\t47904669\t47904669\t0,0,0\t4\t72,120,120,252\t0,5843,12231,13825\t1\tcircRNA\tDIP2A\tNM_206891\t2,3,4,5\tchr21:47879135-47904669|chr21:47918746-47924273\n+chr21\t47916900\t47931527\tcircular_RNA/1\t0\t+\t47916900\t47916900\t0,0,0\t5\t120,252,129,120,198\t0,1594,7373,12269,14429\t1\tcircRNA\tDIP2A\tNM_206891\t4,5,6,7,8\tchr21:47910632-47916900|chr21:47931527-47949004\n+chr21\t48055675\t48056771\tcircular_RNA/1\t1\t+\t48055675\t48055675\t0,0,0\t1\t1096\t0\t1\tciRNA\tPRMT2\tNM_001242865\t1\tchr21:48055675-48056807\n+chr21\t48063446\t48064400\tcircular_RNA/1\t0\t+\t48063446\t48063446\t0,0,0\t2\t105,183\t0,771\t1\tcircRNA\tPRMT2\tNM_001242865\t3,4\tchr21:48056902-48063446|chr21:48064400-48068369\n+chr21\t48063446\t48080874\tcircular_RNA/1\t0\t+\t48063446\t48063446\t0,0,0\t6\t105,183,162,165,176,130\t0,771,4923,6040,15210,17298\t1\tcircRNA\tPRMT2\tNM_001535\t3,4,5,6,7,8\tchr21:48056902-48063446|chr21:48080874-48081711\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_06.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_06.tabular Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,141 @@\n+chr21\t16386664\t16415895\tcircular_RNA/52\t0\t-\t16386664\t16386664\t0,0,0\t2\t123,80\t0,29151\t52\tcircRNA\tNRIP1\tNM_003489\t3,2\tchr21:16340847-16386664|chr21:16415895-16437065\n+chr21\t17135209\t17138460\tcircular_RNA/15\t0\t+\t17135209\t17135209\t0,0,0\t2\t78,145\t0,3106\t15\tcircRNA\tUSP25\tNM_001283041\t2,3\tchr21:17102757-17135209|chr21:17138460-17150222\n+chr21\t17135209\t17172162\tcircular_RNA/2\t0\t+\t17135209\t17135209\t0,0,0\t5\t78,145,124,163,87\t0,3106,15013,28611,36866\t2\tcircRNA\tUSP25\tNM_001283041\t2,3,4,5,6\tchr21:17102757-17135209|chr21:17172162-17177439\n+chr21\t17135209\t17177577\tcircular_RNA/1\t0\t+\t17135209\t17135209\t0,0,0\t6\t78,145,124,163,87,138\t0,3106,15013,28611,36866,42230\t1\tcircRNA\tUSP25\tNM_001283041\t2,3,4,5,6,7\tchr21:17102757-17135209|chr21:17177577-17181127\n+chr21\t17150222\t17177577\tcircular_RNA/1\t0\t+\t17150222\t17150222\t0,0,0\t4\t124,163,87,138\t0,13598,21853,27217\t1\tcircRNA\tUSP25\tNM_001283041\t4,5,6,7\tchr21:17138460-17150222|chr21:17177577-17181127\n+chr21\t26961146\t26973779\tcircular_RNA/1\t0\t-\t26961146\t26961146\t0,0,0\t6\t48,154,66,113,68,100\t0,3977,5058,8467,10964,12533\t1\tcircRNA\tMRPL39\tNM_017446\t9,8,7,6,5,4\tchr21:26958066-26961146|chr21:26973779-26976107\n+chr21\t26969613\t26972178\tcircular_RNA/1\t0\t-\t26969613\t26969613\t0,0,0\t2\t113,68\t0,2497\t1\tcircRNA\tMRPL39\tNM_017446\t6,5\tchr21:26966270-26969613|chr21:26972178-26973679\n+chr21\t27264033\t27347541\tcircular_RNA/1\t0\t-\t27264033\t27264033\t0,0,0\t7\t147,101,54,222,100,129,159\t0,5851,13302,20019,62870,63907,83349\t1\tcircRNA\tAPP\tNM_001136016\t16,15,14,13,12,11,10\tchr21:27254082-27264033|chr21:27347541-27348266\n+chr21\t27269884\t27284274\tcircular_RNA/2\t0\t-\t27269884\t27269884\t0,0,0\t3\t101,54,222\t0,7451,14168\t2\tcircRNA\tAPP\tNM_001136016\t15,14,13\tchr21:27264180-27269884|chr21:27284274-27326903\n+chr21\t27277335\t27284274\tcircular_RNA/2\t0\t-\t27277335\t27277335\t0,0,0\t2\t54,222\t0,6717\t2\tcircRNA\tAPP\tNM_001136016\t14,13\tchr21:27269985-27277335|chr21:27284274-27326903\n+chr21\t27326903\t27328069\tcircular_RNA/4\t0\t-\t27326903\t27326903\t0,0,0\t2\t100,129\t0,1037\t4\tcircRNA\tAPP\tNM_001136016\t12,11\tchr21:27284274-27326903|chr21:27328069-27347382\n+chr21\t27326903\t27354790\tcircular_RNA/2\t0\t-\t27326903\t27326903\t0,0,0\t5\t100,129,159,75,134\t0,1037,20479,21363,27753\t2\tcircRNA\tAPP\tNM_001136016\t12,11,10,9,8\tchr21:27284274-27326903|chr21:27354790-27372329\n+chr21\t27326903\t27484463\tcircular_RNA/2\t0\t-\t27326903\t27326903\t0,0,0\t11\t100,129,159,75,134,168,203,194,113,130,168\t0,1037,20479,21363,27753,45426,67252,96412,98648,135355,157392\t2\tcircRNA\tAPP\tNM_001136016\t12,11,10,9,8,7,6,5,4,3,2\tchr21:27284274-27326903|chr21:27484463-27512470\n+chr21\t27347382\t27369731\tcircular_RNA/4\t0\t-\t27347382\t27347382\t0,0,0\t4\t159,75,134,57\t0,884,7274,22292\t4\tcircRNA\tAPP\tNM_000484\t11,10,9,8\tchr21:27328069-27347382|chr21:27369731-27372329\n+chr21\t27347382\t27372497\tcircular_RNA/2\t0\t-\t27347382\t27347382\t0,0,0\t4\t159,75,134,168\t0,884,7274,24947\t2\tcircRNA\tAPP\tNM_001136016\t10,9,8,7\tchr21:27328069-27347382|chr21:27372497-27394155\n+chr21\t27394155\t27484463\tcircular_RNA/2\t0\t-\t27394155\t27394155\t0,0,0\t5\t203,194,113,130,168\t0,29160,31396,68103,90140\t2\tcircRNA\tAPP\tNM_001136016\t6,5,4,3,2\tchr21:27372497-27394155|chr21:27484463-27512470\n+chr21\t27423315\t27425664\tcircular_RNA/5\t0\t-\t27423315\t27423315\t0,0,0\t2\t194,113\t0,2236\t5\tcircRNA\tAPP\tNM_001136016\t5,4\tchr21:27394358-27423315|chr21:27425664-27462258\n+chr21\t28215032\t28216543\tcircular_RNA/1\t0\t-\t28215032\t28215032\t0,0,0\t1\t1511\t0\t1\tciRNA\tADAMTS1\tNM_006988\t1\tchr21:28215004-28216543\n+chr21\t30437288\t30442658\tcircular_RNA/1\t0\t-\t30437288\t30437288\t0,0,0\t6\t138,62,181,150,80,91\t0,1748,1923,2588,4455,5279\t1\tcircRNA\tCCT8\tNM_001282907\t8,7,6,5,4,3\tchr21:30435851-30437288|chr21:30442658-30444272\n+chr21\t30677524\t30702014\tcircular_RNA/1\t0\t+\t30677524\t30677524\t0,0,0\t4\t119,294,1335,207\t0,16017,20855,24283\t1\tcircRNA\tBACH1\tNR_027655\t1,2,3,4\tNone|chr21:30702014-30723954\n+chr21\t30693541\t30702014\tcircular_RNA/1\t0\t+\t30693541\t30693541\t0,0,0\t3\t294,1335,207\t0,4838,8266\t1\tcircRNA\tBACH1\tNM_001186\t2,3,4\tchr21:30671274-30693541|chr21:30702014-30714719\n+chr21\t30698379\t30702014\tcircular_RNA/1\t0\t+\t3'..b'6554747-46591524\n+chr21\t46600244\t46605006\tcircular_RNA/1\t0\t+\t46600244\t46600244\t0,0,0\t4\t115,169,149,169\t0,2255,3032,4593\t1\tcircRNA\tADARB1\tNR_027673\t6,7,8,9\tchr21:46596579-46600244|chr21:46605006-46624469\n+chr21\t46893808\t46896394\tcircular_RNA/1\t0\t+\t46893808\t46893808\t0,0,0\t3\t87,60,130\t0,1581,2456\t1\tcircRNA\tCOL18A1\tNM_001379500\t4,5,6\tchr21:46888700-46893808|chr21:46896394-46897324\n+chr21\t46893808\t46902735\tcircular_RNA/1\t0\t+\t46893808\t46893808\t0,0,0\t12\t87,60,130,77,216,27,63,87,54,159,63,27\t0,1581,2456,3516,3855,4432,6007,6175,6572,6805,8068,8900\t1\tcircRNA\tCOL18A1\tNM_001379500\t4,5,6,7,8,9,10,11,12,13,14,15\tchr21:46888700-46893808|chr21:46902735-46906774\n+chr21\t46897401\t46897635\tcircular_RNA/2\t0\t+\t46897401\t46897401\t0,0,0\t1\t234\t0\t2\tciRNA\tCOL18A1\tNM_001379500\t7\tchr21:46897401-46897663\n+chr21\t46901939\t46902675\tcircular_RNA/1\t1\t+\t46901939\t46901939\t0,0,0\t1\t736\t0\t1\tciRNA\tCOL18A1\tNM_001379500\t14\tchr21:46901939-46902708\n+chr21\t46916482\t46916936\tcircular_RNA/2\t1\t+\t46916482\t46916482\t0,0,0\t1\t454\t0\t2\tciRNA\tCOL18A1\tNM_001379500\t30\tchr21:46916482-46916963\n+chr21\t47155305\t47175366\tcircular_RNA/3\t0\t+\t47155305\t47155305\t0,0,0\t2\t38,36\t0,20025\t3\tcircRNA\tPCBP3\tNM_001348239\t3,4\tchr21:47088866-47155305|chr21:47175366-47269874\n+chr21\t47320504\t47321027\tcircular_RNA/1\t0\t+\t47320504\t47320504\t0,0,0\t2\t33,117\t0,406\t1\tcircRNA\tPCBP3\tNM_001348238\t7,8\tchr21:47319536-47320504|chr21:47321027-47329268\n+chr21\t47412724\t47414062\tcircular_RNA/2\t1\t+\t47412724\t47412724\t0,0,0\t1\t1338\t0\t2\tciRNA\tCOL6A1\tNM_001848\t19\tchr21:47412724-47414080\n+chr21\t47538590\t47538919\tcircular_RNA/1\t0\t+\t47538590\t47538590\t0,0,0\t1\t329\t0\t1\tciRNA\tCOL6A2\tNM_058174\t13\tchr21:47538590-47538943\n+chr21\t47641767\t47642652\tcircular_RNA/1\t0\t-\t47641767\t47641767\t0,0,0\t2\t122,76\t0,809\t1\tcircRNA\tLSS\tNM_001145436\t5,4\tchr21:47639486-47641767|chr21:47642652-47647465\n+chr21\t47693301\t47697631\tcircular_RNA/2\t0\t-\t47693301\t47693301\t0,0,0\t3\t198,140,191\t0,1798,4139\t2\tcircRNA\tMCM3AP\tNM_003906\t7,6,5\tchr21:47692743-47693301|chr21:47697631-47699906\n+chr21\t47699906\t47700489\tcircular_RNA/1\t0\t-\t47699906\t47699906\t0,0,0\t2\t145,79\t0,504\t1\tcircRNA\tMCM3AP\tNM_003906\t4,3\tchr21:47697631-47699906|chr21:47700489