| Next changeset 1:a3a92e30a727 (2022-07-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069 |
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added:
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 |
| b |
| diff -r 000000000000 -r d87433f2a54d move_files.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/move_files.py Wed Jun 29 13:06:23 2022 +0000 |
| b |
| @@ -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) |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test.agp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.agp Wed Jun 29 13:06:23 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 + \ No newline at end of file |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test.bam |
| b |
| Binary file test-data/test.bam has changed |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.bed Wed Jun 29 13:06:23 2022 +0000 |
| b |
| @@ -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 - |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fasta Wed Jun 29 13:06:23 2022 +0000 |
| b |
| b'@@ -0,0 +1,100 @@\n+>HiC_scaffold_1\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAAATCTGGTGAAGCTTTCTGCATGTGATGT\n+GCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACA\n+CTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGA\n+CGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGC\n+CATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCAC\n+TGTGTCTCCGTGCCGAGCTAGATCTCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGT'..b'AGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCTGGCATTGTAGGTACCAGACACTAACAAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCTCGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTGCCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n' |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test_01_scaffolds_final.agp --- /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 |
| b |
| @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 + |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test_01_scaffolds_final.fa --- /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 |
| b |
| b'@@ -0,0 +1,133 @@\n+>scaffold_1\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGC\n+CATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACA\n+CTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGG\n+TACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTG\n+AAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGT\n+GTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCAC\n+TGTGTCTCCGTGCCGAGCTAGATCTCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n'..b'CCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCTGGCATTGTAGGTACCAGACACTAACAAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCTCGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTGCCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n' |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test_02_no_break.agp --- /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 |
| b |
| @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 + |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test_02_scaffolds_final.agp --- /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 |
| b |
| @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 + |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test_02_scaffolds_final.fa --- /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 |
| b |
| b'@@ -0,0 +1,133 @@\n+>scaffold_1\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGC\n+CATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACA\n+CTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGG\n+TACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTG\n+AAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGT\n+GTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCAC\n+TGTGTCTCCGTGCCGAGCTAGATCTCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n'..b'CCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCTGGCATTGTAGGTACCAGACACTAACAAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCTCGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTGCCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n' |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test_03_initial_break.agp --- /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 |
| b |
| @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 + |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test_03_scaffolds_final.agp --- /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 |
| b |
| @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 + |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test_03_scaffolds_final.fa --- /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 |
| b |
