| Previous changeset 0:f8cb84c49623 (2022-10-24) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 398a2e3e845ada656b3a7e0a6542e1668a8bcf17 |
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modified:
hicup2juicer.xml hicup_macros.xml test-data/dataset1_2.filt.bam test-data/dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg test-data/dataset1_2.filt.bam.deduplicator_uniques_barchart.svg test-data/dataset1_2.filt.sam test-data/dataset1_2.hicup.bam test-data/dataset1_2.pair.bam test-data/dataset1_2.pair.bam.filter_piechart.svg test-data/dataset1_2_contiguous.filter.bam test-data/dataset1_2_invalid.filter.bam test-data/dataset1_2_re_ligation.filter.bam test-data/dataset1_2_same_circularised.filter.bam test-data/dataset1_2_same_dangling_ends.filter.bam test-data/dataset1_2_same_internal.filter.bam |
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added:
test-data/HiCUP_summary_report_aQdQORylpl_22-59-39_22-02-2023.txt test-data/dataset1.fastq.truncation_barchart.svg test-data/dataset1.trunc.fastq.gz.mapper_barchart.svg test-data/dataset1_2.ditag_size_distribution_report.txt test-data/dataset1_2.hicup.bam.prejuicer1 test-data/dataset1_2.hicup.bam.prejuicer2 test-data/dataset2.fastq.truncation_barchart.svg test-data/dataset2.trunc.fastq.gz.mapper_barchart.svg test-data/digest_file.txt |
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removed:
test-data/HiCUP_summary_report.html test-data/HiCUP_summary_report.txt test-data/dataset1.mapper_barchart.svg test-data/dataset1.truncation_barchart.svg test-data/dataset1_2.hicup.bam.prejuicer test-data/dataset2.mapper_barchart.svg test-data/dataset2.truncation_barchart.svg test-data/digester_file.txt |
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| diff -r f8cb84c49623 -r b4e7244246e2 hicup2juicer.xml --- a/hicup2juicer.xml Mon Oct 24 16:09:44 2022 +0000 +++ b/hicup2juicer.xml Thu Feb 23 18:05:02 2023 +0000 |
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| @@ -11,11 +11,27 @@ #set ext='sam' #end if ln -s '$input_file' input.$ext && - hicup2juicer input.$ext + hicup2juicer + #if str($digester.provide_digester) == 'yes': + --digest '${digester.digester_file}' + '${digester.usemid}' + #end if + input.$ext ]]> </command> <inputs> <param name="input_file" type="data" format="qname_sorted.bam,sam" label="Output of HiCUP to convert" /> + <conditional name="digester"> + <param name="provide_digester" type="select" label="Provide digester file" help="With digester file you have correct fragment id and can use option -usemid"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="digester_file" type="data" format="tabular" label="Digester file: Output of HiCUP Digester" /> + <param argument="--usemid" type="boolean" truevalue="--usemid" falsevalue="" checked="false" label="Use middle