-47703528\n+chr21\t47746290\t47754682\tcircular_RNA/1\t0\t+\t47746290\t47746290\t0,0,0\t2\t213,372\t0,8020\t1\tcircRNA\tPCNT\tNM_006031\t2,3\tchr21:47744196-47746290|chr21:47754682-47766041\n+chr21\t47754310\t47754682\tcircular_RNA/3\t0\t+\t47754310\t47754310\t0,0,0\t1\t372\t0\t3\tcircRNA\tPCNT\tNM_006031\t3\tchr21:47746503-47754310|chr21:47754682-47766041\n+chr21\t47768925\t47769734\tcircular_RNA/1\t0\t+\t47768925\t47768925\t0,0,0\t2\t175,137\t0,672\t1\tcircRNA\tPCNT\tNM_006031\t7,8\tchr21:47767426-47768925|chr21:47769734-47771342\n+chr21\t47783394\t47787054\tcircular_RNA/1\t0\t+\t47783394\t47783394\t0,0,0\t2\t455,556\t0,3104\t1\tcircRNA\tPCNT\tNM_006031\t14,15\tchr21:47777106-47783394|chr21:47787054-47801608\n+chr21\t47801608\t47805898\tcircular_RNA/6\t0\t+\t47801608\t47801608\t0,0,0\t2\t147,152\t0,4138\t6\tcircRNA\tPCNT\tNM_006031\t16,17\tchr21:47787054-47801608|chr21:47805898-47808656\n+chr21\t47904669\t47917020\tcircular_RNA/1\t0\t+\t47904669\t47904669\t0,0,0\t3\t72,120,120\t0,5843,12231\t1\tcircRNA\tDIP2A\tNM_206891\t2,3,4\tchr21:47879135-47904669|chr21:47917020-47918494\n+chr21\t47904669\t47918746\tcircular_RNA/1\t0\t+\t47904669\t47904669\t0,0,0\t4\t72,120,120,252\t0,5843,12231,13825\t1\tcircRNA\tDIP2A\tNM_206891\t2,3,4,5\tchr21:47879135-47904669|chr21:47918746-47924273\n+chr21\t47916900\t47931527\tcircular_RNA/1\t0\t+\t47916900\t47916900\t0,0,0\t5\t120,252,129,120,198\t0,1594,7373,12269,14429\t1\tcircRNA\tDIP2A\tNM_206891\t4,5,6,7,8\tchr21:47910632-47916900|chr21:47931527-47949004\n+chr21\t48055675\t48056771\tcircular_RNA/1\t1\t+\t48055675\t48055675\t0,0,0\t1\t1096\t0\t1\tciRNA\tPRMT2\tNM_001242865\t1\tchr21:48055675-48056807\n+chr21\t48063446\t48064400\tcircular_RNA/1\t0\t+\t48063446\t48063446\t0,0,0\t2\t105,183\t0,771\t1\tcircRNA\tPRMT2\tNM_001242865\t3,4\tchr21:48056902-48063446|chr21:48064400-48068369\n+chr21\t48063446\t48080874\tcircular_RNA/1\t0\t+\t48063446\t48063446\t0,0,0\t6\t105,183,162,165,176,130\t0,771,4923,6040,15210,17298\t1\tcircRNA\tPRMT2\tNM_001535\t3,4,5,6,7,8\tchr21:48056902-48063446|chr21:48080874-48081711\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_07_annotated.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_07_annotated.txt Fri Aug 26 22:43:38 2022 +0000 |
| b |
| @@ -0,0 +1,125 @@ +chr21 35122447 35134290 circular_RNA/1 0 + ITSN1 +chr21 45089764 45093836 circular_RNA/1 0 + RRP1B +chr21 32537278 32567621 circular_RNA/4 0 - TIAM1 +chr21 35279644 35281515 circular_RNA/1 0 - ATP5PO +chr21 32617803 32624505 circular_RNA/1 0 - TIAM1 +chr21 34906884 34911662 circular_RNA/1 0 - GART +chr21 27326903 27484463 circular_RNA/2 0 - APP +chr21 40762623 40763762 circular_RNA/1 0 + GET1 +chr21 33750753 33756773 circular_RNA/1 0 - URB1 +chr21 27264033 27347541 circular_RNA/1 0 - APP +chr21 35138178 35140132 circular_RNA/2 0 + ITSN1 +chr21 34787194 34787327 circular_RNA/1 0 + IFNGR2 +chr21 45494204 45495034 circular_RNA/1 0 + TRAPPC10 +chr21 45475578 45483666 circular_RNA/1 0 + TRAPPC10 +chr21 17135209 17172162 circular_RNA/2 0 + USP25 +chr21 35127601 35140132 circular_RNA/1 0 + ITSN1 +chr21 44270150 44279832 circular_RNA/2 0 - WDR4 +chr21 37635843 37649398 circular_RNA/1 0 + DOP1B +chr21 32638325 32649224 circular_RNA/1 0 - TIAM1 +chr21 34832719 34839429 circular_RNA/1 0 - TMEM50B +chr21 30693541 30702014 circular_RNA/1 0 + BACH1 +chr21 33740711 33747792 circular_RNA/1 0 - URB1 +chr21 35091101 35094956 circular_RNA/22 0 + ITSN1 +chr21 47783394 47787054 circular_RNA/1 0 + PCNT +chr21 40590077 40590586 circular_RNA/1 0 - BRWD1 +chr21 26961146 26973779 circular_RNA/1 0 - MRPL39 +chr21 46893808 46902735 circular_RNA/1 0 + COL18A1 +chr21 34721396 34721849 circular_RNA/1 0 + IFNAR1 +chr21 45215069 45217576 circular_RNA/2 0 + RRP1 +chr21 37705943 37711219 circular_RNA/1 0 + MORC3 +chr21 44279771 44283706 circular_RNA/1 0 - WDR4 +chr21 47904669 47917020 circular_RNA/1 0 + DIP2A +chr21 44272364 44296877 circular_RNA/5 0 - WDR4 +chr21 17150222 17177577 circular_RNA/1 0 + USP25 +chr21 39086513 39087434 circular_RNA/1 0 - KCNJ6 +chr21 44293660 44296877 circular_RNA/1 0 - WDR4 +chr21 34066537 34067592 circular_RNA/2 0 - SYNJ1 +chr21 46281077 46285362 circular_RNA/1 0 - PTTG1IP +chr21 40619626 40622815 circular_RNA/3 0 - BRWD1 +chr21 45451971 45457808 circular_RNA/1 0 + TRAPPC10 +chr21 35134226 35138316 circular_RNA/1 0 + ITSN1 +chr21 37429406 37429775 circular_RNA/1 0 - SETD4 +chr21 40641824 40646398 circular_RNA/4 0 - BRWD1 +chr21 32711557 32711737 circular_RNA/1 0 - TIAM1 +chr21 38516824 38519903 circular_RNA/1 0 + TTC3 +chr21 47320504 47321027 circular_RNA/1 0 + PCBP3 +chr21 27347382 27372497 circular_RNA/2 0 - APP +chr21 38792600 38845182 circular_RNA/8 0 + DYRK1A +chr21 37619814 37620866 circular_RNA/3 0 + DOP1B +chr21 27326903 27354790 circular_RNA/2 0 - APP +chr21 40636385 40636945 circular_RNA/1 0 - BRWD1 +chr21 30437288 30442658 circular_RNA/1 0 - CCT8 +chr21 45537700 45537844 circular_RNA/1 0 + LOC102724159 +chr21 47768925 47769734 circular_RNA/1 0 + PCNT +chr21 32554737 32567621 circular_RNA/1 0 - TIAM1 +chr21 47746290 47754682 circular_RNA/1 0 + PCNT +chr21 32833536 32836348 circular_RNA/1 0 - TIAM1 +chr21 37775055 37783902 circular_RNA/10 0 + CHAF1B +chr21 34713304 34717666 circular_RNA/1 0 + IFNAR1 +chr21 27326903 27328069 circular_RNA/4 0 - APP +chr21 27277335 27284274 circular_RNA/2 0 - APP +chr21 37734480 37736557 circular_RNA/2 0 + MORC3 +chr21 44482420 44493451 circular_RNA/1 0 - CBSL +chr21 48063446 48064400 circular_RNA/1 0 + PRMT2 +chr21 47754310 47754682 circular_RNA/3 0 + PCNT +chr21 30677524 30702014 circular_RNA/1 0 + BACH1 +chr21 37410447 37412953 circular_RNA/1 0 - SETD4 +chr21 46600244 46605006 circular_RNA/1 0 + ADARB1 +chr21 34951655 34957074 circular_RNA/2 0 - DONSON +chr21 47155305 47175366 circular_RNA/3 0 + PCBP3 +chr21 17135209 17177577 circular_RNA/1 0 + USP25 +chr21 34906884 34907626 circular_RNA/4 0 - GART +chr21 47916900 47931527 circular_RNA/1 0 + DIP2A +chr21 44424435 44448984 circular_RNA/3 0 + PKNOX1 +chr21 34837648 34839429 circular_RNA/1 0 - TMEM50B +chr21 45153949 45163688 circular_RNA/2 0 + PDXK +chr21 40596333 40604424 circular_RNA/1 0 - BRWD1 +chr21 37771818 37775149 circular_RNA/1 0 + CHAF1B +chr21 45475578 45479095 circular_RNA/1 0 + TRAPPC10 +chr21 44424435 44430334 circular_RNA/1 0 + PKNOX1 +chr21 27394155 27484463 circular_RNA/2 0 - APP +chr21 34053805 34056429 circular_RNA/2 0 - SYNJ1 +chr21 45050202 45053302 circular_RNA/2 0 - HSF2BP +chr21 38560795 38564514 circular_RNA/1 0 + TTC3 +chr21 37775055 37781763 circular_RNA/1 0 + CHAF1B +chr21 47693301 47697631 circular_RNA/2 0 - MCM3AP +chr21 44483062 44493451 circular_RNA/1 0 - CBSL +chr21 37571367 37572799 circular_RNA/1 0 + DOP1B +chr21 16386664 16415895 circular_RNA/52 0 - NRIP1 +chr21 45499444 45500008 circular_RNA/1 0 + TRAPPC10 +chr21 45736126 45739298 circular_RNA/1 0 + PFKL +chr21 27423315 27425664 circular_RNA/5 0 - APP +chr21 44282391 44296877 circular_RNA/1 0 - WDR4 +chr21 47904669 47918746 circular_RNA/1 0 + DIP2A +chr21 27347382 27369731 circular_RNA/4 0 - APP +chr21 34804483 34805178 circular_RNA/7 0 + IFNGR2 +chr21 40619626 40630598 circular_RNA/6 0 - BRWD1 +chr21 46893808 46896394 circular_RNA/1 0 + COL18A1 +chr21 45165959 45168961 circular_RNA/3 0 + PDXK +chr21 37609559 37610999 circular_RNA/1 0 + DOP1B +chr21 40600425 40601362 circular_RNA/9 0 - BRWD1 +chr21 46275124 46276279 circular_RNA/1 0 - PTTG1IP +chr21 44424435 44445057 circular_RNA/1 0 + PKNOX1 +chr21 32537278 32575328 circular_RNA/2 0 - TIAM1 +chr21 47699906 47700489 circular_RNA/1 0 - MCM3AP +chr21 40181958 40186316 circular_RNA/1 0 + ETS2 +chr21 43938386 43955660 circular_RNA/1 0 + SLC37A1 +chr21 48063446 48080874 circular_RNA/1 0 + PRMT2 +chr21 45472160 45483666 circular_RNA/1 0 + TRAPPC10 +chr21 17135209 17138460 circular_RNA/15 0 + USP25 +chr21 32554737 32575328 circular_RNA/1 0 - TIAM1 +chr21 45745035 45745147 circular_RNA/2 0 + PFKL +chr21 38439561 38441924 circular_RNA/1 0 - PIGP +chr21 47801608 47805898 circular_RNA/6 0 + PCNT +chr21 46275124 46281186 circular_RNA/7 0 - PTTG1IP +chr21 46548316 46554747 circular_RNA/20 0 + ADARB1 +chr21 30698379 30702014 circular_RNA/1 0 + BACH1 +chr21 35091101 35107509 circular_RNA/5 0 + ITSN1 +chr21 47641767 47642652 circular_RNA/1 0 - LSS +chr21 32567539 32575328 circular_RNA/1 0 - TIAM1 +chr21 32559316 32567621 circular_RNA/1 0 - TIAM1 +chr21 44492094 44493451 circular_RNA/2 0 - CBSL +chr21 37716876 37721706 circular_RNA/1 0 + MORC3 +chr21 27269884 27284274 circular_RNA/2 0 - APP +chr21 26969613 26972178 circular_RNA/1 0 - MRPL39 |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_07_combined.