Mercurial > repos > iuc > yahs
changeset 0:d87433f2a54d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
| author | iuc |
|---|---|
| date | Wed, 29 Jun 2022 13:06:23 +0000 |
| parents | |
| children | a3a92e30a727 |
| files | move_files.py test-data/test.agp test-data/test.bam test-data/test.bed test-data/test.fasta test-data/test_01_scaffolds_final.agp test-data/test_01_scaffolds_final.fa test-data/test_02_no_break.agp test-data/test_02_scaffolds_final.agp test-data/test_02_scaffolds_final.fa test-data/test_03_initial_break.agp test-data/test_03_scaffolds_final.agp test-data/test_03_scaffolds_final.fa test-data/test_04_initial_break.agp test-data/test_05.fasta yahs.xml |
| diffstat | 16 files changed, 1208 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/move_files.py Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,13 @@ +import os +import shutil + +files = os.listdir() +for file in files: + if "yahs_out" in file and "final" in file: + shutil.move(file, "final_outs/" + file) + elif "yahs_out_init" in file: + shutil.move(file, "initial_break/" + file) + elif "_break.agp" in file: + shutil.move(file, "agp_break/" + file) + elif "yahs_out" in file and ".agp" in file: + shutil.move(file, "agp_out/" + file)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.agp Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.bed Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fasta Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,100 @@ +>HiC_scaffold_1 +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAAATCTGGTGAAGCTTTCTGCATGTGATGT +GCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACA +CTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGA +CGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGC +CATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCAC +TGTGTCTCCGTGCCGAGCTAGATCTCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCTGGCATTGTAGGTACCAGACACTAACAAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCTCGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTGCCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_01_scaffolds_final.agp Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_01_scaffolds_final.fa Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,133 @@ +>scaffold_1 +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGC +CATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACA +CTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGG +TACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTG +AAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGT +GTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCAC +TGTGTCTCCGTGCCGAGCTAGATCTCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCTGGCATTGTAGGTACCAGACACTAACAAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCTCGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTGCCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_02_no_break.agp Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_02_scaffolds_final.agp Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_02_scaffolds_final.fa Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,133 @@ +>scaffold_1 +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGC +CATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACA +CTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGG +TACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTG +AAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGT +GTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCAC +TGTGTCTCCGTGCCGAGCTAGATCTCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCTGGCATTGTAGGTACCAGACACTAACAAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCTCGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTGCCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03_initial_break.agp Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03_scaffolds_final.agp Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03_scaffolds_final.fa Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,133 @@ +>scaffold_1 +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGC +CATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACA +CTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGG +TACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTG +AAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGT +GTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCAC +TGTGTCTCCGTGCCGAGCTAGATCTCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCCATCTGGCATTGTAGGTACCAGACACTAACAAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCTCGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTGCCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04_initial_break.agp Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_05.fasta Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,397 @@ +>scaffold_1 +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGAGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAAATCTGGTG +AAGCTTTCTGCATGTGATGT +GCCTTGTGTGGATCCGTGGC +CATCGCATTGTGTCTGGTGT +GTAGGTACCCAGACACTTAA +GCAAACTCGATCGTTGTACA +CTTTGATGGGCAACCATCAC +TGTGTCTCCGTGCCGTGCTA +GATCTCCCCTAGCCGTAAGG +TACTTTGAACGCCCCTTCGA +CGACGAGTTACAAGAGTGTG +GTATGTGTCATAATCTGGTG +AAGCTTTCTGCATGTGATGT +GCCTTGTGTGGATCCGTGGC +CATCGCATTGTGTCTGGTGT +GTAGGTACCCAGACACTTAA +GCAAACTCGATCGTTGTACA +CTTTGATGGGCAACCATCAC +TGTGTCTCCGTGCCGAGCTA +GATCTCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGAGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGAGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGAGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGAGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGT +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCGCATTGTGTCTGGTGTG +TAGGTACCCAGACACTTAAG +CAAACTCGATCGTTGTACAC +TTTGATGGGCAACCATCACT +GTGTCTCCGTGCCGTGCTAG +ATCTCCCCTAGCCGTAAGGC +ACTTTGAACGCCCCTTCGAC +GACGAGTTACAAGAGTGTGG +TATGTGTCATAATCTGGTGA +AGCTTTCTGCATGTGATGTG +CCTTGTGTGGATCCGTGGCC +ATCTGGCATTGTAGGTACCA +GACACTAACAAACTCGTCGT +CGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCT +AGCTCGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTGC +CTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGT +CGAAGGGGCGTTCAAAGTAC +CTTACGGCTAGGGGAGATCT +AGCACGGCACGGAGACACAG +TGATGGTTGCCCATCAAAGT +GTACAACGATCGAGTTTGCT +TAAGTGTCTGGGTACCTACA +CACCAGACACAATGCGATGG +CCACGGATCCACACAAGGCA +CATCACATGCAGAAAGCTTC +ACCAGATTATGACACATACC +ACACTCTTGTAACTCGTCGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/yahs.xml Wed Jun 29 13:06:23 2022 +0000 @@ -0,0 +1,227 @@ +<tool id="yahs" name="YAHS" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>yet another HI-C scaffolding tool</description> + <macros> + <token name="@VERSION@">1.1a.2</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">yahs</requirement> + <requirement type="package" version="1.11">samtools</requirement> + <requirement type="package" version="3.9">python</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if $function.function_select == "yahs": + ln -s '$function.fasta' input.fasta && + #if $function.bfile.ext == "bam": + ln -s '$function.bfile' input.bam && + #else if $function.bfile.ext == "bed": + ln -s '$function.bfile' input.bed && + #end if + #if $function.agp: + ln -s '$function.agp' input.agp && + #end if + samtools faidx input.fasta && + mkdir initial_break agp_out agp_break final_outs && + yahs input.fasta + #if $function.bfile.ext == "bam": + input.bam + #else if $function.bfile.ext == "bed": + input.bed + #end if + #if $agp: + -a input.agp + #end if + #if $function.res: + -r $function.res + #end if + #if $function.enzyme_conditional.enzyme_options == 'preconfigured': + #if $function.enzyme_conditional.preconfigured_enzymes == 'dovetail' + -e 'GATC' + #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima1' + -e 'GATC,GANTC' + #else + -e 'GATC,GANTC,CTNAG,TTAA' + #end if + #else if $function.enzyme_conditional.enzyme_options == 'specific': + -e '${function.enzyme_conditional.manual_enzyme}' + #end if + #if $function.length: + -l $function.length + #end if + #if $function.quality: + -q $function.quality + #end if + $function.no_contig_ec + $function.no_scaffold_ec + -o yahs_out && + ls -lah && + python '$__tool_directory__/move_files.py' + && ls -lah ./* + #else: + ln -s '$function.fasta' input.fasta && + ln -s '$function.agp' input.agp && + agp_to_fasta input.agp input.fasta + #if $function.length: + -l $function.length + #end if + -o output.fasta + #end if + ]]></command> + <inputs> + <conditional name="function"> + <param name="function_select" type="select" label="Which function would you like to run?"