diff --git a/testdata/v2/bigwig/S1.Signal.Unique.str1.out.wig.bw b/testdata/v2/bigwig/S1.Signal.Unique.str1.out.wig.bw new file mode 100644 index 000000000..38a21eb17 Binary files /dev/null and b/testdata/v2/bigwig/S1.Signal.Unique.str1.out.wig.bw differ diff --git a/testdata/v2/bigwig/S1.Signal.Unique.str2.out.wig.bw b/testdata/v2/bigwig/S1.Signal.Unique.str2.out.wig.bw new file mode 100644 index 000000000..914c5922a Binary files /dev/null and b/testdata/v2/bigwig/S1.Signal.Unique.str2.out.wig.bw differ diff --git a/testdata/v2/bigwig/S2.Signal.Unique.str1.out.wig.bw b/testdata/v2/bigwig/S2.Signal.Unique.str1.out.wig.bw new file mode 100644 index 000000000..fb1f7fd12 Binary files /dev/null and b/testdata/v2/bigwig/S2.Signal.Unique.str1.out.wig.bw differ diff --git a/testdata/v2/bigwig/S2.Signal.Unique.str2.out.wig.bw b/testdata/v2/bigwig/S2.Signal.Unique.str2.out.wig.bw new file mode 100644 index 000000000..51526b1c4 Binary files /dev/null and b/testdata/v2/bigwig/S2.Signal.Unique.str2.out.wig.bw differ diff --git a/testdata/v2/S1.fastq.gz b/testdata/v2/fastq/S1.fastq.gz similarity index 100% rename from testdata/v2/S1.fastq.gz rename to testdata/v2/fastq/S1.fastq.gz diff --git a/testdata/v2/S2.fastq.gz b/testdata/v2/fastq/S2.fastq.gz similarity index 100% rename from testdata/v2/S2.fastq.gz rename to testdata/v2/fastq/S2.fastq.gz diff --git a/testdata/v2/intermediate_cagerobj/annotated_cagexp.rds b/testdata/v2/intermediate_cagerobj/annotated_cagexp.rds new file mode 100644 index 000000000..b463ae274 Binary files /dev/null and b/testdata/v2/intermediate_cagerobj/annotated_cagexp.rds differ diff --git a/testdata/v2/intermediate_cagerobj/initial_cagexp.rds b/testdata/v2/intermediate_cagerobj/initial_cagexp.rds new file mode 100644 index 000000000..2833f0a62 Binary files /dev/null and b/testdata/v2/intermediate_cagerobj/initial_cagexp.rds differ diff --git a/testdata/v2/intermediate_cagerobj/nonTSS_enhancers.rds b/testdata/v2/intermediate_cagerobj/nonTSS_enhancers.rds new file mode 100644 index 000000000..2054d2c92 Binary files /dev/null and b/testdata/v2/intermediate_cagerobj/nonTSS_enhancers.rds differ diff --git a/testdata/v2/intermediate_cagerobj/normalized_clustered_cagexp.rds b/testdata/v2/intermediate_cagerobj/normalized_clustered_cagexp.rds new file mode 100644 index 000000000..a0af5fceb Binary files /dev/null and b/testdata/v2/intermediate_cagerobj/normalized_clustered_cagexp.rds differ diff --git a/testdata/v2/intermediate_cagerobj/supported_enhancers.rds b/testdata/v2/intermediate_cagerobj/supported_enhancers.rds new file mode 100644 index 000000000..0af180c02 Binary files /dev/null and b/testdata/v2/intermediate_cagerobj/supported_enhancers.rds differ diff --git a/testdata/v2/star_genomegenerate/star/Genome b/testdata/v2/star_genomegenerate/star/Genome new file mode 100644 index 000000000..c724a7b79 Binary files /dev/null and b/testdata/v2/star_genomegenerate/star/Genome differ diff --git a/testdata/v2/star_genomegenerate/star/Log.out b/testdata/v2/star_genomegenerate/star/Log.out new file mode 100644 index 000000000..44be49118 --- /dev/null +++ b/testdata/v2/star_genomegenerate/star/Log.out @@ -0,0 +1,90 @@ +STAR version=2.7.11b +STAR compilation time,server,dir=2025-01-09T12:33:46+0000 :/opt/conda/conda-bld/star_1736425784849/work/source +##### Command Line: +/opt/conda/bin/STAR-avx --runMode genomeGenerate --genomeDir star/ --genomeFastaFiles sacCer3chrIII.fa --sjdbGTFfile sacCer3chrIII.gtf --runThreadN 12 --genomeSAindexNbases 8 --limitGenomeGenerateRAM 77209411328 +##### Initial USER parameters from Command Line: +###### All USER parameters from Command Line: +runMode genomeGenerate ~RE-DEFINED +genomeDir star/ ~RE-DEFINED +genomeFastaFiles sacCer3chrIII.fa ~RE-DEFINED +sjdbGTFfile sacCer3chrIII.gtf ~RE-DEFINED +runThreadN 12 ~RE-DEFINED +genomeSAindexNbases 8 ~RE-DEFINED +limitGenomeGenerateRAM 77209411328 ~RE-DEFINED +##### Finished reading parameters from all sources + +##### Final user re-defined parameters-----------------: +runMode genomeGenerate +runThreadN 12 +genomeDir star/ +genomeFastaFiles sacCer3chrIII.fa +genomeSAindexNbases 8 +limitGenomeGenerateRAM 77209411328 +sjdbGTFfile sacCer3chrIII.gtf + +------------------------------- +##### Final effective command line: +/opt/conda/bin/STAR-avx --runMode genomeGenerate --runThreadN 12 --genomeDir star/ --genomeFastaFiles sacCer3chrIII.fa --genomeSAindexNbases 8 --limitGenomeGenerateRAM 77209411328 --sjdbGTFfile sacCer3chrIII.gtf +---------------------------------------- + +Number of fastq files for each mate = 1 +ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters: 3000 0.99 10 +Finished loading and checking parameters +--genomeDir directory exists and will be overwritten: star/ +Apr 10 18:57:38 ... starting to generate Genome files +sacCer3chrIII.fa : chr # 0 "chrIII" chrStart: 0 +Chromosome sequence lengths: +chrIII 316620 +Genome sequence total length = 316620 +Genome size with padding = 524288 +Apr 10 18:57:38 ..... processing annotations GTF +Processing pGe.sjdbGTFfile=sacCer3chrIII.gtf, found: + 202 transcripts + 212 exons (non-collapsed) + 10 collapsed junctions +Total junctions: 10 +Apr 10 18:57:38 ..... finished GTF processing + +Estimated genome size with padding and SJs: total=genome+SJ=201524288 = 524288 + 201000000 +GstrandBit=32 +Number of SA indices: 633240 +Apr 10 18:57:38 ... starting to sort Suffix Array. This may take a long time... +Number of chunks: 12; chunks size limit: 460536 bytes +Apr 10 18:57:38 ... sorting Suffix Array chunks and saving them to disk... +Writing 156568 bytes into star//SA_11 ; empty space on disk = 633757077504 bytes ... done +Writing 436824 bytes into star//SA_0 ; empty space on disk = 633756897280 bytes ... done +Writing 448464 bytes into star//SA_1 ; empty space on disk = 633756438528 bytes ... done +Writing 447336 bytes into star//SA_4 ; empty space on disk = 633755967488 bytes ... done +Writing 442416 bytes into star//SA_8 ; empty space on disk = 633755496448 bytes ... done +Writing 432464 bytes into star//SA_10 ; empty space on disk = 633755029504 bytes ... done +Writing 432544 bytes into star//SA_2 ; empty space on disk = 633754574848 bytes ...Writing 449816 bytes into star//SA_9 ; empty space on disk = 633754120192 bytes ...Writing 460152 bytes into star//SA_3 ; empty space on disk = 633753649152 bytes ... done + done + done +Writing 452704 bytes into star//SA_6 ; empty space on disk = 633753165824 bytes ...Writing 454552 bytes into star//SA_7 ; empty space on disk = 633752690688 bytes ... done + done + done +Writing 452080 bytes into star//SA_5 ; empty space on disk = 633752215552 bytes ... done +Apr 10 18:57:38 ... loading chunks from disk, packing SA... +Apr 10 18:57:38 ... finished generating suffix array +Apr 10 18:57:38 ... generating Suffix Array index +Apr 10 18:57:38 ... completed Suffix Array index +Apr 10 18:57:38 Finished preparing junctions +Apr 10 18:57:38 ..... inserting junctions into the genome indices +Apr 10 18:57:38 Finished SA search: number of new junctions=10, old junctions=0 +Apr 10 18:57:38 Finished sorting SA indicesL nInd=4000 +Genome size with junctions=526298 524288 2010 +GstrandBit1=32 GstrandBit=32 +Apr 10 18:57:38 Finished inserting junction indices +Apr 10 18:57:38 Finished SAi +Apr 10 18:57:38 ..... finished inserting junctions into genome +Apr 10 18:57:38 ... writing Genome to disk ... +Writing 526298 bytes into star//Genome ; empty space on disk = 633756950528 bytes ... done +SA size in bytes: 2628618 +Apr 10 18:57:38 ... writing Suffix Array to disk ... +Writing 2628618 bytes into star//SA ; empty space on disk = 633756401664 bytes ... done +Apr 10 18:57:38 ... writing SAindex to disk +Writing 8 bytes into star//SAindex ; empty space on disk = 633753743360 bytes ... done +Writing 72 bytes into star//SAindex ; empty space on disk = 633753743360 bytes ... done +Writing 382291 bytes into star//SAindex ; empty space on disk = 633753743360 bytes ... done +Apr 10 18:57:38 ..... finished successfully +DONE: Genome generation, EXITING diff --git a/testdata/v2/star_genomegenerate/star/SA b/testdata/v2/star_genomegenerate/star/SA new file mode 100644 index 000000000..b5374eed1 Binary files /dev/null and b/testdata/v2/star_genomegenerate/star/SA differ diff --git a/testdata/v2/star_genomegenerate/star/SAindex b/testdata/v2/star_genomegenerate/star/SAindex new file mode 100644 index 000000000..1034c6d78 Binary files /dev/null and b/testdata/v2/star_genomegenerate/star/SAindex differ diff --git a/testdata/v2/star_genomegenerate/star/chrLength.txt b/testdata/v2/star_genomegenerate/star/chrLength.txt new file mode 100644 index 000000000..3684b3ca7 --- /dev/null +++ b/testdata/v2/star_genomegenerate/star/chrLength.txt @@ -0,0 +1 @@ +316620 diff --git a/testdata/v2/star_genomegenerate/star/chrName.txt b/testdata/v2/star_genomegenerate/star/chrName.txt new file mode 100644 index 000000000..ad2f22503 --- /dev/null +++ b/testdata/v2/star_genomegenerate/star/chrName.txt @@ -0,0 +1 @@ +chrIII diff --git a/testdata/v2/star_genomegenerate/star/chrNameLength.txt b/testdata/v2/star_genomegenerate/star/chrNameLength.txt new file mode 100644 index 000000000..d46694f36 --- /dev/null +++ b/testdata/v2/star_genomegenerate/star/chrNameLength.txt @@ -0,0 +1 @@ +chrIII 316620 diff --git a/testdata/v2/star_genomegenerate/star/chrStart.txt 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MissingGeneType +snR189 snR189 MissingGeneType +YCR032W YCR032W MissingGeneType +YCR033W YCR033W MissingGeneType +YCR034W YCR034W MissingGeneType +YCR035C YCR035C MissingGeneType +YCR036W YCR036W MissingGeneType +YCR037C YCR037C MissingGeneType +YCR038C YCR038C MissingGeneType +YCR038W-A YCR038W-A MissingGeneType +YCR039C YCR039C MissingGeneType +YCR040W YCR040W MissingGeneType +YCR041W YCR041W MissingGeneType +YCR042C YCR042C MissingGeneType +YCR043C YCR043C MissingGeneType +YCR044C YCR044C MissingGeneType +YCR045C YCR045C MissingGeneType +YCR045W-A YCR045W-A MissingGeneType +YCR046C YCR046C MissingGeneType +YCR047C YCR047C MissingGeneType +YCR047W-A YCR047W-A MissingGeneType +YCR049C YCR049C MissingGeneType +YCR048W YCR048W MissingGeneType +YCR050C YCR050C MissingGeneType +YCR051W YCR051W MissingGeneType +YCR052W YCR052W MissingGeneType +YCR053W YCR053W MissingGeneType +YCR054C YCR054C MissingGeneType +YCR057C YCR057C MissingGeneType +YCR059C YCR059C MissingGeneType +YCR060W YCR060W MissingGeneType +YCR061W YCR061W MissingGeneType +tS(CGA)C tS(CGA)C MissingGeneType +YCR064C YCR064C MissingGeneType +YCR063W YCR063W MissingGeneType +YCR065W YCR065W MissingGeneType +YCR066W YCR066W MissingGeneType +YCR067C YCR067C MissingGeneType +YCR068W YCR068W MissingGeneType +YCR069W YCR069W MissingGeneType +YCR071C YCR071C MissingGeneType +YCR072C YCR072C MissingGeneType +YCR073C YCR073C MissingGeneType +YCR073W-A YCR073W-A MissingGeneType +YCR075C YCR075C MissingGeneType +YCR075W-A YCR075W-A MissingGeneType +YCR076C YCR076C MissingGeneType +YCR077C YCR077C MissingGeneType +YCR079W YCR079W MissingGeneType +YCR081W YCR081W MissingGeneType +YCR081C-A YCR081C-A MissingGeneType +YCR082W YCR082W MissingGeneType +YCR083W YCR083W MissingGeneType +YCR084C YCR084C MissingGeneType +YCR085W YCR085W MissingGeneType +YCR086W YCR086W MissingGeneType +YCR087W YCR087W MissingGeneType +YCR087C-A YCR087C-A MissingGeneType +YCR088W YCR088W MissingGeneType +YCR089W YCR089W MissingGeneType +YCR090C YCR090C MissingGeneType +YCR091W YCR091W MissingGeneType +YCR092C YCR092C MissingGeneType +YCR093W YCR093W MissingGeneType +YCR094W YCR094W MissingGeneType +YCR095C YCR095C MissingGeneType +YCR095W-A YCR095W-A MissingGeneType +YCR096C YCR096C MissingGeneType +YCR097W YCR097W MissingGeneType +YCR097W-A YCR097W-A MissingGeneType +tT(AGU)C tT(AGU)C MissingGeneType +YCR098C YCR098C MissingGeneType +YCR099C YCR099C MissingGeneType +YCR100C YCR100C MissingGeneType +YCR101C YCR101C MissingGeneType +YCR102C YCR102C MissingGeneType +YCR102W-A YCR102W-A MissingGeneType +YCR104W YCR104W MissingGeneType +YCR105W YCR105W MissingGeneType +YCR106W YCR106W MissingGeneType +YCR107W YCR107W MissingGeneType +YCR108C YCR108C MissingGeneType diff --git a/testdata/v2/star_genomegenerate/star/genomeParameters.txt