| Previous changeset 2:fc925f53cae7 (2022-07-27) Next changeset 4:425e63adcc5d (2023-03-09) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 968382ccb84765d3e8a6e67c43f095a8cc5ab8f5 |
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modified:
test-data/test.bam test-data/test_04_initial_break.agp yahs.xml |
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added:
test-data/test2.bam test-data/test2.bed test-data/test2.fasta test-data/test_04_scaffolds_final.agp test-data/test_04_scaffolds_final.fa |
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| diff -r fc925f53cae7 -r 39495e107274 test-data/test.bam |
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| Binary file test-data/test.bam has changed |
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| diff -r fc925f53cae7 -r 39495e107274 test-data/test2.bam |
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| Binary file test-data/test2.bam has changed |
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| diff -r fc925f53cae7 -r 39495e107274 test-data/test2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.bed Wed Sep 28 09:41:02 2022 +0000 |
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| b'@@ -0,0 +1,14275 @@\n+LYZE01000001.1_1-71562\t634\t700\tSRR5077823.49272673/2\t16\t-\n+LYZE01000001.1_1-71562\t5697\t5763\tSRR5077823.26979388/2\t60\t-\n+LYZE01000001.1_1-71562\t23370\t23436\tSRR5077823.38393278/1\t15\t+\n+LYZE01000001.1_1-71562\t30743\t30809\tSRR5077823.27391164/1\t60\t+\n+LYZE01000001.1_1-71562\t46557\t46623\tSRR5077823.55365122/2\t60\t-\n+LYZE01000001.1_1-71562\t47146\t47212\tSRR5077823.26730266/2\t60\t-\n+LYZE01000001.1_1-71562\t51049\t51115\tSRR5077823.3825433/2\t60\t+\n+LYZE01000001.1_1-71562\t52230\t52261\tSRR5077823.34234964/1\t60\t-\n+LYZE01000001.1_1-71562\t54556\t54622\tSRR5077823.23328045/1\t60\t+\n+LYZE01000001.1_71573-153119\t12923\t12989\tSRR5077823.18744162/1\t60\t+\n+LYZE01000001.1_71573-153119\t13523\t13589\tSRR5077823.43442898/1\t60\t-\n+LYZE01000001.1_71573-153119\t16338\t16404\tSRR5077823.5541643/2\t60\t-\n+LYZE01000001.1_71573-153119\t52377\t52443\tSRR5077823.7784200/2\t60\t+\n+LYZE01000001.1_71573-153119\t54011\t54077\tSRR5077823.22317178/1\t60\t-\n+LYZE01000001.1_71573-153119\t56258\t56322\tSRR5077823.14335870/2\t60\t+\n+LYZE01000001.1_153130-217945\t4161\t4227\tSRR5077823.31997788/2\t60\t-\n+LYZE01000001.1_153130-217945\t23019\t23081\tSRR5077823.9533867/1\t60\t+\n+LYZE01000001.1_153130-217945\t25021\t25087\tSRR5077823.46685262/1\t60\t-\n+LYZE01000001.1_153130-217945\t34575\t34641\tSRR5077823.43524240/1\t60\t+\n+LYZE01000001.1_217956-235578\t5593\t5659\tSRR5077823.15722078/1\t23\t+\n+LYZE01000002.1_1-25845\t16644\t16710\tSRR5077823.54668248/1\t60\t-\n+LYZE01000002.1_1-25845\t18674\t18711\tSRR5077823.28163456/2\t60\t-\n+LYZE01000002.1_25856-44065\t1861\t1927\tSRR5077823.46555600/2\t60\t+\n+LYZE01000002.1_25856-44065\t10607\t10673\tSRR5077823.20887455/2\t60\t+\n+LYZE01000002.1_25856-44065\t12690\t12756\tSRR5077823.24193214/1\t60\t+\n+LYZE01000002.1_44076-123682\t1941\t2007\tSRR5077823.22683073/2\t60\t-\n+LYZE01000002.1_44076-123682\t4825\t4891\tSRR5077823.15083117/2\t60\t-\n+LYZE01000002.1_44076-123682\t6674\t6740\tSRR5077823.4494256/1\t60\t+\n+LYZE01000002.1_44076-123682\t12349\t12415\tSRR5077823.24806638/2\t60\t+\n+LYZE01000002.1_44076-123682\t15599\t15665\tSRR5077823.15461599/1\t60\t+\n+LYZE01000002.1_44076-123682\t25775\t25841\tSRR5077823.41709596/1\t60\t-\n+LYZE01000002.1_44076-123682\t32825\t32855\tSRR5077823.17044630/2\t60\t-\n+LYZE01000002.1_44076-123682\t45987\t46053\tSRR5077823.20724856/1\t60\t-\n+LYZE01000002.1_44076-123682\t58956\t59022\tSRR5077823.36445538/1\t60\t+\n+LYZE01000002.1_44076-123682\t66031\t66097\tSRR5077823.5546581/1\t60\t-\n+LYZE01000002.1_44076-123682\t71714