| Previous changeset 0:5799092ffdff (2022-03-09) Next changeset 2:ad1149b4f795 (2022-06-01) |
|
Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2" |
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modified:
gfastats.xml macros.xml test-data/test_01.fasta.gz test-data/test_03_stats.tabular test-data/test_04_stats.tabular test-data/test_05_stats.tabular test-data/test_07_stats.tabular test-data/test_08.fasta.gz |
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added:
test-data/dataset_05.agp test-data/test_09.fasta.gz test-data/test_10.gfa |
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| diff -r 5799092ffdff -r 2b8b4cacb83d gfastats.xml --- a/gfastats.xml Wed Mar 09 10:29:20 2022 +0000 +++ b/gfastats.xml Mon Apr 25 09:38:18 2022 +0000 |
| [ |
| @@ -30,7 +30,9 @@ #if $mode_condition.sort --sort $mode_condition.sort #end if - $mode_condition.homopolymer_compress + #if $mode_condition.homopolymer_compress + --homopolymer-compress $mode_condition.homopolymer_compress + #end if -o dataset.$mode_condition.output_condition.out_format #if $mode_condition.output_condition.out_format == 'fasta' #if $mode_condition.output_condition.line_length @@ -41,7 +43,7 @@ --line-length $mode_condition.output_condition.line_length #end if #end if - #else + #else if $mode_condition.selector == "statistics" #if $mode_condition.statistics_condition.selector == 'size' --out-size $mode_condition.statistics_condition.out_size #else if $mode_condition.statistics_condition.selector == 'coordinates' @@ -52,9 +54,13 @@ --seq-report $mode_condition.statistics_condition.out_sequence #end if - $mode_condition.tabular > '$stats' + $mode_condition.tabular > '$stats' + #else + --agp-to-path $mode_condition.agp_to_path + $mode_condition.discover_paths + -o dataset.gfa #end if - #if $mode_condition.selector == 'manipulation' + #if $mode_condition.selector == 'manipulation' or $mode_condition.selector == 'scaffolding' && mv dataset* output_dataset #end if ]]></command> @@ -95,6 +101,7 @@ <param name="selector" type="select" label="Tool mode"> <option value="statistics">Summary statistics generation</option> <option value="manipulation">Genome assembly manipulation</option> + <option value="scaffolding">Scaffolding</option> </param> <when value="manipulation"> <param argument="--swiss-army-knife" type="data" @@ -128,8 +135,7 @@ <option value="largest">Largest</option> <option value="smallest">Smallest</option> </param> - <param argument="--homopolymer-compress" type="boolean" truevalue="--homopolymer-compress" falsevalue="" checked="false" - label="Homopolymer compression" help="Compress all the homopolymers in the input"/> + <param argument="--homopolymer-compress" type="integer" min="0" value="" optional="true" label="Homopolymer compression" help="Compress all the homopolymers in the input above the given threshhold" /> </when> <when value="statistics"> <conditional name="statistics_condition"> @@ -167,6 +173,11 @@ <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true" label="Tabular-format output" help="Generate output in tabular format"/> </when> + <when value="scaffolding"> + <param argument="--agp-to-path" type="data" format="agp" label="Input AGP file" help="Integrate the