b/testdata/v2/star_genomegenerate/star/genomeParameters.txt new file mode 100644 index 000000000..0146abaa9 --- /dev/null +++ b/testdata/v2/star_genomegenerate/star/genomeParameters.txt @@ -0,0 +1,19 @@ +### /opt/conda/bin/STAR-avx --runMode genomeGenerate --runThreadN 12 --genomeDir star/ --genomeFastaFiles sacCer3chrIII.fa --genomeSAindexNbases 8 --limitGenomeGenerateRAM 77209411328 --sjdbGTFfile sacCer3chrIII.gtf +### GstrandBit 32 +versionGenome 2.7.4a +genomeType Full +genomeFastaFiles sacCer3chrIII.fa +genomeSAindexNbases 8 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeTransformType None +genomeTransformVCF - +sjdbOverhang 100 +sjdbFileChrStartEnd - +sjdbGTFfile sacCer3chrIII.gtf +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbInsertSave Basic +genomeFileSizes 526298 2628618 diff --git a/testdata/v2/star_genomegenerate/star/sjdbInfo.txt b/testdata/v2/star_genomegenerate/star/sjdbInfo.txt new file mode 100644 index 000000000..fd27e7f8b --- /dev/null +++ b/testdata/v2/star_genomegenerate/star/sjdbInfo.txt @@ -0,0 +1,11 @@ +10 100 +90896 90927 0 0 0 1 +101633 101699 2 0 1 2 +107033 107109 1 0 0 1 +107191 107286 1 0 0 1 +111557 111632 2 0 0 2 +173115 173197 2 0 1 2 +177906 178212 2 0 0 2 +227978 227996 0 0 0 1 +293939 293992 1 0 0 1 +294239 294290 1 1 0 1 diff --git a/testdata/v2/star_genomegenerate/star/sjdbList.fromGTF.out.tab b/testdata/v2/star_genomegenerate/star/sjdbList.fromGTF.out.tab new file mode 100644 index 000000000..c92627a7f --- /dev/null +++ b/testdata/v2/star_genomegenerate/star/sjdbList.fromGTF.out.tab @@ -0,0 +1,10 @@ +chrIII 90897 90928 + 59 +chrIII 101634 101700 - 64 +chrIII 107034 107110 + 70 +chrIII 107192 107287 + 70 +chrIII 111558 111633 - 74 +chrIII 173116 173198 - 118 +chrIII 177907 178213 - 121 +chrIII 227979 227997 + 153 +chrIII 293940 293993 + 189 +chrIII 294240 294291 + 189 diff --git a/testdata/v2/star_genomegenerate/star/sjdbList.out.tab b/testdata/v2/star_genomegenerate/star/sjdbList.out.tab new file mode 100644 index 000000000..39d173b3b --- /dev/null +++ b/testdata/v2/star_genomegenerate/star/sjdbList.out.tab @@ -0,0 +1,10 @@ +chrIII 90897 90928 + +chrIII 101634 101700 - +chrIII 107034 107110 + +chrIII 107192 107287 + +chrIII 111558 111633 - +chrIII 173116 173198 - +chrIII 177907 178213 - +chrIII 227979 227997 + +chrIII 293940 293993 + +chrIII 294240 294291 + diff --git a/testdata/v2/star_genomegenerate/star/transcriptInfo.tab b/testdata/v2/star_genomegenerate/star/transcriptInfo.tab new file mode 100644 index 000000000..922dccfb5 --- /dev/null +++ b/testdata/v2/star_genomegenerate/star/transcriptInfo.tab @@ -0,0 +1,203 @@ +202 +YCL076W_mRNA 1391 2134 2134 1 1 0 0 +YCL075W 2125 2565 2134 1 1 1 1 +YCL074W 2823 3749 2565 1 1 2 2 +YCL073C_mRNA 6478 8325 3749 2 1 3 3 +YCL069W_mRNA 9705 11081 8325 1 1 4 4 +YCL068C_mRNA 11502 12284 11081 2 1 5 5 +YCL067C_mRNA 12385 13017 12284 2 1 6 6 +YCL066W_mRNA 13281 13808 13017 1 1 7 7 +YCL065W_mRNA 13750 14118 13808 1 1 8 8 +YCL064C_mRNA 15797 16879 14118 2 1 9 9 +YCL063W_mRNA 17289 18560 16879 1 1 10 10 +YCL061C_mRNA 18815 22105 18560 2 1 11 11 +YCL059C_mRNA 22428 23378 22105 2 1 12 12 +YCL058C_mRNA 23522 23980 23378 2 1 13 13 +YCL058W-A_mRNA 23583 23924 23980 1 1 14 14 +YCL057C-A_mRNA 24031 24324 23980 2 1 15 15 +YCL057W_mRNA 24767 26905 24324 1 1 16 16 +YCL056C_mRNA 26924 27358 26905 2 1 17 17 +YCL055W_mRNA 27928 28935 27358 1 1 18 18 +YCL054W-A_mRNA 30909 30995 28935 1 1 19 19 +YCL054W_mRNA 31448 33973 30995 1 1 20 20 +YCL052C_mRNA 34142 35392 33973 2 1 21 21 +YCL051W_mRNA 35864 37615 35392 1 1 22 22 +YCL050C_mRNA 37835 38800 37615 2 1 23 23 +YCL049C_mRNA 39785 40723 38800 2 1 24 24 +YCL048W-A_mRNA 41487 41726 40723 1 1 25 25 +YCL048W_mRNA 42164 43555 41726 1 1 26 26 +YCL047C_mRNA 43660 44436 43555 2 1 27 27 +YCL045C_mRNA 44622 46904 44436 2 1 28 28 +YCL046W_mRNA 46639 46962 46904 1 1 29 29 +YCL044C_mRNA 47110 48363 46962 2 1 30 30 +YCL043C_mRNA 48652 50220 48363 2 1 31 31 +YCL041C_mRNA 50132 50626 50220 2 1 32 32 +YCL042W_mRNA 50583 50942 50626 1 1 33 33 +YCL040W_mRNA 50837 52339 50942 1 1 34 34 +YCL039W_mRNA 52644 54881 52339 1 1 35 35 +YCL038C_mRNA 54940 56526 54881 2 1 36 36 +YCL037C_mRNA 57373 58677 56526 2 1 37 37 +YCL036W_mRNA 59025 60725 58677 1 1 38 38 +YCL035C_mRNA 60840 61172 60725 2 1 39 39 +YCL034W_mRNA 61657 62721 61172 1 1 40 40 +YCL033C_mRNA 62775 63281 62721 2 1 41 41 +YCL032W_mRNA 63440 64480 63281 1 1 42 42 +YCL031C_mRNA 64674 65567 64480 2 1 43 43 +YCL030C_mRNA 65933 68332 65567 2 1 44 44 +YCL029C_mRNA 68598 69920 68332 2 1 45 45 +YCL028W_mRNA 70149 71366 69920 1 1 46 46 +YCL027W_mRNA 71802 73340 71366 1 1 47 47 +YCL026C-B_mRNA 73404 73985 73340 2 1 48 48 +YCL026C-A_mRNA 74703 75284 73985 2 1 49 49 +YCL025C_mRNA 76017 77918 75284 2 1 50 50 +YCL023C_mRNA 78948 79295 77918 2 1 51 51 +YCL024W_mRNA 79161 82274 79295 1 1 52 52 +YCL022C_mRNA 81569 82084 82274 2 1 53 53 +tE(UUC)C_tRNA 82461 82532 82274 2 1 54 54 +YCL021W-A_mRNA 83619 83996 82532 1 1 55 55 +YCL020W 85101 86417 83996 1 1 56 56 +YCL019W 85101 90414 86417 1 1 57 57 +tL(CAA)C_tRNA 90858 90971 90414 1 2 58 58 +YCL018W_mRNA 91323 92417 90971 1 1 60 59 +YCL017C_mRNA 92776 94269 92417 2 1 61 60 +YCL016C_mRNA 94620 95762 94269 2 1 62 61 +YCL014W_mRNA 96280 101190 95762 1 1 63 62 +YCL012C_mRNA 101316 101787 101190 2 2 64 63 +YCL011C_mRNA 102074 103357 101787 2 1 66 64 +YCL010C_mRNA 103570 104349 103357 2 1 67 65 +YCL009C_mRNA 104618 105547 104349 2 1 68 66 +YCL008C_mRNA 105695 106852 105547 2 1 69 67 +YCL007C_mRNA 106973 107365 106852 2 1 70 68 +YCL005W-A_mRNA 107022 107416 107365 1 3 71 69 +snR43_snoRNA 107503 107711 107416 2 1 74 70 +YCL005W_mRNA 108020 108790 107711 1 1 75 71 +YCL004W_mRNA 109104 110669 108790 1 1 76 72 +YCL002C_mRNA 110807 111674 110669 2 2 77 73 +YCL001W_mRNA 111915 112481 111674 1 1 79 74 +YCL001W-A_mRNA 113079 113540 112481 1 1 80 75 +YCL001W-B_mRNA 113769 114023 113540 1 1 81 76 +YCR001W_mRNA 115684 115998 114023 1 1 82 77 +YCR002C_mRNA 117379 118347 115998 2 1 83 78 +YCR003W_mRNA 118619 119170 118347 1 1 84 79 +YCR004C_mRNA 119574 120317 119170 2 1 85 80 +YCR005C_mRNA 120945 122327 120317 2 1 86 81 +YCR006C_mRNA 122529 123002 122327 2 1 87 82 +tP(AGG)C_tRNA 123576 123647 123002 2 1 88 83 +YCR007C_mRNA 126010 126729 123647 2 1 89 84 +tN(GUU)C_tRNA 127715 127788 126729 1 1 90 85 +YCR008W_mRNA 128469 130280 127788 1 1 91 86 +YCR009C_mRNA 130744 131541 130280 2 1 92 87 +YCR010C_mRNA 132272 133123 131541 2 1 93 88 +YCR011C_mRNA 133723 136872 133123 2 1 94 89 +YCR012W_mRNA 137745 138995 136872 1 1 95 90 +YCR013C_mRNA 138401 139048 138995 2 1 96 91 +YCR014C_mRNA 139184 140932 139048 2 1 97 92 +YCR015C_mRNA 141216 142169 140932 2 1 98 93 +snR33_snoRNA 142363 142545 142169 2 1 99 94 +tG(GCC)C_tRNA 142700 142770 142545 2 1 100 95 +YCR016W_mRNA 143633 144505 142770 1 1 101 96 +YCR017C_mRNA 144772 147633 144505 2 1 102 97 +YCR018C_mRNA 148237 148902 147633 2 1 103 98 +tM(CAU)C_tRNA 149919 149990 148902 1 1 104 99 +tK(CUU)C_tRNA 151283 151355 149990 2 1 105 100 +YCR018C-A_mRNA 151607 151861 151355 2 1 106 101 +YCR019W_mRNA 152836 153927 151861 1 1 107 102 +YCR020C_mRNA 154011 154658 153927 2 1 108 103 +YCR020C-A_mRNA 154829 155095 154658 2 1 109 104 +YCR020W-B_mRNA 155319 155555 155095 1 1 110 105 +YCR021C_mRNA 156108 157106 155555 2 1 111 106 +YCR022C_mRNA 157420 157764 157106 2 1 112 107 +YCR023C_mRNA 158537 160372 157764 2 1 113 108 +YCR024C_mRNA 160743 162221 160372 2 1 114 109 +YCR024C-B_mRNA 162598 162864 162221 2 1 115 110 +YCR024C-A_mRNA 162944 163066 162864 2 1 116 111 +YCR025C_mRNA 163445 163855 163066 2 1 117 112 +YCR026C_mRNA 164110 166338 163855 2 1 118 113 +YCR027C_mRNA 167369 167998 166338 2 1 119 114 +tQ(UUG)C_tRNA 168300 168371 167998 2 1 120 115 +YCR028C_mRNA 170885 172423 168371 2 1 121 116 +YCR028C-A_mRNA 172949 173439 172423 2 2 122 117 +YCR030C_mRNA 173825 176437 173439 2 1 124 118 +snR65_snoRNA 177182 177281 176437 1 1 125 119 +YCR031C_mRNA 177499 178219 177281 2 2 126 120 +snR189_snoRNA 178609 178797 178219 2 1 128 121 +YCR032W_mRNA 179519 186022 178797 1 1 129 122 +YCR033W_mRNA 186488 190168 186022 1 1 130 123 +YCR034W_mRNA 190591 191634 190168 1 1 131 124 +YCR035C_mRNA 191833 193017 191634 2 1 132 125 +YCR036W_mRNA 193296 194297 193017 1 1 133 126 +YCR037C_mRNA 194413 197184 194297 2 1 134 127 +YCR038C_mRNA 197620 199548 197184 2 1 135 128 +YCR038W-A_mRNA 199292 199417 199548 1 1 136 129 +YCR039C_mRNA 199545 200177 199548 2 1 137 130 +YCR040W_mRNA 200441 200968 200177 1 1 138 131 +YCR041W_mRNA 200910 201242 200968 1 1 139 132 +YCR042C_mRNA 201173 205396 201242 2 1 140 133 +YCR043C_mRNA 206260 206643 205396 2 1 141 134 +YCR044C_mRNA 206876 207949 206643 2 1 142 135 +YCR045C_mRNA 208134 209609 207949 2 1 143 136 +YCR045W-A_mRNA 208750 209100 209609 1 1 144 137 +YCR046C_mRNA 209913 210422 209609 2 1 145 138 +YCR047C_mRNA 210717 211544 210422 2 1 146 139 +YCR047W-A_mRNA 211300 211506 211544 1 1 147 140 +YCR049C_mRNA 211870 212316 211544 2 1 148 141 +YCR048W_mRNA 211928 213760 212316 1 1 149 142 +YCR050C_mRNA 213463 213771 213760 2 1 150 143 +YCR051W_mRNA 214070 214738 213771 1 1 151 144 +YCR052W_mRNA 214993 216444 214738 1 1 152 145 +YCR053W_mRNA 216696 218240 216444 1 1 153 146 +YCR054C_mRNA 218375 220066 218240 2 1 154 147 +YCR057C_mRNA 220456 223227 220066 2 1 155 148 +YCR059C_mRNA 223453 224229 223227 2 1 156 149 +YCR060W_mRNA 224398 224733 224229 1 1 157 150 +YCR061W_mRNA 225562 227457 224733 1 1 158 151 +tS(CGA)C_tRNA 227941 228041 227457 1 2 159 152 +YCR064C_mRNA 228094 228504 228041 2 1 161 153 +YCR063W_mRNA 228317 228790 228504 1 1 162 154 +YCR065W_mRNA 229309 231003 228790 1 1 163 155 +YCR066W_mRNA 231499 232962 231003 1 1 164 156 +YCR067C_mRNA 233124 236321 232962 2 1 165 157 +YCR068W_mRNA 237213 238775 236321 1 1 166 158 +YCR069W_mRNA 239054 240010 238775 1 1 167 159 +YCR071C_mRNA 240102 240542 240010 2 1 168 160 +YCR072C_mRNA 240804 242351 240542 2 1 169 161 +YCR073C_mRNA 242587 246582 242351 2 1 170 162 +YCR073W-A_mRNA 246962 247909 246582 1 1 171 163 +YCR075C_mRNA 248032 248814 247909 2 1 172 164 +YCR075W-A_mRNA 248974 249201 248814 1 1 173 165 +YCR076C_mRNA 249292 250044 249201 2 1 174 166 +YCR077C_mRNA 250237 252627 250044 2 1 175 167 +YCR079W_mRNA 252844 254172 252627 1 1 176 168 +YCR081W_mRNA 254370 258653 254172 1 1 177 169 +YCR081C-A_mRNA 258414 258650 258653 2 1 178 170 +YCR082W_mRNA 258882 259268 258653 1 1 179 171 +YCR083W_mRNA 259577 259960 259268 1 1 180 172 +YCR084C_mRNA 260310 262451 259960 2 1 181 173 +YCR085W_mRNA 262915 263268 262451 1 1 182 174 +YCR086W_mRNA 263391 263963 263268 1 1 183 175 +YCR087W_mRNA 263975 264490 263963 1 1 184 176 +YCR087C-A_mRNA 264005 264466 264490 2 1 185 177 +YCR088W_mRNA 265067 266845 264490 1 1 186 178 +YCR089W_mRNA 267433 272262 266845 1 1 187 179 +YCR090C_mRNA 272314 272862 272262 2 1 188 180 +YCR091W_mRNA 274403 276565 272862 1 1 189 181 +YCR092C_mRNA 276763 279819 276565 2 1 190 182 +YCR093W_mRNA 280116 286442 279819 1 1 191 183 +YCR094W_mRNA 286761 287936 286442 1 1 192 184 +YCR095C_mRNA 288169 289257 287936 2 1 193 185 +YCR095W-A_mRNA 289638 289796 289257 1 1 194 186 +YCR096C_mRNA 293178 293537 289796 2 1 195 187 +YCR097W_mRNA 293834 294320 293537 1 3 196 188 +YCR097W-A_mRNA 294438 294704 294320 1 1 199 189 +tT(AGU)C_tRNA 295483 295555 294704 1 1 200 190 +YCR098C_mRNA 297048 298604 295555 2 1 201 191 +YCR099C_mRNA 300831 301298 298604 2 1 202 192 +YCR100C_mRNA 301270 302220 301298 2 1 203 193 +YCR101C_mRNA 302481 303029 302220 2 1 204 194 +YCR102C_mRNA 304360 305466 303029 2 1 205 195 +YCR102W-A_mRNA 306734 306931 305466 1 1 206 196 +YCR104W_mRNA 307800 308174 306931 1 1 207 197 +YCR105W_mRNA 309069 310154 308174 1 1 208 198 +YCR106W_mRNA 310957 313455 310154 1 1 209 199 +YCR107W_mRNA 313889 314980 313455 1 1 210 200 +YCR108C_mRNA 315996 316187 314980 2 1 211 201 diff --git a/testdata/v2/tracks/S1_normalized_minus.bw b/testdata/v2/tracks/S1_normalized_minus.bw new file mode 100644 index 000000000..7e0af36b8 Binary files /dev/null and b/testdata/v2/tracks/S1_normalized_minus.bw differ diff --git a/testdata/v2/tracks/S1_normalized_plus.bw b/testdata/v2/tracks/S1_normalized_plus.bw new file mode 100644 index 000000000..778764acd Binary files /dev/null and b/testdata/v2/tracks/S1_normalized_plus.bw differ diff --git a/testdata/v2/tracks/S1_raw_minus.bw b/testdata/v2/tracks/S1_raw_minus.bw new file mode 100644 index 000000000..d62cd0add Binary files /dev/null and b/testdata/v2/tracks/S1_raw_minus.bw differ diff --git a/testdata/v2/tracks/S1_raw_plus.bw b/testdata/v2/tracks/S1_raw_plus.bw new file mode 100644 index 000000000..38a21eb17 Binary files /dev/null and b/testdata/v2/tracks/S1_raw_plus.bw differ diff --git a/testdata/v2/tracks/S1_tagClusters.bed b/testdata/v2/tracks/S1_tagClusters.bed new file mode 100644 index 000000000..30dd47ddb --- /dev/null +++ b/testdata/v2/tracks/S1_tagClusters.bed @@ -0,0 +1,261 @@ +track name=TC description="CAGE Tag Clusters (TC)" visibility=full +chrIII 686 687 . 