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_07_combined.txt Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,1945 @@\n+CUFF.45981.2\tCUFF.45981.2\tchr21\t+\t9825464\t9827165\t9827165\t9827165\t2\t9825464,9827066,\t9825471,9827165,\n+CUFF.45982.1\tCUFF.45982.1\tchr21\t.\t9826847\t9827165\t9827165\t9827165\t1\t9826847,\t9827165,\n+CUFF.45983.1\tCUFF.45983.1\tchr21\t.\t15279914\t15280175\t15280175\t15280175\t1\t15279914,\t15280175,\n+CUFF.45988.1\tCUFF.45988.1\tchr21\t.\t15426534\t15427029\t15427029\t15427029\t1\t15426534,\t15427029,\n+CUFF.45989.1\tCUFF.45989.1\tchr21\t.\t15427319\t15428127\t15428127\t15428127\t1\t15427319,\t15428127,\n+CUFF.45990.1\tCUFF.45990.1\tchr21\t.\t15433507\t15434847\t15434847\t15434847\t1\t15433507,\t15434847,\n+CUFF.45984.1\tCUFF.45984.1\tchr21\t.\t15457362\t15458120\t15458120\t15458120\t1\t15457362,\t15458120,\n+CUFF.45991.1\tCUFF.45991.1\tchr21\t.\t15470615\t15471670\t15471670\t15471670\t1\t15470615,\t15471670,\n+CUFF.45985.1\tCUFF.45985.1\tchr21\t.\t15459562\t15460287\t15460287\t15460287\t1\t15459562,\t15460287,\n+CUFF.45986.1\tCUFF.45986.1\tchr21\t.\t15471760\t15473743\t15473743\t15473743\t1\t15471760,\t15473743,\n+CUFF.45987.1\tCUFF.45987.1\tchr21\t.\t15473986\t15475464\t15475464\t15475464\t1\t15473986,\t15475464,\n+CUFF.45992.1\tCUFF.45992.1\tchr21\t.\t15477957\t15478236\t15478236\t15478236\t1\t15477957,\t15478236,\n+CUFF.45998.1\tCUFF.45998.1\tchr21\t.\t16308473\t16309217\t16309217\t16309217\t1\t16308473,\t16309217,\n+CUFF.45996.1\tCUFF.45996.1\tchr21\t.\t16306827\t16307182\t16307182\t16307182\t1\t16306827,\t16307182,\n+CUFF.45993.1\tCUFF.45993.1\tchr21\t.\t16300305\t16300480\t16300480\t16300480\t1\t16300305,\t16300480,\n+CUFF.45999.1\tCUFF.45999.1\tchr21\t.\t16309313\t16309843\t16309843\t16309843\t1\t16309313,\t16309843,\n+CUFF.45995.1\tCUFF.45995.1\tchr21\t.\t16305403\t16306276\t16306276\t16306276\t1\t16305403,\t16306276,\n+CUFF.45994.1\tCUFF.45994.1\tchr21\t.\t16301777\t16301995\t16301995\t16301995\t1\t16301777,\t16301995,\n+CUFF.46000.1\tCUFF.46000.1\tchr21\t.\t16310431\t16311362\t16311362\t16311362\t1\t16310431,\t16311362,\n+CUFF.45997.1\tCUFF.45997.1\tchr21\t.\t16307817\t16308182\t16308182\t16308182\t1\t16307817,\t16308182,\n+CUFF.46001.1\tCUFF.46001.1\tchr21\t.\t16311444\t16312269\t16312269\t16312269\t1\t16311444,\t16312269,\n+CUFF.46006.1\tCUFF.46006.1\tchr21\t.\t17195172\t17195567\t17195567\t17195567\t1\t17195172,\t17195567,\n+CUFF.46021.2\tCUFF.46021.2\tchr21\t-\t16340591\t16437067\t16437067\t16437067\t4\t16340591,16386664,16415815,16437065,\t16340847,16386787,16415895,16437067,\n+CUFF.46021.1\tCUFF.46021.1\tchr21\t-\t16340591\t16437067\t16437067\t16437067\t5\t16340591,16386664,16412683,16415815,16437065,\t16340847,16386787,16412737,16415895,16437067,\n+CUFF.46021.3\tCUFF.46021.3\tchr21\t-\t16340591\t16438047\t16438047\t16438047\t4\t16340591,16386664,16415815,16438045,\t16340847,16386787,16415895,16438047,\n+CUFF.46021.4\tCUFF.46021.4\tchr21\t-\t16340591\t16438047\t16438047\t16438047\t5\t16340591,16386664,16387465,16415815,16438045,\t16340847,16386787,16387546,16415895,16438047,\n+CUFF.46021.5\tCUFF.46021.5\tchr21\t-\t16340591\t16438047\t16438047\t16438047\t6\t16340591,16386664,16387465,16412683,16415815,16438045,\t16340847,16386787,16387546,16412737,16415895,16438047,\n+CUFF.46021.6\tCUFF.46021.6\tchr21\t-\t16363428\t16437067\t16437067\t16437067\t5\t16363428,16386664,16387465,16415815,16437065,\t16363627,16386787,16387546,16415895,16437067,\n+CUFF.46009.1\tCUFF.46009.1\tchr21\t.\t17768984\t17769561\t17769561\t17769561\t1\t17768984,\t17769561,\n+CUFF.46007.1\tCUFF.46007.1\tchr21\t+\t17205670\t17214859\t17214859\t17214859\t2\t17205670,17214716,\t17205867,17214859,\n+CUFF.46007.2\tCUFF.46007.2\tchr21\t+\t17208302\t17214859\t17214859\t17214859\t2\t17208302,17214716,\t17208361,17214859,\n+CUFF.46008.1\tCUFF.46008.1\tchr21\t.\t17208396\t17209259\t17209259\t17209259\t1\t17208396,\t17209259,\n+CUFF.46002.3\tCUFF.46002.3\tchr21\t+\t17102754\t17177974\t17177974\t17177974\t7\t17102754,17135209,17138315,17150222,17163820,17172075,17177439,\t17102757,17135287,17138460,17150346,17163983,17172162,17177974,\n+CUFF.46002.1\tCUFF.46002.1\tchr21\t+\t17102754\t17177974\t17177974\t17177974\t8\t17102754,17135209,17136556,17138315,17150222,17163820,17172075,17177439,\t17102757,17135287,17136616,17138460,17150346,17163983,17172162,17177974,\n+CUFF.46002.2\tCUFF.46002.2\tchr21\t+\t17102754\t17177974\t17177974\t17177974\t9\t17102754,17135209,17136556,17137100,17138320,17150222,171'..b'7362364\t47269999\t47361620\t18\t47063638,47088787,47155305,47175330,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359943,47361583,\t47063782,47088866,47155343,47175366,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNR_145492\tchr21\t+\t47063638\t47362364\t47362364\t47362364\t18\t47063638,47088787,47155305,47175330,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359950,47361583,\t47063782,47088866,47155343,47175366,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_001348243\tchr21\t+\t47167927\t47362364\t47269999\t47361620\t16\t47167927,47169294,47175330,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349833,47355166,47359943,47361583,\t47168053,47169389,47175366,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47355219,47360113,47362364,\n+PCBP3\tNM_001382277\tchr21\t+\t47167927\t47362364\t47269999\t47361620\t16\t47167927,47169294,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359943,47361583,\t47168053,47169389,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_001130141\tchr21\t+\t47268063\t47362364\t47269999\t47361620\t14\t47268063,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47337501,47349833,47350699,47355166,47359943,47361583,\t47268315,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_001382278\tchr21\t+\t47268063\t47362364\t47269999\t47361620\t15\t47268063,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349833,47350699,47355166,47359943,47361583,\t47268315,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_001382279\tchr21\t+\t47268063\t47362364\t47269999\t47361620\t15\t47268063,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359943,47361583,\t47268315,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47334008,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_020528\tchr21\t+\t47268063\t47362364\t47269999\t47361620\t15\t47268063,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359943,47361583,\t47268315,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+IFNAR2\tNM_001385054\tchr21\t+\t34602242\t34637968\t34614227\t34634882\t8\t34602242,34614190,34615977,34617255,34619022,34621013,34624966,34634865,\t34602521,34614282,34616019,34617379,34619195,34621159,34625135,34637968,\n+IFNAR2\tNM_001385055\tchr21\t+\t34602242\t34637968\t34614227\t34637276\t10\t34602242,34614190,34615977,34617255,34619022,34621013,34624966,34632901,34635097,34637238,\t34602521,34614282,34616019,34617379,34619195,34621159,34625135,34633032,34635575,34637968,\n+SH3BGR\tNM_001317740\tchr21\t+\t40823895\t40887428\t40824022\t40883702\t6\t40823895,40834300,40847060,40880924,40883606,40887014,\t40824067,40834486,40847141,40880954,40883736,40887428,\n+SH3BGR\tNM_007341\tchr21\t+\t40823895\t40887428\t40824022\t40883702\t7\t40823895,40834300,40847060,40871748,40880924,40883606,40887014,\t40824067,40834486,40847141,40871841,40880954,40883736,40887428,\n+APP\tNM_001385253\tchr21\t-\t27252860\t27543088\t27253980\t27542938\t17\t27252860,27264033,27269884,27277335,27284052,27326903,27327940,27347382,27348266,27354656,27369674,27394155,27423315,27425551,27462258,27484295,27542881,\t27254082,27264180,27269985,27277389,27284274,27327003,27328069,27347541,27348341,27354790,27369731,27394358,27423509,27425664,27462388,27484463,27543088,\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_07_full.