AGP information into the assembly graph as paths. The scaffolding information is converted into paths through the graph" /> + <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="generates the initial set of paths" help="In the graph space an assembly + is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" /> + </when> </conditional> </inputs> <outputs> @@ -177,7 +188,7 @@ </change_format> </data> <data name="output" format="fastq" from_work_dir="output_dataset" label="${tool.name} on ${on_string}: edited sequences"> - <filter>mode_condition['selector'] == 'manipulation'</filter> + <filter>mode_condition['selector'] == 'manipulation' or mode_condition['selector'] == 'scaffolding'</filter> <change_format> <when input="mode_condition.output_condition.out_format" value="fasta" format="fasta"/> <when input="mode_condition.output_condition.out_format" value="fasta.gz" format="fasta.gz"/> @@ -185,6 +196,7 @@ <when input="mode_condition.output_condition.out_format" value="fastq.gz" format="fastq.gz"/> <when input="mode_condition.output_condition.out_format" value="gfa" format="gfa1"/> <when input="mode_condition.output_condition.out_format" value="gfa.gz" format="gfa1.gz"/> + <when input="mode_condition.selector" value="scaffolding" format="gfa1"/> </change_format> </data> </outputs> @@ -288,10 +300,31 @@ <param name="out_format" value="fasta.gz"/> </conditional> <param name="sort" value="ascending"/> - <param name="homopolymer_compress" value="true"/> </conditional> <output name="output" value="test_08.fasta.gz" ftype="fasta.gz"/> </test> + <!--Test 09 --> + <test expect_num_outputs="1"> + <param name="input_file" value="dataset_03.fasta"/> + <conditional name="mode_condition"> + <param name="selector" value="manipulation"/> + <conditional name="output_condition"> + <param name="out_format" value="fasta.gz"/> + </conditional> + <param name="homopolymer_compress" value="10"/> + </conditional> + <output name="output" value="test_09.fasta.gz" ftype="fasta.gz"/> + </test> + <!--Test 10 --> + <test expect_num_outputs="1"> + <param name="input_file" value="dataset_04.gfa"/> + <conditional name="mode_condition"> + <param name="selector" value="scaffolding"/> + <param name="agp_to_path" value="dataset_05.agp"/> + <param name="discover_paths" value="true"/> + </conditional> + <output name="output" value="test_10.gfa" ftype="gfa1"/> + </test> </tests> <help><![CDATA[ |
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| diff -r 5799092ffdff -r 2b8b4cacb83d macros.xml --- a/macros.xml Wed Mar 09 10:29:20 2022 +0000 +++ b/macros.xml Mon Apr 25 09:38:18 2022 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.2.0</token> + <token name="@TOOL_VERSION@">1.2.1</token> <token name="@SUFFIX_VERSION@">0</token> <xml name="requirements"> <requirements> |
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| diff -r 5799092ffdff -r 2b8b4cacb83d test-data/dataset_05.agp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_05.agp Mon Apr 25 09:38:18 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +## agp-version 2.1 +# AGP created by RagTag v2.1.0 +NC_004545.1 1 103120 1 W NC_004545.1_1_103120_+ 1 103120 + |
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| diff -r 5799092ffdff -r 2b8b4cacb83d test-data/test_01.fasta.gz |
