Mercurial > repos > iuc > ucsc_mafcoverage
changeset 0:2b1884fdb849 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit fe43201294560762b7aab73785df2f1f7828cb9e
| author | iuc |
|---|---|
| date | Thu, 14 Aug 2025 11:59:27 +0000 |
| parents | |
| children | |
| files | mafCoverage.xml test-data/componentFilter.txt test-data/filter_in.maf test-data/gorGor3.bed test-data/hg38.bed test-data/mafFetch.bed test-data/mafFetch.maf test-data/mafFrag_in.bed test-data/mafFrag_in12.bed test-data/mafIn.maf test-data/malformed.maf test-data/panTro4.bed test-data/ref.2bit test-data/ref.fa test-data/restrict.bed test-data/speciesFilter.txt |
| diffstat | 16 files changed, 470 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mafCoverage.xml Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,131 @@ +<tool id="ucsc_mafcoverage" name="mafCoverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> + <description>Analyse coverage by MAF files</description> + <macros> + <token name="@TOOL_VERSION@">482</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">24.2</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">ucsc-mafcoverage</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + cp '$ucsc_db_connection' "\${HOME}/.hg.conf" && + chmod 600 "\${HOME}/.hg.conf" && + mafCoverage + '$genome' + '$maf_file' + #if $restrict_option.restrict_select == "yes": + -restrict='$restrict_option.restrict_bed' + #end if + #if $count != "": + -count=$count + #end if + > coverage.txt + ]]> + </command> + <configfiles> + <configfile name="ucsc_db_connection"><![CDATA[ +#European MariaDB server +db.host=genome-euro-mysql.soe.ucsc.edu +db.user=genomep +db.password=password +central.db=hgcentral +central.host=genome-euro-mysql.soe.ucsc.edu +central.user=genomep +central.password=password +gbdbLoc1=http://hgdownload.soe.ucsc.edu/gbdb/ +forceTwoBit=on + ]]></configfile> + </configfiles> + <inputs> + <param name="maf_file" type="data" format="maf" label="Input MAF file" help="Input MAF file for which coverage needs to be analysed. MAF file must be sorted by chromosome, tStart"/> + <param name="genome" type="text" optional="false" label="Enter Genome database name" help="Name should match with the UCSC Table Browser Entries (For Eg. mm10, hg19, hg38)"/> + <conditional name="restrict_option"> + <param name="restrict_select" type="select" label="Restrict to a specific parts of input BED file" help="Restrict the MAF coverage to a specific part of the input BED file. If not selected, the entire BED file will be used."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="restrict_bed" type="data" format="bed" label="Restrict BED file" help="Select a BED file to restrict the MAF coverage to specific regions."/> + </when> + <when value="no"/> + </conditional> + <param name="count" type="integer" value="" optional="true" label="Number of matching species to count coverage" help="Number of species to count coverage for. Default is 3"/> + </inputs> + <outputs> + <data name="output" format="txt" from_work_dir="coverage.txt" label="${tool.name} on ${on_string}:Output Coverage"/> + </outputs> + <tests> + <!-- Test 01: Testing with default options --> + <test expect_num_outputs="1"> + <param name="maf_file" value="mafFetch.maf"/> + <param name="genome" value="hg19"/> + <conditional name="restrict_option"> + <param name="restrict_select" value="no"/> + </conditional> + <output name="output" ftype="txt"> + <assert_contents> + <has_n_lines n="16"/> + <has_text_matching expression="all\t330\t0.00\t170\t0.00\t25\t0.00\t145\t0.00"/> + <has_text_matching expression="chr13\t214\t0.00\t101\t0.00\t17\t0.00\t84\t0.00"/> + <has_text_matching expression="chr17\t116\t0.00\t69\t0.00\t8\t0.00\t61\t0.00"/> + </assert_contents> + </output> + </test> + + <!-- Test 02: Testing -count option --> + <test expect_num_outputs="1"> + <param name="maf_file" value="mafFetch.maf"/> + <param name="genome" value="hg19"/> + <conditional name="restrict_option"> + <param name="restrict_select" value="no"/> + </conditional> + <param name="count" value="2"/> + <output name="output" ftype="txt"> + <assert_contents> + <has_n_lines n="16"/> + <has_text_matching expression="all\t330\t0.00\t170\t0.00\t25\t0.00\t145\t0.00"/> + <has_text_matching expression="chr13\t214\t0.00\t101\t0.00\t17\t0.00\t84\t0.00"/> + <has_text_matching expression="chr17\t116\t0.00\t69\t0.00\t8\t0.00\t61\t0.00"/> + </assert_contents> + </output> + </test> + + <!