| b'@@ -0,0 +1,133 @@\n+>scaffold_1\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGC\n+CATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACA\n+CTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGG\n+TACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTG\n+AAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGT\n+GTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCAC\n+TGTGTCTCCGTGCCGAGCTAGATCTCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGAGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGAGCTAGATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGAC\n'..b'CCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGC\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGTACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTGTAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACTGTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGACGACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTGCCTTGTGTGGATCCGTGGCCATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAGCAAACTCGATCGTTGTACACTTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAGATCTCCCCTAGCCGTAAGGCACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGGTATGTGTCATAATCTGGTGAAGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCCATCTGGCATTGTAGGTACCAGACACTAACAAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCTCGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTGCCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGGCCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACCACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCTAGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCTTAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCACATCACATGCAGAAAGCTTCACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGTCGAAGGGGCGTTCAAAGTACCTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAGTGATGGTTGCCCATCAAAGTGTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACACACCAGACACAATGCGATGGCCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTCACCAGATTATGACACATACCACACTCTTGTAACTCGTCGT\n' |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test_04_initial_break.agp --- /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 |
| b |
| @@ -0,0 +1,1 @@ +scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 + |
| b |
| diff -r 000000000000 -r d87433f2a54d test-data/test_05.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_05.fasta Wed Jun 29 13:06:23 2022 +0000 |
| b |
| b'@@ -0,0 +1,397 @@\n+>scaffold_1\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGAGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAAATCTGGTG\n+AAGCTTTCTGCATGTGATGT\n+GCCTTGTGTGGATCCGTGGC\n+CATCGCATTGTGTCTGGTGT\n+GTAGGTACCCAGACACTTAA\n+GCAAACTCGATCGTTGTACA\n+CTTTGATGGGCAACCATCAC\n+TGTGTCTCCGTGCCGTGCTA\n+GATCTCCCCTAGCCGTAAGG\n+TACTTTGAACGCCCCTTCGA\n+CGACGAGTTACAAGAGTGTG\n+GTATGTGTCATAATCTGGTG\n+AAGCTTTCTGCATGTGATGT\n+GCCTTGTGTGGATCCGTGGC\n+CATCGCATTGTGTCTGGTGT\n+GTAGGTACCCAGACACTTAA\n+GCAAACTCGATCGTTGTACA\n+CTTTGATGGGCAACCATCAC\n+TGTGTCTCCGTGCCGAGCTA\n+GATCTCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGAGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGAGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGAGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGC\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGC\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGC\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGA'..b'AGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGC\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGT\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCGCATTGTGTCTGGTGTG\n+TAGGTACCCAGACACTTAAG\n+CAAACTCGATCGTTGTACAC\n+TTTGATGGGCAACCATCACT\n+GTGTCTCCGTGCCGTGCTAG\n+ATCTCCCCTAGCCGTAAGGC\n+ACTTTGAACGCCCCTTCGAC\n+GACGAGTTACAAGAGTGTGG\n+TATGTGTCATAATCTGGTGA\n+AGCTTTCTGCATGTGATGTG\n+CCTTGTGTGGATCCGTGGCC\n+ATCTGGCATTGTAGGTACCA\n+GACACTAACAAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCT\n+AGCTCGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTGC\n+CTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGT\n+CGAAGGGGCGTTCAAAGTAC\n+CTTACGGCTAGGGGAGATCT\n+AGCACGGCACGGAGACACAG\n+TGATGGTTGCCCATCAAAGT\n+GTACAACGATCGAGTTTGCT\n+TAAGTGTCTGGGTACCTACA\n+CACCAGACACAATGCGATGG\n+CCACGGATCCACACAAGGCA\n+CATCACATGCAGAAAGCTTC\n+ACCAGATTATGACACATACC\n+ACACTCTTGTAACTCGTCGT\n' |
| b |
| diff -r 000000000000 -r d87433f2a54d yahs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/yahs.xml Wed Jun 29 13:06:23 2022 +0000 |
| [ |