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_07_full.txt Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,195 @@\n+chr21\t16386664\t16415895\tcircular_RNA/52\t0\t-\t16386664\t16386664\t0,0,0\t2\t123,80\t0,29151\t52\tcircRNA\tNRIP1\tNM_003489\t3,2\tchr21:16340847-16386664|chr21:16415895-16437065\n+chr21\t17135209\t17138460\tcircular_RNA/15\t0\t+\t17135209\t17135209\t0,0,0\t2\t78,145\t0,3106\t15\tcircRNA\tUSP25\tNM_001283041\t2,3\tchr21:17102757-17135209|chr21:17138460-17150222\n+chr21\t17135209\t17172162\tcircular_RNA/2\t0\t+\t17135209\t17135209\t0,0,0\t5\t78,145,124,163,87\t0,3106,15013,28611,36866\t2\tcircRNA\tUSP25\tNM_001283041\t2,3,4,5,6\tchr21:17102757-17135209|chr21:17172162-17177439\n+chr21\t17135209\t17172162\tcircular_RNA/2\t0\t+\t17135209\t17135209\t0,0,0\t4\t78,145,163,87\t0,3106,28611,36866\t2\tcircRNA\tUSP25\tNM_001352561\t2,3,4,5\tchr21:17102757-17135209|chr21:17172162-17177439\n+chr21\t17135209\t17177577\tcircular_RNA/1\t0\t+\t17135209\t17135209\t0,0,0\t6\t78,145,124,163,87,138\t0,3106,15013,28611,36866,42230\t1\tcircRNA\tUSP25\tNM_001283041\t2,3,4,5,6,7\tchr21:17102757-17135209|chr21:17177577-17181127\n+chr21\t17135209\t17177577\tcircular_RNA/1\t0\t+\t17135209\t17135209\t0,0,0\t5\t78,145,163,87,138\t0,3106,28611,36866,42230\t1\tcircRNA\tUSP25\tNM_001352561\t2,3,4,5,6\tchr21:17102757-17135209|chr21:17177577-17181127\n+chr21\t17150222\t17177577\tcircular_RNA/1\t0\t+\t17150222\t17150222\t0,0,0\t4\t124,163,87,138\t0,13598,21853,27217\t1\tcircRNA\tUSP25\tNM_001283041\t4,5,6,7\tchr21:17138460-17150222|chr21:17177577-17181127\n+chr21\t26961146\t26973779\tcircular_RNA/1\t0\t-\t26961146\t26961146\t0,0,0\t6\t48,154,66,113,68,100\t0,3977,5058,8467,10964,12533\t1\tcircRNA\tMRPL39\tNM_017446\t9,8,7,6,5,4\tchr21:26958066-26961146|chr21:26973779-26976107\n+chr21\t26969613\t26972178\tcircular_RNA/1\t0\t-\t26969613\t26969613\t0,0,0\t2\t113,68\t0,2497\t1\tcircRNA\tMRPL39\tNM_017446\t6,5\tchr21:26966270-26969613|chr21:26972178-26973679\n+chr21\t27264033\t27347541\tcircular_RNA/1\t0\t-\t27264033\t27264033\t0,0,0\t7\t147,101,54,222,100,129,159\t0,5851,13302,20019,62870,63907,83349\t1\tcircRNA\tAPP\tNM_001136016\t16,15,14,13,12,11,10\tchr21:27254082-27264033|chr21:27347541-27348266\n+chr21\t27264033\t27347541\tcircular_RNA/1\t0\t-\t27264033\t27264033\t0,0,0\t6\t147,101,222,100,129,159\t0,5851,20019,62870,63907,83349\t1\tcircRNA\tAPP\tNM_001204301\t16,15,14,13,12,11\tchr21:27254082-27264033|chr21:27347541-27348266\n+chr21\t27269884\t27284274\tcircular_RNA/2\t0\t-\t27269884\t27269884\t0,0,0\t3\t101,54,222\t0,7451,14168\t2\tcircRNA\tAPP\tNM_001136016\t15,14,13\tchr21:27264180-27269884|chr21:27284274-27326903\n+chr21\t27269884\t27284274\tcircular_RNA/2\t0\t-\t27269884\t27269884\t0,0,0\t2\t101,222\t0,14168\t2\tcircRNA\tAPP\tNM_001204301\t15,14\tchr21:27264180-27269884|chr21:27284274-27326903\n+chr21\t27277335\t27284274\tcircular_RNA/2\t0\t-\t27277335\t27277335\t0,0,0\t2\t54,222\t0,6717\t2\tcircRNA\tAPP\tNM_001136016\t14,13\tchr21:27269985-27277335|chr21:27284274-27326903\n+chr21\t27326903\t27328069\tcircular_RNA/4\t0\t-\t27326903\t27326903\t0,0,0\t2\t100,129\t0,1037\t4\tcircRNA\tAPP\tNM_001136016\t12,11\tchr21:27284274-27326903|chr21:27328069-27347382\n+chr21\t27326903\t27354790\tcircular_RNA/2\t0\t-\t27326903\t27326903\t0,0,0\t5\t100,129,159,75,134\t0,1037,20479,21363,27753\t2\tcircRNA\tAPP\tNM_001136016\t12,11,10,9,8\tchr21:27284274-27326903|chr21:27354790-27372329\n+chr21\t27326903\t27484463\tcircular_RNA/2\t0\t-\t27326903\t27326903\t0,0,0\t11\t100,129,159,75,134,168,203,194,113,130,168\t0,1037,20479,21363,27753,45426,67252,96412,98648,135355,157392\t2\tcircRNA\tAPP\tNM_001136016\t12,11,10,9,8,7,6,5,4,3,2\tchr21:27284274-27326903|chr21:27484463-27512470\n+chr21\t27326903\t27484463\tcircular_RNA/2\t0\t-\t27326903\t27326903\t0,0,0\t12\t100,129,159,75,134,57,168,203,194,113,130,168\t0,1037,20479,21363,27753,42771,45426,67252,96412,98648,135355,157392\t2\tcircRNA\tAPP\tNM_000484\t13,12,11,10,9,8,7,6,5,4,3,2\tchr21:27284274-27326903|chr21:27484463-27542881\n+chr21\t27326903\t27484463\tcircular_RNA/2\t0\t-\t27326903\t27326903\t0,0,0\t10\t100,129,159,75,134,203,194,113,130,168\t0,1037,20479,21363,27753,67252,96412,98648,135355,157392\t2\tcircRNA\tAPP\tNM_001204303\t11,10,9,8,7,6,5,4,3,2\tchr21:27284274-27326903|chr21:27484463-27542881\n+chr21\t27326903\t27484463\tcircular_RNA/2\t0\t-\t27326903\t27326903\t0,0,0\t11\t100,129,159,75,134,57,203,194,113,130,168\t0,1037,20479,21363,2775'..b'4,5\tchr21:35446045-35467161|chr21:35497780-35514707\n+chr21\t35467161\t35497780\tcircular_RNA/2\t0\t+\t35467161\t35467161\t0,0,0\t3\t8046,23,140\t0,8634,30479\t2\tcircRNA\tCUFF.46946.6\tCUFF.46946.6\t2,3,4\tchr21:35446045-35467161|chr21:35497780-35514707\n+chr21\t35475133\t35497780\tcircular_RNA/4\t0\t+\t35475133\t35475133\t0,0,0\t3\t74,23,140\t0,662,22507\t4\tcircRNA\tCUFF.46946.5\tCUFF.46946.5\t3,4,5\tchr21:35472588-35475133|chr21:35497780-35514707\n+chr21\t37775055\t37783902\tcircular_RNA/10\t0\t+\t37775055\t37775055\t0,0,0\t4\t94,70,46,142\t0,6003,6755,8705\t10\tcircRNA\tCUFF.46349.3\tCUFF.46349.3\t2,3,4,5\tchr21:37771903-37775055|chr21:37783902-37785181\n+chr21\t38792600\t38794168\tcircular_RNA/91\t0\t+\t38792600\t38792600\t0,0,0\t2\t86,93\t0,1475\t91\tcircRNA\tCUFF.46430.1\tCUFF.46430.1\t2,3\tchr21:38747419-38792600|chr21:38794168-38794883\n+chr21\t38792600\t38798083\tcircular_RNA/9\t0\t+\t38792600\t38792600\t0,0,0\t3\t86,93,92\t0,1475,5391\t9\tcircRNA\tCUFF.46430.3\tCUFF.46430.3\t2,3,4\tchr21:38782972-38792600|chr21:38798083-38802570\n+chr21\t38792600\t38798083\tcircular_RNA/9\t0\t+\t38792600\t38792600\t0,0,0\t2\t86,92\t0,5391\t9\tcircRNA\tCUFF.46430.4\tCUFF.46430.4\t2,3\tchr21:38787867-38792600|chr21:38798083-38801168\n+chr21\t38792600\t38802702\tcircular_RNA/19\t0\t+\t38792600\t38792600\t0,0,0\t4\t86,93,92,132\t0,1475,5391,9970\t19\tcircRNA\tCUFF.46430.3\tCUFF.46430.3\t2,3,4,5\tchr21:38782972-38792600|chr21:38802702-38828431\n+chr21\t38792600\t38802702\tcircular_RNA/19\t0\t+\t38792600\t38792600\t0,0,0\t4\t86,92,42,132\t0,5391,8568,9970\t19\tcircRNA\tCUFF.46430.4\tCUFF.46430.4\t2,3,4,5\tchr21:38787867-38792600|chr21:38802702-38828431\n+chr21\t38792600\t38802702\tcircular_RNA/19\t0\t+\t38792600\t38792600\t0,0,0\t5\t86,93,92,42,132\t0,1475,5391,8568,9970\t19\tcircRNA\tCUFF.46430.5\tCUFF.46430.5\t2,3,4,5,6\tchr21:38787867-38792600|chr21:38802702-38828431\n+chr21\t38792600\t38828610\tcircular_RNA/6\t0\t+\t38792600\t38792600\t0,0,0\t2\t86,179\t0,35831\t6\tcircRNA\tCUFF.46430.2\tCUFF.46430.2\t2,3\tchr21:38747419-38792600|chr21:38828610-38844985\n+chr21\t38792600\t38845182\tcircular_RNA/8\t0\t+\t38792600\t38792600\t0,0,0\t3\t86,179,197\t0,35831,52385\t8\tcircRNA\tCUFF.46430.2\tCUFF.46430.2\t2,3,4\tchr21:38747419-38792600|chr21:38845182-38850509\n+chr21\t40641824\t40646398\tcircular_RNA/4\t0\t-\t40641824\t40641824\t0,0,0\t3\t68,151,99\t0,384,4475\t4\tcircRNA\tCUFF.46438.4\tCUFF.46438.4\t7,6,5\tchr21:40636945-40641824|chr21:40646398-40648098\n+chr21\t45472160\t45483666\tcircular_RNA/1\t0\t+\t45472160\t45472160\t0,0,0\t4\t197,118,112,248\t0,3496,6823,11258\t1\tcircRNA\tCUFF.46596.2\tCUFF.46596.2\t3,4,5,6\tchr21:45457