-- Test 03: Testing with restrict option --> + <test expect_num_outputs="1"> + <param name="maf_file" value="mafFetch.maf"/> + <param name="genome" value="hg19"/> + <conditional name="restrict_option"> + <param name="restrict_select" value="yes"/> + <param name="restrict_bed" value="restrict.bed"/> + </conditional> + <param name="count" value="3"/> + <output name="output" ftype="txt"> + <assert_contents> + <has_n_lines n="17"/> + <has_text_matching expression="all\t207\t94.09\t78\t35.45\t6\t2.73\t72\t32.73"/> + <has_text_matching expression="chr13\t107\t89.17\t16\t13.33\t0\t0.00\t16\t13.33"/> + <has_text_matching expression="chr17\t100\t100.00\t62\t62.00\t6\t6.00\t56\t56.00"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +mafCoverage is a command-line tool from the UCSC Genome Browser suite that analyses the coverage by MAF files chromosome by chromosome and genome-wide. + + ]]></help> + <citations> + <citation type="bibtex"> + @misc{mafCoverage, + author = {Kent UCSC}, + title = {mafCoverage: A tool for analysing coverage by MAF files chromosome by chromosome and genome-wide}, + note = {Tool for analysing coverage by MAF files chromosome by chromosome and genome-wide} + </citation> + </citations> + <creator> + <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12" identifier="https://orcid.org/0009-0003-9935-828X"/> + <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/> + </creator> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/componentFilter.txt Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,3 @@ +human.chr1 +mouse.chr1 +dog.chr1 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filter_in.maf Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,32 @@ +##maf version=1 scoring=example +a score=1000.0 +s human.chr1 100 10 + 1000 ACGTACGTAC +s mouse.chr1 200 10 + 2000 ACGTACGTAC +s dog.chr1 300 10 + 3000 ACGTACGTAC + +a score=500.0 +s human.chr2 150 5 + 1000 ACGTA +s mouse.chr2 250 5 + 2000 ACGT- + +a score=200.0 +s human.chr3 200 15 + 1000 ACGTACGTACGTACG +s cat.chr3 350 15 + 4000 ACGTACGTACGTACG +s dog.chr3 450 15 + 5000 ACGTACGTACGTACG +s rat.chr3 550 15 + 6000 ACGTACGTACGTACG + +a score=50.0 +s human.chr4 110 10 + 1000 ACGTACGTAC +s mouse.chr4 210 10 + 2000 ACGTACGTAC + +a score=3000.0 +s human.chr5 105 10 + 1000 ACGTACGTAC +s mouse.chr5 205 10 + 2000 ACGTACGTAC +s dog.chr5 305 10 + 3000 ACGTACGTAC +s cat.chr5 405 10 + 4000 ACGTACGTAC +s rat.chr5 505 10 + 5000 ACGTACGTAC +s cow.chr5 605 10 + 6000 ACGTACGTAC + +a score=600.0 +s human.chr6 100 10 + 1000 ACGTACGTAC +s mouse.chr6 200 10 + 2000 ACGTACGTAC +s dog.chr6 300 10 + 3000 ACGTACGTAC \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gorGor3.bed Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,2 @@ +chr7 1006 1007 +chr7 1013 1014 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg38.bed Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,2 @@ +chr7 1005 1006 +chr7 1010 1012 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafFetch.bed Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,1 @@ +chr17 7578370 7578550 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafFetch.maf Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,254 @@ +##maf version=1 +##maf version=1 scoring=autoMZ.v1 +a score=3796057.000000 +s hg19.chr17 7578364 116 + 81195210 GC---TC---ACCA---TCGCTA----TCTGAG--CAGCGCTC-ATGGTGGGGG-CAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTT-GTAGAT-GGC----CATGGCGCGGACGC---GGGTGCCGGGCGGGGG------T +s xenTro2.scaffold_440 77711 119 + 1031938 ---GATT---ACCA---TCCCCTGGC-TCCACG--CTGCGCTC-ATGGTGGGGG-CACCTCTTGACCACCTCGGCCACGTGCTCGGATTTCTT-GTACAC-GGC----CGTAGCCCGGAGAA---TGGAGCCGAGCGGCGG------G +i xenTro2.scaffold_440 I 804 C 0 +s ornAna1.Contig14337 7793 116 + 24454 CC---TC---ACCG---TCACCG----TCGGAA--GAGCGCTC-GTGGTGGGGG-CACCTCTTCACCACCTCGGCCCTGTGGTCGGTCTTCTT-GTAGAC-GGC----CATggcccggaccc---gggcccccggcggggg------c +i ornAna1.Contig14337 C 0 C 0 +s macEug1.Scaffold144598 15841 104 - 16042 GC---TC---A-------------------GTG--CATCGTTC-ATGGTGGGGA-CAGCGCTTAACCACCTCAGTCATGTGTTCTGACTTCTT-ATAAAT-AGC----CATAGCGCGAACTC---GGGCACCAGCAGGTGG------T +i macEug1.Scaffold144598 C 0 C 0 +s dasNov2.scaffold_2289 70843 119 + 182311 CC---TC---ACCA---TCCCCATGT-TCTGAG--CAGCGCTC-GTGGTGGGGG-CAGCGCCTCACGACCTCCGTCATGTGCTCGGACTTCTT-GTAGAC-AGC----CATGGCCCGGACGC---GGGCCCCAGGAGGGGG------T +i dasNov2.scaffold_2289 C 0 C 0 +s proCap1.scaffold_6241 18925 119 + 60317 CC---TC---ACCA---TCGTTATAG-TCAGAG--CAGCGCTC-GTGGTGGGGG-CAGCGCTTCACAACCTCTGTCATGTGCTCTGACTTCTT-GTAGAT-GGC----CATGGTGCGAACAC---AGGTGCCTGGCGGGGG------T +i proCap1.scaffold_6241 C 0 C 0 +s loxAfr3.scaffold_47 11692611 119 + 18382006 CC---TC---ACCA---TCGCTAGAG-TCAGAG--CAGCGCTC-ATGGTGGGGG-CAGCGCTTGACGACCTCCGTCATATGCTCTGACTTCTT-GTAGAT-GGC----CATGGTGCGAACAC---GGGTGCCGGGCGGGGG------T +i loxAfr3.scaffold_47 C 0 C 0 +s sorAra1.scaffold_223295 4340 119 - 5675 