| b'@@ -0,0 +1,227 @@\n+<tool id="yahs" name="YAHS" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n+ <description>yet another HI-C scaffolding tool</description>\n+ <macros>\n+ <token name="@VERSION@">1.1a.2</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">yahs</requirement>\n+ <requirement type="package" version="1.11">samtools</requirement>\n+ <requirement type="package" version="3.9">python</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $function.function_select == "yahs":\n+ ln -s \'$function.fasta\' input.fasta &&\n+ #if $function.bfile.ext == "bam":\n+ ln -s \'$function.bfile\' input.bam &&\n+ #else if $function.bfile.ext == "bed":\n+ ln -s \'$function.bfile\' input.bed &&\n+ #end if\n+ #if $function.agp:\n+ ln -s \'$function.agp\' input.agp &&\n+ #end if\n+ samtools faidx input.fasta &&\n+ mkdir initial_break agp_out agp_break final_outs &&\n+ yahs input.fasta \n+ #if $function.bfile.ext == "bam":\n+ input.bam\n+ #else if $function.bfile.ext == "bed":\n+ input.bed\n+ #end if\n+ #if $agp:\n+ -a input.agp\n+ #end if\n+ #if $function.res:\n+ -r $function.res\n+ #end if\n+ #if $function.enzyme_conditional.enzyme_options == \'preconfigured\':\n+ #if $function.enzyme_conditional.preconfigured_enzymes == \'dovetail\'\n+ -e \'GATC\'\n+ #else if $function.enzyme_conditional.preconfigured_enzymes == \'arima1\'\n+ -e \'GATC,GANTC\'\n+ #else\n+ -e \'GATC,GANTC,CTNAG,TTAA\'\n+ #end if\n+ #else if $function.enzyme_conditional.enzyme_options == \'specific\':\n+ -e \'${function.enzyme_conditional.manual_enzyme}\'\n+ #end if\n+ #if $function.length:\n+ -l $function.length\n+ #end if\n+ #if $function.quality:\n+ -q $function.quality\n+ #end if\n+ $function.no_contig_ec\n+ $function.no_scaffold_ec\n+ -o yahs_out &&\n+ ls -lah &&\n+ python \'$__tool_directory__/move_files.py\'\n+ && ls -lah ./*\n+ #else:\n+ ln -s \'$function.fasta\' input.fasta &&\n+ ln -s \'$function.agp\' input.agp &&\n+ agp_to_fasta input.agp input.fasta\n+ #if $function.length:\n+ -l $function.length\n+ #end if\n+ -o output.fasta\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <conditional name="function">\n+ <param name="function_select" type="select" label="Which function would you like to run?">\n+ <option value="yahs">YAHS</option>\n+ <option value="agp_to_fasta">AGP to fasta</option>\n+ </param>\n+ <when value="yahs">\n+ <param name="fasta" type="data" format="fasta" label="Input contig sequences"/>\n+ <param name="bfile" type="data" format="bam,bed" label="Alignment file of Hi-C reads to contigs"/>\n+ <param name="agp" argument="-a" type="data" format="agp" optional="true" label="Input AGP file (for rescaffolding)"\n+ 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"/>\n+ <param name="res" argument="-r" type="text" label="Resolutions" optional="true" \n+ 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"/>\n+ '..b'd-ec"/>\n+ </conditional>\n+ <output name="final_agp_out" file="test_02_scaffolds_final.agp" ftype="agp"/>\n+ <output name="final_fasta_out" file="test_02_scaffolds_final.fa" ftype="fasta"/>\n+ <output_collection name="agp_break">\n+ <element name="yahs_out_no_break" file="test_02_no_break.agp" ftype="agp"/>\n+ </output_collection>\n+ <!-- COMMAND: yahs test.fasta test.bed -\\-no-contig-ec -\\-no-scaffold-ec -o test_2 -->\n+ </test>\n+ <test expect_num_outputs="5">\n+ <conditional name="function">\n+ <param name="function_select" value="yahs"/>\n+ <param name="fasta" value="test.fasta"/>\n+ <param name="bfile" value="test.bam"/>\n+ <param name="qual" value="10"/>\n+ <param name="length" value="20"/>\n+ <conditional name="enzyme_conditional">\n+ <param name="enzyme_options" value="specific"/>\n+ <param name="manual_enzyme" value="GATC,GANT"/>\n+ </conditional>\n+ </conditional>\n+ <output name="final_agp_out" file="test_03_scaffolds_final.agp" ftype="agp"/>\n+ <output name="final_fasta_out" file="test_03_scaffolds_final.fa" ftype="fasta"/>\n+ <output_collection name="initial_agp_break">\n+ <element name="yahs_out_inital_break_01" file="test_03_initial_break.agp" ftype="agp"/>\n+ </output_collection>\n+ <!-- COMMAND: yahs test.fasta test.bed -q 10 -l 20 -e \'GATC,GANT\' -o test_3 -->\n+ </test>\n+ <test expect_num_outputs="5">\n+ <conditional name="function">\n+ <param name="function_select" value="yahs"/>\n+ <param name="fasta" value="test.fasta"/>\n+ <param name="bfile" value="test.bam"/>\n+ <param name="qual" value="10"/>\n+ <param name="length" value="20"/>\n+ <conditional name="enzyme_conditional">\n+ <param name="enzyme_options" value="preconfigured"/>\n+ <param name="preconfigured_enzymes" value="arima1"/>\n+ </conditional>\n+ </conditional>\n+ <output name="final_agp_out" file="test_03_scaffolds_final.agp" ftype="agp"/>\n+ <output name="final_fasta_out" file="test_03_scaffolds_final.fa" ftype="fasta"/>\n+ <output_collection name="initial_agp_break">\n+ <element name="yahs_out_inital_break_01" file="test_04_initial_break.agp" ftype="agp"/>\n+ </output_collection>\n+ <!-- COMMAND: yahs test.fasta test.bed -q 10 -l 20 -e \'GATC,GANT\' -o test_3 -->\n+ </test>\n+ <test expect_num_outputs="1">\n+ <conditional name="function">\n+ <param name="function_select" value="agp_to_fasta"/>\n+ <param name="fasta" value="test.fasta"/>\n+ <param name="agp" value="test.agp"/>\n+ <param name="length" value="20"/>\n+ </conditional>\n+ <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/>\n+ <!-- COMMAND: agp_to_fasta teast.fasta test.agp -l 20 -o test_4 -->\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ 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.\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.5281/zenodo.5848772</citation>\n+ </citations>\n+</tool>\n' |