808-45472160|chr21:45483666-45494204\n+chr21\t46538478\t46548488\tcircular_RNA/1\t0\t+\t46538478\t46538478\t0,0,0\t3\t56,166,172\t0,2230,9838\t1\tcircRNA\tCUFF.46822.4\tCUFF.46822.4\t2,3,4\tchr21:46536953-46538478|chr21:46548488-46553473\n+chr21\t46538478\t46554747\tcircular_RNA/1\t0\t+\t46538478\t46538478\t0,0,0\t5\t56,166,172,107,118\t0,2230,9838,14995,16151\t1\tcircRNA\tCUFF.46822.4\tCUFF.46822.4\t2,3,4,5,6\tchr21:46536953-46538478|chr21:46554747-46564545\n+chr21\t46548316\t46554747\tcircular_RNA/20\t0\t+\t46548316\t46548316\t0,0,0\t4\t172,92,107,118\t0,3813,5157,6313\t20\tcircRNA\tCUFF.46822.3\tCUFF.46822.3\t2,3,4,5\tchr21:46494708-46548316|chr21:46554747-46563056\n+chr21\t46548316\t46554747\tcircular_RNA/20\t0\t+\t46548316\t46548316\t0,0,0\t2\t172,76\t0,6355\t20\tcircRNA\tCUFF.46822.1\tCUFF.46822.1\t2,3\tchr21:46494708-46548316|chr21:46554747-46591524\n+chr21\t46548316\t46554747\tcircular_RNA/20\t0\t+\t46548316\t46548316\t0,0,0\t3\t172,92,118\t0,3813,6313\t20\tcircRNA\tCUFF.46822.2\tCUFF.46822.2\t2,3,4\tchr21:46494708-46548316|chr21:46554747-46591524\n+chr21\t46548316\t46554747\tcircular_RNA/20\t0\t+\t46548316\t46548316\t0,0,0\t3\t172,107,118\t0,5157,6313\t20\tcircRNA\tCUFF.46822.4\tCUFF.46822.4\t4,5,6\tchr21:46540874-46548316|chr21:46554747-46564545\n+chr21\t46548316\t46554747\tcircular_RNA/20\t0\t+\t46548316\t46548316\t0,0,0\t3\t172,34,118\t0,5157,6313\t20\tcircRNA\tCUFF.46822.5\tCUFF.46822.5\t2,3,4\tchr21:46536953-46548316|chr21:46554747-46591524\n+chr21\t46600244\t46605006\tcircular_RNA/1\t0\t+\t46600244\t46600244\t0,0,0\t6\t115,37,169,149,120,169\t0,1150,2255,3032,4144,4593\t1\tcircRNA\tCUFF.46822.1\tCUFF.46822.1\t6,7,8,9,10,11\tchr21:46596579-46600244|chr21:46605006-46624469\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_07_novel.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_07_novel.txt Fri Aug 26 22:43:38 2022 +0000 |
| b |
| @@ -0,0 +1,9 @@ +chr21 38792600 38802702 circular_RNA/19 0 + Annotated Novel +chr21 38792600 38828610 circular_RNA/6 0 + Annotated Novel +chr21 46538478 46554747 circular_RNA/1 0 + Novel Annotated +chr21 38792600 38794168 circular_RNA/91 0 + Annotated Novel +chr21 35475133 35497780 circular_RNA/4 0 + Novel Annotated +chr21 38792600 38798083 circular_RNA/9 0 + Annotated Novel +chr21 16386664 16387546 circular_RNA/1 0 - Annotated Novel +chr21 35467161 35497780 circular_RNA/2 0 + Annotated Annotated +chr21 46538478 46548488 circular_RNA/1 0 + Novel Annotated |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_08_a3bs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_08_a3bs.txt Fri Aug 26 22:43:38 2022 +0000 |
| b |
| @@ -0,0 +1,33 @@ +chr21 27326903 27484463 - chr21 27326903 8 0.250000 +chr21 40619626 40622815 - chr21 40619626 9 0.333333 +chr21 27347382 27369731 - chr21 27347382 6 0.666667 +chr21 46548316 46554747 + chr21 46554747 21 0.952381 +chr21 30677523 30702014 + chr21 30702014 4 0.250000 +chr21 32537278 32567621 - chr21 32537278 6 0.666667 +chr21 45472160 45483666 + chr21 45483666 2 0.500000 +chr21 34906884 34911662 - chr21 34906884 5 0.200000 +chr21 16386664 16387546 - chr21 16386664 53 0.018868 +chr21 32554737 32567621 - chr21 32554737 2 0.500000 +chr21 47754310 47754682 + chr21 47754682 4 0.750000 +chr21 35467161 35497780 + chr21 35497780 6 0.333333 +chr21 35475133 35497780 + chr21 35497780 6 0.666667 +chr21 45475578 45483666 + chr21 45483666 2 0.500000 +chr21 40619626 40630598 - chr21 40619626 9 0.666667 +chr21 35138178 35140132 + chr21 35140132 3 0.666667 +chr21 17135209 17177577 + chr21 17177577 2 0.500000 +chr21 46275124 46281186 - chr21 46275124 8 0.875000 +chr21 16386664 16415895 - chr21 16386664 53 0.981132 +chr21 32554737 32575328 - chr21 32554737 2 0.500000 +chr21 30698379 30702014 + chr21 30702014 4 0.250000 +chr21 46538478 46554747 + chr21 46554747 21 0.047619 +chr21 35127601 35140132 + chr21 35140132 3 0.333333 +chr21 32537278 32575328 - chr21 32537278 6 0.333333 +chr21 34906884 34907626 - chr21 34906884 5 0.800000 +chr21 27326903 27354790 - chr21 27326903 8 0.250000 +chr21 17150222 17177577 + chr21 17177577 2 0.500000 +chr21 47746290 47754682 + chr21 47754682 4 0.250000 +chr21 46275124 46276279 - chr21 46275124 8 0.125000 +chr21 27347382 27372497 - chr21 27347382 6 0.333333 +chr21 27326903 27328069 - chr21 27326903 8 0.500000 +chr21 30677524 30702014 + chr21 30702014 4 0.250000 +chr21 30693541 30702014 + chr21 30702014 4 0.250000 |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_08_a5bs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_08_a5bs.txt Fri Aug 26 22:43:38 2022 +0000 |
| b |
| @@ -0,0 +1,45 @@ +chr21 46893808 46896394 + chr21 46893808 2 0.500000 +chr21 45475578 45479095 + chr21 45475578 2 0.500000 +chr21 27326903 27484463 - chr21 27484463 4 0.500000 +chr21 38792600 38798083 + chr21 38792600 133 0.067669 +chr21 44424435 44445057 + chr21 44424435 5 0.200000 +chr21 44482420 44493451 - chr21 44493451 4 0.250000 +chr21 46538478 46548488 + chr21 46538478 2 0.500000 +chr21 44272364 44296877 - chr21 44296877 7 0.714286 +chr21 32537278 32567621 - chr21 32567621 6 0.666667 +chr21 44483062 44493451 - chr21 44493451 4 0.250000 +chr21 38792600 38802702 + chr21 38792600 133 0.142857 +chr21 48063446 48080874 + chr21 48063446 2 0.500000 +chr21 32554737 32567621 - chr21 32567621 6 0.166667 +chr21 35122447 35134290 + chr21 35122447 2 0.500000 +chr21 17135209 17138460 + chr21 17135209 18 0.833333 +chr21 47904669 47917020 + chr21 47904669 2 0.500000 +chr21 17135209 17172162 + chr21 17135209 18 0.111111 +chr21 44282391 44296877 - chr21 44296877 7 0.142857 +chr21 44492094 44493451 - chr21 44493451 4 0.500000 +chr21 45475578 45483666 + chr21 45475578 2 0.500000 +chr21 37775055 37781763 + chr21 37775055 11 0.090909 +chr21 17135209 17177577 + chr21 17135209 18 0.055556 +chr21 32554737 32575328 - chr21 32575328 4 0.250000 +chr21 46538478 46554747 + chr21 46538478 2 0.500000 +chr21 48063446 48064400 + chr21 48063446 2 0.500000 +chr21 35091101 35094956 + chr21 35091101 27 0.814815 +chr21 27277335 27284274 - chr21 27284274 4 0.500000 +chr21 38792600 38828610 + chr21 38792600 133 0.045113 +chr21 35091101 35107509 + chr21 35091101 27 0.185185 +chr21 32559316 32567621 - chr21 32567621 6 0.166667 +chr21 44293660 44296877 - chr21 44296877 7 0.142857 +chr21 32537278 32575328 - chr21 32575328 4 0.500000 +chr21 38792600 38845182 + chr21 38792600 133 0.060150 +chr21 47904669 47918746 + chr21 47904669 2 0.500000 +chr21 34832719 34839429 - chr21 34839429 2 0.500000 +chr21 37775055 37783902 + chr21 37775055 11 0.909091 +chr21 27394155 27484463 - chr21 27484463 4 0.500000 +chr21 44424435 44448984 + chr21 44424435 5 0.600000 +chr21 35122447 35122627 + chr21 35122447 2 0.500000 +chr21 32567539 32575328 - chr21 32575328 4 0.250000 +chr21 27269884 27284274 - chr21 27284274 4 0.500000 +chr21 38792600 38794168 + chr21 38792600 133 0.684211 +chr21 46893808 46902735 + chr21 46893808 2 0.500000 +chr21 34837648 34839429 - chr21 34839429 2 0.500000 +chr21 44424435 44430334 + chr21 44424435 5 0.200000 |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_08_annotated.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_08_annotated.txt Fri Aug 26 22:43:38 2022 +0000 |
| b |