of fragments instead of 5' of reads" /> + </when> + <when value="no"/> + </conditional> </inputs> <outputs> <data name="output" format="tabular" label="${tool.name} on ${on_string}: Pairs in juicebox format" from_work_dir="*.prejuicer" /> @@ -23,7 +39,19 @@ <tests> <test expect_num_outputs="1"> <param name="input_file" value="dataset1_2.hicup.bam"/> - <output name="output" value="dataset1_2.hicup.bam.prejuicer"/> + <conditional name="digester"> + <param name="provide_digester" value="no"/> + </conditional> + <output name="output" value="dataset1_2.hicup.bam.prejuicer1"/> + </test> + <test expect_num_outputs="1"> + <param name="input_file" value="dataset1_2.hicup.bam"/> + <conditional name="digester"> + <param name="provide_digester" value="yes"/> + <param name="digester_file" value="digest_file.txt" ftype="tabular"/> + <param name="usemid" value="true"/> + </conditional> + <output name="output" value="dataset1_2.hicup.bam.prejuicer2"/> </test> </tests> <help><![CDATA[ |
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| diff -r f8cb84c49623 -r b4e7244246e2 hicup_macros.xml --- a/hicup_macros.xml Mon Oct 24 16:09:44 2022 +0000 +++ b/hicup_macros.xml Thu Feb 23 18:05:02 2023 +0000 |
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| @@ -1,10 +1,13 @@ <macros> - <token name="@VERSION@">0.8.3</token> + <token name="@VERSION@">0.9.2</token> <xml name="requirements_hicup"> <requirements> <requirement type="package" version="@VERSION@">hicup</requirement> <requirement type="package" version="2.4.5">bowtie2</requirement> <requirement type="package" version="1.16.1">samtools</requirement> + <!-- without this dependency, hicup_hicup could not generate the html + The error is: /usr/local/bin/pandoc: error while loading shared libraries: libgmp.so.10: cannot open shared object file: No such file or directory --> + <requirement type="package" version="6.2.1">gmp</requirement> <yield/> </requirements> <version_command>hicup --version</version_command> |
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| diff -r f8cb84c49623 -r b4e7244246e2 test-data/HiCUP_summary_report.html --- a/test-data/HiCUP_summary_report.html Mon Oct 24 16:09:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r f8cb84c49623 -r b4e7244246e2 test-data/HiCUP_summary_report.txt --- a/test-data/HiCUP_summary_report.txt Mon Oct 24 16:09:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -File Total_Reads_1 Total_Reads_2 Not_Truncated_Reads_1 Not_Truncated_Reads_2 Truncated_Read_1 Truncated_Read_2 Average_Length_Truncated_1 Average_Length_Truncated_2 Too_Short_To_Map_Read_1 Too_Short_To_Map_Read_2 Unique_Alignments_Read_1 Unique_Alignments_Read_2 Multiple_Alignments_Read_1 Multiple_Alignments_Read_2 Failed_To_Align_Read_1 Failed_To_Align_Read_2 Paired_Read_1 Paired_Read_2 