# HG changeset patch # User bgruening # Date 1670255265 0 # Node ID e661a3269313f2f651f38d3061d83b2b4c2158c7 # Parent e4c01dcece8b0b4e88033e579c4aa13763c3c23d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 diff -r e4c01dcece8b -r e661a3269313 alevin.xml --- a/alevin.xml Thu Jul 22 14:05:58 2021 +0000 +++ b/alevin.xml Mon Dec 05 15:47:45 2022 +0000 @@ -1,5 +1,5 @@ - - Quantification and analysis of 3’ tagged-end single-cell sequencing data + + Quantification and analysis of 3-prime tagged-end single-cell sequencing data macros.xml @@ -61,7 +61,10 @@ #end if -o ./output -p "\${GALAXY_SLOTS:-4}" - ${protocol} + ${protocol_cond.protocol} + #if $protocol_cond.protocol == '--indropV2' + --w1 '${protocol_cond.w1}' + #end if --tgMap ./alevinmap.tsv #if $whitelist: --whitelist '${optional.whitelist}' @@ -85,39 +88,40 @@ --keepCBFraction '${optional.keepCBFraction}' #end if ${optional.noDedup} - ${optional.dumpBfh} - ${optional.dumpFeatures} - ${optional.dumpUmiGraph} + #if 'dumpBfh' in $output_files: + --dumpBfh + #end if + #if 'dumpFeatures' in $output_files: + --dumpFeatures + #end if + #if 'dumpUmiGraph' in $output_files: + --dumpUmiGraph + #end if ${optional.dumpMtx} - #if $optional.lowRegionMinNumBarcodes: - --lowregionMinNumBarcodes '${optional.lowRegionMinNumBarcodes}' - #end if #if $optional.maxNumBarcodes: --maxNumBarcodes '${optional.maxNumBarcodes}' #end if #if $optional.freqThreshold: --freqThreshold '${optional.freqThreshold}' #end if - + ## && gunzip output/alevin/quants_tier_mat.gz -> the output is binary file #if $optional.dumpMtx != "--dumpMtx": && python '$__tool_directory__/vpolo_convert.py' -m #else: && gunzip output/alevin/quants_mat.mtx.gz #end if - #if $optional.dumpUmiGraph: + #if 'dumpUmiGraph' in $output_files: && python '$__tool_directory__/vpolo_convert.py' -u && sh '$__tool_directory__/umiout.sh' #end if - - && gunzip output/alevin/quants_tier_mat.gz - #if $optional.numCellBootstraps: - && gunzip output/alevin/quants_mean_mat.gz - && gunzip output/alevin/quants_var_mat.gz + ## those gzip file include binary datasets + ## #if $optional.numCellBootstraps: + ## && gunzip output/alevin/quants_mean_mat.gz + ## && gunzip output/alevin/quants_var_mat.gz + ## #end if + #if 'auxiliar_info' in $output_files + && tar -zcvf aux_info.tar.gz output/aux_info #end if - - && gunzip output/aux_info/fld.gz - && gunzip output/aux_info/observed_bias.gz - && gunzip output/aux_info/observed_bias_3p.gz ]]> @@ -128,8 +132,8 @@ - - + + @@ -137,91 +141,136 @@ - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + [ATGC]+ + + + + + - -
- - - - - - - - - - - - + + + + + + + + +
+ + + + + + + + + - - - - + + +
- + optional["dumpMtx"] is not True - + optional["dumpMtx"] - - optional["dumpFeatures"] + + + + + + + output_files and 'dumpFeatures' in output_files - - - - - allout + + + + output_files and 'auxiliar_info' in output_files - - - - optional["dumpBfh"] + + output_files and 'salmon_log' in output_files + + + output_files and 'commands' in output_files - - optional["numCellBootstraps"] + + output_files and 'fragment_length' in output_files - + + output_files and 'dumpBfh' in output_files + + optional["numCellBootstraps"] - + + optional["numCellBootstraps"] + + optional["numCellBootstraps"] - - allout - - - allout - - - allout - - - - - - - allout - - - optional["dumpUmiGraph"] - + + output_files and 'dumpUmiGraph' in output_files + - - allout - + + + +
+ +
+
+ + + + + + + + + + + + +
+ + + +
+ +
@@ -236,15 +285,45 @@ - + + + +
- + - +
- + +
+ + + +
+ +
+
+ + + + + + + + + + + + + +
+ + + +
+
@@ -260,16 +339,35 @@ - + + + +
- - - - - +
- + + + + + + + + + + + + + + + + + + + + +
- 1.5.1 - galaxy0 + 1.9.0 + 1 q7 20.01 - salmon + salmon seqtk - samtools + samtools vpolo - pandas - scipy + pandas + graphviz + scipy @@ -72,10 +73,14 @@
- + + + help="Build the index using a perfect hash rather than a dense hash. This will require less memory (especially during quantification), + but will take longer to construct"/>