| @@ -0,0 +1,128 @@ +chr21 35122447 35134290 circular_RNA/1 0 + ITSN1 +chr21 45089764 45093836 circular_RNA/1 0 + RRP1B +chr21 32537278 32567621 circular_RNA/4 0 - TIAM1 +chr21 35279644 35281515 circular_RNA/1 0 - ATP5PO +chr21 32617803 32624505 circular_RNA/1 0 - TIAM1 +chr21 34906884 34911662 circular_RNA/1 0 - GART +chr21 27326903 27484463 circular_RNA/2 0 - APP +chr21 40762623 40763762 circular_RNA/1 0 + GET1 +chr21 33750753 33756773 circular_RNA/1 0 - URB1 +chr21 27264033 27347541 circular_RNA/1 0 - APP +chr21 35138178 35140132 circular_RNA/2 0 + ITSN1 +chr21 34787194 34787327 circular_RNA/1 0 + IFNGR2 +chr21 45494204 45495034 circular_RNA/1 0 + TRAPPC10 +chr21 45475578 45483666 circular_RNA/1 0 + TRAPPC10 +chr21 17135209 17172162 circular_RNA/2 0 + USP25 +chr21 35127601 35140132 circular_RNA/1 0 + ITSN1 +chr21 44270150 44279832 circular_RNA/2 0 - WDR4 +chr21 37635843 37649398 circular_RNA/1 0 + DOP1B +chr21 32638325 32649224 circular_RNA/1 0 - TIAM1 +chr21 34832719 34839429 circular_RNA/1 0 - TMEM50B +chr21 30693541 30702014 circular_RNA/1 0 + BACH1 +chr21 33740711 33747792 circular_RNA/1 0 - URB1 +chr21 35091101 35094956 circular_RNA/22 0 + ITSN1 +chr21 47783394 47787054 circular_RNA/1 0 + PCNT +chr21 40590077 40590586 circular_RNA/1 0 - BRWD1 +chr21 26961146 26973779 circular_RNA/1 0 - MRPL39 +chr21 46893808 46902735 circular_RNA/1 0 + COL18A1 +chr21 34721396 34721849 circular_RNA/1 0 + IFNAR1 +chr21 45215069 45217576 circular_RNA/2 0 + RRP1 +chr21 37705943 37711219 circular_RNA/1 0 + MORC3 +chr21 44279771 44283706 circular_RNA/1 0 - WDR4 +chr21 47904669 47917020 circular_RNA/1 0 + DIP2A +chr21 44272364 44296877 circular_RNA/5 0 - WDR4 +chr21 17150222 17177577 circular_RNA/1 0 + USP25 +chr21 39086513 39087434 circular_RNA/1 0 - KCNJ6 +chr21 44293660 44296877 circular_RNA/1 0 - WDR4 +chr21 34066537 34067592 circular_RNA/2 0 - SYNJ1 +chr21 46281077 46285362 circular_RNA/1 0 - PTTG1IP +chr21 40619626 40622815 circular_RNA/3 0 - BRWD1 +chr21 45451971 45457808 circular_RNA/1 0 + TRAPPC10 +chr21 35134226 35138316 circular_RNA/1 0 + ITSN1 +chr21 37429406 37429775 circular_RNA/1 0 - SETD4 +chr21 40641824 40646398 circular_RNA/4 0 - BRWD1 +chr21 32711557 32711737 circular_RNA/1 0 - TIAM1 +chr21 38516824 38519903 circular_RNA/1 0 + TTC3 +chr21 47320504 47321027 circular_RNA/1 0 + PCBP3 +chr21 27347382 27372497 circular_RNA/2 0 - APP +chr21 38792600 38845182 circular_RNA/8 0 + DYRK1A +chr21 37619814 37620866 circular_RNA/3 0 + DOP1B +chr21 27326903 27354790 circular_RNA/2 0 - APP +chr21 40636385 40636945 circular_RNA/1 0 - BRWD1 +chr21 30437288 30442658 circular_RNA/1 0 - CCT8 +chr21 45537700 45537844 circular_RNA/1 0 + LOC102724159 +chr21 47768925 47769734 circular_RNA/1 0 + PCNT +chr21 32554737 32567621 circular_RNA/1 0 - TIAM1 +chr21 47746290 47754682 circular_RNA/1 0 + PCNT +chr21 32833536 32836348 circular_RNA/1 0 - TIAM1 +chr21 37775055 37783902 circular_RNA/10 0 + CHAF1B +chr21 34713304 34717666 circular_RNA/1 0 + IFNAR1 +chr21 27326903 27328069 circular_RNA/4 0 - APP +chr21 27277335 27284274 circular_RNA/2 0 - APP +chr21 37734480 37736557 circular_RNA/2 0 + MORC3 +chr21 44482420 44493451 circular_RNA/1 0 - CBSL +chr21 48063446 48064400 circular_RNA/1 0 + PRMT2 +chr21 47754310 47754682 circular_RNA/3 0 + PCNT +chr21 30677524 30702014 circular_RNA/1 0 + BACH1 +chr21 37410447 37412953 circular_RNA/1 0 - SETD4 +chr21 46600244 46605006 circular_RNA/1 0 + ADARB1 +chr21 34951655 34957074 circular_RNA/2 0 - DONSON +chr21 47155305 47175366 circular_RNA/3 0 + PCBP3 +chr21 17135209 17177577 circular_RNA/1 0 + USP25 +chr21 34906884 34907626 circular_RNA/4 0 - GART +chr21 47916900 47931527 circular_RNA/1 0 + DIP2A +chr21 44424435 44448984 circular_RNA/3 0 + PKNOX1 +chr21 34837648 34839429 circular_RNA/1 0 - TMEM50B +chr21 45153949 45163688 circular_RNA/2 0 + PDXK +chr21 40596333 40604424 circular_RNA/1 0 - BRWD1 +chr21 37771818 37775149 circular_RNA/1 0 + CHAF1B +chr21 45475578 45479095 circular_RNA/1 0 + TRAPPC10 +chr21 44424435 44430334 circular_RNA/1 0 + PKNOX1 +chr21 27394155 27484463 circular_RNA/2 0 - APP +chr21 34053805 34056429 circular_RNA/2 0 - SYNJ1 +chr21 35122447 35122627 circular_RNA/1 1 + ITSN1 +chr21 45050202 45053302 circular_RNA/2 0 - HSF2BP +chr21 38560795 38564514 circular_RNA/1 0 + TTC3 +chr21 37775055 37781763 circular_RNA/1 0 + CHAF1B +chr21 47693301 47697631 circular_RNA/2 0 - MCM3AP +chr21 44483062 44493451 circular_RNA/1 0 - CBSL +chr21 37571367 37572799 circular_RNA/1 0 + DOP1B +chr21 16386664 16415895 circular_RNA/52 0 - NRIP1 +chr21 45499444 45500008 circular_RNA/1 0 + TRAPPC10 +chr21 45736126 45739298 circular_RNA/1 0 + PFKL +chr21 33064661 33065797 circular_RNA/1 1 - SCAF4 +chr21 37711071 37717005 circular_RNA/11 3 + MORC3 +chr21 27423315 27425664 circular_RNA/5 0 - APP +chr21 44282391 44296877 circular_RNA/1 0 - WDR4 +chr21 47904669 47918746 circular_RNA/1 0 + DIP2A +chr21 27347382 27369731 circular_RNA/4 0 - APP +chr21 34804483 34805178 circular_RNA/7 0 + IFNGR2 +chr21 40619626 40630598 circular_RNA/6 0 - BRWD1 +chr21 46893808 46896394 circular_RNA/1 0 + COL18A1 +chr21 45165959 45168961 circular_RNA/3 0 + PDXK +chr21 37609559 37610999 circular_RNA/1 0 + DOP1B +chr21 40600425 40601362 circular_RNA/9 0 - BRWD1 +chr21 46275124 46276279 circular_RNA/1 0 - PTTG1IP +chr21 44424435 44445057 circular_RNA/1 0 + PKNOX1 +chr21 32537278 32575328 circular_RNA/2 0 - TIAM1 +chr21 47699906 47700489 circular_RNA/1 0 - MCM3AP +chr21 40181958 40186316 circular_RNA/1 0 + ETS2 +chr21 43938386 43955660 circular_RNA/1 0 + SLC37A1 +chr21 48063446 48080874 circular_RNA/1 0 + PRMT2 +chr21 45472160 45483666 circular_RNA/1 0 + TRAPPC10 +chr21 17135209 17138460 circular_RNA/15 0 + USP25 +chr21 32554737 32575328 circular_RNA/1 0 - TIAM1 +chr21 45745035 45745147 circular_RNA/2 0 + PFKL +chr21 38439561 38441924 circular_RNA/1 0 - PIGP +chr21 47801608 47805898 circular_RNA/6 0 + PCNT +chr21 46275124 46281186 circular_RNA/7 0 - PTTG1IP +chr21 46548316 46554747 circular_RNA/20 0 + ADARB1 +chr21 30698379 30702014 circular_RNA/1 0 + BACH1 +chr21 35091101 35107509 circular_RNA/5 0 + ITSN1 +chr21 47641767 47642652 circular_RNA/1 0 - LSS +chr21 32567539 32575328 circular_RNA/1 0 - TIAM1 +chr21 32559316 32567621 circular_RNA/1 0 - TIAM1 +chr21 44492094 44493451 circular_RNA/2 0 - CBSL +chr21 37716876 37721706 circular_RNA/1 0 + MORC3 +chr21 27269884 27284274 circular_RNA/2 0 - APP +chr21 26969613 26972178 circular_RNA/1 0 - MRPL39 |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_08_combined.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_08_combined.txt Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,1945 @@\n+CUFF.45981.2\tCUFF.45981.2\tchr21\t+\t9825464\t9827165\t9827165\t9827165\t2\t9825464,9827066,\t9825471,9827165,\n+CUFF.45982.1\tCUFF.45982.1\tchr21\t.\t9826847\t9827165\t9827165\t9827165\t1\t9826847,\t9827165,\n+CUFF.45983.1\tCUFF.45983.1\tchr21\t.\t15279914\t15280175\t15280175\t15280175\t1\t15279914,\t15280175,\n+CUFF.45988.1\tCUFF.45988.1\tchr21\t.\t15426534\t15427029\t15427029\t15427029\t1\t15426534,\t15427029,\n+CUFF.45989.1\tCUFF.45989.1\tchr21\t.\t15427319\t15428127\t15428127\t15428127\t1\t15427319,\t15428127,\n+CUFF.45990.1\tCUFF.45990.1\tchr21\t.\t15433507\t15434847\t15434847\t15434847\t1\t15433507,\t15434847,\n+CUFF.45984.1\tCUFF.45984.1\tchr21\t.\t15457362\t15458120\t15458120\t15458120\t1\t15457362,\t15458120,\n+CUFF.45991.1\tCUFF.45991.1\tchr21\t.\t15470615\t15471670\t15471670\t15471670\t1\t15470615,\t15471670,\n+CUFF.45985.1\tCUFF.45985.1\tchr21\t.\t15459562\t15460287\t15460287\t15460287\t1\t15459562,\t15460287,\n+CUFF.45986.1\tCUFF.45986.1\tchr21\t.\t15471760\t15473743\t15473743\t15473743\t1\t15471760,\t15473743,\n+CUFF.45987.1\tCUFF.45987.1\tchr21\t.\t15473986\t15475464\t15475464\t15475464\t1\t15473986,\t15475464,\n+CUFF.45992.1\tCUFF.45992.1\tchr21\t.\t15477957\t15478236\t15478236\t15478236\t1\t15477957,\t15478236,\n+CUFF.45998.1\tCUFF.45998.1\tchr21\t.\t16308473\t16309217\t16309217\t16309217\t1\t16308473,\t16309217,\n+CUFF.45996.1\tCUFF.45996.1\tchr21\t.\t16306827\t16307182\t16307182\t16307182\t1\t16306827,\t16307182,\n+CUFF.45993.1\tCUFF.45993.1\tchr21\t.\t16300305\t16300480\t16300480\t16300480\t1\t16300305,\t16300480,\n+CUFF.45999.1\tCUFF.45999.1\tchr21\t.\t16309313\t16309843\t16309843\t16309843\t1\t16309313,\t16309843,\n+CUFF.45995.1\tCUFF.45995.1\tchr21\t.\t16305403\t16306276\t16306276\t16306276\t1\t16305403,\t16306276,\n+CUFF.45994.1\tCUFF.45994.1\tchr21\t.\t16301777\t16301995\t16301995\t16301995\t1\t16301777,\t16301995,\n+CUFF.46000.1\tCUFF.46000.1\tchr21\t.