# HG changeset patch # User iuc # Date 1590009822 14400 # Node ID bc0b40dec7d25a59944a950c86b5f8e344683e1e "planemo upload for repository https://github.com/nebiolabs/tasmanian-mismatch commit a64a371ca1ed117c9bd8af743d847128fbce461c" diff -r 000000000000 -r bc0b40dec7d2 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,16 @@ +Galaxy wrappers for tasmanian_mismatch tool +=========================================== + +These wrappers are available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/iuc/tasmanian_mismatch + +The tasmanian_mismatch repository: + - Provides tasmanian-mismatch wrapper + - Downloads and builds tasmanian-mismatch and all its dependencies on the Linux or Mac operating system + +To collaborate with this project and for more information, please visit https://github.com/nebiolabs/tasmanian-mismatch + + + + + diff -r 000000000000 -r bc0b40dec7d2 Tasmanian.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Tasmanian.xml Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,158 @@ + + + tasmanian-mismatch + samtools + + + '${output_table}' + + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + keepHTML_conditional == "yes" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + = +bases in the boundary region in a separate group. This is useful when the bed refers to repeat regions. Since these +regions might not have been correctly placed in the assembly or are not the same in different individuals, we can +include this *confidence* repeat regions where we have high confidence on the reference genome to which we mapped the reads. + +.. image:: ${static_path}/images/intersections_tasmanian.jpg + :height: 150 + :width: 650 + +Softclips are critical in FFPE (Formalin-fixed paraffin-embedded) experiments as mismatches tend to accumulate at the ends of the reads. Most often, softclips +are all accepted during the analysis and many real mismatches are indirectly excluded from the analysis. Hence, this tool +provides different ways to deal with this: + +The *softclips* field allows for 3 different ways at treating softclips: +0) Exclude these region if there is less than 2/3 identity with the reference genome +1) Exclude all softclipped bases +2) Include all softclipped bases + +.. class:: warningmark + +BAM/SAM file must be **sorted** if not using a bed file. + + ]]> + + + + @misc{githubtasmanian, + author = {Langhorst B., Others, Erijman A.