@@ -155,9 +160,20 @@ - + + + + + + + + + + + @@ -315,10 +331,21 @@ mkdir ./index && mkdir ./output && #if $quant_type.refTranscriptSource.TranscriptSource != "indexed": + #if $quant_type.refTranscriptSource.s_index.genome + cat '${quant_type.refTranscriptSource.s_index.genome}' | grep "^>" | cut -d " " -f 1 > 'decoys.txt' && + sed -i.bak -e 's/>//g' 'decoys.txt' && + cat '${quant_type.refTranscriptSource.s_index.fasta}' '${quant_type.refTranscriptSource.s_index.genome}' > 'input_index.fasta' && + #else + ln -s '${quant_type.refTranscriptSource.s_index.fasta}' 'input_index.fasta' && + #end if salmon index -i ./index --kmerLen '${quant_type.refTranscriptSource.s_index.kmer}' --gencode - --transcripts '${quant_type.refTranscriptSource.s_index.fasta}' + --threads "\${GALAXY_SLOTS:-4}" + --transcripts 'input_index.fasta' + #if $quant_type.refTranscriptSource.s_index.genome + --decoy 'decoys.txt' + #end if && #set $index_path = './index' #else @@ -453,7 +480,10 @@ #end if ${quant_type.dovetail} ${quant_type.recoverOrphans} - ${quant_type.writeMappings} + ${quant_type.bam_options.writeMappings} + #if $quant_type.bam_options.writeMappings: + ${quant_type.bam_options.writeQualities} + #end if ${quant_type.consistentHits} #if $quant_type.quasiCoverage: --quasiCoverage '${quant_type.quasiCoverage}' diff -r e4c01dcece8b -r e661a3269313 test-data/alevin_mat.mtx --- a/test-data/alevin_mat.mtx Thu Jul 22 14:05:58 2021 +0000 +++ b/test-data/alevin_mat.mtx Mon Dec 05 15:47:45 2022 +0000 @@ -1,5 +1,5 @@ %%MatrixMarket matrix coordinate real general -95 61 99 +14 61 15 1 9 1.000000 2 28 1.000000 3 38 1.000000 @@ -11,91 +11,7 @@ 9 28 1.000000 10 30 1.000000 11 53 1.000000 -12 4 1.000000 +12 3 0.500000 +12 4 0.500000 13 28 1.000000 14 56 1.000000 -15 9 1.000000 -16 43 0.500000 -16 45 0.500000 -17 42 0.500000 -17 44 0.500000 -18 28 1.000000 -19 46 1.000000 -20 38 1.000000 -21 40 1.000000 -22 19 1.000000 -23 9 1.000000 -24 56 1.000000 -25 8 1.000000 -26 28 1.000000 -27 53 1.000000 -28 56 1.000000 -29 28 1.000000 -30 30 1.000000 -31 38 1.000000 -32 28 1.000000 -33 30 1.000000 -34 34 1.000000 -35 30 1.000000 -36 28 1.000000 -37 34 1.000000 -38 16 1.000000 -39 19 1.000000 -40 47 1.000000 -41 38 1.000000 -42 28 1.000000 -43 56 1.000000 -44 28 1.000000 -45 9 1.000000 -46 19 1.000000 -47 23 1.000000 -48 43 0.500000 -48 45 0.500000 -49 38 1.000000 -50 57 1.000000 -51 40 1.000000 -52 38 1.000000 -53 19 1.000000 -54 16 1.000000 -55 15 1.000000 -56 56 1.000000 -57 53 1.000000 -58 30 1.000000 -59 9 1.000000 -60 34 1.000000 -61 30 1.000000 -62 24 1.000000 -63 30 1.000000 -64 56 1.000000 -65 9 1.000000 -66 23 1.000000 -67 61 1.000000 -68 38 1.000000 -69 21 1.000000 -70 38 1.000000 -71 38 1.000000 -72 16 1.000000 -73 30 1.000000 -74 16 1.000000 -75 30 1.000000 -76 40 1.000000 -77 52 1.000000 -78 53 1.000000 -79 42 0.500000 -79 44 0.500000 -80 34 1.000000 -81 9 1.000000 -82 15 1.000000 -83 45 1.000000 -84 47 1.000000 -85 40 1.000000 -86 56 1.000000 -87 56 1.000000 -88 34 1.000000 -89 56 1.000000 -90 38 1.000000 -91 53 1.000000 -92 56 1.000000 -93 53 1.000000 -94 38 1.000000 -95 53 1.000000 diff -r e4c01dcece8b -r e661a3269313 test-data/alevin_mat_01.mtx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alevin_mat_01.mtx Mon Dec 05 15:47:45 2022 +0000 @@ -0,0 +1,105 @@ +%%MatrixMarket matrix coordinate real general +96 61 103 +1 9 1.000000 +2 28 1.000000 +3 38 1.000000 +4 28 1.000000 +5 42 1.000000 +6 9 1.000000 +7 56 1.000000 +8 28 1.000000 +9 28 1.000000 +10 30 1.000000 +11 53 1.000000 +12 3 0.500000 +12 4 0.500000 +13 28 1.000000 +14 56 1.000000 +15 9 1.000000 +16 43 0.500000 +16 45 0.500000 +17 42 0.500000 +17 44 0.500000 +18 28 1.000000 +19 46 1.000000 +20 38 1.000000 +21 40 1.000000 +22 19 1.000000 +23 9 1.000000 +24 56 1.000000 +25 8 1.000000 +26 28 1.000000 +27 53 1.000000 +28 56 1.000000 +29 28 1.000000 +30 30 1.000000 +31 38 1.000000 +32 28 1.000000 +33 30 1.000000 +34 34 1.000000 +35 30 1.000000 +36 28 1.000000 +37 34 1.000000 +38 16 1.000000 +39 19 1.000000 +40 47 1.000000 +41 38 1.000000 +42 28 1.000000 +43 56 1.000000 +44 28 1.000000 +45 9 1.000000 +46 19 1.000000 +47 23 1.000000 +48 43 0.500000 +48 45 0.500000 +49 38 1.000000 +50 56 0.500000 +50 57 0.500000 +51 40 1.000000 +52 38 1.000000 +53 19 1.000000 +54 16 1.000000 +55 15 1.000000 +56 56 1.000000 +57 53 1.000000 +58 30 1.000000 +59 9 1.000000 +60 34 1.000000 +61 30 1.000000 +62 24 1.000000 +63 30 1.000000 +64 56 1.000000 +65 9 1.000000 +66 23 1.000000 +67 61 1.000000 +68 38 1.000000 +69 38 1.000000 +70 21 1.000000 +71 38 1.000000 +72 38 1.000000 +73 16 1.000000 +74 30 1.000000 +75 16 1.000000 +76 30 1.000000 +77 40 1.000000 +78 52 0.500000 +78 53 0.500000 +79 53 1.000000 +80 42 0.500000 +80 44 0.500000 +81 34 1.000000 +82 9 1.000000 +83 15 1.000000 +84 45 1.000000 +85 47 1.000000 +86 40 1.000000 +87 56 1.000000 +88 56 1.000000 +89 34 1.000000 +90 56 1.000000 +91 38 1.000000 +92 53 1.000000 +93 56 1.000000 +94 53 1.000000 +95 38 1.000000 +96 53 1.000000 diff -r e4c01dcece8b -r e661a3269313 test-data/alevin_mat_02.mtx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alevin_mat_02.mtx Mon Dec 05 15:47:45 2022 +0000 @@ -0,0 +1,105 @@ +%%MatrixMarket matrix coordinate