Valid_Pairs Valid_Cis_Close Valid_Cis_Far Valid_Trans Invalid_Pairs Same_Circularised Same_Dangling_Ends Same_Fragment_Internal Re_Ligation Contiguous_Sequence Wrong_Size Deduplication_Read_Pairs_Uniques Deduplication_Cis_Close_Uniques Deduplication_Cis_Far_Uniques Deduplication_Trans_Uniques Percentage_Mapped Percentage_Valid Percentage_Uniques Percentage_Unique_Trans Percentage_Ditags_Passed_Through_HiCUP -dataset1_2.hicup.bam 99742 99742 92512 92628 7230 7114 22.45 22.63 2658 2476 3885 3725 12437 12679 80762 80862 1143 1143 544 44 440 60 599 21 73 466 39 0 0 544 44 440 60 1.15 47.59 100.00 11.03 0.55 |
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| diff -r f8cb84c49623 -r b4e7244246e2 test-data/HiCUP_summary_report_aQdQORylpl_22-59-39_22-02-2023.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HiCUP_summary_report_aQdQORylpl_22-59-39_22-02-2023.txt Thu Feb 23 18:05:02 2023 +0000 |
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| @@ -0,0 +1,2 @@ +File Total_Reads_1 Total_Reads_2 Not_Truncated_Reads_1 Not_Truncated_Reads_2 Truncated_Read_1 Truncated_Read_2 Average_Length_Truncated_1 Average_Length_Truncated_2 Too_Short_To_Map_Read_1 Too_Short_To_Map_Read_2 Unique_Alignments_Read_1 Unique_Alignments_Read_2 Multiple_Alignments_Read_1 Multiple_Alignments_Read_2 Failed_To_Align_Read_1 Failed_To_Align_Read_2 Paired_Read_1 Paired_Read_2 Valid_Pairs Valid_Cis_Close Valid_Cis_Far Valid_Trans Invalid_Pairs Same_Circularised Same_Dangling_Ends Same_Fragment_Internal Re_Ligation Contiguous_Sequence Wrong_Size Deduplication_Read_Pairs_Uniques Deduplication_Cis_Close_Uniques Deduplication_Cis_Far_Uniques Deduplication_Trans_Uniques Percentage_Mapped Percentage_Valid Percentage_Uniques Percentage_Unique_Trans Percentage_Ditags_Passed_Through_HiCUP +dataset1_2.hicup.bam 99742 99742 92512 92628 7230 7114 22.45 22.63 2658 2476 3885 3725 12437 12679 80762 80862 1143 1143 544 44 440 60 599 21 73 466 39 0 0 544 44 440 60 1.15 47.59 100.00 11.03 0.55 |
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| diff -r f8cb84c49623 -r b4e7244246e2 test-data/dataset1.fastq.truncation_barchart.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset1.fastq.truncation_barchart.svg Thu Feb 23 18:05:02 2023 +0000 |
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| diff -r f8cb84c49623 -r b4e7244246e2 test-data/dataset1.truncation_barchart.svg --- a/test-data/dataset1.truncation_barchart.svg Mon Oct 24 16:09:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r f8cb84c49623 -r b4e7244246e2 test-data/dataset1_2.filt.bam |
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| b |
| diff -r f8cb84c49623 -r b4e7244246e2 test-data/dataset1_2.filt.sam --- a/test-data/dataset1_2.filt.sam Mon Oct 24 16:09:44 2022 +0000 +++ b/test-data/dataset1_2.filt.sam Thu Feb 23 18:05:02 2023 +0000 |