\t71744\tSRR5077823.15392560/1\t60\t+\n+LYZE01000002.1_44076-123682\t74753\t74798\tSRR5077823.55328821/2\t60\t-\n+LYZE01000002.1_123693-145330\t5884\t5950\tSRR5077823.2752637/1\t60\t-\n+LYZE01000002.1_123693-145330\t6766\t6832\tSRR5077823.926187/1\t60\t+\n+LYZE01000002.1_123693-145330\t16224\t16290\tSRR5077823.32327628/1\t60\t+\n+LYZE01000002.1_123693-145330\t20786\t20852\tSRR5077823.15421166/1\t60\t-\n+LYZE01000002.1_147751-227410\t5604\t5670\tSRR5077823.56419088/1\t60\t+\n+LYZE01000002.1_147751-227410\t6006\t6040\tSRR5077823.41669606/1\t60\t+\n+LYZE01000002.1_147751-227410\t6795\t6861\tSRR5077823.51820348/2\t60\t-\n+LYZE01000002.1_147751-227410\t29210\t29276\tSRR5077823.19600886/1\t60\t+\n+LYZE01000002.1_147751-227410\t29214\t29280\tSRR5077823.53053717/1\t60\t+\n+LYZE01000002.1_147751-227410\t31246\t31312\tSRR5077823.21897185/1\t60\t+\n+LYZE01000002.1_147751-227410\t31268\t31334\tSRR5077823.24426997/1\t60\t-\n+LYZE01000002.1_227421-332338\t37905\t37971\tSRR5077823.28416201/2\t60\t+\n+LYZE01000002.1_227421-332338\t38284\t38350\tSRR5077823.18861784/1\t60\t-\n+LYZE01000002.1_227421-332338\t47154\t47220\tSRR5077823.43089267/2\t60\t-\n+LYZE01000002.1_227421-332338\t55037\t55087\tSRR5077823.54706899/2\t60\t-\n+LYZE01000002.1_227421-332338\t57447\t57513\tSRR5077823.54710249/1\t60\t-\n+LYZE01000002.1_227421-332338\t66523\t66562\tSRR5077823.53617202/2\t60\t-\n+LYZE01000002.1_227421-332338\t73760\t73797\tSRR5077823.6003587/2\t60\t-\n+LYZE01000002.1_227421-332338\t84454\t84520\tSRR5077823.9384399/1\t60\t-\n+LYZE01000002.1_227421-332338\t88853\t88919\tSRR5077823.7037147/1\t60\t-\n+LYZE01000002.1_227421-332338\t91647\t91705\tSRR5077823.39231294/1\t60\t+\n+LYZE01000002.1_345455-556941\t9826\t9892\tSRR5077823.57423941/2\t60\t-\n+LYZE01000002.1_345455-556941\t15392\t1545'..b'2\t60\t+\n+LYZE01000016.1_918909-981380\t38533\t38599\tSRR5077823.23419676/1\t60\t+\n+LYZE01000016.1_918909-981380\t38543\t38609\tSRR5077823.31948344/2\t60\t-\n+LYZE01000016.1_918909-981380\t38543\t38609\tSRR5077823.53724277/1\t60\t-\n+LYZE01000016.1_918909-981380\t38546\t38612\tSRR5077823.57025094/2\t60\t+\n+LYZE01000016.1_918909-981380\t38550\t38616\tSRR5077823.42109324/2\t60\t+\n+LYZE01000016.1_918909-981380\t38552\t38618\tSRR5077823.4430755/2\t60\t-\n+LYZE01000016.1_918909-981380\t38563\t38629\tSRR5077823.41479059/2\t60\t+\n+LYZE01000016.1_918909-981380\t38566\t38632\tSRR5077823.3402163/2\t60\t+\n+LYZE01000016.1_918909-981380\t38567\t38633\tSRR5077823.26283341/1\t60\t+\n+LYZE01000016.1_918909-981380\t38569\t38635\tSRR5077823.37735252/2\t60\t+\n+LYZE01000016.1_918909-981380\t38572\t38638\tSRR5077823.15736102/1\t60\t+\n+LYZE01000016.1_918909-981380\t38578\t38644\tSRR5077823.26283341/2\t60\t-\n+LYZE01000016.1_918909-981380\t38580\t38646\tSRR5077823.47762445/1\t60\t+\n+LYZE01000016.1_918909-981380\t38581\t38647\tSRR5077823.49284847/2\t60\t+\n+LYZE01000016.1_918909-981380\t38585\t38651\tSRR5077823.55127496/2\t60\t+\n+LYZE01000016.1_918909-981380\t38586\t38652\tSRR5077823.23419676/2\t60\t-\n+LYZE01000016.1_918909-981380\t38589\t38654\tSRR5077823.38201215/1\t60\t+\n+LYZE01000016.1_918909-981380\t38592\t38652\tSRR5077823.12039377/1\t60\t-\n+LYZE01000016.1_918909-981380\t38594\t38659\tSRR5077823.12039377/2\t60\t+\n+LYZE01000016.1_918909-981380\t38604\t38670\tSRR5077823.46054703/2\t60\t-\n+LYZE01000016.1_918909-981380\t38606\t38672\tSRR5077823.29953044/1\t60\t-\n+LYZE01000016.1_918909-981380\t38608\t38674\tSRR5077823.50530898/2\t60\t+\n+LYZE01000016.1_918909-981380\t38608\t38674\tSRR5077823.3402163/1\t60\t-\n+LYZE01000016.1_918909-981380\t38612\t38678\tSRR5077823.52349012/2\t60\t+\n+LYZE01000016.1_918909-981380\t38615\t38681\tSRR5077823.53277668/1\t60\t+\n+LYZE01000016.1_918909-981380\t38615\t38681\tSRR5077823.52349012/1\t60\t-\n+LYZE01000016.1