\t16310431\t16311362\t16311362\t16311362\t1\t16310431,\t16311362,\n+CUFF.45997.1\tCUFF.45997.1\tchr21\t.\t16307817\t16308182\t16308182\t16308182\t1\t16307817,\t16308182,\n+CUFF.46001.1\tCUFF.46001.1\tchr21\t.\t16311444\t16312269\t16312269\t16312269\t1\t16311444,\t16312269,\n+CUFF.46006.1\tCUFF.46006.1\tchr21\t.\t17195172\t17195567\t17195567\t17195567\t1\t17195172,\t17195567,\n+CUFF.46021.2\tCUFF.46021.2\tchr21\t-\t16340591\t16437067\t16437067\t16437067\t4\t16340591,16386664,16415815,16437065,\t16340847,16386787,16415895,16437067,\n+CUFF.46021.1\tCUFF.46021.1\tchr21\t-\t16340591\t16437067\t16437067\t16437067\t5\t16340591,16386664,16412683,16415815,16437065,\t16340847,16386787,16412737,16415895,16437067,\n+CUFF.46021.3\tCUFF.46021.3\tchr21\t-\t16340591\t16438047\t16438047\t16438047\t4\t16340591,16386664,16415815,16438045,\t16340847,16386787,16415895,16438047,\n+CUFF.46021.4\tCUFF.46021.4\tchr21\t-\t16340591\t16438047\t16438047\t16438047\t5\t16340591,16386664,16387465,16415815,16438045,\t16340847,16386787,16387546,16415895,16438047,\n+CUFF.46021.5\tCUFF.46021.5\tchr21\t-\t16340591\t16438047\t16438047\t16438047\t6\t16340591,16386664,16387465,16412683,16415815,16438045,\t16340847,16386787,16387546,16412737,16415895,16438047,\n+CUFF.46021.6\tCUFF.46021.6\tchr21\t-\t16363428\t16437067\t16437067\t16437067\t5\t16363428,16386664,16387465,16415815,16437065,\t16363627,16386787,16387546,16415895,16437067,\n+CUFF.46009.1\tCUFF.46009.1\tchr21\t.\t17768984\t17769561\t17769561\t17769561\t1\t17768984,\t17769561,\n+CUFF.46007.1\tCUFF.46007.1\tchr21\t+\t17205670\t17214859\t17214859\t17214859\t2\t17205670,17214716,\t17205867,17214859,\n+CUFF.46007.2\tCUFF.46007.2\tchr21\t+\t17208302\t17214859\t17214859\t17214859\t2\t17208302,17214716,\t17208361,17214859,\n+CUFF.46008.1\tCUFF.46008.1\tchr21\t.\t17208396\t17209259\t17209259\t17209259\t1\t17208396,\t17209259,\n+CUFF.46002.3\tCUFF.46002.3\tchr21\t+\t17102754\t17177974\t17177974\t17177974\t7\t17102754,17135209,17138315,17150222,17163820,17172075,17177439,\t17102757,17135287,17138460,17150346,17163983,17172162,17177974,\n+CUFF.46002.1\tCUFF.46002.1\tchr21\t+\t17102754\t17177974\t17177974\t17177974\t8\t17102754,17135209,17136556,17138315,17150222,17163820,17172075,17177439,\t17102757,17135287,17136616,17138460,17150346,17163983,17172162,17177974,\n+CUFF.46002.2\tCUFF.46002.2\tchr21\t+\t17102754\t17177974\t17177974\t17177974\t9\t17102754,17135209,17136556,17137100,17138320,17150222,171'..b'7362364\t47269999\t47361620\t18\t47063638,47088787,47155305,47175330,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359943,47361583,\t47063782,47088866,47155343,47175366,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNR_145492\tchr21\t+\t47063638\t47362364\t47362364\t47362364\t18\t47063638,47088787,47155305,47175330,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359950,47361583,\t47063782,47088866,47155343,47175366,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_001348243\tchr21\t+\t47167927\t47362364\t47269999\t47361620\t16\t47167927,47169294,47175330,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349833,47355166,47359943,47361583,\t47168053,47169389,47175366,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47355219,47360113,47362364,\n+PCBP3\tNM_001382277\tchr21\t+\t47167927\t47362364\t47269999\t47361620\t16\t47167927,47169294,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359943,47361583,\t47168053,47169389,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_001130141\tchr21\t+\t47268063\t47362364\t47269999\t47361620\t14\t47268063,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47337501,47349833,47350699,47355166,47359943,47361583,\t47268315,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_001382278\tchr21\t+\t47268063\t47362364\t47269999\t47361620\t15\t47268063,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349833,47350699,47355166,47359943,47361583,\t47268315,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_001382279\tchr21\t+\t47268063\t47362364\t47269999\t47361620\t15\t47268063,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359943,47361583,\t47268315,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47334008,47337543,47349909,47350759,47355219,47360113,47362364,\n+PCBP3\tNM_020528\tchr21\t+\t47268063\t47362364\t47269999\t47361620\t15\t47268063,47269874,47316121,47319512,47320504,47320910,47329268,47330815,47333864,47337501,47349830,47350699,47355166,47359943,47361583,\t47268315,47270009,47316276,47319536,47320537,47321027,47329400,47330944,47333939,47337543,47349909,47350759,47355219,47360113,47362364,\n+IFNAR2\tNM_001385054\tchr21\t+\t34602242\t34637968\t34614227\t34634882\t8\t34602242,34614190,34615977,34617255,34619022,34621013,34624966,34634865,\t34602521,34614282,34616019,34617379,34619195,34621159,34625135,34637968,\n+IFNAR2\tNM_001385055\tchr21\t+\t34602242\t34637968\t34614227\t34637276\t10\t34602242,34614190,34615977,34617255,34619022,34621013,34624966,34632901,34635097,34637238,\t34602521,34614282,34616019,34617379,34619195,34621159,34625135,34633032,34635575,34637968,\n+SH3BGR\tNM_001317740\tchr21\t+\t40823895\t40887428\t40824022\t40883702\t6\t40823895,40834300,40847060,40880924,40883606,40887014,\t40824067,40834486,40847141,40880954,40883736,40887428,\n+SH3BGR\tNM_007341\tchr21\t+\t40823895\t40887428\t40824022\t40883702\t7\t40823895,40834300,40847060,40871748,40880924,40883606,40887014,\t40824067,40834486,40847141,40871841,40880954,40883736,40887428,\n+APP\tNM_001385253\tchr21\t-\t27252860\t27543088\t27253980\t27542938\t17\t27252860,27264033,27269884,27277335,27284052,27326903,27327940,27347382,27348266,27354656,27369674,27394155,27423315,27425551,27462258,27484295,27542881,\t27254082,27264180,27269985,27277389,27284274,27327003,27328069,27347541,27348341,27354790,27369731,27394358,27423509,27425664,27462388,27484463,27543088,\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_08_full.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_08_full.txt Fri Aug 26 22:43:38 2022 +0000 |
| b |
| b'@@ -0,0 +1,201 @@\n+chr21\t16386664\t16415895\tcircular_RNA/52\t0\t-\t16386664\t16386664\t0,0,0\t2\t123,80\t0,29151\t52\tcircRNA\tNRIP1\tNM_003489\t3,2\tchr21:16340847-16386664|chr21:16415895-16437065\n+chr21\t17135209\t17138460\tcircular_RNA/15\t0\t+\t17135209\t17135209\t0,0,0\t2\t78,145\t0,3106\t15\tcircRNA\tUSP25\tNM_001283041\t2,3\tchr21:17102757-17135209|chr21:17138460-17150222\n+chr21\t17135209\t17172162\tcircular_RNA/2\t0\t+\t17135209\t17135209\t0,0,0\t5\t78,145,124,163,87\t0,3106,15013,28611,36866\t2\tcircRNA\tUSP25\tNM_001283041\t2,3,4,5,6\tchr21:17102757-17135209|chr21:17172162-17177439\n+chr21\t17135209\t17172162\tcircular_RNA/2\t0\t+\t17135209\t17135209\t0,0,0\t4\t78,145,163,87\t0,3106,28611,36866\t2\tcircRNA\tUSP25\tNM_001352561\t2,3,4,5\tchr21:17102757-17135209|chr21:17172162-17177439\n+chr21\t17135209\t17177577\tcircular_RNA/1\t0\t+\t17135209\t17135209\t0,0,0\t6\t78,145,124,163,87,138\t0,3106,15013,28611,36866,42230\t1\tcircRNA\tUSP25\tNM_001283041\t2,3,4,5,6,7\tchr21:17102757-17135209|chr21:17177577-17181127\n+chr21\t17135209\t17177577\tcircular_RNA/1\t0\t+\t17135209\t17135209\t0,0,0\t5\t78,145,163,87,138\t0,3106,28611,36866,42230\t1\tcircRNA\tUSP25\tNM_001352561\t2,3,4,5,6\tchr21:17102757-17135209|chr21:17177577-17181127\n+chr21\t17150222\t17177577\tcircular_RNA/1\t0\t+\t17150222\t17150222\t0,0,0\t4\t124,163,87,138\t0,13598,21853,27217\t1\tcircRNA\tUSP25\tNM_001283041\t4,5,6,7\tchr21:17138460-17150222|chr21:17177577-17181127\n+chr21\t26961146\t26973779\tcircular_RNA/1\t0\t-\t26961146\t26961146\t0,0,0\t6\t48,154,66,113,68,100\t0,3977,5058,8467,10964,12533\t1\tcircRNA\tMRPL39\tNM_017446\t9,8,7,6,5,4\tchr21:26958066-26961146|chr21:26973779-26976107\n+chr21\t26969613\t26972178\tcircular_RNA/1\t0\t-\t26969613\t26969613\t0,0,0\t2\t113,68\t0,2497\t1\tcircRNA\tMRPL39\tNM_017446