> + <option value="yahs">YAHS</option> + <option value="agp_to_fasta">AGP to fasta</option> + </param> + <when value="yahs"> + <param name="fasta" type="data" format="fasta" label="Input contig sequences"/> + <param name="bfile" type="data" format="bam,bed" label="Alignment file of Hi-C reads to contigs"/> + <param name="agp" argument="-a" type="data" format="agp" optional="true" label="Input AGP file (for rescaffolding)" + help="You can specify a AGP format file to ask YaHS to do scaffolding with the scaffolds in the AGP file as the start point"/> + <param name="res" argument="-r" type="text" label="Resolutions" optional="true" + help="Comma separated, ascending list of range of resolutions with no spaces. Ex. 50000,100000,200000,500000,1000000,2000000,5000000. By default and the upper limit is automatically adjusted with the genome size"/> + <conditional name="enzyme_conditional"> + <param name="enzyme_options" type="select" label="Restriction enzyme used in Hi-C experiment" help="Hi-C experiments can use different restriction enzymes. + The enzyme frequency in contigs is used to normalize the Hi-C interaction frequency. Note that you need to specify the actual + sequence of the cutting site for a restriction enzyme and not the enzyme name. You can also specify DNASE as an enzyme if you + use an enzyme-free prep, e.g. Omin-C."> + <option value="not_especified">Not especified</option> + <option value="preconfigured">Preconfigured restriction enzymes</option> + <option value="specific">Enter a specific sequence</option> + </param> + <when value="not_especified"/> + <when value="preconfigured"> + <param name="preconfigured_enzymes" argument="-e" type="select" label="Preconfigured enzymes"> + <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option> + <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option> + <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option> + </param> + </when> + <when value="specific"> + <param name="manual_enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)" + help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT')."> + <validator type="expression" message="Only alphabetical letters and the comma can be used in to define restriction enzym sequences.">value.replace(',', '').isalpha()</validator> + </param> + </when> + </conditional> + <param name="length" argument="-l" type="integer" label="Minimum contig length included for scaffolding" min="1" optional="true"/> + <param name="quality" argument="-q" type="integer" label="Minimum read mapping quality (for BAM input only)" min="1" optional="true"/> + <param argument="--no-contig-ec" type="boolean" label="Skip assembly error correction step" truevalue="--no-contig-ec" falsevalue="" help="Automatically active if AGP output is set"/> + <param argument="--no-scaffold-ec" type="boolean" label="Skip assembly/scaffolding error check each round" truevalue="--no-scaffold-ec" falsevalue="" help="Will also prevent any break.agp output files"/> + </when> + <when value="agp_to_fasta"> + <param name="agp" type="data" format="agp" label="Input AGP file"/> + <param name="fasta" type="data" format="fasta" label="Contig fasta file"/> + <param name="length" type='integer' label="Output fasta line length" value="60" min="1"/> + </when> + </conditional> + </inputs> + <outputs> + <!-- INITIAL ROUNDS --> + <collection name="initial_agp_break" type="list" label="${tool.name} on ${on_string}: AGP initial break files"> + <filter>function['function_select'] == "yahs"</filter> + <discover_datasets pattern="__name_and_ext__" directory="initial_break" ext="agp"/> + </collection> + <collection name="agp_break" type="list" label="${tool.name} on ${on_string}: AGP break files"> + <filter> function['function_select'] == "yahs"</filter> + <discover_datasets pattern="__name_and_ext__" directory="agp_break" ext="agp"/> + </collection> + <collection name="agp_out" type="list" label="${tool.name} on ${on_string}: AGP scaffolding results files"> + <filter>function['function_select'] == "yahs"</filter> + <discover_datasets pattern="__name_and_ext__" directory="agp_out" ext="agp"/> + </collection> + <!