| [ |
| @@ -1,13 +1,14 @@ -@HD VN:1.5 SO:queryname +@HD VN:1.5 SO:unsorted GO:query @SQ SN:chr21 LN:46709983 @SQ SN:chr22 LN:50818468 -@PG ID:bowtie2 PN:bowtie2 VN:2.4.5 CL:"/home/ldelisle/miniconda3/envs/__hicup@0.8.3/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome --threads 1 --reorder - --passthrough" -@PG ID:HiCUP Mapper VN:0.8.3 -@PG ID:samtools PN:samtools PP:HiCUP Mapper VN:1.16.1 CL:samtools view -bSh - -@PG ID:samtools.1 PN:samtools PP:samtools VN:1.15.1 (pysam) CL:samtools sort -n -@1 -T /tmp/tmpqwp310ym/sorted -O BAM -o /tmp/tmpqwp310ym/sorted.bam /tmp/tmprolrrufe/job_working_directory/000/1/outputs/galaxy_dataset_2f0aefeb-faca-49dc-a585-09a611400a5e.dat -@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.16.1 CL:/home/ldelisle/miniconda3/envs/__hicup@0.8.3/bin/samtools view -h ./0.bam -@PG ID:HiCUP Filter VN:0.8.3 DS:"Max insert 0 Min insert 0 Digest file /tmp/tmprolrrufe/files/c/8/e/dataset_c8ea51e8-38b0-4467-b22b-1b5878b2ab5f.dat" -@PG ID:samtools.3 PN:samtools PP:samtools.2 VN:1.16.1 CL:samtools view -bSh - +@PG ID:bowtie2 PN:bowtie2 VN:2.4.5 CL:"/home/ldelisle/miniconda3/envs/mulled-v1-5c1994247e0ff8cda611e273476d9ea98cc0e3e62bd124f468f1ea5f3d75bca4/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome --threads 1 --reorder - --passthrough" +@PG ID:HiCUP Mapper VN:0.9.2 +@PG ID:HiCUP Truncater VN:0.9.2 DS:"Restriction enzyme re1_unspecified [A^AGCTT]" +@PG ID:samtools PN:samtools PP:HiCUP Truncater VN:1.16.1 CL:samtools view -bSh - +@PG ID:samtools.1 PN:samtools PP:samtools VN:1.16.1 CL:/home/ldelisle/miniconda3/envs/mulled-v1-5c1994247e0ff8cda611e273476d9ea98cc0e3e62bd124f468f1ea5f3d75bca4/bin/samtools view -h dataset1_2.pair.bam +@PG ID:HiCUP Filter VN:0.9.2 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" +@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.16.1 CL:samtools view -bSh - +@PG ID:samtools.3 PN:samtools PP:samtools.2 VN:1.16.1 CL:samtools view -h dataset1_2.filt.bam SRR071233.29547 115 chr22 31119191 42 40M = 28742824 0 GCCTCTAACCTACATGGCTCTGCTGCTTGAGATCCCCTCG CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC8CCCCCCCCC AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:40 YT:Z:UU CT:Z:FAR SRR071233.29547 179 chr22 28742824 42 40M = 31119191 0 TGGGCGAGGCCTGAGGGAAAAGTGAGAATTGGAGGGAGAG CDCDBCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:40 YT:Z:UU CT:Z:FAR SRR071233.80581 99 chr21 27660196 42 40M = 15297495 0 TGCATATTCACTAACCGGGACAGTTAAAAATTAATATATT CCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCC AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:40 YT:Z:UU CT:Z:FAR |
| b |
| diff -r f8cb84c49623 -r b4e7244246e2 test-data/dataset1_2.hicup.bam |
| b |
| Binary file test-data/dataset1_2.hicup.bam has changed |
| b |