AC---GC---ACCG---TCATTATAG-TCAGAG--CAGCGCTC-GTGGTGCGGG-CAGCGCCGCACCACTTCTGTCATATACTCGGATTTCTT-GTAGAT-GGC----CATGGCACGGACTC---GTGCGCCCTGTGGGGG------T +i sorAra1.scaffold_223295 C 0 C 0 +s eriEur1.scaffold_369359 787 116 + 53529 TC---TC---ACCA---TCATTGCAG-TCCG-----AGCGCTC-ATGGTGGGGG-CAGCGCCTCACAACCTCTGTCATATGCTCTGACTTCTT-GTAGAT-GGC----CATGGCGCGAACAT---GGCTACCCATTGGTGG------T +i eriEur1.scaffold_369359 C 0 C 0 +s pteVam1.scaffold_3215 83447 124 + 151245 -CACTTC---ACCA---TCGCTATAATTCTGGA--CAGCGTTC-ATGGTGGGGGCCAGCGCCTCACCACCTCTGTCATGTCCTCAGATTTCTT-GAATATGGGC----CATGTCTCGGACAC---GGGTGCCAAGTGGGGG------T +i pteVam1.scaffold_3215 C 0 M 669 +s felCat3.scaffold_213592 202966 119 + 335748 GC---TC---ACCA---TCGCTACTG-TCAGGG--CAGCGCTC-GTGGTGGGGA-CAGCGCCTCACGACCTCTGTCATGAACTCTGACTTCTT-ATAAAT-GGC----CATGGCGCGGACAC---AGGTTCCCGGTGGGGG------C +i felCat3.scaffold_213592 C 0 C 0 +s canFam2.chr5 35559471 119 + 91976430 GC---TT---ACCG---TCACTACTG-TCAGAG--CAGCGTTC-ATGGTGGGGG-CAGCGCCGCACAACCTCGGTCACGAACTCCGACTTCTT-ATAGAT-GGC----CATAGCGCGGACGC---AGGTATTGGGTGGGGG------T +i canFam2.chr5 C 0 C 0 +s equCab2.chr11 50614770 119 + 61308211 AC---TC---ACCA---TCGCTACTG-TCAGAG--CAGCGTTC-ATGGTGGGGG-CAGCGCCTCACGACCTCCGTCATGAACTCTGACTTCTT-GTAGAT-GGC----CATGGCCCGGACAC---GGGTGCCGGGTGGGGG------T +i equCab2.chr11 C 0 C 0 +s myoLuc1.scaffold_182347 10113 118 + 17583 -C---TC---ACCG---TCACTATAG-TCAGAG--CAGCGCTC-ATGGTGGGGG-CAGCGCCGCACGACCTCCGTCATGTGCTCGGACTTCTT-GTAGAT-GGC----CATGGCACGGACCC---GGGAGCTGAGCGGGGG------T +i myoLuc1.scaffold_182347 C 0 C 0 +s bosTau4.chr19 27882876 119 + 65312493 GC---TC---ACCA---TCGCTATAG-TCAGAG--GAGCGCTC-ATGGTGGGGA-CAACGCCTCACAACCTCCGTCATGTGCTCCAACTTCTT-GTAGAT-GGC----CATGGCGCGGACGC---GGGTGCCGGGCGGGGG------T +i bosTau4.chr19 C 0 C 0 +s turTru1.scaffold_109828 111640 119 + 563998 GC---TC---ACCG---TCGCTATAG-TCAGAG--CAGCGCTC-ATGGTGGGGA-CAGCGCCTCACAACCTCCGTCATGTACTCTGACTTCTT-ATAGAT-GGC----CATGGCGCGGACCC---GGGTGCCGGGCGGGGG------T +i turTru1.scaffold_109828 C 0 C 0 +s ochPri2.scaffold_2885 39191 116 + 176626 AC---TC---ACCA---TCGCTA----TCCGAG--CAGCGCTC-GTGGTGGGGG-CAGCGCTTCACAATCTCGGTCACATGCTGCGACTTCTT-GTAGAT-GGC----CATGGCCCGCACGC---GGGTGCCAGGCGGGGG------T +i ochPri2.scaffold_2885 C 0 C 0 +s oryCun2.chr19 45751305 116 - 57279966 AC---TC---ACCA---TCGCTG----TCGGAG--CAGCGCTC-GTGGTGGGGG-CAGCGTCTGACAACTTCCGTCATGTGCTGAGACTTCTT-GTAGAT-GGC----CATGGCCCGGACGC---GGCTGCCAGGCGGGGG------C +i oryCun2.chr19 C 0 C 0 +s cavPor3.scaffold_61 1734708 116 - 10725151 AC---TC---ACCA---TCACTA----TCGGAA--CAGCGCTC-GTGATGGGGG-CAGCGTCTCACCACCTCCGTCATGTGCTGTGACTTCTT-GTAGAT-GGC----CAGGGCACGGACTC---GGGTGCCAGGTGGGGG------T +i cavPor3.scaffold_61 C 0 C 0 +s rn4.chr10 54310678 116 - 110718848 GC---TC---ACCG---TCACCA----TCAGAG--CAACGCTC-ATGGTGGGGG-CAGCGTCTCACGACCTCAGTCATGTGTTGTGACTTCTT-GTAGAT-GGC----CATGGCACGGACAC---GGGTACCAGGTGGAGG------T +i rn4.chr10 C 0 C 0 +s mm9.chr11 52441801 116 - 121843856 GC---TT---ACCA---TCACCA----TCGGAG--CAGCGCTC-ATGGTGGGGG-CAGCGTCTCACGACCTCCGTCATGTGCTGTGACTTCTT-GTAGAT-GGC----CATGGCGCGGACAC---GGCTCCCAGCTGGAGG------T +i mm9.chr11 C 0 C 0 +s panTro2.chr17 7856405 116 + 83384210 GC---TC---ACCA---TCGCTA----TCTGAG--CAGCGCTC-ATGGTGGGGG-CAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTT-GTAGAT-GGC----CATGGCGCGGACGC---GGGTGCCAGGTGGGGG------T +i panTro2.chr17 C 0 C 0 +s gorGor1.Supercontig_0189236 487 116 + 3737 GC---TC---ACCA---TCGCTA----TCTGAG--CAGCGCTC-ATGGTGGGGG-CAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTT-ATAGAT-GGC----CATGGCGCGGACGC---GGGTGCCGGGCGGGGG------T +i gorGor1.Supercontig_0189236 C 0 C 0 +s ponAbe2.chr17 7682674 116 + 73212453 GC---TC---ACCA---TCACTA----TCTGAG--CAGCGCTC-ATGGTGGGGA-CAGCGCCTCACGACCTCCGTCATGTGCTGTGACTGCTT-GTAGAT-GGC----CATGGCGCGGACGC---GGGTGCCAGGTGGGGG------T +i ponAbe2.chr17 C 0 C 0 +s rheMac2.chr16 7405993 116 + 78773432 GC---TC---ACCA---TCGCTG----TCTGAG--CAGCGCTC-ATGGTGGGGG-CAGCGCCTCACGACCTCCGTCATGTGCTGTGACTGCTT-GTAGAT-GGC----CATGGCGCGGACGC---GGCTGCCGGGTGGGGG------T +i rheMac2.chr16 C 0 C 0 +s papHam1.scaffold7284 33446 116 + 103654 GC---TC---ACCA---TCGCTG----TCTGAG--CAGCGCTC-ATGGTGGGGG-CAGCGCCTCACGACCTCCGTCATGTGCTGTGACTGCTT-GTAGAT-GGC----CATGGCGCGGACGC---GGCTGCCGGGCGGGGG------T +i papHam1.scaffold7284 C 0 C 0 +s calJac1.Contig2760 258379 116 + 385592 GC---TC---ACCA---TCGCTA----TCTGAG--CAGCGCTC-ATGGTGGGGG-CAGCGCCTCACGACCTCCGTCATGTGCTGTGACTGCTT-GTAGAT-GGC----CATGGCGCGGACGC---GGGTGCCACGTGGGGG------T +i calJac1.Contig2760 C 0 C 0 +s tarSyr1.scaffold_121145 321 116 + 7117 AC---TC---ACCA---TCGCTA----TCTGAG--CAACGCTC-ATGGTGGGGG-CAGCGCCTTACCACCTCTGTCATGTATTGTGACTGCTT-GTAGAT-GGC----CATGGCGCGGACGC---GGGTGCCAGGCGGGGG------T +i tarSyr1.scaffold_121145 C 0 C 0 +s micMur1.scaffold_3128 