-- FINAL FILES --> + <data format="agp" name="final_agp_out" label="${tool.name} on ${on_string}: Final scaffolds agp output" from_work_dir="final_outs/yahs_out_scaffolds_final.agp"> + <filter>function['function_select'] == "yahs"</filter> + </data> + <data format="fasta" name="final_fasta_out" label="${tool.name} on ${on_string}: Final scaffolds fasta output" from_work_dir="final_outs/yahs_out_scaffolds_final.fa"> + <filter>function['function_select'] == "yahs"</filter> + </data> + <data format="fasta" name="fasta_from_agp" label="${tool.name} on ${on_string}: agp to fasta" from_work_dir="output.fasta"> + <filter>function['function_select'] == "agp_to_fasta"</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="5"> + <conditional name="function"> + <param name="function_select" value="yahs"/> + <param name="fasta" value="test.fasta"/> + <param name="bfile" value="test.bed"/> + <param name="agp" value="test.agp"/> + <param name="res" value="50000,100000,150000,2000000,1000000"/> + </conditional> + <output name="final_agp_out" file="test_01_scaffolds_final.agp" ftype="agp"/> + <output name="final_fasta_out" file="test_01_scaffolds_final.fa" ftype="fasta"/> + <!-- COMMAND: yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 --> + </test> + <test expect_num_outputs="5"> + <conditional name="function"> + <param name="function_select" value="yahs"/> + <param name="fasta" value="test.fasta"/> + <param name="bfile" value="test.bed"/> + <param name="no_contig_ec" value="--no-contig-ec"/> + <param name="no_scaffold_ec" value="--no-scaffold-ec"/> + </conditional> + <output name="final_agp_out" file="test_02_scaffolds_final.agp" ftype="agp"/> + <output name="final_fasta_out" file="test_02_scaffolds_final.fa" ftype="fasta"/> + <output_collection name="agp_break"> + <element name="yahs_out_no_break" file="test_02_no_break.agp" ftype="agp"/> + </output_collection> + <!-- COMMAND: yahs test.fasta test.bed -\-no-contig-ec -\-no-scaffold-ec -o test_2 --> + </test> + <test expect_num_outputs="5"> + <conditional name="function"> + <param name="function_select" value="yahs"/> + <param name="fasta" value="test.fasta"/> + <param name="bfile" value="test.bam"/> + <param name="qual" value="10"/> + <param name="length" value="20"/> + <conditional name="enzyme_conditional"> + <param name="enzyme_options" value="specific"/> + <param name="manual_enzyme" value="GATC,GANT"/> + </conditional> + </conditional> + <output name="final_agp_out" file="test_03_scaffolds_final.agp" ftype="agp"/> + <output name="final_fasta_out" file="test_03_scaffolds_final.fa" ftype="fasta"/> + <output_collection name="initial_agp_break"> + <element name="yahs_out_inital_break_01" file="test_03_initial_break.agp" ftype="agp"/> + </output_collection> + <!-- COMMAND: yahs test.fasta test.bed -q 10 -l 20 -e 'GATC,GANT' -o test_3 --> + </test> + <test expect_num_outputs="5"> + <conditional name="function"> + <param name="function_select" value="yahs"/> + <param name="fasta" value="test.fasta"/> + <param name="bfile" value="test.bam"/> + <param name="qual" value="10"/> + <param name="length" value="20"/> + <conditional name="enzyme_conditional"> + <param name="enzyme_options" value="preconfigured"/> + <param name="preconfigured_enzymes" value="arima1"/> + </conditional> + </conditional> + <output name="final_agp_out" file="test_03_scaffolds_final.agp" ftype="agp"/> + <output name="final_fasta_out" file="test_03_scaffolds_final.fa" ftype="fasta"/> + <output_collection name="initial_agp_break"> + <element name="yahs_out_inital_break_01" file="test_04_initial_break.agp" ftype="agp"/> + </output_collection> + <!-- COMMAND: yahs test.fasta test.bed -q 10 -l 20 -e 'GATC,GANT' -o test_3 --> + </test> + <test expect_num_outputs="1"> + <conditional name="function"> + <param name="function_select" value="agp_to_fasta"/> + <param name="fasta" value="test.fasta"/> + <param name="agp" value="test.agp"/> + <param name="length" value="20"/> + </conditional> + <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/> + <!-- COMMAND: agp_to_fasta teast.fasta test.agp -l 20 -o test_4 --> + </test> + </tests> + <help><![CDATA[ + YaHS is scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. YaHS has been tested in a wide range of genome assemblies. Compared to other Hi-C scaffolding tools, it usually generates more contiguous scaffolds - especially with a higher N90 and L90 statistics. It is also super fast - takes less than 5 minutes to reconstruct the human genome from an assembly of 5,483 contigs with ~45X Hi-C data. + ]]></help> + <citations> + <citation type="doi">10.5281/zenodo.5848772</citation> + </citations> +</tool>