real general +96 61 103 +1 9 1.000000 +2 28 1.000000 +3 38 1.000000 +4 28 1.000000 +5 42 1.000000 +6 9 1.000000 +7 56 1.000000 +8 28 1.000000 +9 28 1.000000 +10 30 1.000000 +11 53 1.000000 +12 3 0.500000 +12 4 0.500000 +13 28 1.000000 +14 56 1.000000 +15 9 1.000000 +16 43 0.500000 +16 45 0.500000 +17 42 0.500000 +17 44 0.500000 +18 28 1.000000 +19 46 1.000000 +20 38 1.000000 +21 40 1.000000 +22 19 1.000000 +23 9 1.000000 +24 56 1.000000 +25 8 1.000000 +26 28 1.000000 +27 53 1.000000 +28 56 1.000000 +29 28 1.000000 +30 30 1.000000 +31 38 1.000000 +32 28 1.000000 +33 30 1.000000 +34 34 1.000000 +35 30 1.000000 +36 28 1.000000 +37 34 1.000000 +38 16 1.000000 +39 19 1.000000 +40 47 1.000000 +41 38 1.000000 +42 28 1.000000 +43 56 1.000000 +44 28 1.000000 +45 9 1.000000 +46 19 1.000000 +47 23 1.000000 +48 43 0.500000 +48 45 0.500000 +49 38 1.000000 +50 56 0.500000 +50 57 0.500000 +51 40 1.000000 +52 38 1.000000 +53 19 1.000000 +54 16 1.000000 +55 15 1.000000 +56 56 1.000000 +57 53 1.000000 +58 30 1.000000 +59 9 1.000000 +60 34 1.000000 +61 30 1.000000 +62 24 1.000000 +63 30 1.000000 +64 56 1.000000 +65 9 1.000000 +66 23 1.000000 +67 61 1.000000 +68 38 1.000000 +69 38 1.000000 +70 21 1.000000 +71 38 1.000000 +72 38 1.000000 +73 16 1.000000 +74 30 1.000000 +75 16 1.000000 +76 30 1.000000 +77 40 1.000000 +78 52 0.500000 +78 53 0.500000 +79 53 1.000000 +80 42 0.500000 +80 44 0.500000 +81 34 1.000000 +82 9 1.000000 +83 15 1.000000 +84 45 1.000000 +85 47 1.000000 +86 40 1.000000 +87 56 1.000000 +88 56 1.000000 +89 34 1.000000 +90 56 1.000000 +91 38 1.000000 +92 53 1.000000 +93 56 1.000000 +94 53 1.000000 +95 38 1.000000 +96 53 1.000000 diff -r e4c01dcece8b -r e661a3269313 test-data/alevin_mat_indropV2.mtx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alevin_mat_indropV2.mtx Mon Dec 05 15:47:45 2022 +0000 @@ -0,0 +1,105 @@ +%%MatrixMarket matrix coordinate real general +96 61 103 +1 9 1.000000 +2 28 1.000000 +3 38 1.000000 +4 28 1.000000 +5 42 1.000000 +6 9 1.000000 +7 56 1.000000 +8 28 1.000000 +9 28 1.000000 +10 30 1.000000 +11 53 1.000000 +12 3 0.500000 +12 4 0.500000 +13 28 1.000000 +14 56 1.000000 +15 16 1.000000 +16 9 1.000000 +17 43 0.500000 +17 45 0.500000 +18 28 1.000000 +19 42 0.500000 +19 44 0.500000 +20 40 1.000000 +21 46 1.000000 +22 38 1.000000 +23 19 1.000000 +24 9 1.000000 +25 56 1.000000 +26 8 1.000000 +27 9 1.000000 +28 28 1.000000 +29 53 1.000000 +30 56 1.000000 +31 28 1.000000 +32 30 1.000000 +33 34 1.000000 +34 38 1.000000 +35 28 1.000000 +36 30 1.000000 +37 30 1.000000 +38 28 1.000000 +39 34 1.000000 +40 19 1.000000 +41 47 1.000000 +42 38 1.000000 +43 28 1.000000 +44 19 1.000000 +45 56 1.000000 +46 28 1.000000 +47 23 1.000000 +48 43 0.500000 +48 45 0.500000 +49 38 1.000000 +50 56 0.500000 +50 57 0.500000 +51 40 1.000000 +52 38 1.000000 +53 19 1.000000 +54 16 1.000000 +55 15 1.000000 +56 56 1.000000 +57 23 1.000000 +58 30 1.000000 +59 53 1.000000 +60 30 1.000000 +61 9 1.000000 +62 34 1.000000 +63 24 1.000000 +64 30 1.000000 +65 56 1.000000 +66 9 1.000000 +67 61 1.000000 +68 21 1.000000 +69 38 1.000000 +70 38 1.000000 +71 16 1.000000 +72 38 1.000000 +73 38 1.000000 +74 30 1.000000 +75 53 1.000000 +76 16 1.000000 +77 30 1.000000 +78 40 1.000000 +79 52 0.500000 +79 53 0.500000 +80 42 0.500000 +80 44 0.500000 +81 34 1.000000 +82 9 1.000000 +83 15 1.000000 +84 45 1.000000 +85 47 1.000000 +86 40 1.000000 +87 56 1.000000 +88 34 1.000000 +89 56 1.000000 +90 56 1.000000 +91 38 1.000000 +92 53 1.000000 +93 56 1.000000 +94 53 1.000000 +95 38 1.000000 +96 53 1.000000 diff -r e4c01dcece8b -r e661a3269313 test-data/full_data_structure.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/full_data_structure.txt Mon Dec 05 15:47:45 2022 +0000 @@ -0,0 +1,551 @@ +322 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+ENST00000461106.6 +ENST00000461465.5 +ENST00000470596.5 +ENST00000496325.5 +ENST00000481140.5 +ENST00000482686.5 +ENST00000486681.5 +ENST00000470986.5 +ENST00000470511.5 +ENST00000471018.6 +ENST00000466352.5 +ENST00000497183.5 +ENST00000478770.6 +ENST00000400919.7 +ENST00000428120.5 +ENST00000414253.5 +ENST00000400918.7 +ENST00000378543.2 +ENST00000378546.9 +ENST00000440825.6 +ENST00000420515.1 +ENST00000378536.5 +ENST00000378531.8 +ENST00000378529.7 +ENST00000449373.2 +ENST00000378525.2 +ENST00000494279.2 +ENST00000378513.7 +ENST00000378518.5 +ENST00000605895.6 +ENST00000306256.13 +ENST00000378512.5 +ENST00000443438.5 +ENST00000488353.2 +ENST00000288774.7 +ENST00000650293.1 +ENST00000447513.6 +ENST00000507596.5 +ENST00000510434.1 +ENST00000508384.5 +ENST00000502666.1 +ENST00000514502.1 +ENST00000609981.5 +ENST00000449969.5 +ENST00000378486.8 +ENST00000419816.6 +ENST00000278878.6 +ENST00000378466.8 +ENST00000435556.8 +ENST00000505228.5 +ENST00000651094.1 +ENST00000502512.1 +ENST00000468002.2 +ENST00000486396.1 +ENST00000502770.2 +ENST00000378453.4 +ENST00000426449.5 +ENST00000434817.5 +ENST00000435221.6 +ENST00000451778.5 +ENST00000409119.5 +ENST00000355716.4 +GGATTACCATAGGATA +CTCTGGTAGGAGTAGA +GCTTGAAGTCGGATCC +CTGCTGTGTTACGTCA +TTAACTCAGCTAACAA +CATTATCTCAACTCTT +CTCGAGGGTCGCCATG +CGAACATGTTACAGAA +AAGGCAGCACCATCCT +TCATTACGTCTCATCC +GGTATTGTCTGACCTC +GACGTTACAAGAAGAG +TGTTCCGAGCGCTCCA +CGCTATCTCTTAACCT +GTATTCTGTAGTGAAT +GTCGGGTGTGCAGTAG +ATCATGGCAGCCAATT +AGTTGGTTCGCGATCG +AGAATAGTCCTATTCA +TTGCGTCAGCTAAACA +GAACGGAGTCGTCTTC +CATGACAGTACCGAGA +CACATAGTCATGTGGT +TACTTACTCAAAGTAG +GGGCATCGTAGCTTGT +GACAGAGAGGGTGTGT +AGCCTAATCATTCACT +CATCGAATCTGCGGCA +GCTTCCAAGAGCTGGT +CATGACAGTAGCCTCG +CAGCATAAGACTTGAA +TTGTAGGCACCATCCT +GACTACACAACGATGG +CGAATGTGTACCATCA +ATAGACCTCTCACATT +AGTGGGATCTTAACCT +TGGACGCGTAGAAGGA +CCGTGGAAGTAGGCCA +CTCACACTCGCCTGTT +AGTAGTCGTAACGACG +GTCTCGTGTGATGTGG +GTAACTGGTTCACGGC +CTTAGGAGTCTCCATC +GGTGAAGCAATGACCT +ACGATACAGCCCAGCT +TGTTCCGCAGCATGAG +TTAGGCAAGCCGCCTA +TGACTTTTCGCTAGCG +GGACATTCACTCTGTC +GATCGTATCGCACTCT +TACACGAGTGCACTTA +GTACTCCCAACTTGAC +GCGACCACAGTCGATT +CTGTTTAGTCCGTCAG +CCGGGATCATGAGCGA +ACTGAACTCTTTAGTC +AACCATGAGAGTACCG +TAGAGCTCACGAGAGT +ACGCAGCCATAAAGGT +CTCGAGGCATGCCTTC +AGCGTATAGATACACA +ACGCCAGAGGGTATCG +TGATTTCAGTGGGCTA +TTCTCAAAGTACGTAA +TCATTTGTCCATGAGT +AGAATAGCAGTGGGAT +AAAGTAGAGTCAAGGC +TACTTGTAGGGAACGG +TACCTATCAGATGGGT +CTGAAGTTCCACGTGG +ACCAGTATCTCATTCA +AAACGGGAGCGGCTTC +AAACCTGCAGGCGATA +CACAGGCGTGATGTCT +CACAAACGTGCTTCTC +TGACTAGAGTACGCGA +CGACCTTAGGAGCGTT +ATAGACCTCTCGATGA +AACCGCGAGACACTAA +TCGAGGCGTCTACCTC +TACGGATAGATGTTAG +CAGTCCTCACGAAGCA +GTGCTTCAGGCTAGAC +GCGCCAAGTCATGCAT +CCACGGAGTAATAGCA +CAAGTTGAGATCCTGT +ATCCGAAGTAACGCGA +AATCCAGAGCCAACAG +TTCGGTCCATTGTGCA +TCTCTAACAACACCCG +TCATTACCACAGAGGT +GCATGTAAGTACGTAA +ACGGGCTAGTTCGATC +GTCCTCATCACAATGC +GGCCGATAGGTACTCT +GACGTTAAGGGAAACA +CGAATGTCATACAGCT +CATGGCGAGCTGAAAT +CACACCTAGTGAACGC +TTTATGCAGGCCCTTG +GTACTTTCACGTCAGC +GGATGTTTCAGTCAGT +GAAATGAGTAGCGTAG +CATGCCTCAGACAAAT +AGCATACTCTTGCAAG +AAAGCAATCTGCCCTA +GTCGGGTTCACGGTTA +GGTGCGTGTCAGGACA +CTGTGCTGTAAACCTC +CGATGTAAGTTCGCGC +ATGGGAGCAGCTCGCA +GCTCTGTAGTTTCCTT +CACAGGCCACGAAAGC +GTGCTTCGTTGTCTTT +GTGCTTCAGGCTCTTA +GAAATGAAGACAGACC +CTCGGAGGTCGACTGC +CAACCAACACAGACAG +TTCTCAAAGCTCCTCT +GTACTTTAGTCCTCCT +TGTGGTAGTTACGACT +TAGAGCTGTGGACGAT +GTCTTCGGTTTCCACC +GGTGCGTTCAAACCGT +GGACATTCATTGCGGC +GCTGCGACATAACCTG +TCTCATAAGTTAGCGG +TAGTGGTAGAAGGTGA +GCGAGAACAAGTTGTC +GACTACAGTTGTACAC +CCTAGCTGTCGCGTGT +ATTACTCGTACTCAAC +AGCAGCCAGATGTCGG +AGATCTGTCTGCGTAA +ACGCCAGTCAAGCCTA +AAGGCAGGTAGTGAAT +TTAACTCGTCTGATTG +TGACGGCCATGCTGGC +GGAAAGCTCGAATGCT +CTCGTACCATTAACCG +CATGGCGTCCATGAGT +CAGCATACAAGTTAAG +CACCTTGGTGGTCCGT +ACTGAGTCATCCCATC +AAGCCGCCAATCTGCA +TTAGGCACAACGATGG +GTACGTACACACGCTG +CTGTGCTTCCGCGGTA +ACCAGTAAGGGCTCTC +AACTTTCTCATCGGAT +AACACGTCACCTGGTG +TCAATCTCATGCCACG +GTCATTTAGGCAGTCA +GTCACAAGTATTCGTG +GGAGCAATCGCTTGTC +GATGAGGTCCATTCTA +GATGAAAGTGATGTCT +GATCAGTAGGGTTTCT +GAAACTCAGTACTTGC +CTACATTGTCACTGGC +CGATTGACATACGCCG +AGTTGGTGTACCGGCT +TTAGGACTCGTGACAT +GTGCATAGTAACGACG +GTACGTAGTAAGTTCC +GTAACGTTCCACGTGG +GGACAAGTCTCAAGTG +GGAAAGCAGGAGTAGA +CTCCTAGAGCAGACTG +AGCGTCGGTGTTCGAT +TTTGTCACAGGTCCAC +GTCACGGGTAAGTTCC +GTATCTTTCATCATTC +GACGTGCGTAGCAAAT +GAACATCGTATAAACG +CTGTTTATCAGTCAGT +CTCGGGACACATCCAA +CTAACTTTCAGCTTAG +CGATCGGAGGTGGGTT +CGACCTTCATTGGGCC +AATCCAGCAGCCTGTG +TTAGTTCCATGTAAGA +TGGCTGGCAATTGCTG +GTATTCTGTAGGCTGA +GTAGTCATCCAGTATG +GGGATGAAGAGGGATA +GCTTCCAAGGAATCGC +CTTTGCGCACAGGAGT +CCGGGATTCTTGTCAT +CCATTCGGTAGCCTAT +CAGCCGACAGATTGCT +CACAAACTCTTAACCT +CAACTAGTCCTCTAGC +ATCGAGTGTACAGCAG +TTATGCTAGAGATGAG +TGGCGCAGTCTCGTTC +TCAGCTCTCTGCTTGC +GTTACAGAGTTATCGC +GTAGTCATCAGCTCTC +GGGAGATGTGCTTCTC +GCGCCAAGTACGAAAT +CTGCGGAAGTACGCGA +CCATTCGAGCTAACTC +ATCTACTTCTGAGTGT +AACTCAGGTTTGACAC +AACCGCGGTAAGTGTA +TGCCCTATCCACTCCA +TCATTTGAGCAAATCA +GTGAAGGAGCCAGAAC +CTCTGGTGTTAAGGGC +CCTTCGACACTATCTT +CATCCACAGGCTATCT +CACCACTTCATCGGAT +ATCATCTCATCCAACA +AGGTCATTCCGCGGTA +AGACGTTAGACCACGA +AACGTTGCAGTTAACC +AAAGCAAAGTGTCCAT +8 198 199 200 201 202 203 204 205 1 1 32 1 TACGGGCTGC 1 +1 170 1 1 21 1 GAACATTTGT 1 +3 29 30 31 2 2 34 1 CGGCGTCCGG 1 1 1 AGCGGCTGGT 1 +11 5 6 7 8 9 10 11 12 13 14 16 1 1 93 1 TTGACACCAT 1 +1 146 1 1 46 1 AACACAGATA 1 +4 287 289 291 293 2 2 140 1 CCGTACGGGG 1 35 1 GGATTCAGTA 1 +3 273 274 275 1 1 86 1 CCGACTCGTT 1 +4 134 135 136 137 5 5 30 1 ACGAATGTTT 1 95 1 ACAGAGCTAA 1 45 1 AGTTTACACT 1 3 1 ACCTATGTTC 1 41 1 GACTATGGAT 1 diff -r e4c01dcece8b -r e661a3269313 test-data/genome.