110288 116 + 169956 AC---TC---ACCA---TCGCTA----TCGGAG--CAGCGCTC-GTGGTGGGGG-CAGCGCCTCACGACCTCCGTCATGTGTTGTGACTGCTT-GTAGAT-GGC----CATGGCGCGGATGC---GGCTGCCTGGCGGGGG------C +i micMur1.scaffold_3128 C 0 C 0 +s petMar1.Contig11049 1942 117 + 16916 -----TT---ACCA---TCGTTGAAC-TCCTTG--GAGATCTC-GTGGTTGGGG-CACCGCTTTACGACCTCGGTCAGGTGGTCGGCCTTCTT-GTACAC-GGG----CATGGCACGCACTA---CGCAACCGGTCGGCAC------C +i petMar1.Contig11049 I 752 C 0 +s danRer6.chr6 30982895 119 - 61647013 ------GCATACCG---TCATTGAAC-TCTCTG--CTCAGCTC-GTGGTTCGGG-CATCGTTTGACCACCTCAGTAACATGCTCTGCTTTCTT-ATAGAC-AGG----CATGGCCCGTATGA---CTGCACCCTGGGGTGG------G +i danRer6.chr6 C 0 C 0 +s oryLat2.chr18 15469404 116 - 29908082 ------G---TCTGTTTTCCTTACAG-TCCTCG--TT---TTG-GTGGTGGGGA-CACCTCCTCACCACGTCCGCCACGTGCTCCGTCTTCTT-GTAGAC-CGC----AGTGGCCCTGAGAA---TGGCGCCCTTTGGAGG------C +i oryLat2.chr18 C 0 C 0 +s gasAcu1.chrVIII 1698226 116 - 19368704 ------G---ACCG---TCGTTGAAC-TCGCGG--CTGAGCTC-GTGGTTCGGG-CAGCGCTTCACCACCTCCGTCACGTGCTCCGCCTTCTT-GTAGAC-GGG----CATGGCCCGGATGA---CGGCGCCCTGCGGCGG------G +i gasAcu1.chrVIII C 0 C 0 +s fr2.chrUn 269239176 124 - 400509343 ----------GCTG---CCGTTTCTC-TTACAGTCCTCGTTTTGGTGGTGGGGG-CACCGGCGGACCACATCTGCCACGTGTTCGATCTTCTT-GTAAAT-GGC----TGTAGCCCTCAGGA---CGGCGCCCGCAGGAGGCTTCTTG +i fr2.chrUn C 0 C 0 +s tetNig2.chr1 12256769 114 - 22981688 -----------CCG---TCGTTGAAC-TCGCGG--CTCAGCTC-GTGGTTCGGG-CAGCGCTTCACCACTTCAGTCACGTGTTCGGCCTTTTT-GTACAC-GGG----CATGGCCCGGACGA---CGGCGCCCTGCGGCGG------G +i tetNig2.chr1 C 0 C 0 +s dipOrd1.scaffold_14566 2290 108 - 35663 -------------A---TCATTA----TCAGAA--CAG-GCTC-ATGATGTGGG-CAGCGCCTCACAACTTCTGTCATGGGCTGGGACTTCTT-GTAGAT-GGC----CATGGTGCGGACTC---GTGTGCCAGGTGGAGG------G +i dipOrd1.scaffold_14566 C 0 C 0 +s tupBel1.scaffold_141935.1-6425 4503 107 + 6425 -----------------TCACTG----TCAG-G--CAGCGCTC-GTGTCGGCGC-AAG---CTCTCCACCGCTATCATAC-TTGAGACTGCTTCGAAGAA-GGC----CAATCGGCCGATACACGAGGTGCCCGCCGGGAG------C +i tupBel1.scaffold_141935.1-6425 I 1462 C 0 +s choHof1.scaffold_240329 1872 111 - 2109 -----------------TCATTGAAT-TCACAG--CTCAGCTC-ATGGTTGGGG-CACCATTTCCCCACCTCAGTGACATGCTCAGCTTTCTT-GTAGAT-AGG----CATGGCACAGATCA---CAGCACCCTGAGGAGG------T +i choHof1.scaffold_240329 C 0 C 0 +s echTel1.scaffold_129816 820 114 - 1574 -----------GCA---TCGATATAG-TCAGAG--CAACGCTC-CTGGTGGGGA-CAGCGCTTCACAACCTCCGTCATGTGCTCAGACTTCTT-GTAAAT-GGC----CATGGTGCGCACAC---GGGTGCCAGGCGGGGG------C +i echTel1.scaffold_129816 C 0 C 0 +s otoGar1.scaffold_118233.1-50963 5339 86 + 50963 ------C---ACCC---CCA--------------------------GATGGGGG-CAGCACCTCGCGACC----TTATGCGTAGTGATGGCTA-GTGAGT-GACTGGGCGTGCCGTGG----------TGTCC-ATGGTGG------C +i otoGar1.scaffold_118233.1-50963 C 0 C 0 +e monDom5.chr2 286665505 12170 - 541556283 I +e speTri1.scaffold_150122 1470 33750 + 48993 M + +a score=4696355.000000 +s hg19.chr13 32914423 162 + 115169878 TTTAGCACAGCAAGTGG-AAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTT--------------CTGA---AATAGAAGATA---GTAC----------CAAGCAAGTCTTTTCCAA----AGTATTGTTTAAA----AGTAACGAA-----CAT---T-----------CAGACCAGCTCACAAGAGAAGAAAATACT +s panTro2.chr13 32107304 162 + 115868456 TTTAGCACAGCAAGTGG-AAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTT--------------CTGA---AATAGAAGACA---GTAC----------CAAGCAAGTCTTTTCCAA----AGTATTGTTTAAA----AGTAACGAA-----CAT---T-----------CAGACCAGCTCACAAGAGAAGAAAATACT +i panTro2.chr13 C 0 C 0 +s gorGor1.Supercontig_0026501 3880 162 + 8047 TTTAGCACAGCAAGTGG-AAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTT--------------CTGA---AATAGAAGATA---GTAC----------CAAGCAAGTCTTTTCCAA----AGTATTGTTTAAA----AGTAACGAA-----CAT---T-----------CAGACCAGCTCACAAGAGAAGAAAATACT +i gorGor1.Supercontig_0026501 C 0 C 0 +s ponAbe2.chr13 31875809 162 + 117095149 TTTAGCACAGCAAGTGG-AAAATCTGTCCAGATATCAGATGCTTCATTACAAAAGGCAAGACAAGTGTTTT--------------CTGA---AATAGAAGATA---GTAC----------CAAGCAAGTCTTTTCCAA----AGTATTGTTTAAG----AGTAACGAA-----CAT---T-----------CAGACCAGCTCACAAGACAAGAAAATACT +i ponAbe2.chr13 C 0 C 0 +s rheMac2.chr17 11711748 162 + 94452569 TTTAGCACAGCAAGTGG-AAAATCTGTCCAGGTATCAGATGCTTCATTACAAAAGGCAAGACAAGTGTTTT--------------CTGA---AATAGAAGATA---GTAC----------CAAGCAAGTCTTTTCCAA----AGTATTGTTTAAA----AGTAATGAA-----CAT---T-----------CAGACCAGCTCACAAGAGAAGAAAATACT +i rheMac2.chr17 C 0 C 0 +s papHam1.scaffold8860 29325 162 - 91400 TTTAGCACAGCAAGTGG-AAAATCTGTCCAGGTATCAGATGCTTCATTACAAAAGGCAAGACAAGTGTTTT--------------CTGA---AATAGAAGATA---GTAC----------CAAGCAAGTCTTTTCCAA----AGTATTGTTTAAA----AGTAATGAA-----CAT---T-----------CAGACCAGCTCACAAGAGAAGAAAATACT +i papHam1.scaffold8860 C 0 C 0 +s calJac1.Contig1458 176003 162 + 405365 