41.0223592494323 + 686 687 0 1 1 0 +chrIII 17249 17274 . 455.673161933904 + 17249 17250 0 2 17,1 0,24 +chrIII 23551 23562 . 1175.18113511716 + 23561 23562 0 1 11 0 +chrIII 24750 24793 . 3708.98051198223 + 24764 24765 0 3 1,27,1 0,5,42 +chrIII 27888 27946 . 745.672456457998 + 27913 27914 0 3 1,33,1 0,13,57 +chrIII 27967 27968 . 41.0223592494323 + 27967 27968 0 1 1 0 +chrIII 29355 29361 . 82.0447184988646 + 29355 29356 0 1 6 0 +chrIII 31401 31442 . 2134.55730008315 + 31431 31432 0 3 1,15,1 0,16,40 +chrIII 41434 41435 . 82.4800962429387 + 41434 41435 0 1 1 0 +chrIII 50771 50829 . 7430.74967305521 + 50795 50796 0 3 1,31,1 0,10,57 +chrIII 50936 50937 . 41.0223592494323 + 50936 50937 0 1 1 0 +chrIII 51316 51317 . 41.0223592494323 + 51316 51317 0 1 1 0 +chrIII 51674 51675 . 82.4800962429387 + 51674 51675 0 1 1 0 +chrIII 52610 52625 . 623.978213904952 + 52624 52625 0 2 1,9 0,6 +chrIII 57046 57047 . 41.0223592494323 + 57046 57047 0 1 1 0 +chrIII 61607 61637 . 786.222258927324 + 61636 61637 0 2 1,25 0,5 +chrIII 63392 63434 . 745.20968040264 + 63410 63411 0 2 39,1 0,41 +chrIII 70086 70091 . 290.128051454369 + 70090 70091 0 1 5 0 +chrIII 70111 70123 . 1167.8676294392 + 70111 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88640 88650 . 2561.79056835583 + 88640 88641 0 1 10 0 +chrIII 88681 88682 . 417.499715858619 + 88681 88682 0 1 1 0 +chrIII 88717 88736 . 1960.37381348808 + 88718 88719 0 2 1,18 0,1 +chrIII 88811 88812 . 165.835568717042 + 88811 88812 0 1 1 0 +chrIII 88845 88851 . 82.0447184988646 + 88845 88846 0 1 6 0 +chrIII 88939 88972 . 414.505883177905 + 88958 88959 0 2 1,14 0,19 +chrIII 88992 88995 . 165.126128452184 + 88992 88993 0 1 3 0 +chrIII 89028 89034 . 3168.65011572173 + 89028 89029 0 1 6 0 +chrIII 89063 89065 . 584.860367636822 + 89064 89065 0 2 1,1 0,1 +chrIII 89137 89138 . 207.64795521143 + 89137 89138 0 1 1 0 +chrIII 89194 89196 . 751.038994080318 + 89195 89196 0 1 2 0 +chrIII 89219 89223 . 710.671511375634 + 89222 89223 0 1 4 0 +chrIII 89261 89275 . 206.583865445691 + 89261 89262 0 1 14 0 +chrIII 89299 89313 . 82.0447184988646 + 89299 89300 0 1 14 0 +chrIII 89357 89386 . 4111.30104908278 + 89380 89381 0 2 1,23 0,6 +chrIII 89415 89460 . 495.675225445604 + 89429 89430 0 2 36,1 0,44 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-0,0 +1,261 @@ +track name=TC description="CAGE Tag Clusters (TC)" visibility=full +chrIII 686 687 . 40.1589826054152 + 686 687 0 1 1 0 +chrIII 17249 17274 . 398.13097331648 + 17261 17262 0 1 25 0 +chrIII 23551 23562 . 277.83881846769 + 23561 23562 0 1 11 0 +chrIII 24750 24793 . 3638.16301311042 + 24759 24760 0 3 1,25,1 0,7,42 +chrIII 27888 27946 . 873.760115445495 + 27913 27914 0 3 1,33,1 0,13,57 +chrIII 27967 27968 . 40.1589826054152 + 27967 27968 0 1 1 0 +chrIII 29355 29361 . 80.3179652108304 + 29355 29356 0 1 6 0 +chrIII 31401 31442 . 675.097926109637 + 31417 31418 0 3 1,15,1 0,16,40 +chrIII 41434 41435 . 40.1589826054152 + 41434 41435 0 1 1 0 +chrIII 50771 50829 . 7338.14325184551 + 50795 50796 0 3 1,31,1 0,10,57 +chrIII 50936 50937 . 40.1589826054152 + 50936 50937 0 1 1 0 +chrIII 51316 51317 . 79.8940004472695 + 51316 51317 0 1 1 0 +chrIII 51674 51675 . 40.1589826054152 + 51674 51675 0 1 1 0 +chrIII 52610 52625 . 711.573130989202 + 52624 52625 0 2 1,9 0,6 +chrIII 57046 57047 . 40.1589826054152 + 57046 57047 0 1 1 0 +chrIII 61607 61637 . 1346.92352326631 + 61617 61618 0 2 1,22 0,8 +chrIII 63392 63434 . 1109.84071829973 + 63410 63411 0 2 25,1 0,41 +chrIII 70086 70091 . 475.155638839462 + 70090 70091 0 1 5 0 +chrIII 70111 70123 . 1928.90381789236 + 70111 70112 0 1 12 0 +chrIII 71684 71685 . 40.1589826054152 + 71684 71685 0 1 1 0 +chrIII 79089 79100 . 199.10352983624 + 79099 79100 0 1 11 0 +chrIII 82714 82715 . 40.1589826054152 + 82714 82715 0 1 1 0 +chrIII 83005 83006 . 40.1589826054152 + 83005 83006 0 1 1 0 +chrIII 85144 85163 . 438.474748889351 + 85156 85157 0 3 1,17,1 0,1,18 +chrIII 85242 85243 . 119.470552740074 + 85242 85243 0 1 1 0 +chrIII 85292 85293 . 355.417693527281 + 85292 85293 0 1 1 0 +chrIII 85340 85341 . 158.944547230825 + 85340 85341 0 1 1 0 +chrIII 85549 85568 . 397.78309490892 + 85549 85550 0 1 19 0 +chrIII 85641 85643 . 159.629535345489 + 85642 85643 0 1 2 0 +chrIII 85674 85675 . 40.1589826054152 + 85674 85675 0 1 1 0 +chrIII 85702 85707 . 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89222 89223 0 1 4 0 +chrIII 89261 89275 . 238.838547678095 + 89261 89262 0 1 14 0 +chrIII 89299 89313 . 199.10352983624 + 89312 89313 0 1 14 0 +chrIII 89357 89386 . 1700.09371497256 + 89379 89380 0 2 1,23 0,6 +chrIII 89415 89460 . 439.20949594161 + 89450 89451 0 1 45 0 +chrIII 89519 89557 . 1496.97967678139 + 89520 89521 0 3 1,14,1 0,1,37 +chrIII 89579 89619 . 676.863004385479 + 89602 89603 0 1 40 0 +chrIII 89657 89706 . 914.358765560068 + 89688 89689 0 2 1,48 0,1 +chrIII 89740 89770 . 909.166705113919 + 89769 89770 0 2 1,15 0,15 +chrIII 89857 89858 . 79.8940004472695 + 89857 89858 0 1 1 0 +chrIII 89881 89901 . 318.39543841826 + 89898 89899 0 1 20 0 +chrIII 89925 89926 . 40.1589826054152 + 89925 89926 0 1 1 0 +chrIII 89947 89948 . 40.1589826054152 + 89947 89948 0 1 1 0 +chrIII 89973 89976 . 80.3179652108304 + 89973 89974 0 1 3 0 +chrIII 90038 90069 . 2150.70513857409 + 90053 90054 0 3 1,1,1 0,15,30 +chrIII 90112 90113 . 119.470552740074 + 90112 90113 0 1 1 0 +chrIII 90214 90215 . 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0 1 1 0 +chrIII 274329 274345 . 