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fasta Mon Dec 05 15:47:45 2022 +0000 @@ -0,0 +1,239 @@ +>chrM +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG +GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC +CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA +ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC +ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA +AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC +TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA +CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC +AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC +ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA +GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC +AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA +ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA +TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT +CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC +ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC +AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC +CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA +CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC +AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT +GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA +AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA +TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA +GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA +GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG +ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA +ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC +AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA +AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT +AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC +CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG +TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC +ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG +TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC +AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA +AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC +ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA +AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT +TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA +TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT +AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG +TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA +GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG +ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG +AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT +ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA +ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT +TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA +TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC +CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC +ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC +CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG +CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC +AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC +TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG +CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTC +CGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATAC +ACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCC +CTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAAC +AGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA +GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATAT +GTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTAGGACTATGA +GAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAAGTAAGGTC +AGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCT +GGCCCAACCCGTCATCTACTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT +TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTC +GTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTAT +CCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTCATCATTAATA +ATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAG +GCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA +AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGA +GGTGGATTAAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAA +TAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCCTAACTACTAC +CGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACTATCTCGCACCTGAAACAAGCTA +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT +TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCAC +CATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATA +TCTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCG +CCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATTTAGGTTAAATAC +AGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA +CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGA +CTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCC +GCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGA +AAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCA +GCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG +AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCC +GAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCAT +TTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAAT +AATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTC +CTACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG +CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTC +CTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATAC +CAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAG +CTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGG +AGACCCCATTCTATACCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA +GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTA +TGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGG +AATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAA +GTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAG +GATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT +ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATC +ATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCC +ATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAAT +GCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTC +ATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC +TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGA +AGAACCCGTATACATAAAATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAA +CCCCATGGCCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAAT +TATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCT +ATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC +TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGA +AACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTAC +ATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACG +AGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGA +CCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA +TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTC +TAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGC +AAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTT +ACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTT +AAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT +AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTA +CCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCT +GTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCT +CTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAAC +TAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT +AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTA +TCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTA +AAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGA +AACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCAC +CTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA +TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCAC +ACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAA +AACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATT +TCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGG +CGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG +GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAG +CCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAA +GTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAA +TAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCT +CCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT +GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCC +AACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGT +AGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGT +ACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTAA +TAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT +AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAA +TTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAG +CCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAG +TCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAAT +GATTTCGACTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG +CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGA +AGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAAT +ATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAA +TCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCA +ACAATTATATTACTACCACTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA +GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCC +AACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATC +ATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCT +CCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAAC +CACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA +TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCC +TAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTT +AATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCT +AAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCT +ATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT +ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCA +TACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCG +GCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTA +CGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTT +TGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG +TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGC +CCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAA +CCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACC +CCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAA +CAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC +AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCA +ACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCC +ATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCAT +CCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAA +CTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA +TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACC +CAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA +CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA +TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT +TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA +CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT +CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA +TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC +TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC +AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC +CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC +CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC +ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA +AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC +TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC +ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC +TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA +CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC +AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA +TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT +AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA +ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA +TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA +CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA +CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC +TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC +CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC +CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG +ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC +CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC +CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC +CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA +ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA +CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC +ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC +TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC +AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC +TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA +GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT +CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC +ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT +TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC +TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA +GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC +AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT +AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC +TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC +CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA +GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC +ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA +TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA +ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA +ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG +TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC +TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG +CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC +ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG + diff -r e4c01dcece8b -r e661a3269313 test-data/length_distribution.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/length_distribution.txt Mon Dec 05 15:47:45 2022 +0000 @@ -0,0 +1,2 @@ +3.09819e-24 4.61802e-24 6.8724e-24 1.02109e-23 1.51471e-23 2.24335e-23 3.31719e-23 4.89721e-23 7.21827e-23 1.06224e-22 1.56069e-22 2.28937e-22 3.3529e-22 4.90265e-22 7.15724e-22 1.0432e-21 1.51807e-21 2.20558e-21 3.19933e-21 4.6334e-21 6.69956e-21 9.67159e-21 1.39397e-20 2.00594e-20 2.88194e-20 4.13387e-20 5.92018e-20 8.46483e-20 1.20839e-19 1.72226e-19 2.45075e-19 3.48179e-19 4.93869e-19 6.994e-19 9.88884e-19 1.39595e-18 1.96743e-18 2.76844e-18 3.88934e-18 5.45534e-18 7.63964e-18 1.06814e-17 1.49104e-17 2.07805e-17 2.89154e-17 4.01703e-17 5.5717e-17 7.7157e-17 1.06676e-16 1.47254e-16 2.02941e-16 2.7924e-16 3.83611e-16 5.2615e-16 7.205e-16 9.85061e-16 1.34461e-15 1.83247e-15 2.49334e-15 3.38713e-15 4.59396e-15 6.22082e-15 8.41034e-15 1.13523e-14 1.52989e-14 2.05846e-14 2.76522e-14 3.70869e-14 4.96613e-14 6.63927e-14 8.86192e-14 1.18097e-13 1.5713e-13 2.08729e-13 2.76828e-13 3.66559e-13 4.84599e-13 6.39627e-13 8.429e-13 1.109e-12 1.45677e-12 1.91054e-12 2.50165e-12 3.2704e-12 4.26856e-12 5.56247e-12 7.237e-12 9.40059e-12 1.21915e-11 1.57857e-11 2.04068e-11 2.63386e-11 3.39402e-11 4.36659e-11 5.60887e-11 7.19306e-11 9.20994e-11 1.17735e-10 1.50265e-10 1.91478e-10 2.43603e-10 3.09422e-10 3.92397e-10 4.96828e-10 6.28046e-10 7.9265e-10 9.98796e-10 1.25654e-09 1.57828e-09 1.97922e-09 2.47806e-09 3.09765e-09 3.86598e-09 4.81717e-09 5.99279e-09 7.4434e-09 9.23037e-09 1.1428e-08 1.41264e-08 1.74339e-08 2.14814e-08 2.64263e-08 3.24575e-08 3.98015e-08 4.87292e-08 5.9564e-08 7.26915e-08 8.85704e-08 1.07745e-07 1.30862e-07 1.58685e-07 1.92115e-07 2.32216e-07 2.80239e-07 3.37653e-07 4.06179e-07 4.87832e-07 5.84962e-07 7.0031e-07 8.37062e-07 9.9892e-07 1.19017e-06 1.41577e-06 1.68144e-06 1.99377e-06 2.36034e-06 2.78984e-06 3.29222e-06 3.87885e-06 4.56271e-06 5.35856e-06 6.28317e-06 7.35554e-06 8.59717e-06 1.00323e-05 1.16883e-05 1.35959e-05 1.57896e-05 1.83079e-05 2.11939e-05 2.44956e-05 2.82664e-05 3.25656e-05 3.74586e-05 4.3018e-05 4.93235e-05 5.64628e-05 6.45322e-05 7.36369e-05 8.38919e-05 9.54223e-05 0.000108364 0.000122864 0.000139082 0.000157188 0.000177368 0.000199819 0.000224752 0.000252392 0.000282977 0.000316762 0.000354014 0.000395015 0.000440059 0.000489456 0.000543527 0.000602608 0.000667042 0.000737185 0.000813403 0.000896065 0.000985551 0.00108224 0.00118652 0.00129876 0.00141935 0.00154865 0.00168704 0.00183485 0.00199242 0.00216007 0.00233808 0.00252671 0.0027262 0.00293674 0.00315848 0.00339153 0.00363595 0.00389176 0.00415891 0.00443729 0.00472674 0.00502702 0.00533784 0.0056588 0.00598948 0.00632935 0.00667781 0.0070342 0.00739776 0.00776767 0.00814304 0.00852291 0.00890624 0.00929193 0.00967883 0.0100657 0.0104513 0.0108344 0.0112135 0.0115874 0.0119546 0.0123137 0.0126633 0.013002 0.0133284 0.0136412 0.013939 0.0142206 0.0144846 0.01473 0.0149556 0.0151603 0.0153433 0.0155037 0.0156407 0.0157537 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3.25656e-05 2.82664e-05 2.44956e-05 2.11939e-05 1.83079e-05 1.57896e-05 1.35959e-05 1.16883e-05 1.00323e-05 8.59717e-06 7.35554e-06 6.28317e-06 5.35856e-06 4.56271e-06 3.87885e-06 3.29222e-06 2.78984e-06 2.36034e-06 1.99377e-06 1.68144e-06 1.41577e-06 1.19017e-06 9.9892e-07 8.37062e-07 7.0031e-07 5.84962e-07 4.87832e-07 4.06179e-07 3.37653e-07 2.80239e-07 2.32216e-07 1.92115e-07 1.58685e-07 1.30862e-07 1.07745e-07 8.85704e-08 7.26915e-08 5.9564e-08 4.87292e-08 3.98015e-08 3.24575e-08 2.64263e-08 2.14814e-08 1.74339e-08 1.41264e-08 1.1428e-08 9.23037e-09 7.4434e-09 5.99279e-09 4.81717e-09 3.86598e-09 3.09765e-09 2.47806e-09 1.97922e-09 1.57828e-09 1.25654e-09 9.98796e-10 7.9265e-10 6.28045e-10 4.96828e-10 3.92397e-10 3.09422e-10 2.43603e-10 1.91478e-10 1.50265e-10 1.17735e-10 9.20994e-11 7.19305e-11 5.60888e-11 4.36658e-11 3.39403e-11 2.63386e-11 2.04068e-11 1.57857e-11 1.21915e-11 9.40059e-12 7.23699e-12 5.56244e-12 4.26859e-12 3.27038e-12 2.50167e-12 1.91058e-12 1.45672e-12 1.109e-12 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