TTTAGCACAGCAAGTGG-AAAATCTGTACAGGTATCAAATGCTTCATTGCAAAAGGCAAGACAAGTGTTTT--------------CTGA---GATAGATGATA---GTAC----------CAAGCAACTCTCTTCCGA----AGTATTGTTTACA----AATAATGAA-----CAT---T-----------CAGACCAGCTCACAAGAGAAGAAAATACT +i calJac1.Contig1458 C 0 C 0 +s tarSyr1.scaffold_132783 990 156 - 6023 TTTAGCACAGCAAGTGG-AAAATCTGTACAAGTTTCAGATGCTTCATTACAAAAGGCAAGACAGGTGTTTT--------------CTGA---GGTAGATGATA---ATAC----------CGAACAACTCTTTTCCAA----AGTATCATTTAAA----AGTA-----------AT---T-----------CAGATCAGTTTACAAAGGAAGAGACTACT +i tarSyr1.scaffold_132783 C 0 C 0 +s micMur1.scaffold_6236 97203 158 + 100975 TTTAGTACAGCAAGTGG-AAAATCCATACAAGTATCAGATGCTTCATTACAAAAGGCAAGACAGGTGTTTT--------------CTGA---GATAGATGATA---GTGC----------CAAGCAACTCTTTTCCAA----AATATCCTTTAAA----AGTAATAAAGA---TAT---T-----------TAGACCAGTTCAC---AGAGAGAAA---A +i micMur1.scaffold_6236 C 0 C 0 +s otoGar1.scaffold_101144.1-52040 43355 162 - 52040 TTTAGCACAGCAAGTGG-AAAATCCATACAGGTATCAGAGTCTTCATTACAACAGGCAAGACAGGTGTTTT--------------CTGA---GATAGAAGAGC---ATGC----------CAAGCAACACTTTTCAAA----AGTATCCTTTAAA----AATAATGAAGA--GTAT---T-----------CAGACCAGTTCACAAGAGAAGAAAA---A +i otoGar1.scaffold_101144.1-52040 C 0 C 0 +s tupBel1.scaffold_131324.1-77451 10960 135 - 77451 TTTAGCACAGCAAGTGG-AAAATCCATACATGTATCAGATGTTTCATTACAAAAAGCAAGACAGGTGTTTT--------------CTGA---GATAGAAGATA---ATGC----------CAA-------------------------------A----AATAATGAA-----CAT---T-----------TAGATCAGTTCACAAGAGAAGAAAATACT +i tupBel1.scaffold_131324.1-77451 C 0 C 0 +s rn4.chr12 42474610 162 - 46782294 TTTAGCACAGCAAGTGG-AAAAGCTGTACAAGTATCTGATGCTTCATTGGAAAAGGCACGGCAAGTGTTTT--------------CTGA---GATAGATGGTG---ATGC----------TAAACAGTTAGCTTCCAT----GGTGTCACTGGAA----GGTAATGAA-----AAA---T-----------CACATCACTCTGTGAAAAGAGAAAGCTCT +i rn4.chr12 C 0 C 0 +s mm9.chr5 151345137 162 + 152537259 TTTAGCACAGCAAGTGG-AAAAGCTATACAAGTATCAGATGCTTCATTAGAAAAGGCAAGGCAAGTGTTTT--------------CTGA---GATGGATGGTG---ATGC----------TAAACAGTTATCTTCCAT----GGTGTCACTGGAA----GGTAATGAA-----AAA---C-----------CACATCACTCTGTGAAAAGAGAAAACTCT +i mm9.chr5 C 0 C 0 +s cavPor3.scaffold_6 33813162 159 + 61187194 TTTAGCACGGCAAGTGG-AAAATCTGTACAAGTATCAAATGGTTCATTACAAAAGGCAAAACAGATGTTTT--------------CTAA---AACAGAAGATA---GTGC----------CAAGCAGCTGTTTTCCAA----AGT---ATTTAAA----AGCAGTGAA-----CAT---T-----------CAGACCAATTCACAAAAGAAGAAATTACT +i cavPor3.scaffold_6 C 0 C 0 +s speTri1.scaffold_136871 52128 165 - 149453 TTTAGCACAGCTAGTGG-AAAATCTGTACAAGTATCAGATACTTCGTTACAAAAGGCAAGACAGATATTTT--------------CTGA---GATAGAAGATA---ATGC----------CAACCAACTCTTTTCCAA----AGTATCACTTAAA----AGCAACGAA-----GAACATT-----------CAAACCCGTTCACAAGAGAAAAAAGTACT +i speTri1.scaffold_136871 C 0 C 0 +s oryCun2.chrUn0004 3065495 162 + 7969563 TTTAGCACAGCAAGTGG-AAAATCTGTGCATGTGTCAGATGCTTCCTTACAAAAGGCGAAAGAGATGTTTT--------------CTGA---GACAGAAGATA---GTGC----------TGAACAACTCTTTTCCAA----AGTATCTTTTAAA----AGTAAAGAA-----TGT---T-----------CAGACCAATTCACCAGAGAAGAGAATTCT +i oryCun2.chrUn0004 C 0 C 0 +s ochPri2.scaffold_63227 3283 162 + 7289 TTCAGCACAGCAAATGG-AAAGCCTGTACATGTGTCAGATGCTGCATTACAAAAGGCAAAGCAGATGTTTT--------------CTGA---AACTGAAGGTA---GTGC----------AGAACAACTCTTCAGCAA----AGTATCATTTAAA----GGTAAAGAA-----CGC---T-----------CAGACCAGTTCACAGGAGACGAAAGTGCT +i ochPri2.scaffold_63227 C 0 C 0 +s vicPac1.scaffold_1303 214051 162 - 397986 TTTAGCACAGCAAGTGG-AAAATCTGTACACATATCAGATGCTGCATTCCAAAAGGCAAAACAGGTATTTT--------------CTAA---GATAGAAGATG---ATGC----------TAAGCAACTCCTTTCCAA----AGTATCATTTAAA----AGTAATGAAGA--ACAG---T-----------CGGATAAGTTCTCAGG---GGAAAATACT +i vicPac1.scaffold_1303 C 0 C 0 +s turTru1.scaffold_99052 59316 165 - 340450 TTTAGCACAGCAAGTGG-AAAATCTGTACAAGTATCAGATGCTGCCTTACAAAAGGCAAGACAGGTATTTT--------------CTAA---GACAGAAGATA---GTGG----------TAAGCAACTCTTTCCCCA----AGTATCATTTAAA----AGTAATGAAGA--ACAT---T-----------CAAACAAGTTTGCAAGAGAAGAAAATACT +i turTru1.scaffold_99052 C 0 C 0 +s bosTau4.chr12 56910197 165 - 85358539 TTTAACACAGCAAGTGG-AAAATCTGTCCAAGTGTCAGATTCTGCATTACAAAAAGCGAGACAGGTATTTT--------------CTAA---GTCAGAAGACA---GTGC----------CAAGCAGTTCTTTTCCAG----AGTATCATTTAAA----AGTAATGAAGA--GCAT---T-----------CAGACATATTCACAAGAAAAGAAAATACT +i bosTau4.chr12 C 0 C 0 +s equCab2.chr17 11530646 165 + 80757907 TTTAGCACAGCAAGTGG-AAAATCTGTGCAAGTATCAGATGCTGCATTACAAAAGGCAAGACAGGTATTTT--------------CTAA---GATAGAAGATG---GTGA----------CAATCAGCTCTTTTCCAA----AGTATCACTTAAA----AATAATAAAGA--ACAT---T-----------CAGACAAGTTCACAAGAGAAGAAAATACT +i equCab2.chr17 C 0 C 0 +s felCat3.scaffold_141508 959 165 + 43838 TTTAGCACAGCAAGTGG-AAAATGTGTACAAGTATCAGATGCTGCACTACAAAAGGCAAGACAGGTGTTTT--------------CTAA---GGTAGAAGACA---GTGC----------CAAGCAGCCCTTTTCCAA----AGTATCATTTAAA----CATAATGAGGA--TCAC---T-----------CAGACAAGTTCACAAGAGAAGAAAATACT +i felCat3.scaffold_141508 C 0 C 0 +s canFam2.chr25 43807475 165 - 54563659 