_918909-981380\t38617\t38683\tSRR5077823.1583103/2\t60\t+\n+LYZE01000016.1_918909-981380\t38617\t38683\tSRR5077823.25767601/2\t60\t+\n+LYZE01000016.1_918909-981380\t38621\t38687\tSRR5077823.55542217/1\t60\t-\n+LYZE01000016.1_918909-981380\t38635\t38701\tSRR5077823.25767601/1\t60\t-\n+LYZE01000016.1_918909-981380\t38643\t38709\tSRR5077823.49586875/2\t60\t+\n+LYZE01000016.1_918909-981380\t38643\t38709\tSRR5077823.22322788/1\t60\t-\n+LYZE01000016.1_918909-981380\t38643\t38709\tSRR5077823.42109324/1\t60\t-\n+LYZE01000016.1_918909-981380\t38646\t38712\tSRR5077823.30654112/1\t60\t+\n+LYZE01000016.1_918909-981380\t38646\t38712\tSRR5077823.5505773/1\t60\t-\n+LYZE01000016.1_918909-981380\t38651\t38717\tSRR5077823.52577438/2\t60\t+\n+LYZE01000016.1_918909-981380\t38653\t38693\tSRR5077823.41479059/1\t60\t+\n+LYZE01000016.1_918909-981380\t38656\t38722\tSRR5077823.3587523/2\t60\t+\n+LYZE01000016.1_918909-981380\t38656\t38722\tSRR5077823.38533860/1\t60\t+\n+LYZE01000016.1_918909-981380\t38656\t38722\tSRR5077823.37735252/1\t60\t-\n+LYZE01000016.1_918909-981380\t38657\t38723\tSRR5077823.23432423/1\t60\t+\n+LYZE01000016.1_918909-981380\t38660\t38726\tSRR5077823.3587523/1\t60\t-\n+LYZE01000016.1_918909-981380\t38685\t38751\tSRR5077823.57025094/1\t60\t-\n+LYZE01000016.1_918909-981380\t38687\t38753\tSRR5077823.56977718/1\t60\t+\n+LYZE01000016.1_918909-981380\t38695\t38761\tSRR5077823.15736102/2\t60\t-\n+LYZE01000016.1_918909-981380\t38699\t38765\tSRR5077823.8028560/1\t60\t-\n+LYZE01000016.1_918909-981380\t38699\t38765\tSRR5077823.54731625/2\t60\t-\n+LYZE01000016.1_918909-981380\t38699\t38765\tSRR5077823.55127496/1\t60\t-\n+LYZE01000016.1_918909-981380\t38700\t38766\tSRR5077823.38533860/2\t60\t-\n+LYZE01000016.1_918909-981380\t38704\t38770\tSRR5077823.56977718/2\t60\t-\n+LYZE01000016.1_918909-981380\t38708\t38774\tSRR5077823.15583941/2\t60\t+\n+LYZE01000016.1_918909-981380\t38709\t38775\tSRR5077823.51411392/1\t60\t+\n+LYZE01000016.1_918909-981380\t38710\t38776\tSRR5077823.12756732/2\t60\t+\n+LYZE01000016.1_918909-981380\t38714\t38780\tSRR5077823.51913584/2\t60\t+\n+LYZE01000016.1_918909-981380\t38718\t38784\tSRR5077823.36521698/1\t60\t-\n+LYZE01000016.1_918909-981380\t38725\t38791\tSRR5077823.15583941/1\t60\t-\n+LYZE01000016.1_918909-981380\t38725\t38791\tSRR5077823.49284847/1\t60\t-\n+LYZE01000016.1_918909-981380\t38729\t38795\tSRR5077823.887847/2\t60\t-\n' |
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| diff -r fc925f53cae7 -r 39495e107274 test-data/test2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.fasta Wed Sep 28 09:41:02 2022 +0000 |
| b |
| b'@@ -0,0 +1,4 @@\n+>LYZE01000016.1_918909-981380\n+TACGAAGCAGGTGCTAAGATATCTTGAACAGCAAAGAAGTGTCAAAAACGTTTCTAATAAGGTTTTAAATGAAGAATGGGCTTTGTATTTGCAAAGAGAACACGAAGTACTGAGAAAAAGGAGGTTGAAACCTAAGCACAAGGATTTTCAGATACTGACACAAGTTGGACAGGGTGGTTATGGGCAAGTTTATCTTGCAAAAAAAAAAGACAGTGATGAAATTTGTGCTTTGAAAATATTAAACAAGAAACTTTTATTCAAACTAAACGAGACGAATCACGTCCTTACTGAGAGGGACATACTAACCACAACTAGATCTGACTGGCTTGTGAAGTTGCTTTATGCATTTCAGGATCCAGAGAGCCTATATTTAGCAATGGAATTTGTACCTGGTGGTGATTTTCGCACATTGTTAATAAATACAAGGATATTGAAGAGCGGTCACGCAAGGTTCTATATCAGCGAAATGTTTTGTGCCGTGAACGCGTTGCATGAACTTGGTTACACTCACCGGGATTTAAAGCCGGAGAATTTCTTGATTGATGCTACAGGGCATATCAAGCTGACCGATTTTGGTCTAGCAGCAGGGACCGTATCAAATGAAAGAATCGAAAGCATGAAAATACGCTTAGAAGAAGTAAAGAATTTGGAATTTCCTGCTTTCACAGAAAGGTCTATCGAGGATAGAAGGAAAATATATCATAACATGAGGAAGACAGAAATTAATTACGCTAACTCTATGGTCGGTTCGCCTGATTATATGGCCCTAGAAGTTCTGGAAGGTAAAAAATACGATTTTACAGTGGATTATTGGTCATTAGGCTGTATGCTTTTTGAAAGTTTGGTTGGATATACACCTTTTAGTGGTTCTTCTACTAATGAAACTTACGAGAATTTAAGATATTGGAAAAAAACTTTAAGAAGGCCCCGTACTGAGGATAGAAGAGCAGCATTCTCAGATAGAACCTGGGATTTAATTACAAGACTAATAGCTGACCCCATCAACAGAGTACGATCTTTTGAGCAAGTTCGCAAAATGTCTTATTTCGCAGAGATCAATTTTGAAACCCTAAGAACAAGTTCTCCACCATTTATTCCTCAATTAGATGATGAAACGGATGCAGGTTATTTCGATGACTTCACAAATGAAGAAGATATGGCTAAATATGCAGATGTCTTCAAAAGACAGAACAAATTATCTGCAATGGTCGATGACTCTGCCGTTGATTCCAAGCTTGTTGGATTTACTTTTAGGCATAGAGATGGAAAACAAGGTTCAAGCGGGATACTTTACAATGGTTCAGAACATTCAGACCCTTTTTCAACTTTTTATTAAGATTACGTCCCTACAATTTAATTTTGTATAGCATAACAGATACATTGACAACAGCAACAAGATGTGCTAACATTTTCCATTTTGAATGATTACCAAAATTATGAAACCAAGGCAACATGTAATTTTTAAGTTTAGTAATCTTTTTCGGGATGAGATGTTTTGAAGAGTTTTATGCTATTAAAGTAGTAATATGATTTATATATTCAAATAAAATGTAAATTATGAAAGAAAAATACGATAAGCTGATAGGGTAAACTAGAAACCTTCGTTTTCTTCATCATCCACATCCAGTTTCTTTCTACCGCCCCCATTTCTTAAGGCAGCCATCTCATTAGTGGCAACTTGCTTTCTAACCTTCTTTGTCATCCTGGCTATCTCTTCTTCAGCGTCAACTGCATCTTCTTCTGCATATTGCATTACCAATCTGCGGCCCAGTAAATGGACACCGTGCAACTGATCCATAGCATTTTCTGCTTCCTTTGGAAGTAAAAATTCCACGAACGCAAAACCTCTTGCAGACTTGTCGAACTTCTTTGGAACTCTAACAGATTTTAATTGACCAAAAGAATTGAATAATTCGAAAACGTCTTTCCTAGTAGCTTCAAATGGAAGATTCTTAACAATGATTTTACCGCTTTTCTTATTGGATTTAGTCTTTGTATTACCGCTCTGAGATGCTTGTCTATGGGATAACTTCAATTGAATCTTATGGCCGTCGATTACCGTCCCATCCATTGCAGCTATCACGGCATTAGCTTGTTCCTTGGTCCTGAATTCTACAAAACCAAACCCCATTGACAAGGTCTTGCCTTGATGTTTTGGATCAGGTTTTGTCTTCACTTGGGCAACAACAAAACCAGTGAAAACCTTGAACCTATCAGTAAGATTTTGGTTCGTCGTGGAGAAGTTTAGATTCTTTATGAAAATTGAGACAGTTGGACCATCAATAACGTCTTCATCATGAGCATTAGATGACCCTTCAGTTACATCCTTGTTTGCTTCCATTAAGTCATTTGATGAAGGTTTTACCTCTACCGGGTTTTCTTCTTCTTTTGCAGAAGTGTTATTTATCAAATCATCGGCCTCAGCTGGTTTAGTAAAGCAATCCTTAGGCCCCCTTTCTAGATATATTATGCCGTCCTTAAATCTTTTATACGATAGTTTAGTGAAAGCTGCCCTTGCTGACGTTGTGTCCCTGAATTGCACTATAGCTATTGTACCAGCTGGTGGCATGAGCAATCTTTCCAATTTACCATATGGCAAAAACATTTCGCCAAGCTCTTCTCTAGTTGTCCCAAAAGGAAAATTTTTAACCAGTATCACTTTATCGTCTCTTTGATTTGTAGATTTTAACTGTGAAAACTTGGTCAGATCAACACCTTTGGATTCAAAGTATTTTCTAACATCACCAATAACATGGGCTTCAGCCAAAGCTTGTTTGACAGCCGAACTTGAGTTTTCAGCATCGATCAATTGAGATTTTTCTAGACCCAATTTGGCTGCCACACTACCCAAAACAGCATCTTGGTTCATATACAAGGAGTTCCAAGAAAATGTTTGTCTGGATGCAGCTGCCTTCCTTTTCAATTCCTTTTGCTTTTTCAATGGCATATTCTTTAAATCAAACTCATCTAATCTATGGCTTTTTTTTTCTTCACCAGGAAGAATATGCAATAGTCTTCCTTGAAAAATCTGTTTATCCAATTCAACATAGGCGTTCACTGCATTCTTAGAATCCTTAAATAGAACGTATGCAAATCCTTTGGATTGACCAGTCCTGGTATCCAAAGCCACATGAACCTCCTCTAACTCTCCAAATGGACTAAATAGTTTCCTGAAATCTTCTTCTTTGGAGGTATACAAGATATTACGTAAGAATAAACGGCCAGTTTGGTTAATTTTTTCAATAGCCAGTTCTTCGTCCGTCTTTTGCGGCACAGCACGTTCTGGTTGTTCTTCCTTCTTGGTATCGAGACTTTCATTTTGTTCAGTAGCGTATGATGATGATTTTTCCCTTGTTTCCGCTTCACTTTCTTTGATTCTTACACGGCGTTGTTTGAACCAATCTAGGTCAGAAACCTTTTCATCTTGGGCGAGGTTTCTCCTCTTTTCATTCTCTTTTTCATCACTATTAGCGTCATCATTAACTAAACCTATATCAGTATCCTTCAAATTGCTAATACTTATCATCTTTTCTTCCTCTCCGGCATCTTCTTGATCTTCATCCCTGTTTCTGTTGAGAGCCGAATATTCATCGTCACTTTCATTCTCAATGACCAAATTTGGTGCTTCGTCTTTATTATTCTCTTCCTTTAAGGCTAATGCATGAGCCAATAGAGAATTCCCTTGCACGCTGGAGTCCTCTTCTTCCCGTTTTAGTTTTTCGTCCTCTATGCTCTTGTCAATGCCAACTTTTTCCCATGATGTGACTTGTGAGCTTGGCTTCATAGTCTCCATGAACTCTTGTAATTGCTTGTTCTTGCGAATCTCGTCATCAATGTTGCTGTGCTTATTTTCATCCACTTTCTTTTTCTTTCGATTTTCTTCTTGTAGCAATTTTTCTTCCTTTTCCCTAAACCTTTTCAGAGCTTCTCTTCTCTTCTCCTTCATGGGCT'..b'GATCAACTGCCCCAGTTTAATAGTATAATACTTTGATGATTGAGTGACCATATCAAGTCTTTCGTGCACTATACCGCGAGGTATATCAGAAACCAATGAAGCTATTTCAATTGGTTTCTTCGGTAGCCCGACAAACCTGAAGTTCCGAATCACCATAAATTTGTTTATTCTTGGGCGTATTTTTTCTAGTAAATCAACTGACAAGGCCTTTAGGGACCATTTTTGATGCGACAGTTTTTTCTTATTTACATCCTTCAAAACAGTTTGAGATAAAAGACGTATTGTCGATACTGAATTTTGTAAACAGTAAAGAAAAGACTTTAGGATTGAATCACTTACTGTTTTGTAGTACTGTTCAGCTTCATACACGGCAGGTAAACCTTGGACGCATTCGTTGGTCACAGAATAGTAGCACAATAATATAATGTACTCAAATATGGCTTGGCTAACAAGATATTGCAAATCTCCGTCTTCAAAGGATGAGGGATCAGCAATGTCCTTGCAAATATTGTATAGCAAATCAAAAGGCACCGAACAATAAGAGTCAATATTGTCAGTTTTGATTGAAATGCAGATTTTTTCAACAATTGACCTGATCAATTGTAATTGATCTTGTAACCTACTTAGTTCTTCATTTTCCTCACGTACGTCTTGAATCAATTGTTGCTGTGAATCAAATGCAACCTCTCGTAGTGATTCCTCTAATGAATGACTTATCTCTTCAAAAGATTTCAAAATACGCCTATTGATGATCATTTAAGAATATTAATTAAGGAACCTGCAATTTTGCAATAGGACTATTTTGTTGACTTTGTTGTTATTACTAAGTTTTAAAGTGGAAAAGAATTCCGACCCTTTGTTTAGTGAGTGGGGGTCAATCAAATTCGTATTCCTCGGTCAAATGAGGAGGAATGTAAAAACCGAAAATAAAGTCATCGCATAGGTACAAGAAGAATGAACTTGAGAAGTTCAAATTTCTAATTCAATTTTTTTTTTTTTCTATACATATAAATTAATAAAGTTACTCACGGTTTGAAGGTCAATCAATATATTTGTTTAGGATAGCAATAGATAAAAGAACAATAGAGAAAGAATGTAAAATACGTAAAAATATATGTACATTACTGTCGGATAATGGTTTGAATGCATGTTTGATATGTTTGCTTATGTTTGCTTATGTTTGCTTATGTTTTTATCATTACTACTACTATAATTTTTCATTATTATGCTCGATTCGTAAAATCGTTACTCTTATTCAATACTATCTATGGAATAATCCTTCTTGGATAACTTATGTCTCAAACCTTTGCCCCAGTAAGAAAATGCAAAAGGTAAAGCAATCATAGCAGTGGAGATGAAAGCCAACAACCAAGAACCCCAGTGCAGATTCAATTTGTGGTACATTTGAATGGTAAACAAGGGGAAGGCAGCACCACCGGCGGATCTTAAGAAAACCTTTGTAGCCAGAGCACTGGATGCGTATTGGACGTAGCAATCAATAATGTAATTATTCAATGAATAATAAATCAACACCATACCGAAACCAAAAGCTAAACCAGCTGAAGCTGGACCAACCCAAATAATATGTTTATAAGCGGTAGCACCCAGGATCCATAAAGCAATTGCAGCAAATGGAGCACCGATCTTAGCACCTAGCAAACGATCTTCAGGAGTAGGTTTACGCTGTTTGACAATTTGTAAATACTTGTTTTCACAGTAGAAAGTTGTGGCTAACGCCCAAAGAGCACCGATAACAATAGGAATAAACATCAAACCCACAAGGTTGTCTTTGTAGCCATATAGTTCACCGAAAATGACAGGGAAGGCAAAGAAGAACGCATATAGTAGAGAGTAAATCAAACACACGTAGAAACAAGTAGCAACTAGAACAGGTTCAGTGACAGAGAAGTACAAAGGTCTCAACAGACAAGCCCTCATCATTTCACCCATACTGACACCTTGCGCTTCCTGCTCAGTCATAATCTTGGGATTACCAGTTTCCTTTCTTAATCTAGCAGCCTTTCTCTTCAAGATAACTGGAGCGTACGTTTCTGGGATGGCAGAAGATATGATCCACATAACACCTGCAAAGGCCATATTGACCCAGAAAATCAGGTCCATACGTCCGGTAGAAACGGAAATAAAACCGTTAACTAGTGGACCAACAACGGGACCAACGTAAGGAGCAAAAGCGAAGAAAGCAATAGCCTTACCTCTTGTTTCACTTGGGAACATATCGGCAATAGACCCACCAACTAAACACAAACCAGATGATGACCAAACACCACATAAAAATCTACAAGCTAAAAGACTACCTAGATTTGGAGCTAAGGCGCAAGGGATATTGAAGATGACATAAAGACCCATAGAAACAAAGTAAGCAACTCTTCTACCGTAAAGATCACTAACAGGAGACCAAATCAAAGGACCCAGCGAGAACCCAATAACCATTAAAGAAACCGATAAAATAGCGGCTTCCATACCTACATGGTATTTCTTTTCAACGGTTCCCAACCCACCACTGATACAAGCAGACCCGTAGGCGACACAAATAACTAAGATTGACAGTAGGACAGTGTAACTCCAACGGATCCATGCAGGCCAGTTATGGGGGTTTTCTGGATCGCCAGTCACAAAGGTAACGAATTCAATTTCCGGATCTAGATCTGGAGCTTCGTCATTCGCACCACTAGAGTCGCCTTCTTTACCCTTTTCGTTATTATCACTTTCTAAAGCATCTTCATTAGAAGAAGGCGAAGAAGCGCCATCGATCTGTCTAGTTCTCGTACGGGAAATCGCAGTAGAAGTTCTACCTATGGAATGTAGAGTGGCGACAGGAACTAAACCTGTAGGGGTTTCTAAAGTATATTCTTCAGGAAAAATCTTATTCTTGCTAGATTGAGGAGCATTAACATCAGGAACGGGGGCTTTGGAGCTCACACCCATGTCCTGCAATGACTTCACGGTTTCCGTCCGGGTCAACTTCAGTTGATTAGGAGCCATGTTGGATTTAGATCCACTCTCTGAAGGGATATATTGTTGCGGCTGCTGACTTTCTACATCAGACAACGAAGATGTTTCGTCTGAATTAAACGAATTTATGGATTCCTGTCTGTTCATTTCTGTTTATCTTTGGCTAGAGGAGTACTAATGCAAAATTAAAATAATGAAGTAAGAAGGGAGAAAGTAATTAGTTATATTAGAAAACTAGACCACGAAATTTGTAGTATAATTATGGGTATGACAATTAAAGAATTAGGGTGAACGCTACCGGTGAGGACAAAAAAGGCTGAACGAAGAAGAAAAATAAAAAGAAGATTAGATCAACGCACCTAGACGAAAAAGAGCAAATACTGCTTATTGTATTCACTTTGGAGAACAGGTTGTAACAGGACAGCTGACAATTGCTAAGTTAAGTAGATTACAAAGACAAATGTTCTTAGGCGAAAAGAATATATAAACTAAAAGAAAAAGTGGAAAAAGGGTACGTGTAAAAAGAGACTAGGATGGTTGAGCAGCGAATGATTGCAAGATATATAAAAGAAACGAGCCAGTTTTACAGCGTTTAACGCAGATCCAGAATATGAACAAAATGCATTAGGAAATAAATGAAAAAAATGGCTCTATGGATCAGGGATCATCATGGCTGCCGGAAACTACGCCGTTCTGTTTTGTTTTTGTTTTTCCTTTTTCCCGTTTGGGTGAAATCAGTGAGCTGTTCCGATCCGTTGGGCGAAGACATTGCCGCAGTGACGAAGCCCGGCTAGTCCGATTGGGCTCCAGTAAACCCCTCGCCAAGCACAGAGAAGCTAGTCAGAGGCCCGCTAGACTGTACTTACTGGTCTTTAGCACACGACGACCGTACTTTGCACGTGGCTGCAGACACATTTTGTATGGAGGGAATGCTTGATTATATAAAGAGCTCTGTTTTTATGTTACCCGTCCAACGTTCTCACCCGGCTCCGCGCTATTTTTTTTTTTTTTTTTTTTTTTTTTTT\n' |
| b |
| diff -r fc925f53cae7 -r 39495e107274 test-data/test_04_initial_break.agp --- a/test-data/test_04_initial_break.agp Wed Jul 27 09:26:18 2022 +0000 +++ b/test-data/test_04_initial_break.agp Wed Sep 28 09:41:02 2022 +0000 |
| b |
| @@ -1,1 +1,2 @@ -scaffold_1 1 7920 1 W HiC_scaffold_1 1 7920 + +scaffold_1 1 62472 1 W LYZE01000016.1_918909-981380 1 62472 + +scaffold_2 1 35123 1 W LYZE01000016.1_62044-97166 1 35123 + |
| b |
| diff -r fc925f53cae7 -r 39495e107274 test-data/test_04_scaffolds_final.agp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04_scaffolds_final.agp Wed Sep 28 09:41:02 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +scaffold_1 1 62472 1 W LYZE01000016.1_918909-981380 1 62472 + +scaffold_2 1 35123 1 W LYZE01000016.1_62044-97166 1 35123 + |