317.81300810565 + 274344 274345 0 1 16 0 +chrIII 280037 280055 . 160.2119656581 + 280037 280038 0 1 18 0 +chrIII 280082 280087 . 475.155638839462 + 280086 280087 0 1 5 0 +chrIII 286696 286748 . 558.097618369074 + 286708 286709 0 2 32,1 0,51 +chrIII 289500 289501 . 79.8940004472695 + 289500 289501 0 1 1 0 +chrIII 293821 293867 . 1188.13480679135 + 293822 293823 0 3 1,31,1 0,1,45 +chrIII 7056 7057 . 40.1589826054152 - 7056 7057 0 1 1 0 +chrIII 22121 22122 . 40.1589826054152 - 22121 22122 0 1 1 0 +chrIII 22153 22162 . 159.629535345489 - 22153 22154 0 1 9 0 +chrIII 23399 23444 . 358.554421023676 - 23403 23404 0 1 45 0 +chrIII 24324 24377 . 6644.55172937318 - 24354 24355 0 3 1,19,1 0,20,52 +chrIII 27360 27393 . 398.729106374687 - 27382 27383 0 1 33 0 +chrIII 27775 27776 . 40.1589826054152 - 27775 27776 0 1 1 0 +chrIII 35409 35467 . 955.989419889448 - 35432 35433 0 3 1,43,1 0,2,57 +chrIII 38816 38841 . 517.362354260449 - 38840 38841 0 1 25 0 +chrIII 38862 38871 . 2387.17855919486 - 38862 38863 0 2 6,1 0,8 +chrIII 40755 40797 . 1850.33384069085 - 40778 40779 0 3 1,11,1 0,23,41 +chrIII 41858 41859 . 40.1589826054152 - 41858 41859 0 1 1 0 +chrIII 44439 44466 . 1148.38634047239 - 44439 44440 0 1 27 0 +chrIII 46926 46971 . 559.206571247299 - 46944 46945 0 3 1,37,1 0,6,44 +chrIII 48380 48408 . 319.417536240028 - 48404 48405 0 1 28 0 +chrIII 50236 50289 . 10202.4390405504 - 50257 50258 0 3 1,23,1 0,21,52 +chrIII 56519 56520 . 40.1589826054152 - 56519 56520 0 1 1 0 +chrIII 56601 56628 . 160.635930421661 - 56617 56618 0 1 27 0 +chrIII 58733 58761 . 1452.23372870771 - 58744 58745 0 3 1,4,1 0,11,27 +chrIII 61197 61248 . 7622.69533494234 - 61236 61237 0 3 1,28,1 0,12,50 +chrIII 63231 63267 . 912.592969004457 - 63266 63267 0 1 36 0 +chrIII 65575 65576 . 40.1589826054152 - 65575 65576 0 1 1 0 +chrIII 65600 65630 . 2364.49331989819 - 65600 65601 0 2 19,1 0,29 +chrIII 66426 66427 . 40.1589826054152 - 66426 66427 0 1 1 0 +chrIII 66507 66508 . 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103402 0 1 26 0 +chrIII 104361 104410 . 831.769896350011 - 104365 104366 0 3 1,5,1 0,4,48 +chrIII 105533 105605 . 9053.05579102942 - 105562 105563 0 3 1,28,1 0,29,71 +chrIII 106828 106829 . 158.944547230825 - 106828 106829 0 1 1 0 +chrIII 106853 106872 . 1380.8988974239 - 106863 106864 0 3 1,8,1 0,3,18 +chrIII 107381 107382 . 40.1589826054152 - 107381 107382 0 1 1 0 +chrIII 111701 111712 . 159.629535345489 - 111701 111702 0 1 11 0 +chrIII 116189 116190 . 40.1589826054152 - 116189 116190 0 1 1 0 +chrIII 118392 118403 . 830.268475070012 - 118402 118403 0 2 1,4 0,7 +chrIII 120321 120342 . 159.788000894539 - 120321 120322 0 1 21 0 +chrIII 120433 120434 . 79.8940004472695 - 120433 120434 0 1 1 0 +chrIII 120480 120538 . 5090.3013515238 - 120499 120500 0 3 1,14,1 0,19,57 +chrIII 122372 122404 . 20326.4785322785 - 122387 122388 0 3 1,12,1 0,10,31 +chrIII 122474 122475 . 40.1589826054152 - 122474 122475 0 1 1 0 +chrIII 127553 127554 . 40.1589826054152 - 127553 127554 0 1 1 0 +chrIII 131560 131561 . 198.342455365576 - 131560 131561 0 1 1 0 +chrIII 131584 131623 . 2019.54987289302 - 131597 131598 0 2 23,1 0,38 +chrIII 132786 132787 . 40.1589826054152 - 132786 132787 0 1 1 0 +chrIII 133232 133233 . 1018.47869598515 - 133232 133233 0 1 1 0 +chrIII 137000 137034 . 359.576518845444 - 137012 137013 0 1 34 0 +chrIII 142179 142206 . 478.203617921804 - 142205 142206 0 2 1,23 0,4 +chrIII 142545 142546 . 119.470552740074 - 142545 142546 0 1 1 0 +chrIII 142760 142761 . 40.1589826054152 - 142760 142761 0 1 1 0 +chrIII 147662 147678 . 947.34385257132 - 147662 147663 0 1 16 0 +chrIII 148569 148601 . 240.105966105369 - 148569 148570 0 1 32 0 +chrIII 155095 155126 . 908.742740350358 - 155113 155114 0 3 1,10,1 0,9,30 +chrIII 157206 157220 . 357.971990711065 - 157206 157207 0 1 14 0 +chrIII 160426 160457 . 517.177561292994 - 160456 160457 0 1 31 0 +chrIII 162240 162241 . 79.8940004472695 - 162240 162241 0 1 1 0 +chrIII 163144 163154 . 357.732818914959 - 163144 163145 0 1 10 0 +chrIII 163205 163275 . 16225.7944460977 - 163217 163218 0 3 1,21,1 0,9,69 +chrIII 163301 163302 . 158.944547230825 - 163301 163302 0 1 1 0 +chrIII 166388 166413 . 1144.51535989844 - 166393 166394 0 3 1,14,1 0,5,24 +chrIII 166661 166662 . 40.1589826054152 - 166661 166662 0 1 1 0 +chrIII 168166 168174 . 238.501437970991 - 168173 168174 0 1 8 0 +chrIII 168578 168598 . 1265.47706219018 - 168590 168591 0 2 13,1 0,19 +chrIII 168708 168709 . 40.1589826054152 - 168708 168709 0 1 1 0 +chrIII 169344 169345 . 79.8940004472695 - 169344 169345 0 1 1 0 +chrIII 172434 172441 . 120.052983052685 - 172434 172435 0 1 7 0 +chrIII 172464 172488 . 437.865991158335 - 172478 172479 0 2 1,16 0,8 +chrIII 172511 172542 . 635.700017974887 - 172522 172523 0 2 1,26 0,5 +chrIII 173450 173548 . 5723.45769283007 - 173479 173480 0 3 1,62,1 0,15,97 +chrIII 176516 176538 . 910.58133455181 - 176536 176537 0 3 1,15,1 0,6,21 +chrIII 178230 178270 . 27576.0114984467 - 178240 178241 0 3 1,10,1 0,10,39 +chrIII 178797 178798 . 40.1589826054152 - 178797 178798 0 1 1 0 +chrIII 193024 193056 . 558.782606483738 - 193037 193038 0 2 26,1 0,31 +chrIII 197226 197244 . 554.805771260847 - 197228 197229 0 2 3,1 0,17 +chrIII 205419 205423 . 278.236455812845 - 205419 205420 0 1 4 0 +chrIII 206667 206677 . 239.523535792759 - 206676 206677 0 1 10 0 +chrIII 206702 206703 . 394.590977898754 - 206702 206703 0 1 1 0 +chrIII 207947 207982 . 1266.95518375326 - 207956 207957 0 3 1,12,1 0,9,34 +chrIII 210420 210470 . 3203.48423281198 - 210469 210470 0 2 1,44 0,6 +chrIII 211633 211638 . 120.052983052685 - 211633 211634 0 1 5 0 +chrIII 220121 220137 . 120.052983052685 - 220121 220122 0 1 16 0 +chrIII 223277 223299 . 517.677612412555 - 223289 223290 0 2 1,19 0,3 +chrIII 224243 224266 . 872.78004778773 - 224248 224249 0 2 1,20 0,3 +chrIII 236423 236441 . 199.10352983624 - 236440 236441 0 1 18 0 +chrIII 240554 240592 . 1190.48841349891 - 240591 240592 0 2 1,36 0,2 +chrIII 242385 242386 . 40.1589826054152 - 242385 242386 0 1 1 0 +chrIII 246647 246648 . 119.470552740074 - 246647 246648 0 1 1 0 +chrIII 248791 248813 . 