| diff -r f8cb84c49623 -r b4e7244246e2 test-data/dataset1_2.hicup.bam.prejuicer --- a/test-data/dataset1_2.hicup.bam.prejuicer Mon Oct 24 16:09:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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|
| b |
| diff -r f8cb84c49623 -r b4e7244246e2 test-data/dataset1_2.hicup.bam.prejuicer1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset1_2.hicup.bam.prejuicer1 Thu Feb 23 18:05:02 2023 +0000 |
| b |
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|
| b |
| diff -r f8cb84c49623 -r b4e7244246e2 test-data/dataset1_2.hicup.bam.prejuicer2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset1_2.hicup.bam.prejuicer2 Thu Feb 23 18:05:02 2023 +0000 |
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| diff -r f8cb84c49623 -r b4e7244246e2 test-data/dataset1_2.pair.bam |
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| Binary file test-data/dataset1_2.pair.bam has changed |
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| b |
| diff -r f8cb84c49623 -r b4e7244246e2 test-data/dataset2.truncation_barchart.svg --- a/test-data/dataset2.truncation_barchart.svg Mon Oct 24 16:09:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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| b |
| diff -r f8cb84c49623 -r b4e7244246e2 test-data/digest_file.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/digest_file.txt Thu Feb 23 18:05:02 2023 +0000 |
| [ |
| b"@@ -0,0 +1,19943 @@\n+Genome:chr21And22FromHg38\tRestriction_Enzyme1:re1_unspecified [A^AGCTT]\tRestriction_Enzyme2:None\tHicup Digester version 0.9.2\n+Chromosome\tFragment_Start_Position\tFragment_End_Position\tFragment_Number\tRE1_Fragment_Number\t5'_Restriction_Site\t3'_Restriction_Site\n+chr21\t1\t5011282\t1\t1\tNone\tRe1\n+chr21\t5011283\t5011467\t2\t2\tRe1\tRe1\n+chr21\t5011468\t5021436\t3\t3\tRe1\tRe1\n+chr21\t5021437\t5024121\t4\t4\tRe1\tRe1\n+chr21\t5024122\t5024614\t5\t5\tRe1\tRe1\n+chr21\t5024615\t5029202\t6\t6\tRe1\tRe1\n+chr21\t5029203\t5029336\t7\t7\tRe1\tRe1\n+chr21\t5029337\t5034470\t8\t8\tRe1\tRe1\n+chr21\t5034471\t5036477\t9\t9\tRe1\tRe1\n+chr21\t5036478\t5038831\t10\t10\tRe1\tRe1\n+chr21\t5038832\t5045607\t11\t11\tRe1\tRe1\n+chr21\t5045608\t5045959\t12\t12\tRe1\tRe1\n+chr21\t5045960\t5047552\t13\t13\tRe1\tRe1\n+chr21\t5047553\t5049458\t14\t14\tRe1\tRe1\n+chr21\t5049459\t5050222\t15\t15\tRe1\tRe1\n+chr21\t5050223\t5055227\t16\t16\tRe1\tRe1\n+chr21\t5055228\t5062258\t17\t17\tRe1\tRe1\n+chr21\t5062259\t5068162\t18\t18\tRe1\tRe1\n+chr21\t5068163\t5069453\t19\t19\tRe1\tRe1\n+chr21\t5069454\t5084093\t20\t20\tRe1\tRe1\n+chr21\t5084094\t5092669\t21\t21\tRe1\tRe1\n+chr21\t5092670\t5109145\t22\t22\tRe1\tRe1\n+chr21\t5109146\t5110690\t23\t23\tRe1\tRe1\n+chr21\t5110691\t5116382\t24\t24\tRe1\tRe1\n+chr21\t5116383\t5129707\t25\t25\tRe1\tRe1\n+chr21\t5129708\t5136842\t26\t26\tRe1\tRe1\n+chr21\t5136843\t5137635\t27\t27\tRe1\tRe1\n+chr21\t5137636\t5149807\t28\t28\tRe1\tRe1\n+chr21\t5149808\t5150628\t29\t29\tRe1\tRe1\n+chr21\t5150629\t5151858\t30\t30\tRe1\tRe1\n+chr21\t5151859\t5152502\t31\t31\tRe1\tRe1\n+chr21\t5152503\t5159839\t32\t32\tRe1\tRe1\n+chr21\t5159840\t5160172\t33\t33\tRe1\tRe1\n+chr21\t5160173\t5160847\t34\t34\tRe1\tRe1\n+chr21\t5160848\t5163528\t35\t35\tRe1\tRe1\n+chr21\t5163529\t5165131\t36\t36\tRe1\tRe1\n+chr21\t5165132\t5223272\t37\t37\tRe1\tRe1\n+chr21\t5223273\t5224520\t38\t38\tRe1\tRe1\n+chr21\t5224521\t5225694\t39\t39\tRe1\tRe1\n+chr21\t5225695\t5226427\t40\t40\tRe1\tRe1\n+chr21\t5226428\t5227994\t41\t41\tRe1\tRe1\n+chr21\t5227995\t5232313\t42\t42\tRe1\tRe1\n+chr21\t5232314\t5232736\t43\t43\tRe1\tRe1\n+chr21\t5232737\t5235077\t44\t44\tRe1\tRe1\n+chr21\t5235078\t5236330\t45\t45\tRe1\tRe1\n+chr21\t5236331\t5238447\t46\t46\tRe1\tRe1\n+chr21\t5238448\t5245210\t47\t47\tRe1\tRe1\n+chr21\t5245211\t5245228\t48\t48\tRe1\tRe1\n+chr21\t5245229\t5250715\t49\t49\tRe1\tRe1\n+chr21\t5250716\t5255183\t50\t50\tRe1\tRe1\n+chr21\t5255184\t5255853\t51\t51\tRe1\tRe1\n+chr21\t5255854\t5258863\t52\t52\tRe1\tRe1\n+chr21\t5258864\t5261077\t53\t53\tRe1\tRe1\n+chr21\t5261078\t5270995\t54\t54\tRe1\tRe1\n+chr21\t5270996\t5277649\t55\t55\tRe1\tRe1\n+chr21\t5277650\t5279633\t56\t56\tRe1\tRe1\n+chr21\t5279634\t5290243\t57\t57\tRe1\tRe1\n+chr21\t5290244\t5291132\t58\t58\tRe1\tRe1\n+chr21\t5291133\t5291264\t59\t59\tRe1\tRe1\n+chr21\t5291265\t5299284\t60\t60\tRe1\tRe1\n+chr21\t5299285\t5300652\t61\t61\tRe1\tRe1\n+chr21\t5300653\t5302881\t62\t62\tRe1\tRe1\n+chr21\t5302882\t5303836\t63\t63\tRe1\tRe1\n+chr21\t5303837\t5304351\t64\t64\tRe1\tRe1\n+chr21\t5304352\t5307669\t65\t65\tRe1\tRe1\n+chr21\t5307670\t5311235\t66\t66\tRe1\tRe1\n+chr21\t5311236\t5311301\t67\t67\tRe1\tRe1\n+chr21\t5311302\t5316052\t68\t68\tRe1\tRe1\n+chr21\t5316053\t5316565\t69\t69\tRe1\tRe1\n+chr21\t5316566\t5320146\t70\t70\tRe1\tRe1\n+chr21\t5320147\t5330771\t71\t71\tRe1\tRe1\n+chr21\t5330772\t5332201\t72\t72\tRe1\tRe1\n+chr21\t5332202\t5333001\t73\t73\tRe1\tRe1\n+chr21\t5333002\t5333441\t74\t74\tRe1\tRe1\n+chr21\t5333442\t5337368\t75\t75\tRe1\tRe1\n+chr21\t5337369\t5343285\t76\t76\tRe1\tRe1\n+chr21\t5343286\t5343574\t77\t77\tRe1\tRe1\n+chr21\t5343575\t5344658\t78\t78\tRe1\tRe1\n+chr21\t5344659\t5346862\t79\t79\tRe1\tRe1\n+chr21\t5346863\t5350509\t80\t80\tRe1\tRe1\n+chr21\t5350510\t5352398\t81\t81\tRe1\tRe1\n+chr21\t5352399\t5355495\t82\t82\tRe1\tRe1\n+chr21\t5355496\t5357543\t83\t83\tRe1\tRe1\n+chr21\t5357544\t5364287\t84\t84\tRe1\tRe1\n+chr21\t5364288\t5365650\t85\t85\tRe1\tRe1\n+chr21\t5365651\t5367002\t86\t86\tRe1\tRe1\n+chr21\t5367003\t5368510\t87\t87\tRe1\tRe1\n+chr21\t5368511\t5372592\t88\t88\tRe1\tRe1\n+chr21\t5372593\t5375546\t