TTTAGCACAGCAAGTGG-AAAATCTGTACAAGTATCAGATGCTGCAATACAAAAGGCAAGAGAGGTGTTTT--------------CTAA---GCTAGAAGATA---GTGC----------CAAGCAACTCTTTCCTGA----AGTATCACTTAAA----GATAATGAAGA--ACAT---T-----------CAGAAAAGTTCACAAATGAAGAAAATACT +i canFam2.chr25 C 0 C 0 +s myoLuc1.scaffold_166230 5395 165 - 15142 TTTAGCACAGCAAGTGG-AAAATGTGTACAAGTGTCAGATGCTGCCTTACAGAAGACCAGATGCATCTTTT--------------CTAA---GCTAGAAGAGA---GTGC----------CGAGCAGCTCTTTTCCAA----AGTATCATTTGAA----TCTAATGAAGA--ACAT---T-----------CAGACAGGCTCACAAGAGAAGAAAATACT +i myoLuc1.scaffold_166230 C 0 C 0 +s pteVam1.scaffold_6136 29260 165 - 97493 TTTAGCACGGCGGGTGG-GAAGTTGGTACAGGTGTCGGGCGCTGCACTGCAAAAGGCCAGGCAGATATTTT--------------CTAG---GCTAGAAGATA---GTGC----------CGAGCAGCTCGGGGCCAG----AATAGCCTTTGAA----CATGATGAAGA--TCAT---T-----------CAGAGAATGCCACAAGAAAAGACGATACC +i pteVam1.scaffold_6136 C 0 C 0 +s eriEur1.scaffold_292860 9251 165 + 12208 TTTAGCACAGCAAGTGG-AAAATCTGTACAAGTATCAGATGCTGCATTACAAAAGGCAAGAAAGGTATTTT--------------CTAAACTAGAAGAAGATA---GTGC----------TGACCAACTCCTCTCCAA----AGAGTC---ATTG----AAAAATAGTGA--ACAT---T-----------CAGACAACCTCACAAGAGATAAAAGTACT +i eriEur1.scaffold_292860 I 630 C 0 +s sorAra1.scaffold_231034 27222 162 + 64674 TTTAGCACAGCAAGTGG-AAAAGCTGTACAAGTATCAGATGCTTCTTTGCAAAAGGCAAGACAAGTGTTTT--------------CAAA---GGTAGAAGATA---ATGC----------TGATCAGCCTTTTTctga----agtatt---taaa----aataatagaga--acAT---T-----------CGGACaagtacacaaaagaaaaaagtact +i sorAra1.scaffold_231034 C 0 C 0 +s proCap1.scaffold_30001 16489 165 - 22135 TTTAGCACAGCTGGTGG-GAAATCCGTGCAGGTGTCAGATGCTGCCTTAAGAAAGACAAGACAGGTGTTTT--------------CTGA---GATGGAAGATA---GTGC----------CCAGCAGCTTGTGTACAC----AGAATCCTGTCAC----AGTAACAAGGG--ACAT---T-----------CAAACAAGGTCACAAAAGAAAGTAAGGCT +i proCap1.scaffold_30001 C 0 C 0 +s loxAfr3.scaffold_11 62578974 162 - 67275361 TTTAGCACAGCAAGTGG-GAAATCTGTACAGGTGTCAGATGCTTCATTACAAAAGACAAGACAGGTGTTTT--------------CTGA---GATTGAAGAGA---GTAC----------CAAGTATCTCTTTTCCAA----ACTATCCTTTAAA----AGTAATGAAG-----AT---T-----------CAAACAAGTTCACCAAAGAAAAAAATACT +i loxAfr3.scaffold_11 C 0 C 0 +s choHof1.scaffold_37163 7318 162 - 13057 TTTAGCACAGCAAGTGG-GAAATTTGTACAAGTATCAGATGCTTCATTACAAAAGGCAAGTCAGGTATTTT--------------CTGA---GATAGAAGATA---GTGC----------CAAGCAGTTCTTTTCCAA----AGTATCCTTTAAA----ATTAATGAAGA--ACAT---T-----------CAGACAAATTCAC---AGAAGAAAGTACC +i choHof1.scaffold_37163 C 0 C 0 +s dasNov2.scaffold_18245 14882 162 - 37296 TTTAGCACAGCAAGTGG-AAAATCTGTACAAGTATCAGACACTTCATTACAAAAGGCAAGACAGATATTTT--------------CTGA---GACAGAAATTA---GTGC----------CAAGCAGTTCTTTTCCAA----AGTATCCTTTAGA----AGTAAT---GA--ACAT---T-----------CAGACCAATTTACAAAAGAAGAAAATAAT +i dasNov2.scaffold_18245 C 0 C 0 +s macEug1.Scaffold381358 340 162 + 1363 TTTTGTACAGCCAATGG-CAAACCTGTGCAAGTATCAGGTAATTCATTAAAGAAAGCCAgacaggtttttt--------------ctga---aatagaaaata---attc----------tgaGCAATTACTTTCCAT----GACATCCTTTAAA----GATAGTGAAAG--CAAT---C-----------CAGAAAcatt---aatagaagaaaatgcc +i macEug1.Scaffold381358 C 0 C 0 +s monDom5.chr4 304148438 156 + 435153693 TTTTGTACAGCAAATGG-CAAACCTGTACAAGTATCAGATAATTCATTAAAGAAAGCCAGACAAGTATTTT--------------CTGA---AATAGCAAATG---ATTC----------TGAGCAATTACTTTCCA-------------TTAAA----GGTAGTGAAAA--CCAT---C-----------CAGAAACACTAATAGGAGAAGAAAATGCC +i monDom5.chr4 C 0 C 0 +s ornAna1.Ultra336 845659 165 + 10157919 TTTAATACCGCAAGCGG-AAAACCCGTGCGGGTATCAGATGCTTCACTGAAGAAGGCAAAGCAAGTGTTTT--------------CTGC---AATAGAAAATC---ACTC----------TGAGCGACTGCCCTTTGT----AACATCTTTTAAA----GACACTGAAAG--TCAT---C-----------CAGAGAAGGTCATGGATGAAAGCAATCCT +i ornAna1.Ultra336 C 0 C 0 +s galGal3.chr1 22136643 179 - 200994015 TTCAGTACGGCAAGTGG-GAAGCCTGTGCAACTATCAGAAGAGTCGCTAAAGAAAGCTAGACAGCTCTTTT--------------CTGA---AATGGAAGGTAGCCATTCATCAGGGCTACAAGATGCACATTTGCTT----GAAGACGTTGAGA----AAT-CCACAAACCATGG---T-----------GAAGTATTTCCTAGAGAAATGCAGCTACT +i galGal3.chr1 C 0 C 0 +s taeGut1.chr1 50821092 182 + 118548696 tttagtACAGCAAGTGG-AAAGCCTGTACAGCTTTCAGAAGAGTCACTCAGGAAAGCTAGACAGctctttt--------------ctga---aatggaagATAGTCATTCACCACATGTACAAGAAGCATTTTTAGTT-GAGGAAGATGTTGAAA----AGT-CTAAAATGCACAT---T-----------GAAGTACTACCTAGGGAAATGCAGGTAGT +i taeGut1.chr1 C 0 C 0 +s anoCar1.scaffold_312 1391078 185 - 1725611 TTCAGCACAGCGAGTGG-AAAAGCTGTTCAGTTATCTGAAGAGTCATTGAAAAAAGCAAgacagttttttt--------------ctga---aatcGAAGATG---ATTCATTAGGTTGTCAA---ACACATGTATCA----GGTGGTGGTGACC----ATTACTGGAAAGCGTCT---TCTGTCAGGAACAAAGCCACCGCTAAAGAAAATAAACTTCT +i anoCar1.scaffold_312 C 0 C 0 +s xenTro2.scaffold_80 2044187 176 - 3128562 TTTAGTACTGCAAGTGG-CAAGACGGTGCAGTTGTCAGACGAGTCTTTGAAGAAAGCTAGGGTGATTTTTT--------------CTGA---AATAGATACTT---GTCCGTT-------GATGCAACAGCAGACTAATGAAAGCACTGTTGAAGAGATAGTAATAGGAGGAGGAA---T-------------GACAAAATCAAAACAGATGCCATTAAC +i xenTro2.scaffold_80 