358.994088532833 - 248806 248807 0 1 22 0 +chrIII 250017 250070 . 1622.22104811608 - 250056 250057 0 3 1,29,1 0,21,52 +chrIII 252641 252671 . 1738.04670651005 - 252669 252670 0 2 1,25 0,5 +chrIII 261638 261639 . 40.1589826054152 - 261638 261639 0 1 1 0 +chrIII 262484 262485 . 40.1589826054152 - 262484 262485 0 1 1 0 +chrIII 262648 262679 . 280.264948710785 - 262668 262669 0 1 31 0 +chrIII 264464 264465 . 40.1589826054152 - 264464 264465 0 1 1 0 +chrIII 264492 264503 . 396.6243830931 - 264492 264493 0 1 11 0 +chrIII 272877 272910 . 674.574206416206 - 272877 272878 0 1 33 0 +chrIII 279853 279856 . 238.501437970991 - 279855 279856 0 1 3 0 +chrIII 289295 289315 . 160.635930421661 - 289298 289299 0 1 20 0 +chrIII 298578 298579 . 79.8940004472695 - 298578 298579 0 1 1 0 +chrIII 300165 300166 . 40.1589826054152 - 300165 300166 0 1 1 0 +chrIII 302998 302999 . 119.470552740074 - 302998 302999 0 1 1 0 +chrIII 303044 303045 . 40.1589826054152 - 303044 303045 0 1 1 0 +chrIII 303079 303080 . 40.1589826054152 - 303079 303080 0 1 1 0 +chrIII 305536 305537 . 40.1589826054152 - 305536 305537 0 1 1 0 diff --git a/testdata/v2/tracks/consensusClusters.bed b/testdata/v2/tracks/consensusClusters.bed new file mode 100644 index 000000000..65fa87b09 --- /dev/null +++ b/testdata/v2/tracks/consensusClusters.bed @@ -0,0 +1,261 @@ +track name=TC description="CAGE Tag Clusters (TC)" visibility=full +chrIII 686 687 . 81.1813418548475 + 0 +chrIII 17249 17274 . 853.804135250384 + 0 +chrIII 23551 23562 . 1453.01995358485 + 0 +chrIII 24755 24782 . 6493.62885909485 + 0 +chrIII 27901 27934 . 1417.33487035194 + 0 +chrIII 27967 27968 . 81.1813418548475 + 0 +chrIII 29355 29361 . 162.362683709695 + 0 +chrIII 31417 31432 . 2564.21113252978 + 0 +chrIII 41434 41435 . 122.639078848354 + 0 +chrIII 50781 50812 . 13506.2756245299 + 0 +chrIII 50936 50937 . 81.1813418548475 + 0 +chrIII 51316 51317 . 120.916359696702 + 0 +chrIII 51674 51675 . 122.639078848354 + 0 +chrIII 52616 52625 . 1254.37000303931 + 0 +chrIII 57046 57047 . 81.1813418548475 + 0 +chrIII 61612 61637 . 2012.22942249693 + 0 +chrIII 63392 63431 . 1773.86905684753 + 0 +chrIII 70086 70091 . 765.283690293831 + 0 +chrIII 70111 70123 . 3096.77144733157 + 0 +chrIII 71684 71685 . 81.1813418548475 + 0 +chrIII 79089 79100 . 489.042867756035 + 0 +chrIII 82714 82715 . 81.1813418548475 + 0 +chrIII 83005 83006 . 122.639078848354 + 0 +chrIII 85145 85163 . 1565.70287218522 + 0 +chrIII 85242 85243 . 160.492911989507 + 0 +chrIII 85292 85293 . 479.521462730033 + 0 +chrIII 85340 85341 . 241.424643473764 + 0 +chrIII 85549 85568 . 686.847056597549 + 0 +chrIII 85641 85643 . 869.736505033156 + 0 +chrIII 85674 85675 . 415.606563196312 + 0 +chrIII 85702 85707 . 537.490594654548 + 0 +chrIII 85827 85847 . 2566.94075841873 + 0 +chrIII 85895 85896 . 247.806937816845 + 0 +chrIII 85976 85978 . 579.42088842816 + 0 +chrIII 86018 86048 . 368.083172511369 + 0 +chrIII 86181 86182 . 81.1813418548475 + 0 +chrIII 86323 86324 . 287.541955658699 + 0 +chrIII 86480 86492 . 370.446016665199 + 0 +chrIII 86612 86613 . 164.262751808167 + 0 +chrIII 86862 86863 . 162.374096690208 + 0 +chrIII 87005 87018 . 202.097701551549 + 0 +chrIII 87186 87189 . 2207.45033681422 + 0 +chrIII 87210 87216 . 1495.22137794349 + 0 +chrIII 87351 87352 . 245.729569164312 + 0 +chrIII 87458 87459 . 201.950648983013 + 0 +chrIII 87654 87680 . 7283.65516981294 + 0 +chrIII 88020 88021 . 287.541955658699 + 0 +chrIII 88118 88119 . 164.262751808167 + 0 +chrIII 88274 88283 . 573.818092860009 + 0 +chrIII 88517 88518 . 164.262751808167 + 0 +chrIII 88606 88607 . 1403.31078381335 + 0 +chrIII 88640 88650 . 3116.31179171935 + 0 +chrIII 88681 88682 . 536.970268598693 + 0 +chrIII 88717 88736 . 2637.50231708807 + 0 +chrIII 88811 88812 . 285.306121457117 + 0 +chrIII 88845 88851 . 162.362683709695 + 0 +chrIII 88939 88972 . 534.98283099415 + 0 +chrIII 88992 88995 . 245.444093663015 + 0 +chrIII 89028 89034 . 3722.18564085131 + 0 +chrIII 89063 89065 . 862.699186104511 + 0 +chrIII 89137 89138 . 287.541955658699 + 0 +chrIII 89194 89196 . 950.142523916558 + 0 +chrIII 89219 89223 . 870.301046721124 + 0 +chrIII 89261 89275 . 445.422413123786 + 0 +chrIII 89299 89313 . 281.148248335105 + 0 +chrIII 89363 89386 . 5565.66519489103 + 0 +chrIII 89415 89460 . 934.884721387214 + 0 +chrIII 89520 89534 . 6777.55514026349 + 0 +chrIII 89579 89619 . 2094.01384236874 + 0 +chrIII 89658 89706 . 2708.22795694073 + 0 +chrIII 89755 89770 . 2552.812753945 + 0 +chrIII 89857 89858 . 287.541955658699 + 0 +chrIII 89881 89901 . 1487.73392347884 + 0 +chrIII 89925 89926 . 81.1813418548475 + 0 +chrIII 89947 89948 . 205.994551322458 + 0 +chrIII 89973 89976 . 162.362683709695 + 0 +chrIII 90053 90055 . 8889.15421308344 + 0 +chrIII 90112 90113 . 201.950648983013 + 0 +chrIII 90214 90215 . 122.639078848354 + 0 +chrIII 90242 90253 . 326.636848498376 + 0 +chrIII 90303 90304 . 162.374096690208 + 0 +chrIII 91240 91307 . 8440.28796441537 + 0 +chrIII 92621 92622 . 81.1813418548475 + 0 +chrIII 96177 96178 . 484.614908004587 + 0 +chrIII 106996 107008 . 4444.96331441655 + 0 +chrIII 107977 107978 . 81.1813418548475 + 0 +chrIII 107999 108027 . 443.5109320448 + 0 +chrIII 109026 109031 . 366.487463311964 + 0 +chrIII 109093 109094 . 81.1813418548475 + 0 +chrIII 111815 111816 . 201.950648983013 + 0 +chrIII 111837 111855 . 2255.15484178963 + 0 +chrIII 111880 111913 . 3864.28989572712 + 0 +chrIII 116825 116826 . 81.1813418548475 + 0 +chrIII 118594 118605 . 4084.42065688657 + 0 +chrIII 118956 118957 . 203.997769650022 + 0 +chrIII 120895 120896 . 81.1813418548475 + 0 +chrIII 123353 123357 . 202.097701551549 + 0 +chrIII 128026 128027 . 122.639078848354 + 0 +chrIII 137672 137706 . 124009.761004613 + 0 +chrIII 137744 137745 . 160.492911989507 + 0 +chrIII 143603 143636 . 1346.09890794922 + 0 +chrIII 152698 152722 . 605.725267974725 + 0 +chrIII 155287 155310 . 608.173130136831 + 0 +chrIII 156323 156324 . 122.639078848354 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238902 238934 . 3599.13143214426 + 0 +chrIII 242589 242590 . 122.639078848354 + 0 +chrIII 246937 246953 . 3130.13630964582 + 0 +chrIII 248940 248941 . 164.262751808167 + 0 +chrIII 248965 248967 . 