89\t89\tRe1\tRe1\n+chr21\t5375547\t5377246\t90\t90\tRe1\tRe1\n+chr21\t5377247\t5380268\t91\t91\tRe1\tRe1\n+chr21\t5380269\t5380780\t92\t92\tRe1\tRe1\n+chr21\t5380781\t5380952\t93\t93\tRe1\tRe1\n+chr21\t5380953\t5382836\t94\t94\tRe1\tRe1\n+chr21\t5382837\t5383179\t95\t95\tRe1\tRe1\n+chr21\t5383180\t5383351\t96\t96\tRe1\tRe1\n+chr21\t5383352\t5384354\t97\t97\tRe1\tRe1\n+chr21\t5384355\t5384879\t98\t98\tRe1\tRe1\n+chr21\t5384880\t5385049\t99\t99\tRe1\tRe1\n+chr21\t5385050\t5385100\t100\t100\tRe1\tRe1\n+chr21\t5385101\t5385221\t101\t101\tRe1\tRe1\n"..b'chr22\t50282718\t50288350\t8585\t8585\tRe1\tRe1\n+chr22\t50288351\t50294476\t8586\t8586\tRe1\tRe1\n+chr22\t50294477\t50309116\t8587\t8587\tRe1\tRe1\n+chr22\t50309117\t50327992\t8588\t8588\tRe1\tRe1\n+chr22\t50327993\t50342333\t8589\t8589\tRe1\tRe1\n+chr22\t50342334\t50351441\t8590\t8590\tRe1\tRe1\n+chr22\t50351442\t50353246\t8591\t8591\tRe1\tRe1\n+chr22\t50353247\t50355862\t8592\t8592\tRe1\tRe1\n+chr22\t50355863\t50358434\t8593\t8593\tRe1\tRe1\n+chr22\t50358435\t50359656\t8594\t8594\tRe1\tRe1\n+chr22\t50359657\t50363435\t8595\t8595\tRe1\tRe1\n+chr22\t50363436\t50363511\t8596\t8596\tRe1\tRe1\n+chr22\t50363512\t50367080\t8597\t8597\tRe1\tRe1\n+chr22\t50367081\t50379288\t8598\t8598\tRe1\tRe1\n+chr22\t50379289\t50397379\t8599\t8599\tRe1\tRe1\n+chr22\t50397380\t50401722\t8600\t8600\tRe1\tRe1\n+chr22\t50401723\t50401984\t8601\t8601\tRe1\tRe1\n+chr22\t50401985\t50421256\t8602\t8602\tRe1\tRe1\n+chr22\t50421257\t50426383\t8603\t8603\tRe1\tRe1\n+chr22\t50426384\t50428909\t8604\t8604\tRe1\tRe1\n+chr22\t50428910\t50444665\t8605\t8605\tRe1\tRe1\n+chr22\t50444666\t50450724\t8606\t8606\tRe1\tRe1\n+chr22\t50450725\t50450736\t8607\t8607\tRe1\tRe1\n+chr22\t50450737\t50450804\t8608\t8608\tRe1\tRe1\n+chr22\t50450805\t50458364\t8609\t8609\tRe1\tRe1\n+chr22\t50458365\t50466498\t8610\t8610\tRe1\tRe1\n+chr22\t50466499\t50482637\t8611\t8611\tRe1\tRe1\n+chr22\t50482638\t50485316\t8612\t8612\tRe1\tRe1\n+chr22\t50485317\t50486417\t8613\t8613\tRe1\tRe1\n+chr22\t50486418\t50491090\t8614\t8614\tRe1\tRe1\n+chr22\t50491091\t50493790\t8615\t8615\tRe1\tRe1\n+chr22\t50493791\t50495968\t8616\t8616\tRe1\tRe1\n+chr22\t50495969\t50500513\t8617\t8617\tRe1\tRe1\n+chr22\t50500514\t50501346\t8618\t8618\tRe1\tRe1\n+chr22\t50501347\t50509861\t8619\t8619\tRe1\tRe1\n+chr22\t50509862\t50514002\t8620\t8620\tRe1\tRe1\n+chr22\t50514003\t50535493\t8621\t8621\tRe1\tRe1\n+chr22\t50535494\t50555553\t8622\t8622\tRe1\tRe1\n+chr22\t50555554\t50560973\t8623\t8623\tRe1\tRe1\n+chr22\t50560974\t50566738\t8624\t8624\tRe1\tRe1\n+chr22\t50566739\t50574082\t8625\t8625\tRe1\tRe1\n+chr22\t50574083\t50576569\t8626\t8626\tRe1\tRe1\n+chr22\t50576570\t50578973\t8627\t8627\tRe1\tRe1\n+chr22\t50578974\t50598031\t8628\t8628\tRe1\tRe1\n+chr22\t50598032\t50618927\t8629\t8629\tRe1\tRe1\n+chr22\t50618928\t50626366\t8630\t8630\tRe1\tRe1\n+chr22\t50626367\t50628581\t8631\t8631\tRe1\tRe1\n+chr22\t50628582\t50629592\t8632\t8632\tRe1\tRe1\n+chr22\t50629593\t50630215\t8633\t8633\tRe1\tRe1\n+chr22\t50630216\t50630812\t8634\t8634\tRe1\tRe1\n+chr22\t50630813\t50633886\t8635\t8635\tRe1\tRe1\n+chr22\t50633887\t50634576\t8636\t8636\tRe1\tRe1\n+chr22\t50634577\t50640196\t8637\t8637\tRe1\tRe1\n+chr22\t50640197\t50640456\t8638\t8638\tRe1\tRe1\n+chr22\t50640457\t50643142\t8639\t8639\tRe1\tRe1\n+chr22\t50643143\t50645738\t8640\t8640\tRe1\tRe1\n+chr22\t50645739\t50657934\t8641\t8641\tRe1\tRe1\n+chr22\t50657935\t50666016\t8642\t8642\tRe1\tRe1\n+chr22\t50666017\t50668885\t8643\t8643\tRe1\tRe1\n+chr22\t50668886\t50669931\t8644\t8644\tRe1\tRe1\n+chr22\t50669932\t50671729\t8645\t8645\tRe1\tRe1\n+chr22\t50671730\t50676679\t8646\t8646\tRe1\tRe1\n+chr22\t50676680\t50694482\t8647\t8647\tRe1\tRe1\n+chr22\t50694483\t50696303\t8648\t8648\tRe1\tRe1\n+chr22\t50696304\t50713988\t8649\t8649\tRe1\tRe1\n+chr22\t50713989\t50716566\t8650\t8650\tRe1\tRe1\n+chr22\t50716567\t50724541\t8651\t8651\tRe1\tRe1\n+chr22\t50724542\t50726541\t8652\t8652\tRe1\tRe1\n+chr22\t50726542\t50726987\t8653\t8653\tRe1\tRe1\n+chr22\t50726988\t50733406\t8654\t8654\tRe1\tRe1\n+chr22\t50733407\t50735950\t8655\t8655\tRe1\tRe1\n+chr22\t50735951\t50736155\t8656\t8656\tRe1\tRe1\n+chr22\t50736156\t50746610\t8657\t8657\tRe1\tRe1\n+chr22\t50746611\t50749091\t8658\t8658\tRe1\tRe1\n+chr22\t50749092\t50752511\t8659\t8659\tRe1\tRe1\n+chr22\t50752512\t50754396\t8660\t8660\tRe1\tRe1\n+chr22\t50754397\t50760974\t8661\t8661\tRe1\tRe1\n+chr22\t50760975\t50763868\t8662\t8662\tRe1\tRe1\n+chr22\t50763869\t50764496\t8663\t8663\tRe1\tRe1\n+chr22\t50764497\t50765215\t8664\t8664\tRe1\tRe1\n+chr22\t50765216\t50769525\t8665\t8665\tRe1\tRe1\n+chr22\t50769526\t50771588\t8666\t8666\tRe1\tRe1\n+chr22\t50771589\t50773285\t8667\t8667\tRe1\tRe1\n+chr22\t50773286\t50777600\t8668\t8668\tRe1\tRe1\n+chr22\t50777601\t50783896\t8669\t8669\tRe1\tRe1\n+chr22\t50783897\t50786637\t8670\t8670\tRe1\tRe1\n+chr22\t50786638\t50787146\t8671\t8671\tRe1\tRe1\n+chr22\t50787147\t50791313\t8672\t8672\tRe1\tRe1\n+chr22\t50791314\t50791700\t8673\t8673\tRe1\tRe1\n+chr22\t50791701\t50793839\t8674\t8674\tRe1\tRe1\n+chr22\t50793840\t50798861\t8675\t8675\tRe1\tRe1\n+chr22\t50798862\t50799224\t8676\t8676\tRe1\tRe1\n+chr22\t50799225\t50818468\t8677\t8677\tRe1\tNone\n' |
| b |
| diff -r f8cb84c49623 -r b4e7244246e2 test-data/digester_file.txt --- a/test-data/digester_file.txt Mon Oct 24 16:09:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b"@@ -1,19943 +0,0 @@\n-Genome:chr21And22FromHg38\tRestriction_Enzyme1:re1_unspecified [A^AGCTT]\tRestriction_Enzyme2:None\tHicup Digester version 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|