I 4 C 0 +s tetNig2.chr16 4699911 111 + 9031048 TTTCGTACAGCCAGTGGCAAGGCAGCAACCTGCTCGTCTGAA-GCCCTCCAGAAAGCTAAAGCGCTTTTTA--------------GTGA---CAT------CA---GTTC----------CAAT-------------G----AGAATACCGGACA----AGCAGACCA-----------T---------------------------------------- +i tetNig2.chr16 C 0 C 0 +s danRer6.chr15 32393696 147 + 47237297 TTTTCTACAGCAGGTGG-GAGGAAGATGGATATTTCTGTGACTGCACTGCAGAAGGCAAACAACCTCTTTAAAGATTGTGAAGAGGAGA---GTT------TA---GCTT----------CTAG-------------G----AGTCTTGCGCACC----AAGGCTTCA-----------C-----------TA-------CTGCCAGTGGTAAAAATGTT +i danRer6.chr15 C 0 I 102 +e dipOrd1.scaffold_47936 6489 3359 - 10608 I +e echTel1.scaffold_282619 20187 28333 + 54172 I +e oryLat2.chr14 9930930 2 + 33607196 I +e gasAcu1.chrVII 19975244 0 + 27937443 I + +a score=-751512.000000 +s hg19.chr13 32914585 52 + 115169878 -GCTAT-------------ACGT-----------ACTCCAGAACATTTAAT-----AT--CCCAAAAAGGCTTTTCATATAAT-G +s panTro2.chr13 32107466 52 + 115868456 -GCTAT-------------ACGT-----------ACTCCAGAACATTTAAT-----AT--CCCAAAAAGGCTTTTCATATAAT-G +i panTro2.chr13 C 0 C 0 +s gorGor1.Supercontig_0026501 4042 52 + 8047 -GCTAT-------------ACGT-----------ACTCCAGAACATTTAAT-----AT--CCCAAAAAGGCTTTTCATATAAT-G +i gorGor1.Supercontig_0026501 C 0 C 0 +s ponAbe2.chr13 31875971 52 + 117095149 -GCTAT-------------ACAT-----------ACTCCAGAAAATTTAAC-----AT--CCCAAAAAGGCTTTTCATATAAT-G +i ponAbe2.chr13 C 0 C 0 +s rheMac2.chr17 11711910 55 + 94452569 -ACTAT-------------ACAT-----------ACTCCAAAACATTTAATA--TCAT--CCCAAAAAGACTTTTCACATAAT-G +i rheMac2.chr17 C 0 C 0 +s papHam1.scaffold8860 29487 55 - 91400 -ACTAT-------------ACAT-----------ACTCCAAAACATTTAATA--TCAT--CCCAAAAAGACTTTTCATATAAT-G +i papHam1.scaffold8860 C 0 C 0 +s calJac1.Contig1458 176165 54 + 405365 -GCTAC-------------ACAG-----------ATAGCAGAACATTTGATA--CCAT--CCCAAAAAGGCTTTTCATATAAT-- +i calJac1.Contig1458 C 0 C 0 +s tarSyr1.scaffold_132783 1146 55 - 6023 -ATGAT-------------GCAT-----------ACCCCAAAACATTTAATA--GCAC--CCCAAAAAGGCTTTTCACATAAT-G +i tarSyr1.scaffold_132783 C 0 C 0 +s micMur1.scaffold_6236 97361 52 + 100975 -ACAAT-------------GCAT-----------ATCC--CCAAATTTAAT-----ATCACCCCAAAAGGCTTTTCGTATAAT-G +i micMur1.scaffold_6236 C 0 M 467 +s otoGar1.scaffold_101144.1-52040 43517 52 - 52040 -GTAAT-------------TCAT-----------GTCCCACAAAAGTTAAT-----AT--CCCAAAAAGGCTTTTCATGCAAT-G +i otoGar1.scaffold_101144.1-52040 C 0 C 0 +s tupBel1.scaffold_131324.1-77451 11095 55 - 77451 -ATGAC-------------ACAT-----------ACTCCCCAGAATGTATTA--TCAC--CCAAAAAAGGCTTTTCATATAAT-A +i tupBel1.scaffold_131324.1-77451 C 0 C 0 +s rn4.chr12 42474772 55 - 46782294 -GTGGT-------------GCAT-----------AACACCCATGGTGTATTG--TCAC--TCCGAAAAACCCTCCCAGGCAAT-G +i rn4.chr12 C 0 C 0 +s mm9.chr5 151345299 55 + 152537259 -GTGGT-------------GCAT-----------AGCACCCAGGGTGTATTG--TCAC--TCCCAAAACCCCTCCCAGGCAAT-G +i mm9.chr5 C 0 C 0 +s cavPor3.scaffold_6 33813321 55 + 61187194 -GTAAT-------------GCGC-----------ACCCCCTCAAAAGTACCA--TCAC--CTCCGAAAAACTTTCACCATAGT-G +i cavPor3.scaffold_6 C 0 C 0 +s speTri1.scaffold_136871 52293 55 - 149453 -ATGGC-------------ACAT-----------GCCCCCCCAAACGTACTA--TCAC--CCGGGAAAAGCTTTCTGTGTAAC-A +i speTri1.scaffold_136871 C 0 C 0 +s oryCun2.chrUn0004 3065657 55 + 7969563 -ATGAC-------------AGAT-----------ATCCCAAAAAATTTACTG--TCAT--CTCAGAAAGACTTTTCAAATAAT-G +i oryCun2.chrUn0004 C 0 C 0 +s ochPri2.scaffold_63227 3445 52 + 7289 -GTGAC-------------AGAT-----------GGCCCAGAAAACACACTG-----T--TCCAGAAGGACGTTCCATATAAT-G +i ochPri2.scaffold_63227 C 0 C 0 +s vicPac1.scaffold_1303 214213 27 - 397986 -AAGAT-------------ACAT-----------ACCCCTCAAAATTTACTG--------------------------------- +i vicPac1.scaffold_1303 C 0 C 0 +s turTru1.scaffold_99052 59481 27 - 340450 -GTGAT-------------ACAT-----------ACCCCCCAAAATTTACTA--------------------------------- +i turTru1.scaffold_99052 C 0 C 0 +s bosTau4.chr12 56910362 28 - 85358539 -ATGAC-------------ACAT----------AACCCCCCCAAATTTACTA--------------------------------- +i bosTau4.chr12 C 0 C 0 +s equCab2.chr17 11530811 27 + 80757907 -ATGAT-------------ACAT-----------AGCCCCCAAAATTTGCTG--------------------------------- +i equCab2.chr17 C 0 C 0 +s felCat3.scaffold_141508 1124 29 + 43838 -ATGAT-------------ACAT-----------ACCCCCCAAAATTTACTATC------------------------------- +i felCat3.scaffold_141508 C 0 I 913 +s canFam2.chr25 43807640 29 - 54563659 -GTGAT-------------ATAT-----------ACCTCCCAAAATTTACTATC------------------------------- +i canFam2.chr25 C 0 C 0 +s myoLuc1.scaffold_166230 5560 27 - 15142 -ATGAT-------------ACAT-----------ATCCCCCCAAATTTG-------------------------CCA-------- +i myoLuc1.scaffold_166230 C 0 C 0 +s pteVam1.scaffold_6136 29425 27 - 97493 -GTGAT-------------ACGC-----------ACCCCCCAGAATGTC-------------------------CCG-------- +i pteVam1.scaffold_6136 C 0 C 0 +s eriEur1.scaffold_292860 9416 27 + 12208 -GTGGT-------------ACAT-----------ACTACCCCAAATTC----------------AAAA----------------- +i eriEur1.scaffold_292860 C 0 C 0 +s sorAra1.scaffold_231034 27384 24 + 64674 -gtAAT-------------ACAT-----------AGCGCTTCAAAATC-------------------A----------------- +i sorAra1.scaffold_231034 C 0 C 0 +s proCap1.scaffold_30001 16654 55 - 22135 -GTGAT-------------ACAC-----------ACCAAAGACAAATTGCCA--TCAC--CCCTAGCAGGCTTTTCATCTAGA-G +i proCap1.scaffold_30001 C 0 C 0 +s loxAfr3.scaffold_11 62579136 53 - 67275361 -GTGAT-------------ACAT-----------ACCAAAAACAAATTGCTA--CCAC--CCCAGGAAGGCTTTTCGTCTAG--- +i loxAfr3.scaffold_11 C 0 C 0 +s choHof1.scaffold_37163 7480 55 - 13057 -ATGAC-------------ACAC-----------ACCAACAACAATTTACCA--TTAC--CCCAAAAAGATTTTTTATATAA-TG +i choHof1.scaffold_37163 C 0 C 0 +s dasNov2.scaffold_18245 15044 52 - 37296 -ATGAC-------------AC--------------TTAGCAACAGTTTACCA--TCAT--CTCAAAAAGGCTTTTCATGTAA-TG +i dasNov2.scaffold_18245 C 0 C 0 +s macEug1.Scaffold381358 502 52 + 1363 -TTGTT-------------ACAT-----------GC-----AAAAACTAACCTATCAG--AAAAGAAAGACTATTTAAATAAT-A +i macEug1.Scaffold381358 C 0 C 0 +s monDom5.chr4 304148594 52 + 435153693 -ATGCT-------------TTAT-----------GC-----AAAAATCAACCTACCAG--CACAAAAAGACTATTTGAGTAAT-A +i monDom5.chr4 C 0 C 0 +s ornAna1.Ultra336 845824 36 + 10157919 -AACAG-------------AAGTGAAAAACCCCAAGTGCTACAAAAGCAC----------------------------------- +i ornAna1.Ultra336 C 0 C 0 +s galGal3.chr1 22136822 32 - 200994015 -GCTGCCAAGAGGGAAGGAGAAT-----------GCCAGCACGG----------------------------------------- +i galGal3.chr1 C 0 C 0 +s taeGut1.chr1 50821274 32 + 118548696 -ATCAtcaaaaggggaagaaaat-----------accAGCCCTG----------------------------------------- +i taeGut1.chr1 C 0 C 0 +s anoCar1.scaffold_312 1391263 32 - 1725611 -CATGTCCCAAGGGAAAATACTT-----------TCAAATGCAG----------------------------------------- +i anoCar1.scaffold_312 C 0 C 0 +s xenTro2.scaffold_80 2044363 22 - 3128562 -AACAG-------------AAAA-----------AGTCGAAACAACT-------------------------------------- +i xenTro2.scaffold_80 C 0 C 0 +s tetNig2.chr16 4700022 22 + 9031048 GCTGAT-------------CCGG-----------AACAAGAGAAGA--------------------------------------- +i tetNig2.chr16 C 0 C 0 +e dipOrd1.scaffold_47936 6489 3359 - 10608 I +e echTel1.scaffold_282619 20187 28333 + 54172 I +e oryLat2.chr14 9930930 2 + 33607196 I +e gasAcu1.chrVII 19975244 0 + 27937443 I +e danRer6.chr15 32393843 102 + 47237297 I +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafFrag_in.bed Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,1 @@ +chr17 7571738 7590808 TP53 0 - \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafFrag_in12.bed Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,1 @@ +chr17 7571738 7590808 TP53 0 - 7572926 7579912 0 11 1188,1741,1921,1025,1000,398,900,896,900,900,8201 0,1188,2929,4850,5875,6875,7273,8173,9069,9969,10869 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafIn.maf Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,5 @@ +##maf version=1 scoring=blastz +a score=1234 +s hg38.chr7 1000 20 + 248956422 ACGTACGTACGTACGTACGT +s panTro4.chr7 1000 20 + 159345973 ACGTAC-TAC-TACGTACGT +s gorGor3.chr7 1000 20 + 174310764 A-GTACGTAC-TACG-AC-T \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/malformed.maf Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,32 @@ +##maf version=1 scoring=example +a score=1000.0 +s human.chr1 100 10 + 1000 ACGTACGTAC +s mouse.chr1 200 10 + 2000 ACGTACGTAC +s dog.chr1 300 10 + 3000 ACGTACGTAC + +a score=500.0 +s human.chr2 150 5 + 1000 ACGTA +s mouse.chr2 250 5 + 2000 ACGT- + +a score=200.0 +s human.chr3 200 15 + 1000 ACGTACGTACGTACG +s cat.chr3 350 15 + 4000 ACGTACGTACGTACG +s dog.chr3 450 15 + 5000 ACGTACGTACGTACG +s rat.chr3 550 15 + 6000 ACGTACGTACGTACG + +a score=50.0 +s human.chr4 110 10 + 1000 ACGTACGTAC +s mouse.chr4 210 10 + 2000 ACGTACGTAC + +a score=3000.0 +s human.chr5 105 10 + 1000 ACGTACGTAC +s mouse.chr5 205 10 + 2000 ACGTACGTAC +s dog.chr5 305 10 + 3000 ACGTACGTAC +s cat.chr5 405 10 + 4000 ACGTACGTAC +s rat.chr5 505 10 + 5000 ACGTACGTAC +s cow.chr5 605 10 + 6000 ACGTACGTAC + +a score=600.0 +s human.chr6 100 10 + 1000 ACGTACGTAC +s mouse.chr6 200 10 + 2000 ACGTACGTAC +s dog.chr6 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/panTro4.bed Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,1 @@ +chr7 1007 1008 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref.fa Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,2 @@ +>chr7 +NNNNNACGTACGTACGTACGTNNNNNTGCACTGCACTGCACTGCANNNNN \ No newline at end of file