| b |
| diff -r fc925f53cae7 -r 39495e107274 test-data/test_04_scaffolds_final.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04_scaffolds_final.fa Wed Sep 28 09:41:02 2022 +0000 |
| b |
| b'@@ -0,0 +1,1630 @@\n+>scaffold_1\n+TACGAAGCAGGTGCTAAGATATCTTGAACAGCAAAGAAGTGTCAAAAACGTTTCTAATAA\n+GGTTTTAAATGAAGAATGGGCTTTGTATTTGCAAAGAGAACACGAAGTACTGAGAAAAAG\n+GAGGTTGAAACCTAAGCACAAGGATTTTCAGATACTGACACAAGTTGGACAGGGTGGTTA\n+TGGGCAAGTTTATCTTGCAAAAAAAAAAGACAGTGATGAAATTTGTGCTTTGAAAATATT\n+AAACAAGAAACTTTTATTCAAACTAAACGAGACGAATCACGTCCTTACTGAGAGGGACAT\n+ACTAACCACAACTAGATCTGACTGGCTTGTGAAGTTGCTTTATGCATTTCAGGATCCAGA\n+GAGCCTATATTTAGCAATGGAATTTGTACCTGGTGGTGATTTTCGCACATTGTTAATAAA\n+TACAAGGATATTGAAGAGCGGTCACGCAAGGTTCTATATCAGCGAAATGTTTTGTGCCGT\n+GAACGCGTTGCATGAACTTGGTTACACTCACCGGGATTTAAAGCCGGAGAATTTCTTGAT\n+TGATGCTACAGGGCATATCAAGCTGACCGATTTTGGTCTAGCAGCAGGGACCGTATCAAA\n+TGAAAGAATCGAAAGCATGAAAATACGCTTAGAAGAAGTAAAGAATTTGGAATTTCCTGC\n+TTTCACAGAAAGGTCTATCGAGGATAGAAGGAAAATATATCATAACATGAGGAAGACAGA\n+AATTAATTACGCTAACTCTATGGTCGGTTCGCCTGATTATATGGCCCTAGAAGTTCTGGA\n+AGGTAAAAAATACGATTTTACAGTGGATTATTGGTCATTAGGCTGTATGCTTTTTGAAAG\n+TTTGGTTGGATATACACCTTTTAGTGGTTCTTCTACTAATGAAACTTACGAGAATTTAAG\n+ATATTGGAAAAAAACTTTAAGAAGGCCCCGTACTGAGGATAGAAGAGCAGCATTCTCAGA\n+TAGAACCTGGGATTTAATTACAAGACTAATAGCTGACCCCATCAACAGAGTACGATCTTT\n+TGAGCAAGTTCGCAAAATGTCTTATTTCGCAGAGATCAATTTTGAAACCCTAAGAACAAG\n+TTCTCCACCATTTATTCCTCAATTAGATGATGAAACGGATGCAGGTTATTTCGATGACTT\n+CACAAATGAAGAAGATATGGCTAAATATGCAGATGTCTTCAAAAGACAGAACAAATTATC\n+TGCAATGGTCGATGACTCTGCCGTTGATTCCAAGCTTGTTGGATTTACTTTTAGGCATAG\n+AGATGGAAAACAAGGTTCAAGCGGGATACTTTACAATGGTTCAGAACATTCAGACCCTTT\n+TTCAACTTTTTATTAAGATTACGTCCCTACAATTTAATTTTGTATAGCATAACAGATACA\n+TTGACAACAGCAACAAGATGTGCTAACATTTTCCATTTTGAATGATTACCAAAATTATGA\n+AACCAAGGCAACATGTAATTTTTAAGTTTAGTAATCTTTTTCGGGATGAGATGTTTTGAA\n+GAGTTTTATGCTATTAAAGTAGTAATATGATTTATATATTCAAATAAAATGTAAATTATG\n+AAAGAAAAATACGATAAGCTGATAGGGTAAACTAGAAACCTTCGTTTTCTTCATCATCCA\n+CATCCAGTTTCTTTCTACCGCCCCCATTTCTTAAGGCAGCCATCTCATTAGTGGCAACTT\n+GCTTTCTAACCTTCTTTGTCATCCTGGCTATCTCTTCTTCAGCGTCAACTGCATCTTCTT\n+CTGCATATTGCATTACCAATCTGCGGCCCAGTAAATGGACACCGTGCAACTGATCCATAG\n+CATTTTCTGCTTCCTTTGGAAGTAAAAATTCCACGAACGCAAAACCTCTTGCAGACTTGT\n+CGAACTTCTTTGGAACTCTAACAGATTTTAATTGACCAAAAGAATTGAATAATTCGAAAA\n+CGTCTTTCCTAGTAGCTTCAAATGGAAGATTCTTAACAATGATTTTACCGCTTTTCTTAT\n+TGGATTTAGTCTTTGTATTACCGCTCTGAGATGCTTGTCTATGGGATAACTTCAATTGAA\n+TCTTATGGCCGTCGATTACCGTCCCATCCATTGCAGCTATCACGGCATTAGCTTGTTCCT\n+TGGTCCTGAATTCTACAAAACCAAACCCCATTGACAAGGTCTTGCCTTGATGTTTTGGAT\n+CAGGTTTTGTCTTCACTTGGGCAACAACAAAACCAGTGAAAACCTTGAACCTATCAGTAA\n+GATTTTGGTTCGTCGTGGAGAAGTTTAGATTCTTTATGAAAATTGAGACAGTTGGACCAT\n+CAATAACGTCTTCATCATGAGCATTAGATGACCCTTCAGTTACATCCTTGTTTGCTTCCA\n+TTAAGTCATTTGATGAAGGTTTTACCTCTACCGGGTTTTCTTCTTCTTTTGCAGAAGTGT\n+TATTTATCAAATCATCGGCCTCAGCTGGTTTAGTAAAGCAATCCTTAGGCCCCCTTTCTA\n+GATATATTATGCCGTCCTTAAATCTTTTATACGATAGTTTAGTGAAAGCTGCCCTTGCTG\n+ACGTTGTGTCCCTGAATTGCACTATAGCTATTGTACCAGCTGGTGGCATGAGCAATCTTT\n+CCAATTTACCATATGGCAAAAACATTTCGCCAAGCTCTTCTCTAGTTGTCCCAAAAGGAA\n+AATTTTTAACCAGTATCACTTTATCGTCTCTTTGATTTGTAGATTTTAACTGTGAAAACT\n+TGGTCAGATCAACACCTTTGGATTCAAAGTATTTTCTAACATCACCAATAACATGGGCTT\n+CAGCCAAAGCTTGTTTGACAGCCGAACTTGAGTTTTCAGCATCGATCAATTGAGATTTTT\n+CTAGACCCAATTTGGCTGCCACACTACCCAAAACAGCATCTTGGTTCATATACAAGGAGT\n+TCCAAGAAAATGTTTGTCTGGATGCAGCTGCCTTCCTTTTCAATTCCTTTTGCTTTTTCA\n+ATGGCATATTCTTTAAATCAAACTCATCTAATCTATGGCTTTTTTTTTCTTCACCAGGAA\n+GAATATGCAATAGTCTTCCTTGAAAAATCTGTTTATCCAATTCAACATAGGCGTTCACTG\n+CATTCTTAGAATCCTTAAATAGAACGTATGCAAATCCTTTGGATTGACCAGTCCTGGTAT\n+CCAAAGCCACATGAACCTCCTCTAACTCTCCAAATGGACTAAATAGTTTCCTGAAATCTT\n+CTTCTTTGGAGGTATACAAGATATTACGTAAGAATAAACGGCCAGTTTGGTTAATTTTTT\n+CAATAGCCAGTTCTTCGTCCGTCTTTTGCGGCACAGCACGTTCTGGTTGTTCTTCCTTCT\n+TGGTATCGAGACTTTCATTTTGTTCAGTAGCGTATGATGATGATTTTTCCCTTGTTTCCG\n+CTTCACTTTCTTTGATTCTTACACGGCGTTGTTTGAACCAATCTAGGTCAGAAACCTTTT\n+CATCTTGGGCGAGGTTTCTCCTCTTTTCATTCTCTTTTTCATCACTATTAGCGTCATCAT\n+TAACTAAACCTATATCAGTATCCTTCAAATTGCTAATACTTATCATCTTTTCTTCCTCTC\n+CGGCATCTTCTTGATCTTCATCCCTGTTTCTGTTGAGAGCCGAATATTCATCGTCACTTT\n+CATTCTCAATGACCAAATTTGGTGCTTCGTCTTTATTATTCTCTTCCTTTAAGGCTAATG\n+CATGAGCCAATAGAGAATTCCCTTGCACGCTGGAGTCCTCTTCTTCCCGTTTTAGTTTTT\n+CGTCCTCTATGCTCTTGTCAATGCCAACTTTTTCCCATGATGTGACTTGTGAGCTTGGCT\n+TCATAGTCTCCATGAACTCTTGTAATTGCTTGTTCTTGCGAATCTCGTCATCAATGTTGC'..b'ACAAA\n+CCTGAAGTTCCGAATCACCATAAATTTGTTTATTCTTGGGCGTATTTTTTCTAGTAAATC\n+AACTGACAAGGCCTTTAGGGACCATTTTTGATGCGACAGTTTTTTCTTATTTACATCCTT\n+CAAAACAGTTTGAGATAAAAGACGTATTGTCGATACTGAATTTTGTAAACAGTAAAGAAA\n+AGACTTTAGGATTGAATCACTTACTGTTTTGTAGTACTGTTCAGCTTCATACACGGCAGG\n+TAAACCTTGGACGCATTCGTTGGTCACAGAATAGTAGCACAATAATATAATGTACTCAAA\n+TATGGCTTGGCTAACAAGATATTGCAAATCTCCGTCTTCAAAGGATGAGGGATCAGCAAT\n+GTCCTTGCAAATATTGTATAGCAAATCAAAAGGCACCGAACAATAAGAGTCAATATTGTC\n+AGTTTTGATTGAAATGCAGATTTTTTCAACAATTGACCTGATCAATTGTAATTGATCTTG\n+TAACCTACTTAGTTCTTCATTTTCCTCACGTACGTCTTGAATCAATTGTTGCTGTGAATC\n+AAATGCAACCTCTCGTAGTGATTCCTCTAATGAATGACTTATCTCTTCAAAAGATTTCAA\n+AATACGCCTATTGATGATCATTTAAGAATATTAATTAAGGAACCTGCAATTTTGCAATAG\n+GACTATTTTGTTGACTTTGTTGTTATTACTAAGTTTTAAAGTGGAAAAGAATTCCGACCC\n+TTTGTTTAGTGAGTGGGGGTCAATCAAATTCGTATTCCTCGGTCAAATGAGGAGGAATGT\n+AAAAACCGAAAATAAAGTCATCGCATAGGTACAAGAAGAATGAACTTGAGAAGTTCAAAT\n+TTCTAATTCAATTTTTTTTTTTTTCTATACATATAAATTAATAAAGTTACTCACGGTTTG\n+AAGGTCAATCAATATATTTGTTTAGGATAGCAATAGATAAAAGAACAATAGAGAAAGAAT\n+GTAAAATACGTAAAAATATATGTACATTACTGTCGGATAATGGTTTGAATGCATGTTTGA\n+TATGTTTGCTTATGTTTGCTTATGTTTGCTTATGTTTTTATCATTACTACTACTATAATT\n+TTTCATTATTATGCTCGATTCGTAAAATCGTTACTCTTATTCAATACTATCTATGGAATA\n+ATCCTTCTTGGATAACTTATGTCTCAAACCTTTGCCCCAGTAAGAAAATGCAAAAGGTAA\n+AGCAATCATAGCAGTGGAGATGAAAGCCAACAACCAAGAACCCCAGTGCAGATTCAATTT\n+GTGGTACATTTGAATGGTAAACAAGGGGAAGGCAGCACCACCGGCGGATCTTAAGAAAAC\n+CTTTGTAGCCAGAGCACTGGATGCGTATTGGACGTAGCAATCAATAATGTAATTATTCAA\n+TGAATAATAAATCAACACCATACCGAAACCAAAAGCTAAACCAGCTGAAGCTGGACCAAC\n+CCAAATAATATGTTTATAAGCGGTAGCACCCAGGATCCATAAAGCAATTGCAGCAAATGG\n+AGCACCGATCTTAGCACCTAGCAAACGATCTTCAGGAGTAGGTTTACGCTGTTTGACAAT\n+TTGTAAATACTTGTTTTCACAGTAGAAAGTTGTGGCTAACGCCCAAAGAGCACCGATAAC\n+AATAGGAATAAACATCAAACCCACAAGGTTGTCTTTGTAGCCATATAGTTCACCGAAAAT\n+GACAGGGAAGGCAAAGAAGAACGCATATAGTAGAGAGTAAATCAAACACACGTAGAAACA\n+AGTAGCAACTAGAACAGGTTCAGTGACAGAGAAGTACAAAGGTCTCAACAGACAAGCCCT\n+CATCATTTCACCCATACTGACACCTTGCGCTTCCTGCTCAGTCATAATCTTGGGATTACC\n+AGTTTCCTTTCTTAATCTAGCAGCCTTTCTCTTCAAGATAACTGGAGCGTACGTTTCTGG\n+GATGGCAGAAGATATGATCCACATAACACCTGCAAAGGCCATATTGACCCAGAAAATCAG\n+GTCCATACGTCCGGTAGAAACGGAAATAAAACCGTTAACTAGTGGACCAACAACGGGACC\n+AACGTAAGGAGCAAAAGCGAAGAAAGCAATAGCCTTACCTCTTGTTTCACTTGGGAACAT\n+ATCGGCAATAGACCCACCAACTAAACACAAACCAGATGATGACCAAACACCACATAAAAA\n+TCTACAAGCTAAAAGACTACCTAGATTTGGAGCTAAGGCGCAAGGGATATTGAAGATGAC\n+ATAAAGACCCATAGAAACAAAGTAAGCAACTCTTCTACCGTAAAGATCACTAACAGGAGA\n+CCAAATCAAAGGACCCAGCGAGAACCCAATAACCATTAAAGAAACCGATAAAATAGCGGC\n+TTCCATACCTACATGGTATTTCTTTTCAACGGTTCCCAACCCACCACTGATACAAGCAGA\n+CCCGTAGGCGACACAAATAACTAAGATTGACAGTAGGACAGTGTAACTCCAACGGATCCA\n+TGCAGGCCAGTTATGGGGGTTTTCTGGATCGCCAGTCACAAAGGTAACGAATTCAATTTC\n+CGGATCTAGATCTGGAGCTTCGTCATTCGCACCACTAGAGTCGCCTTCTTTACCCTTTTC\n+GTTATTATCACTTTCTAAAGCATCTTCATTAGAAGAAGGCGAAGAAGCGCCATCGATCTG\n+TCTAGTTCTCGTACGGGAAATCGCAGTAGAAGTTCTACCTATGGAATGTAGAGTGGCGAC\n+AGGAACTAAACCTGTAGGGGTTTCTAAAGTATATTCTTCAGGAAAAATCTTATTCTTGCT\n+AGATTGAGGAGCATTAACATCAGGAACGGGGGCTTTGGAGCTCACACCCATGTCCTGCAA\n+TGACTTCACGGTTTCCGTCCGGGTCAACTTCAGTTGATTAGGAGCCATGTTGGATTTAGA\n+TCCACTCTCTGAAGGGATATATTGTTGCGGCTGCTGACTTTCTACATCAGACAACGAAGA\n+TGTTTCGTCTGAATTAAACGAATTTATGGATTCCTGTCTGTTCATTTCTGTTTATCTTTG\n+GCTAGAGGAGTACTAATGCAAAATTAAAATAATGAAGTAAGAAGGGAGAAAGTAATTAGT\n+TATATTAGAAAACTAGACCACGAAATTTGTAGTATAATTATGGGTATGACAATTAAAGAA\n+TTAGGGTGAACGCTACCGGTGAGGACAAAAAAGGCTGAACGAAGAAGAAAAATAAAAAGA\n+AGATTAGATCAACGCACCTAGACGAAAAAGAGCAAATACTGCTTATTGTATTCACTTTGG\n+AGAACAGGTTGTAACAGGACAGCTGACAATTGCTAAGTTAAGTAGATTACAAAGACAAAT\n+GTTCTTAGGCGAAAAGAATATATAAACTAAAAGAAAAAGTGGAAAAAGGGTACGTGTAAA\n+AAGAGACTAGGATGGTTGAGCAGCGAATGATTGCAAGATATATAAAAGAAACGAGCCAGT\n+TTTACAGCGTTTAACGCAGATCCAGAATATGAACAAAATGCATTAGGAAATAAATGAAAA\n+AAATGGCTCTATGGATCAGGGATCATCATGGCTGCCGGAAACTACGCCGTTCTGTTTTGT\n+TTTTGTTTTTCCTTTTTCCCGTTTGGGTGAAATCAGTGAGCTGTTCCGATCCGTTGGGCG\n+AAGACATTGCCGCAGTGACGAAGCCCGGCTAGTCCGATTGGGCTCCAGTAAACCCCTCGC\n+CAAGCACAGAGAAGCTAGTCAGAGGCCCGCTAGACTGTACTTACTGGTCTTTAGCACACG\n+ACGACCGTACTTTGCACGTGGCTGCAGACACATTTTGTATGGAGGGAATGCTTGATTATA\n+TAAAGAGCTCTGTTTTTATGTTACCCGTCCAACGTTCTCACCCGGCTCCGCGCTATTTTT\n+TTTTTTTTTTTTTTTTTTTTTTT\n' |
| b |
| diff -r fc925f53cae7 -r 39495e107274 yahs.xml --- a/yahs.xml Wed Jul 27 09:26:18 2022 +0000 +++ b/yahs.xml Wed Sep 28 09:41:02 2022 +0000 |
| [ |
| @@ -1,8 +1,8 @@ <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@">1.2a</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION@">1.2a.2</token> + <token name="@VERSION_SUFFIX@">0</token> </macros> <requirements> <requirement type="package" version="@VERSION@">yahs</requirement> @@ -22,7 +22,7 @@ #end if samtools faidx input.fasta && mkdir initial_break agp_out agp_break final_outs && - yahs input.fasta + yahs --no-mem-check input.fasta #if $function.bfile.ext == "bam": input.bam #else if $function.bfile.ext == "bed": @@ -152,6 +152,7 @@ </data> </outputs> <tests> + <!-- TEST 1 --> <test expect_num_outputs="5"> <conditional name="function"> <param name="function_select" value="yahs"/> @@ -164,6 +165,7 @@ <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 2 --> <test expect_num_outputs="5"> <conditional name="function"> <param name="function_select" value="yahs"/> @@ -179,44 +181,44 @@ </output_collection> <!-- COMMAND: yahs test.fasta test.bed -\-no-contig-ec -\-no-scaffold-ec -o test_2 --> </test> + <!-- TEST 3 --> + <test expect_num_outputs="6"> + <conditional name="function"> + <param name="function_select" value="yahs"/> + <param name="fasta" value="test2.fasta"/> + <param name="bfile" value="test2.bam"/> + <param name="res" value="1000,2000,5000,10000,20000,50000,100000,200000,500000"/> + <conditional name="enzyme_conditional"> + <param name="enzyme_options" value="not_specified"/> + </conditional> + </conditional> + <param name="log_out" value="yes"/> + <output name="log_file" ftype="txt"> + <assert_contents> + <has_text text="[I::dump_links_from_bam_file] dumped 6399 read pairs from 17675 records: 6297 intra links + 102 inter links" /> + </assert_contents> + </output> + <!-- COMMAND: yahs test.fasta test.bam -r 1000,2000,5000,10000,20000,50000,100000,200000,500000 -o test_3 --> + </test> + <!-- TEST 4 --> <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="fasta" value="test2.fasta"/> + <param name="bfile" value="test2.bed"/> <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"/> + <param name="enzyme_options" value="not_specified"/> </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 name="final_agp_out" file="test_04_scaffolds_final.agp" ftype="agp"/> + <output name="final_fasta_out" file="test_04_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 5 --> <test expect_num_outputs="1"> <conditional name="function"> <param name="function_select" value="agp_to_fasta"/> @@ -227,6 +229,7 @@ <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/> <!-- COMMAND: agp_to_fasta test.fasta test.agp -l 20 -o test_4 --> </test> + <!-- TEST 6 --> <test expect_num_outputs="6"> <conditional name="function"> <param name="function_select" value="yahs"/> |