322.605985328611 + 0 +chrIII 252808 252847 . 649.345391629041 + 0 +chrIII 254348 254357 . 689.270797587396 + 0 +chrIII 258833 258866 . 7145.40556902547 + 0 +chrIII 259542 259569 . 3023.86380679731 + 0 +chrIII 263301 263342 . 766.128330353924 + 0 +chrIII 265021 265036 . 3428.66108497498 + 0 +chrIII 267137 267138 . 160.492911989507 + 0 +chrIII 274329 274345 . 691.296532034122 + 0 +chrIII 280037 280055 . 407.652254386916 + 0 +chrIII 280082 280087 . 2410.86130321041 + 0 +chrIII 286696 286728 . 889.21325191746 + 0 +chrIII 289500 289501 . 120.916359696702 + 0 +chrIII 293822 293853 . 1982.15521928651 + 0 +chrIII 7056 7057 . 81.1813418548475 - 0 +chrIII 22121 22122 . 81.1813418548475 - 0 +chrIII 22153 22162 . 324.755663797674 - 0 +chrIII 23399 23444 . 856.510416188712 - 0 +chrIII 24344 24372 . 8768.49982222681 - 0 +chrIII 27360 27393 . 770.439100272563 - 0 +chrIII 27775 27776 . 81.1813418548475 - 0 +chrIII 35411 35454 . 2206.57265622304 - 0 +chrIII 38816 38841 . 888.745096968727 - 0 +chrIII 38862 38868 . 5696.17657003818 - 0 +chrIII 40778 40789 . 3452.6560719274 - 0 +chrIII 41858 41859 . 81.1813418548475 - 0 +chrIII 44439 44466 . 2103.5085832296 - 0 +chrIII 46932 46969 . 891.293707994179 - 0 +chrIII 48380 48408 . 566.588383191078 - 0 +chrIII 50257 50280 . 20659.6409749656 - 0 +chrIII 56519 56520 . 81.1813418548475 - 0 +chrIII 56601 56628 . 407.80677737271 - 0 +chrIII 58744 58748 . 3824.34968495972 - 0 +chrIII 61201 61237 . 14179.4981586361 - 0 +chrIII 63231 63267 . 1409.12255422149 - 0 +chrIII 65575 65576 . 81.1813418548475 - 0 +chrIII 65600 65619 . 4749.30535577866 - 0 +chrIII 66426 66427 . 81.1813418548475 - 0 +chrIII 66507 66508 . 81.1813418548475 - 0 +chrIII 68376 68417 . 3305.30048346981 - 0 +chrIII 69955 69981 . 811.866540887785 - 0 +chrIII 74012 74026 . 2176.90117163652 - 0 +chrIII 77935 77952 . 998.234075393908 - 0 +chrIII 82744 82783 . 4467.74376745738 - 0 +chrIII 85494 85527 . 799.365490209055 - 0 +chrIII 85603 85606 . 322.605985328611 - 0 +chrIII 94360 94380 . 2801.68272116818 - 0 +chrIII 95783 95795 . 484.98008201882 - 0 +chrIII 99927 99928 . 322.446224568328 - 0 +chrIII 101787 101799 . 803.373131183832 - 0 +chrIII 101819 101822 . 926.554195083019 - 0 +chrIII 101846 101847 . 201.950648983013 - 0 +chrIII 101871 101872 . 81.1813418548475 - 0 +chrIII 103376 103402 . 691.116117157391 - 0 +chrIII 104361 104390 . 1581.62319062591 - 0 +chrIII 105562 105590 . 14581.6515147732 - 0 +chrIII 106828 106829 . 199.966906480257 - 0 +chrIII 106853 106864 . 2467.42713876122 - 0 +chrIII 107381 107382 . 81.1813418548475 - 0 +chrIII 111701 111712 . 324.755663797674 - 0 +chrIII 116189 116190 . 81.1813418548475 - 0 +chrIII 118399 118403 . 1586.50792924059 - 0 +chrIII 120321 120342 . 366.37186634023 - 0 +chrIII 120433 120434 . 120.916359696702 - 0 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166661 166662 . 81.1813418548475 - 0 +chrIII 168166 168174 . 612.954977643656 - 0 +chrIII 168578 168591 . 1973.0377425102 - 0 +chrIII 168708 168709 . 81.1813418548475 - 0 +chrIII 169344 169345 . 162.374096690208 - 0 +chrIII 172434 172441 . 285.179111504869 - 0 +chrIII 172464 172488 . 726.49457510289 - 0 +chrIII 172516 172542 . 967.251029267347 - 0 +chrIII 173465 173527 . 8340.92062761623 - 0 +chrIII 176520 176537 . 1369.59862456279 - 0 +chrIII 178240 178250 . 53832.7766809858 - 0 +chrIII 178797 178798 . 247.806937816845 - 0 +chrIII 193024 193050 . 1265.01394869041 - 0 +chrIII 197226 197229 . 1266.48555785739 - 0 +chrIII 205419 205423 . 778.842841136696 - 0 +chrIII 206667 206677 . 653.75535644988 - 0 +chrIII 206702 206703 . 435.613337148187 - 0 +chrIII 207947 207968 . 2230.18533784227 - 0 +chrIII 210426 210470 . 6547.48318613932 - 0 +chrIII 211633 211638 . 243.555438545056 - 0 +chrIII 220121 220137 . 285.013175538562 - 0 +chrIII 223280 223299 . 1141.58174551035 - 0 +chrIII 224243 224266 . 1326.36882421816 - 0 +chrIII 236423 236441 . 322.605985328611 - 0 +chrIII 240554 240592 . 2435.31347577748 - 0 +chrIII 242385 242386 . 205.994551322458 - 0 +chrIII 246647 246648 . 368.995226972361 - 0 +chrIII 248791 248813 . 523.083525530562 - 0 +chrIII 250032 250070 . 2535.9116319996 - 0 +chrIII 252644 252671 . 3406.21698393582 - 0 +chrIII 261638 261639 . 81.1813418548475 - 0 +chrIII 262484 262485 . 81.1813418548475 - 0 +chrIII 262648 262679 . 693.105428412569 - 0 +chrIII 264464 264465 . 81.1813418548475 - 0 +chrIII 264492 264503 . 1022.04397788456 - 0 +chrIII 272877 272910 . 1296.01860454068 - 0 +chrIII 279853 279856 . 320.546156469856 - 0 +chrIII 289295 289315 . 532.454050874013 - 0 +chrIII 298578 298579 . 120.916359696702 - 0 +chrIII 300165 300166 . 81.1813418548475 - 0 +chrIII 302998 302999 . 160.492911989507 - 0 +chrIII 303044 303045 . 81.1813418548475 - 0 +chrIII 303079 303080 . 205.994551322458 - 0 +chrIII 305536 305537 . 1472.98426298917 - 0 diff --git a/testdata/v2/tracks/enhancers.bed b/testdata/v2/tracks/enhancers.bed new file mode 100644 index 000000000..9077cb561 --- /dev/null +++ b/testdata/v2/tracks/enhancers.bed @@ -0,0 +1,12 @@ +chrIII 8790 9447 chrIII:8791-9447 403.173560907 . 9188 9189 +chrIII 30213 30946 chrIII:30214-30946 324.725367416 . 30579 30580 +chrIII 124814 125424 chrIII:124815-125424 286.293138099 . 125136 125137 +chrIII 126166 126767 chrIII:126167-126767 282.41566676 . 126563 126564 +chrIII 133383 134015 chrIII:133384-134015 160.63593042 . 133694 133695 +chrIII 150882 151871 chrIII:150883-151871 161.499307064 . 151514 151515 +chrIII 202169 202955 chrIII:202170-202955 202.521666313 . 202722 202723 +chrIII 226295 227342 chrIII:226296-227342 364.020973377 . 226906 226907 +chrIII 304414 305392 chrIII:304415-305392 160.63593042 . 304693 304694 +chrIII 305559 306169 chrIII:305560-306169 287.156514743 . 305878 305879 +chrIII 314072 315058 chrIII:314073-315058 405.043332626 . 314687 314688 +chrIII 315587 316381 chrIII:315588-316381 322.574649365 . 315983 315984 diff --git a/testdata/v2/txdb/annotation_from_gtf.sqlite b/testdata/v2/txdb/annotation_from_gtf.sqlite new file mode 100644 index 000000000..bc37780e2 Binary files /dev/null and b/testdata/v2/txdb/annotation_from_gtf.sqlite differ