}, + year = {2020}, + title = {TBD}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nebiolabs/tasmanian-mismatch}, + } + + + diff -r 000000000000 -r bc0b40dec7d2 static/images/intersections_tasmanian.jpg Binary file static/images/intersections_tasmanian.jpg has changed diff -r 000000000000 -r bc0b40dec7d2 static/images/snapshot_good.jpg Binary file static/images/snapshot_good.jpg has changed diff -r 000000000000 -r bc0b40dec7d2 test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,2 @@ +#chrM chrM ChrM ${__HERE__}/cached_locally/picard_BedToIntervalList_ref.fa +hg38 hg38 Human hg38 ${__HERE__}/cached_locally/small_region.fa diff -r 000000000000 -r bc0b40dec7d2 test-data/cached_locally/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/all_fasta.loc Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,1 @@ +hg38 hg38 Human hg38 ${__HERE__}/small_region.fa diff -r 000000000000 -r bc0b40dec7d2 test-data/cached_locally/small_region.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/small_region.fa Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,102 @@ +>chr1 +TCCTCAGAAAATGGATTTTTCTTTTCTATCACAGTGTCATGCTACAAATTTTCTGAACGTTTATGCTCTG +TTTTCCTGTTAAAACTGAGTGCTTTTAACACACCCAAGTCACTCTTGAATGATTTGCTGCTTAGAAATTT +CTTCTGCCAGATACCCTAACTCATCTCCCTCAAGTTCAAAGTTCCACAAATCTCTAGGGCAGGGACAAAA +TGCTGCCAGTCTCTCTCGATAGCAAGAGACACCTTTACTCCAGTTCCCATTGAGTTCCTCATCTCCATCT +GAGACCATCTCAGCCTGGATTTCATTGTCTATATCATTATTTGACATTTTAGTCAAAGCCATTCAACAAG +TCTCTAGGAAGTTCCAAACTTTCCCACATTTTCCTGTCGTTTTCTGAGCCCTCCAAACTGTTTCAACCCC +TGCCTGTTACCCAGTTCCAAAGTCGCTTCCACATTTTTGGGTTATCTTTACAACAGCACCCCACTCTACC +AGTACCAATGTACTGTATTAGTCTGTTTTCATGCTGCTGATAAAGACATACCTGAGACTGAGTGATTTAT +GAAGAAAAAGACACTTAATGGACTCACATTTCCAGGTGGATGGGGAGGCCTCACAATCATGGTGGAAGGC +AAAAGGCACATCTCTACATGATGGCAGACAAGACAGAATGAGAGCTAAGTGAAAGGGGAACCCCCTTATA +AAATCATCAGCTCTTGTGAGACTTATTCAAGACCACGAGAACAGTATGGGGGAAATACTCCTGTGATTCA +GTTATCTCCCGTTGGATCCCTCCCACAAGACACGGAAATTATGGGAGCTACAATTCAAGATGAGATTTGG +GTGGGGACACATCCAAACCATATTGCTGCTGAATAGATCATGTAGACAGGCTCTCAAACTACACGGAGAG +CAAGAGAGGCCCACCTTACCACAACATTTCATCCAATCCACTAATAAAACAGGCACATCACTGAAGCCAC +CTTCAACTCTCCAGACTACCCAGCTGCCAGCTGAATACCACAGATGGCTACAGTTAATACCACATGGAGC +AGAATCATGTAGCTAAGCCCTGCTTGCGCTAATACAAGTCCACAATTTTTTTTAAGTTTGTTGTTTTAAG +CTGCTAAGTTTTGAGGTGGTTTGTGGTACGTGGAATAAGATGTCACTCTAATATAATATAAACTTAAACT +ATGTGGCATTGGCTTTGGAATCAGACAATGGATAGAAGCCAGAAGGATTTCACAAAGACTGTTAGTGAAA +AGTGAACAGACTTCAAGGAAAATGATAGCAAAACCTGTAAAAGCATTCTGGGAACTGACAGTAAACACTG +AATGGTCCTTAAGGAGACTGAAAACTTGAAAGAGCTTAAGAAGTCTACTGGAAAGGGCTTTAAGGATAAT +GAGAAAAAATCATCAGTGGAGGCTGAGGAAAACGCACCAAAGTCATATTCTGATGGGAGAATTAGAAAAC +GCTTGCCTGGAATGATATAAAAAATAGGAAAAATACCGAAAAAGTTTGTGGATCTGGCTGGGGAGATTTT +TGGTGTCAACTAAAGAAAAAAATTAAGCTTTTAAGAAATTAAAGTTAGATTTATTTAGGGGTCTGAGAAC +AAGAGACTGAGGATTACAGCCTAGGAGAAGTCTTCCAGAGAGGTTCTGTCAGACTGCTCTGGTGAAGGTC +TTTAGCCCACAGTTTATATGCAGGCTGTACATATACACCATGGAATACTATGCCGCCATTAAAAAATGAT +ATCATGTCTTTTGCTGGAACATGGATGGACCTTCTATTATCCTTAGCAAACTAATGCAGGAACAGAAAAC +CAAATACAGCATACTCTCAGTTATAAGTGGGAGCTAAATGATGAGAACTCATGAACACAAAGAATAAAAC +AGACACTGGGGTCTACTTGAGGGTGGAGGGTGAGAAAAGGAAGAGAAGCAGAAAAGATAACTATTGGGTA +CTAGGTTTAATACCTGGGTGATGAAATGATCTGTACAATAACCCCCTGTGACACCAGTCTACCTATGTAA +CAAATGCCCCTAAACTTAAAATAAAAGTTAAAAAAAAAGAAAATTAAAATCTCCTTATCATCTACCTGGT +AATATGAAAAACACAAATCTTTCATTCATTCCTTTCAACTGATGAGGAAAATGAGGCATCGGGAGTTAGT +AAAAGTCCACATTGAGATATGAGACCCACCACTGGCTGGACGCAGTGGCTCACACCTGTAATCCCAGCAC +TTTGGGAGGCCGATGCTGGTGGATCACCTAAGGTCAGGAGTTCGGGACCAGGCTGGCCAACATGGTGAAA +CCCCCATCTCTACTAAAAATACAAAAATTAGCTGGGTGTGGTGGCAGGCACCTGTAATACCAGCTACTAG +GGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGGTGGAGTTTACAGTGAGCCAAAATCACGCCATTG +CACTCCAGCCTGGGCAACAAGAGCAAGACTCTGTCGGGGAAAAAAAAGAAAAAAAAAAACCACCGCCATC +ATTTTGCAAGTGTTACCACTATTGTGTGTTAATATTGTAGAAGTATTCCTAATTATGATTTCTTTGTATT +CCTAATTGTAATAGCTTTGTATTTGAAAAATTATTGATTCATACTCTATATGTTATTATTTTGTATGTGA +TGACAACAGAATATATTATCATGCTCCTTTTGTGAATCTCATTCATAATATAAAGTATAAATTTGTGATT +TTGCTTTAATTTGAAATATTAACTTCAAATATGTTATCACAATTTGATACAAACTATTGACAGTAAATCT +GTGGATTAAGTAATGTCTTAGTAGGTATTGGGAAAATTTGAAACTAGTAACATGGAGGACTATTGTCATT +GTTTATTTCAAAGCCAGTTAAAATTCTGCAAAGCAGTGTACATAAAAATAATTTCAAGAAATTTATAAAA +TACCGAGATTATGGTGTATAAACAACTTTAGATTCTTTGTTTAAGAAATTCTGCCAGTTTGTAATATATG +CTTCATTCAAAGTAGCTAAGGGCTGTACCTGGCTAATAGTAGGCACCTAATATTTGTTGAAAAGGAATAC +TGAGTAGCTGGGACCTCCTGAGTAGCTGGGACCACACACATTTAACCTGTATTTATAAAATTACTGTTTA +GAGAATAACATTTGATGGAATCATGCTTTTACTTTCTGCTTACGACTCAATTGTTTGTACTGACATTAAC +ATCCCAAATCCTTAGCATGGCCTACAAGGCCCTGAGCAATGTGGCACCTGCTGAAGCCTGCTGCCTCATT +TAATAACTCTTTGTCTCTTTCCCAGATCCAGCCACTCTAACATTTTTTAGCTCCTGGACCAAGACAAGCT +CTTCCCAGAACCTGACCTTTGTACCTGTTCTTTATTCCTGGAGTATTTTTCCCCTGACAAATTACTTATC +ATCTATCATAATTCAGGTTAAATGGCACTAACTCAGGGAAGGCTTCCCTAACTGCCTCCCTTCTCCAACC +AAATTAGGAACAATTATATGGCCACATAGTATCGAATCAAGTTTATAATTTTAAAATAATTGGGAGATTT +TGTTGTTTAACACTTGTTTTCACTATAAGACTGTAATTACATGCAAGTAAGAACCATGCCTGTTTGTTCA +CTCCTGCCACAGTCAGAATAGTGCCTGGAATATGCAGTAAGGGCTGAACAAGCACTAAATAAATGAACAA +GTGAATAAATGGATATTGTCTCATTTTTAGAACAGAGTACTGAATGGATCATGAACACTATCTGGTATGT +CACGTAGGTAATTTACAAGGGCTACAATTTCAGCTCAGATTTACCTTTTCCTGGATACAGGTCTTGATAG +GTCTCTTGATGTCATTTCACTTCAGATTCTTCTTTAGAAAACTTGGACAATAGCATTTGCTGTCTTGTCC +AAATTGTTACTAAGAATCAAGAGAGATATCTGACATGAAATGACATTGGAAAACATTAAACACGATTGAA +ATAATGCTAGCCAATATGGTTATTATTAGAAACCAATTACATTTTCAACTTAAAAATAGTAATACTTATT +GCAGACTCAAATGTGCTTATTCTAAAACAAGTAAATGTTTGCCTATGGTCTGAGATTCTAATCCACGGAG +TTCATTCTAATCCACATTCAACACTATCATGTACCAGTGGGCCTCATAACCCACCTAGCCCTGTGATTTT +TCAGGTTCACTTTTCTAAACTTGTGAATTAAATATTTATTTTCTTAGTTCAGAAGAGGAAAAAAACTCTT +GTAATTGTTGCCCATTTCAGGAGAAATCTTGCATATGAAAACAAGAGATAAATATACACAACTGAGGGCT +GTGGTTTAAACAAAATCTTGAGAATGTTTTTTGACCTTACACATTTGTGCTTTAGTATAACAAAATGATA +TAGACAAAGGTAACTTTTAATAGAACCAGTCACTAAATTAAAAAAATGACAAATTCTTCTGCTTAGCTAA +GCAACAGAGAAGGTAAAATACTAATTCAATTCATCAATTTAAGCAATACTCATTAAGAGCCAAGTATGTG +CTCACTGAATAAGCTGCTAAGGTTTGGTGGTTACAGAGTGTGCGGTGAAATGATGTCTACATCACAGTCC +AACATTCACAGAGTTTAAAAGCCTACCAAGAATCAAGACAGACACAAATACCTAACATAGACATTTGTAT +ATGATAAGAGAGCCAGAGTACAATTTAGGAGAAGAAATTGTATGGAAGGAAGGTTCATTTCCATTAGACC +AGAAAAGACAGCACATTTGAAGGCCTGAATAAGAAATATTCTGGATAAGATATTGTGGCTGCTACCAGAA +TGGCTCTTGATGATCTCTACCTCTTGGTATTTATACCCTTATATAATCTCTTTCCTATAGTGTAAGCTGG +TCCCAGGTACTTGTTTCTATTGAATAGAATAGAACAAAAGAAATGAGATGCCACTTCTGAGATTAGATTA +TAAGATACTGTGAATTTCTTCTTGTGCCCTCTCCCTCTCTCTCTTTCTCTTGCCCTCTCATTTGAATGAA +GCCAACTGGCATGCTGTCAGTGGCCCAGTGTAAGTCCTGTTACAAGAAATTGATGATTACCTGTAGCCAA +CCCTAAGTGAAGAACTGAGGTCCTCAGTCCTACAAATGGAGAGAAACTGAATCTAGCTAAGAACCATGTG +AGTGAGCTGGGAAGAAGATCCACCCTCAGTTGAAATTTAAGATGACATATTGAGCAGACATACTGAGACA +CACTGAAAGTAAGAGAGCAGGAGGAAACAAAACCAGGGTCATACAAAGAACACAACTGATTTTGAGATTC +TCACATAAGTATTACACCTTCAGTGAGCACGTGTACTAGAAATTTAAAAAATAAATAAAATAAACCTTCA +AAGTGAGCTAGCAAATAAATTTCCCTATGGTCTCAGCTCTGAGTGGAGAGAGAAAATGTTCCCTGTGGAG +TTTATAGCCAGAATCCAGCTCTCAAACAGGTTTCAGCCTGAACTCACACAATCTGTGTGGCTTCCAAATT +TGCAAGCTGAGAATTTAATTCAAAGTGGTCTCAGGTTGATAGCAGTCCAAAATGCTAGGTAGGAAAAAAA +ATCCTCTCTGGACAAATAAATCATCAAAGCAAGCTCATAAGAGCAGGTTTCAAAGGTCATGAGCTTCTAA +CACACACACAAAAATCACACACACAAAATGGGGGTAGCAGCAACATGGGTAGCGTATTCAAACTTGAAAA +GACTTTAAATATTTGTATTATTAGATGTAGATTATGAAACACATATTTTAATGTGGTTAATTTTTTTAAG +GAATCAAAACTATGAGTAAAGACCAAGAAAATTGTGCTGGATGGCCACTTCCACCATGGCTCCCCTCCTA +TTTAAGTCTGGGTACTGTGTCACCCGAAGTCTTCAGGCACATTGTTCCAGGTCTGGGTTTGCCTATGAAA +GAAACTCATGAGAGCTGGAAATGAGGAGTGAAGAGGAGGTCTTCAAATAAAGCAGGCTTAAGGATTAGAC +ATAGCAGGTTTGACAGATGTGATGGCTTGCAGAATCCTTTATGAGCTCCCACTGTCCATCTGGATAAGAT +TTACAGACCTTTCAGAAATTCCTATAAGCTTGGGTTCTGTGCCCACACTCTAGACTGTCAGGCTAAGATC +TCTGATATAAAACAGACCTCTTCTGATTTTGTCTAGCTGCTTTTCTAATATCTATTCACCAAGCTCTTCC +AATAATAGCATAAGGCCCTAATTAATATTAAACTTTTATCATTATAATACATAGGATGTCTTCTGTTTTC +CTGATCAAATTCTGACTACTATTAAAATATAAAGAATTGTCCAGAAATATATAAAAAAAGAATCACACAT +TGATCTTCTTTAAATGAAAATATAACAATTGTATGGACTAGGATGATTACAGTTGTTCAGTTCTGACTGT +TATTTGAAGAAAAAAGCAATAAGAAGCCTCAGCAACTTAACAGAAGGAGCTGCCATTTACTAGGAGAAAA +GATTGTGGATGAGAGTGTAGCAAAGGTCAGAATTCTGTGAAGCTTGAGATGTTTATTATAATGAATTATC +TTTTATACTCACTACAATTTCCTAACAATTTTGGGGTTTATATTTTTGAAAGAGATATACCTTTAATTTT +CTTTCTTTGTACTATTGTTAGGTAACTTTGATGTGCAGATTATACTACAGTGAAAGTTGCCAATGACAAG +GCAAAGTCACTTACATCAGACCCAAAGCAAAGTGGAGCCGGGTCATGAAAAAGGGGATCTTGTGTGTCTG +TCCACGATAAGCACTATCACAAGGACTTTCTATAAACTCACAAGAAATTTCTGCCCACCCAGCACACTCT +GTTTGTCCAGCTCATCCTGTAGGTGTCTCTATAATAGGACCTATCATAAAAAATTCCTCAAGACTGCAGC +ATTTCAGATAAGCCACCCTCACAAGAACACTTGCCTAGCAATGGCTGTTTCTGCCAGTAAGTTAACACCA +GCTCCTGCATCAGACCCTGTGACCAATGATGTTTGTTTCAAAACAGCTTGCATGGACTTCTTTTTGTCTT diff -r 000000000000 -r bc0b40dec7d2 test-data/cached_locally/small_region.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/small_region.fa.fai Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,1 @@ +chr1 7070 7 70 71 diff -r 000000000000 -r bc0b40dec7d2 test-data/small_region.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_region.fa Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,102 @@ +>chr1 +TCCTCAGAAAATGGATTTTTCTTTTCTATCACAGTGTCATGCTACAAATTTTCTGAACGTTTATGCTCTG +TTTTCCTGTTAAAACTGAGTGCTTTTAACACACCCAAGTCACTCTTGAATGATTTGCTGCTTAGAAATTT +CTTCTGCCAGATACCCTAACTCATCTCCCTCAAGTTCAAAGTTCCACAAATCTCTAGGGCAGGGACAAAA +TGCTGCCAGTCTCTCTCGATAGCAAGAGACACCTTTACTCCAGTTCCCATTGAGTTCCTCATCTCCATCT +GAGACCATCTCAGCCTGGATTTCATTGTCTATATCATTATTTGACATTTTAGTCAAAGCCATTCAACAAG +TCTCTAGGAAGTTCCAAACTTTCCCACATTTTCCTGTCGTTTTCTGAGCCCTCCAAACTGTTTCAACCCC +TGCCTGTTACCCAGTTCCAAAGTCGCTTCCACATTTTTGGGTTATCTTTACAACAGCACCCCACTCTACC +AGTACCAATGTACTGTATTAGTCTGTTTTCATGCTGCTGATAAAGACATACCTGAGACTGAGTGATTTAT +GAAGAAAAAGACACTTAATGGACTCACATTTCCAGGTGGATGGGGAGGCCTCACAATCATGGTGGAAGGC +AAAAGGCACATCTCTACATGATGGCAGACAAGACAGAATGAGAGCTAAGTGAAAGGGGAACCCCCTTATA +AAATCATCAGCTCTTGTGAGACTTATTCAAGACCACGAGAACAGTATGGGGGAAATACTCCTGTGATTCA +GTTATCTCCCGTTGGATCCCTCCCACAAGACACGGAAATTATGGGAGCTACAATTCAAGATGAGATTTGG +GTGGGGACACATCCAAACCATATTGCTGCTGAATAGATCATGTAGACAGGCTCTCAAACTACACGGAGAG +CAAGAGAGGCCCACCTTACCACAACATTTCATCCAATCCACTAATAAAACAGGCACATCACTGAAGCCAC +CTTCAACTCTCCAGACTACCCAGCTGCCAGCTGAATACCACAGATGGCTACAGTTAATACCACATGGAGC +AGAATCATGTAGCTAAGCCCTGCTTGCGCTAATACAAGTCCACAATTTTTTTTAAGTTTGTTGTTTTAAG +CTGCTAAGTTTTGAGGTGGTTTGTGGTACGTGGAATAAGATGTCACTCTAATATAATATAAACTTAAACT +ATGTGGCATTGGCTTTGGAATCAGACAATGGATAGAAGCCAGAAGGATTTCACAAAGACTGTTAGTGAAA +AGTGAACAGACTTCAAGGAAAATGATAGCAAAACCTGTAAAAGCATTCTGGGAACTGACAGTAAACACTG +AATGGTCCTTAAGGAGACTGAAAACTTGAAAGAGCTTAAGAAGTCTACTGGAAAGGGCTTTAAGGATAAT +GAGAAAAAATCATCAGTGGAGGCTGAGGAAAACGCACCAAAGTCATATTCTGATGGGAGAATTAGAAAAC +GCTTGCCTGGAATGATATAAAAAATAGGAAAAATACCGAAAAAGTTTGTGGATCTGGCTGGGGAGATTTT +TGGTGTCAACTAAAGAAAAAAATTAAGCTTTTAAGAAATTAAAGTTAGATTTATTTAGGGGTCTGAGAAC +AAGAGACTGAGGATTACAGCCTAGGAGAAGTCTTCCAGAGAGGTTCTGTCAGACTGCTCTGGTGAAGGTC +TTTAGCCCACAGTTTATATGCAGGCTGTACATATACACCATGGAATACTATGCCGCCATTAAAAAATGAT +ATCATGTCTTTTGCTGGAACATGGATGGACCTTCTATTATCCTTAGCAAACTAATGCAGGAACAGAAAAC +CAAATACAGCATACTCTCAGTTATAAGTGGGAGCTAAATGATGAGAACTCATGAACACAAAGAATAAAAC +AGACACTGGGGTCTACTTGAGGGTGGAGGGTGAGAAAAGGAAGAGAAGCAGAAAAGATAACTATTGGGTA +CTAGGTTTAATACCTGGGTGATGAAATGATCTGTACAATAACCCCCTGTGACACCAGTCTACCTATGTAA +CAAATGCCCCTAAACTTAAAATAAAAGTTAAAAAAAAAGAAAATTAAAATCTCCTTATCATCTACCTGGT +AATATGAAAAACACAAATCTTTCATTCATTCCTTTCAACTGATGAGGAAAATGAGGCATCGGGAGTTAGT +AAAAGTCCACATTGAGATATGAGACCCACCACTGGCTGGACGCAGTGGCTCACACCTGTAATCCCAGCAC +TTTGGGAGGCCGATGCTGGTGGATCACCTAAGGTCAGGAGTTCGGGACCAGGCTGGCCAACATGGTGAAA +CCCCCATCTCTACTAAAAATACAAAAATTAGCTGGGTGTGGTGGCAGGCACCTGTAATACCAGCTACTAG +GGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGGTGGAGTTTACAGTGAGCCAAAATCACGCCATTG +CACTCCAGCCTGGGCAACAAGAGCAAGACTCTGTCGGGGAAAAAAAAGAAAAAAAAAAACCACCGCCATC +ATTTTGCAAGTGTTACCACTATTGTGTGTTAATATTGTAGAAGTATTCCTAATTATGATTTCTTTGTATT +CCTAATTGTAATAGCTTTGTATTTGAAAAATTATTGATTCATACTCTATATGTTATTATTTTGTATGTGA +TGACAACAGAATATATTATCATGCTCCTTTTGTGAATCTCATTCATAATATAAAGTATAAATTTGTGATT +TTGCTTTAATTTGAAATATTAACTTCAAATATGTTATCACAATTTGATACAAACTATTGACAGTAAATCT +GTGGATTAAGTAATGTCTTAGTAGGTATTGGGAAAATTTGAAACTAGTAACATGGAGGACTATTGTCATT +GTTTATTTCAAAGCCAGTTAAAATTCTGCAAAGCAGTGTACATAAAAATAATTTCAAGAAATTTATAAAA +TACCGAGATTATGGTGTATAAACAACTTTAGATTCTTTGTTTAAGAAATTCTGCCAGTTTGTAATATATG +CTTCATTCAAAGTAGCTAAGGGCTGTACCTGGCTAATAGTAGGCACCTAATATTTGTTGAAAAGGAATAC +TGAGTAGCTGGGACCTCCTGAGTAGCTGGGACCACACACATTTAACCTGTATTTATAAAATTACTGTTTA +GAGAATAACATTTGATGGAATCATGCTTTTACTTTCTGCTTACGACTCAATTGTTTGTACTGACATTAAC +ATCCCAAATCCTTAGCATGGCCTACAAGGCCCTGAGCAATGTGGCACCTGCTGAAGCCTGCTGCCTCATT +TAATAACTCTTTGTCTCTTTCCCAGATCCAGCCACTCTAACATTTTTTAGCTCCTGGACCAAGACAAGCT +CTTCCCAGAACCTGACCTTTGTACCTGTTCTTTATTCCTGGAGTATTTTTCCCCTGACAAATTACTTATC +ATCTATCATAATTCAGGTTAAATGGCACTAACTCAGGGAAGGCTTCCCTAACTGCCTCCCTTCTCCAACC +AAATTAGGAACAATTATATGGCCACATAGTATCGAATCAAGTTTATAATTTTAAAATAATTGGGAGATTT +TGTTGTTTAACACTTGTTTTCACTATAAGACTGTAATTACATGCAAGTAAGAACCATGCCTGTTTGTTCA +CTCCTGCCACAGTCAGAATAGTGCCTGGAATATGCAGTAAGGGCTGAACAAGCACTAAATAAATGAACAA +GTGAATAAATGGATATTGTCTCATTTTTAGAACAGAGTACTGAATGGATCATGAACACTATCTGGTATGT +CACGTAGGTAATTTACAAGGGCTACAATTTCAGCTCAGATTTACCTTTTCCTGGATACAGGTCTTGATAG +GTCTCTTGATGTCATTTCACTTCAGATTCTTCTTTAGAAAACTTGGACAATAGCATTTGCTGTCTTGTCC +AAATTGTTACTAAGAATCAAGAGAGATATCTGACATGAAATGACATTGGAAAACATTAAACACGATTGAA +ATAATGCTAGCCAATATGGTTATTATTAGAAACCAATTACATTTTCAACTTAAAAATAGTAATACTTATT +GCAGACTCAAATGTGCTTATTCTAAAACAAGTAAATGTTTGCCTATGGTCTGAGATTCTAATCCACGGAG +TTCATTCTAATCCACATTCAACACTATCATGTACCAGTGGGCCTCATAACCCACCTAGCCCTGTGATTTT +TCAGGTTCACTTTTCTAAACTTGTGAATTAAATATTTATTTTCTTAGTTCAGAAGAGGAAAAAAACTCTT +GTAATTGTTGCCCATTTCAGGAGAAATCTTGCATATGAAAACAAGAGATAAATATACACAACTGAGGGCT +GTGGTTTAAACAAAATCTTGAGAATGTTTTTTGACCTTACACATTTGTGCTTTAGTATAACAAAATGATA +TAGACAAAGGTAACTTTTAATAGAACCAGTCACTAAATTAAAAAAATGACAAATTCTTCTGCTTAGCTAA +GCAACAGAGAAGGTAAAATACTAATTCAATTCATCAATTTAAGCAATACTCATTAAGAGCCAAGTATGTG +CTCACTGAATAAGCTGCTAAGGTTTGGTGGTTACAGAGTGTGCGGTGAAATGATGTCTACATCACAGTCC +AACATTCACAGAGTTTAAAAGCCTACCAAGAATCAAGACAGACACAAATACCTAACATAGACATTTGTAT +ATGATAAGAGAGCCAGAGTACAATTTAGGAGAAGAAATTGTATGGAAGGAAGGTTCATTTCCATTAGACC +AGAAAAGACAGCACATTTGAAGGCCTGAATAAGAAATATTCTGGATAAGATATTGTGGCTGCTACCAGAA +TGGCTCTTGATGATCTCTACCTCTTGGTATTTATACCCTTATATAATCTCTTTCCTATAGTGTAAGCTGG +TCCCAGGTACTTGTTTCTATTGAATAGAATAGAACAAAAGAAATGAGATGCCACTTCTGAGATTAGATTA +TAAGATACTGTGAATTTCTTCTTGTGCCCTCTCCCTCTCTCTCTTTCTCTTGCCCTCTCATTTGAATGAA +GCCAACTGGCATGCTGTCAGTGGCCCAGTGTAAGTCCTGTTACAAGAAATTGATGATTACCTGTAGCCAA +CCCTAAGTGAAGAACTGAGGTCCTCAGTCCTACAAATGGAGAGAAACTGAATCTAGCTAAGAACCATGTG +AGTGAGCTGGGAAGAAGATCCACCCTCAGTTGAAATTTAAGATGACATATTGAGCAGACATACTGAGACA +CACTGAAAGTAAGAGAGCAGGAGGAAACAAAACCAGGGTCATACAAAGAACACAACTGATTTTGAGATTC +TCACATAAGTATTACACCTTCAGTGAGCACGTGTACTAGAAATTTAAAAAATAAATAAAATAAACCTTCA +AAGTGAGCTAGCAAATAAATTTCCCTATGGTCTCAGCTCTGAGTGGAGAGAGAAAATGTTCCCTGTGGAG +TTTATAGCCAGAATCCAGCTCTCAAACAGGTTTCAGCCTGAACTCACACAATCTGTGTGGCTTCCAAATT +TGCAAGCTGAGAATTTAATTCAAAGTGGTCTCAGGTTGATAGCAGTCCAAAATGCTAGGTAGGAAAAAAA +ATCCTCTCTGGACAAATAAATCATCAAAGCAAGCTCATAAGAGCAGGTTTCAAAGGTCATGAGCTTCTAA +CACACACACAAAAATCACACACACAAAATGGGGGTAGCAGCAACATGGGTAGCGTATTCAAACTTGAAAA +GACTTTAAATATTTGTATTATTAGATGTAGATTATGAAACACATATTTTAATGTGGTTAATTTTTTTAAG +GAATCAAAACTATGAGTAAAGACCAAGAAAATTGTGCTGGATGGCCACTTCCACCATGGCTCCCCTCCTA +TTTAAGTCTGGGTACTGTGTCACCCGAAGTCTTCAGGCACATTGTTCCAGGTCTGGGTTTGCCTATGAAA +GAAACTCATGAGAGCTGGAAATGAGGAGTGAAGAGGAGGTCTTCAAATAAAGCAGGCTTAAGGATTAGAC +ATAGCAGGTTTGACAGATGTGATGGCTTGCAGAATCCTTTATGAGCTCCCACTGTCCATCTGGATAAGAT +TTACAGACCTTTCAGAAATTCCTATAAGCTTGGGTTCTGTGCCCACACTCTAGACTGTCAGGCTAAGATC +TCTGATATAAAACAGACCTCTTCTGATTTTGTCTAGCTGCTTTTCTAATATCTATTCACCAAGCTCTTCC +AATAATAGCATAAGGCCCTAATTAATATTAAACTTTTATCATTATAATACATAGGATGTCTTCTGTTTTC +CTGATCAAATTCTGACTACTATTAAAATATAAAGAATTGTCCAGAAATATATAAAAAAAGAATCACACAT +TGATCTTCTTTAAATGAAAATATAACAATTGTATGGACTAGGATGATTACAGTTGTTCAGTTCTGACTGT +TATTTGAAGAAAAAAGCAATAAGAAGCCTCAGCAACTTAACAGAAGGAGCTGCCATTTACTAGGAGAAAA +GATTGTGGATGAGAGTGTAGCAAAGGTCAGAATTCTGTGAAGCTTGAGATGTTTATTATAATGAATTATC +TTTTATACTCACTACAATTTCCTAACAATTTTGGGGTTTATATTTTTGAAAGAGATATACCTTTAATTTT +CTTTCTTTGTACTATTGTTAGGTAACTTTGATGTGCAGATTATACTACAGTGAAAGTTGCCAATGACAAG +GCAAAGTCACTTACATCAGACCCAAAGCAAAGTGGAGCCGGGTCATGAAAAAGGGGATCTTGTGTGTCTG +TCCACGATAAGCACTATCACAAGGACTTTCTATAAACTCACAAGAAATTTCTGCCCACCCAGCACACTCT +GTTTGTCCAGCTCATCCTGTAGGTGTCTCTATAATAGGACCTATCATAAAAAATTCCTCAAGACTGCAGC +ATTTCAGATAAGCCACCCTCACAAGAACACTTGCCTAGCAATGGCTGTTTCTGCCAGTAAGTTAACACCA +GCTCCTGCATCAGACCCTGTGACCAATGATGTTTGTTTCAAAACAGCTTGCATGGACTTCTTTTTGTCTT diff -r 000000000000 -r bc0b40dec7d2 test-data/small_region.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_region.fa.fai Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,1 @@ +chr1 7070 7 70 71 diff -r 000000000000 -r bc0b40dec7d2 test-data/test2-bed.output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2-bed.output Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,153 @@ +read,position,Ia_a,Ia_t,Ia_c,Ia_g,It_a,It_t,It_c,It_g,Ic_a,Ic_t,Ic_c,Ic_g,Ig_a,Ig_t,Ig_c,Ig_g,Ca_a,Ca_t,Ca_c,Ca_g,Ct_a,Ct_t,Ct_c,Ct_g,Cc_a,Cc_t,Cc_c,Cc_g,Cg_a,Cg_t,Cg_c,Cg_g,Na_a,Na_t,Na_c,Na_g,Nt_a,Nt_t,Nt_c,Nt_g,Nc_a,Nc_t,Nc_c,Nc_g,Ng_a,Ng_t,Ng_c,Ng_g,cIa_a,cIa_t,cIa_c,cIa_g,cIt_a,cIt_t,cIt_c,cIt_g,cIc_a,cIc_t,cIc_c,cIc_g,cIg_a,cIg_t,cIg_c,cIg_g,cCa_a,cCa_t,cCa_c,cCa_g,cCt_a,cCt_t,cCt_c,cCt_g,cCc_a,cCc_t,cCc_c,cCc_g,cCg_a,cCg_t,cCg_c,cCg_g +1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,0,0,0,2,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +1,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,2,0,0,0,0,1,0,0,0,0,1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1 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newline at end of file diff -r 000000000000 -r bc0b40dec7d2 test-data/test2.bam Binary file test-data/test2.bam has changed diff -r 000000000000 -r bc0b40dec7d2 test-data/test2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.bed Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,4 @@ +chr1 850 879 + L1P5 LINE L1 +chr1 1019 1200 + L1P5 LINE L1 +chr1 5728 5735 + L1P5 LINE L1 +chr1 465 487 + L1P5 LINE L1 diff -r 000000000000 -r bc0b40dec7d2 test-data/test2.output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.output Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,153 @@ 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b/tool-data/all_fasta.loc.sample Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +# +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# diff -r 000000000000 -r bc0b40dec7d2 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+
diff -r 000000000000 -r bc0b40dec7d2 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed May 20 17:23:42 2020 -0400 @@ -0,0 +1,8 @@ + + + + + value, dbkey, name, path + +
+