\t6,5\tchr21:26966270-26969613|chr21:26972178-26973679\n+chr21\t27264033\t27347541\tcircular_RNA/1\t0\t-\t27264033\t27264033\t0,0,0\t7\t147,101,54,222,100,129,159\t0,5851,13302,20019,62870,63907,83349\t1\tcircRNA\tAPP\tNM_001136016\t16,15,14,13,12,11,10\tchr21:27254082-27264033|chr21:27347541-27348266\n+chr21\t27264033\t27347541\tcircular_RNA/1\t0\t-\t27264033\t27264033\t0,0,0\t6\t147,101,222,100,129,159\t0,5851,20019,62870,63907,83349\t1\tcircRNA\tAPP\tNM_001204301\t16,15,14,13,12,11\tchr21:27254082-27264033|chr21:27347541-27348266\n+chr21\t27269884\t27284274\tcircular_RNA/2\t0\t-\t27269884\t27269884\t0,0,0\t3\t101,54,222\t0,7451,14168\t2\tcircRNA\tAPP\tNM_001136016\t15,14,13\tchr21:27264180-27269884|chr21:27284274-27326903\n+chr21\t27269884\t27284274\tcircular_RNA/2\t0\t-\t27269884\t27269884\t0,0,0\t2\t101,222\t0,14168\t2\tcircRNA\tAPP\tNM_001204301\t15,14\tchr21:27264180-27269884|chr21:27284274-27326903\n+chr21\t27277335\t27284274\tcircular_RNA/2\t0\t-\t27277335\t27277335\t0,0,0\t2\t54,222\t0,6717\t2\tcircRNA\tAPP\tNM_001136016\t14,13\tchr21:27269985-27277335|chr21:27284274-27326903\n+chr21\t27326903\t27328069\tcircular_RNA/4\t0\t-\t27326903\t27326903\t0,0,0\t2\t100,129\t0,1037\t4\tcircRNA\tAPP\tNM_001136016\t12,11\tchr21:27284274-27326903|chr21:27328069-27347382\n+chr21\t27326903\t27354790\tcircular_RNA/2\t0\t-\t27326903\t27326903\t0,0,0\t5\t100,129,159,75,134\t0,1037,20479,21363,27753\t2\tcircRNA\tAPP\tNM_001136016\t12,11,10,9,8\tchr21:27284274-27326903|chr21:27354790-27372329\n+chr21\t27326903\t27484463\tcircular_RNA/2\t0\t-\t27326903\t27326903\t0,0,0\t11\t100,129,159,75,134,168,203,194,113,130,168\t0,1037,20479,21363,27753,45426,67252,96412,98648,135355,157392\t2\tcircRNA\tAPP\tNM_001136016\t12,11,10,9,8,7,6,5,4,3,2\tchr21:27284274-27326903|chr21:27484463-27512470\n+chr21\t27326903\t27484463\tcircular_RNA/2\t0\t-\t27326903\t27326903\t0,0,0\t12\t100,129,159,75,134,57,168,203,194,113,130,168\t0,1037,20479,21363,27753,42771,45426,67252,96412,98648,135355,157392\t2\tcircRNA\tAPP\tNM_000484\t13,12,11,10,9,8,7,6,5,4,3,2\tchr21:27284274-27326903|chr21:27484463-27542881\n+chr21\t27326903\t27484463\tcircular_RNA/2\t0\t-\t27326903\t27326903\t0,0,0\t10\t100,129,159,75,134,203,194,113,130,168\t0,1037,20479,21363,27753,67252,96412,98648,135355,157392\t2\tcircRNA\tAPP\tNM_001204303\t11,10,9,8,7,6,5,4,3,2\tchr21:27284274-27326903|chr21:27484463-27542881\n+chr21\t27326903\t27484463\tcircular_RNA/2\t0\t-\t27326903\t27326903\t0,0,0\t11\t100,129,159,75,134,57,203,194,113,130,168\t0,1037,20479,21363,2775'..b'46,23,140\t0,8634,30479\t2\tcircRNA\tCUFF.46946.6\tCUFF.46946.6\t2,3,4\tchr21:35446045-35467161|chr21:35497780-35514707\n+chr21\t35475133\t35497780\tcircular_RNA/4\t0\t+\t35475133\t35475133\t0,0,0\t3\t74,23,140\t0,662,22507\t4\tcircRNA\tCUFF.46946.5\tCUFF.46946.5\t3,4,5\tchr21:35472588-35475133|chr21:35497780-35514707\n+chr21\t37775055\t37783902\tcircular_RNA/10\t0\t+\t37775055\t37775055\t0,0,0\t4\t94,70,46,142\t0,6003,6755,8705\t10\tcircRNA\tCUFF.46349.3\tCUFF.46349.3\t2,3,4,5\tchr21:37771903-37775055|chr21:37783902-37785181\n+chr21\t38792600\t38794168\tcircular_RNA/91\t0\t+\t38792600\t38792600\t0,0,0\t2\t86,93\t0,1475\t91\tcircRNA\tCUFF.46430.1\tCUFF.46430.1\t2,3\tchr21:38747419-38792600|chr21:38794168-38794883\n+chr21\t38792600\t38798083\tcircular_RNA/9\t0\t+\t38792600\t38792600\t0,0,0\t3\t86,93,92\t0,1475,5391\t9\tcircRNA\tCUFF.46430.3\tCUFF.46430.3\t2,3,4\tchr21:38782972-38792600|chr21:38798083-38802570\n+chr21\t38792600\t38798083\tcircular_RNA/9\t0\t+\t38792600\t38792600\t0,0,0\t2\t86,92\t0,5391\t9\tcircRNA\tCUFF.46430.4\tCUFF.46430.4\t2,3\tchr21:38787867-38792600|chr21:38798083-38801168\n+chr21\t38792600\t38802702\tcircular_RNA/19\t0\t+\t38792600\t38792600\t0,0,0\t4\t86,93,92,132\t0,1475,5391,9970\t19\tcircRNA\tCUFF.46430.3\tCUFF.46430.3\t2,3,4,5\tchr21:38782972-38792600|chr21:38802702-38828431\n+chr21\t38792600\t38802702\tcircular_RNA/19\t0\t+\t38792600\t38792600\t0,0,0\t4\t86,92,42,132\t0,5391,8568,9970\t19\tcircRNA\tCUFF.46430.4\tCUFF.46430.4\t2,3,4,5\tchr21:38787867-38792600|chr21:38802702-38828431\n+chr21\t38792600\t38802702\tcircular_RNA/19\t0\t+\t38792600\t38792600\t0,0,0\t5\t86,93,92,42,132\t0,1475,5391,8568,9970\t19\tcircRNA\tCUFF.46430.5\tCUFF.46430.5\t2,3,4,5,6\tchr21:38787867-38792600|chr21:38802702-38828431\n+chr21\t38792600\t38828610\tcircular_RNA/6\t0\t+\t38792600\t38792600\t0,0,0\t2\t86,179\t0,35831\t6\tcircRNA\tCUFF.46430.2\tCUFF.46430.2\t2,3\tchr21:38747419-38792600|chr21:38828610-38844985\n+chr21\t38792600\t38845182\tcircular_RNA/8\t0\t+\t38792600\t38792600\t0,0,0\t3\t86,179,197\t0,35831,52385\t8\tcircRNA\tCUFF.46430.2\tCUFF.46430.2\t2,3,4\tchr21:38747419-38792600|chr21:38845182-38850509\n+chr21\t40641824\t40646398\tcircular_RNA/4\t0\t-\t40641824\t40641824\t0,0,0\t3\t68,151,99\t0,384,4475\t4\tcircRNA\tCUFF.46438.4\tCUFF.46438.4\t7,6,5\tchr21:40636945-40641824|chr21:40646398-40648098\n+chr21\t45472160\t45483666\tcircular_RNA/1\t0\t+\t45472160\t45472160\t0,0,0\t4\t197,118,112,248\t0,3496,6823,11258\t1\tcircRNA\tCUFF.46596.2\tCUFF.46596.2\t3,4,5,6\tchr21:45457808-45472160|chr21:45483666-45494204\n+chr21\t46538478\t46548488\tcircular_RNA/1\t0\t+\t46538478\t46538478\t0,0,0\t3\t56,166,172\t0,2230,9838\t1\tcircRNA\tCUFF.46822.4\tCUFF.46822.4\t2,3,4\tchr21:46536953-46538478|chr21:46548488-46553473\n+chr21\t46538478\t46554747\tcircular_RNA/1\t0\t+\t46538478\t46538478\t0,0,0\t5\t56,166,172,107,118\t0,2230,9838,14995,16151\t1\tcircRNA\tCUFF.46822.4\tCUFF.46822.4\t2,3,4,5,6\tchr21:46536953-46538478|chr21:46554747-46564545\n+chr21\t46548316\t46554747\tcircular_RNA/20\t0\t+\t46548316\t46548316\t0,0,0\t4\t172,92,107,118\t0,3813,5157,6313\t20\tcircRNA\tCUFF.46822.3\tCUFF.46822.3\t2,3,4,5\tchr21:46494708-46548316|chr21:46554747-46563056\n+chr21\t46548316\t46554747\tcircular_RNA/20\t0\t+\t46548316\t46548316\t0,0,0\t2\t172,76\t0,6355\t20\tcircRNA\tCUFF.46822.1\tCUFF.46822.1\t2,3\tchr21:46494708-46548316|chr21:46554747-46591524\n+chr21\t46548316\t46554747\tcircular_RNA/20\t0\t+\t46548316\t46548316\t0,0,0\t3\t172,92,118\t0,3813,6313\t20\tcircRNA\tCUFF.46822.2\tCUFF.46822.2\t2,3,4\tchr21:46494708-46548316|chr21:46554747-46591524\n+chr21\t46548316\t46554747\tcircular_RNA/20\t0\t+\t46548316\t46548316\t0,0,0\t3\t172,107,118\t0,5157,6313\t20\tcircRNA\tCUFF.46822.4\tCUFF.46822.4\t4,5,6\tchr21:46540874-46548316|chr21:46554747-46564545\n+chr21\t46548316\t46554747\tcircular_RNA/20\t0\t+\t46548316\t46548316\t0,0,0\t3\t172,34,118\t0,5157,6313\t20\tcircRNA\tCUFF.46822.5\tCUFF.46822.5\t2,3,4\tchr21:46536953-46548316|chr21:46554747-46591524\n+chr21\t46600244\t46605006\tcircular_RNA/1\t0\t+\t46600244\t46600244\t0,0,0\t6\t115,37,169,149,120,169\t0,1150,2255,3032,4144,4593\t1\tcircRNA\tCUFF.46822.1\tCUFF.46822.1\t6,7,8,9,10,11\tchr21:46596579-46600244|chr21:46605006-46624469\n+chr21\t47538599\t47538914\tcircular_RNA/1\t1\t.\t47538599\t47538599\t0,0,0\t1\t315\t0\t1\tcircRNA\tCUFF.46798.1\tCUFF.46798.1\t1\tNone|None\n' |
| b |
| diff -r 000000000000 -r 465d6578b4d0 test-data/test_08_novel.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_08_novel.txt Fri Aug 26 22:43:38 2022 +0000 |
| b |
| @@ -0,0 +1,12 @@ +chr21 30677523 30702014 circular_RNA/1 1 + Novel Annotated +chr21 38792600 38802702 circular_RNA/19 0 + Annotated Novel +chr21 9827066 9827165 circular_RNA/1 1 + Novel Novel +chr21 38792600 38828610 circular_RNA/6 0 + Annotated Novel +chr21 46538478 46554747 circular_RNA/1 0 + Novel Annotated +chr21 38792600 38794168 circular_RNA/91 0 + Annotated Novel +chr21 35475133 35497780 circular_RNA/4 0 + Novel Annotated +chr21 47538599 47538914 circular_RNA/1 1 . Novel Novel +chr21 38792600 38798083 circular_RNA/9 0 + Annotated Novel +chr21 16386664 16387546 circular_RNA/1 0 - Annotated Novel +chr21 35467161 35497780 circular_RNA/2 0 + Annotated Annotated +chr21 46538478 46548488 circular_RNA/1 0 + Novel Annotated |