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| Binary file test-data/test_01.fasta.gz has changed |
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| diff -r 5799092ffdff -r 2b8b4cacb83d test-data/test_03_stats.tabular --- a/test-data/test_03_stats.tabular Wed Mar 09 10:29:20 2022 +0000 +++ b/test-data/test_03_stats.tabular Mon Apr 25 09:38:18 2022 +0000 |
| b |
| b'@@ -1,1697 +1,210 @@\n-Seq\t1\n-Header\tbf06004a-705a-4fe9-942a-2dcabf04766e.1\n-Comment\t\n-Total segment length\t11188\n-Base composition (ACGT)\t2755, 2648, 2783, 3002\n-GC content %\t48.54\n-# soft-masked bases\t0\n-\n-Seq\t2\n-Header\t106a7186-c3b0-43dd-8289-34f8a0494fcf.1\n-Comment\t\n-Total segment length\t15267\n-Base composition (ACGT)\t3870, 3700, 3835, 3862\n-GC content %\t49.35\n-# soft-masked bases\t0\n-\n-Seq\t3\n-Header\te6a172b9-7593-4d0b-9f09-e85edaab94cf.1\n-Comment\t\n-Total segment length\t15699\n-Base composition (ACGT)\t3946, 3779, 3927, 4047\n-GC content %\t49.09\n-# soft-masked bases\t0\n-\n-Seq\t4\n-Header\t48744a56-dcfe-48e0-97ab-3b903ebdb60a.1\n-Comment\t\n-Total segment length\t14688\n-Base composition (ACGT)\t3551, 3670, 3692, 3775\n-GC content %\t50.12\n-# soft-masked bases\t0\n-\n-Seq\t5\n-Header\t94d29bbc-7b1e-4cc5-abaa-d26d744c82bb.1\n-Comment\t\n-Total segment length\t10592\n-Base composition (ACGT)\t2524, 2631, 2678, 2759\n-GC content %\t50.12\n-# soft-masked bases\t0\n-\n-Seq\t6\n-Header\t813565c4-b858-4289-979d-ed8db9603825.1\n-Comment\t\n-Total segment length\t17906\n-Base composition (ACGT)\t4239, 4509, 4722, 4436\n-GC content %\t51.55\n-# soft-masked bases\t0\n-\n-Seq\t7\n-Header\t392f8e7b-42bc-469c-81cd-199b5c068bd7.1\n-Comment\t\n-Total segment length\t14117\n-Base composition (ACGT)\t3392, 3580, 3794, 3351\n-GC content %\t52.23\n-# soft-masked bases\t0\n-\n-Seq\t8\n-Header\t805d527c-db18-465d-be1d-6ef52fa8f84f.1\n-Comment\t\n-Total segment length\t18959\n-Base composition (ACGT)\t4951, 4579, 4593, 4836\n-GC content %\t48.38\n-# soft-masked bases\t0\n-\n-Seq\t9\n-Header\tf4f56757-4761-4f86-a434-3d8c09be3b37.1\n-Comment\t\n-Total segment length\t8044\n-Base composition (ACGT)\t1909, 2034, 2120, 1981\n-GC content %\t51.64\n-# soft-masked bases\t0\n-\n-Seq\t10\n-Header\tc91c7a17-0d05-4248-b677-59617a91d4ce.1\n-Comment\t\n-Total segment length\t12004\n-Base composition (ACGT)\t3080, 3015, 3137, 2772\n-GC content %\t51.25\n-# soft-masked bases\t0\n-\n-Seq\t11\n-Header\t790136e4-0663-4d7a-b7e2-941f5d007754.1\n-Comment\t\n-Total segment length\t6684\n-Base composition (ACGT)\t1594, 1736, 1777, 1577\n-GC content %\t52.56\n-# soft-masked bases\t0\n-\n-Seq\t12\n-Header\te72d1741-ef41-4bc7-a49e-279c9f9b7263.1\n-Comment\t\n-Total segment length\t11195\n-Base composition (ACGT)\t2787, 2843, 3047, 2518\n-GC content %\t52.61\n-# soft-masked bases\t0\n-\n-Seq\t13\n-Header\t78e01914-94ca-4040-bd8e-6c99d7583512.1\n-Comment\t\n-Total segment length\t6987\n-Base composition (ACGT)\t1621, 1818, 1813, 1735\n-GC content %\t51.97\n-# soft-masked bases\t0\n-\n-Seq\t14\n-Header\te76596da-bcc2-4395-aa51-b96a89bf872f.1\n-Comment\t\n-Total segment length\t7674\n-Base composition (ACGT)\t1816, 1949, 1939, 1970\n-GC content %\t50.66\n-# soft-masked bases\t0\n-\n-Seq\t15\n-Header\ta6565705-c7a4-4365-9fd0-3b28c1919cdd.1\n-Comment\t\n-Total segment length\t7530\n-Base composition (ACGT)\t1920, 1881, 1950, 1779\n-GC content %\t50.88\n-# soft-masked bases\t0\n-\n-Seq\t16\n-Header\t81954f91-3ccd-4af8-9bd4-69a43b777235.1\n-Comment\t\n-Total segment length\t8752\n-Base composition (ACGT)\t1968, 2265, 2251, 2268\n-GC content %\t51.60\n-# soft-masked bases\t0\n-\n-Seq\t17\n-Header\t3328f98c-6f8c-4bad-a998-22e81b0f64d0.1\n-Comment\t\n-Total segment length\t7363\n-Base composition (ACGT)\t1868, 1823, 2003, 1669\n-GC content %\t51.96\n-# soft-masked bases\t0\n-\n-Seq\t18\n-Header\t1aff9669-f6d2-4ffd-8f77-4c99cef14421.1\n-Comment\t\n-Total segment length\t9608\n-Base composition (ACGT)\t2517, 2436, 2578, 2077\n-GC content %\t52.19\n-# soft-masked bases\t0\n-\n-Seq\t19\n-Header\tef00aaf4-8ba0-45ff-8df2-bcc01dbf8d50.1\n-Comment\t\n-Total segment length\t8167\n-Base composition (ACGT)\t2187, 2015, 2143, 1822\n-GC content %\t50.91\n-# soft-masked bases\t0\n-\n-Seq\t20\n-Header\tc22489fb-3bdb-484a-8c2a-e9706b7c40b3.1\n-Comment\t\n-Total segment length\t5406\n-Base composition (ACGT)\t1411, 1339, 1455, 1201\n-GC content %\t51.68\n-# soft-masked bases\t0\n-\n-Seq\t21\n-Header\t3c2169f8-24e7-455d-ae9f-44ca5224d990.1\n-Comment\t\n-Total segment length\t4455\n-Base composition (ACGT)\t967, 1187, 1121, 1180\n-GC content %\t51.81\n-# soft-masked bases\t0\n-\n-Seq\t22\n-Header\tdf422228-a7ac-47c4-bfa9-17b9b694b1de.1\n-Comment\t\n-Total segment length\t6143\n-'..b'\t495\t36.61\t0\n+158\t3b8d7a03-715f-4de8-b947-f5f7ef71e026.1\t\t1503\t532\t261\t289\t421\t36.59\t0\n+159\td291085b-90a4-4cd4-9882-7840c2560a25.1\t\t1711\t519\t293\t373\t526\t38.92\t0\n+160\t2e893f02-50f9-4097-8afe-5cb76b9d0530.1\t\t707\t201\t157\t108\t241\t37.48\t0\n+161\t650a79d4-9afd-4e70-8278-eff31d799303.1\t\t3213\t965\t645\t642\t961\t40.06\t0\n+162\t060418b3-01d6-4930-836c-f463edb86237.1\t\t11792\t3187\t2115\t2145\t4345\t36.13\t0\n+163\t0a342b60-bd55-4512-84d6-2a6de18d68e0.1\t\t13370\t3719\t2405\t2289\t4957\t35.11\t0\n+164\t5d246966-eedb-4165-9470-62b97e96242c.1\t\t8183\t2195\t1502\t1534\t2952\t37.10\t0\n+165\tbdd01c94-237f-4bbf-83d3-b1deef7d16c7.1\t\t10475\t3588\t1856\t2006\t3025\t36.87\t0\n+166\t8f6d70a8-9423-4169-b345-45e744a11e88.1\t\t7755\t2789\t1352\t1442\t2172\t36.03\t0\n+167\tc761e47e-0c8c-4744-854c-f1223df45684.1\t\t9837\t3686\t1672\t1761\t2718\t34.90\t0\n+168\t7652f113-0d63-4ebd-acff-d2d12be43f0e.1\t\t11893\t4384\t1988\t2133\t3388\t34.65\t0\n+169\t16a88a50-c6ac-4f5b-af02-9acdf147b5a3.1\t\t5949\t1683\t1030\t1093\t2143\t35.69\t0\n+170\t424363b0-4eb3-4267-be80-013aab28f207.1\t\t10479\t2877\t1874\t1855\t3873\t35.59\t0\n+171\tcf1fdc14-0b98-47a0-aa21-8489c331d096.1\t\t10090\t2728\t1814\t1763\t3785\t35.45\t0\n+172\tf472fb0c-4ff1-4c0e-a3f3-0326e72ed0b6.1\t\t14971\t4129\t2735\t2702\t5405\t36.32\t0\n+173\t92135d45-94c1-4297-a523-1119cfa480bf.1\t\t4877\t1384\t824\t885\t1784\t35.04\t0\n+174\t054c508f-a936-44f1-a964-7ee2857d63cb.1\t\t11907\t3308\t2098\t2060\t4441\t34.92\t0\n+175\tb5f8232c-3fd2-4aa9-9b80-22fa749bd1fb.1\t\t1458\t459\t277\t253\t469\t36.35\t0\n+176\ta9ab6f29-eb7c-4ef4-a510-26cdd495208d.1\t\t1110\t384\t169\t195\t362\t32.79\t0\n+177\t55cb3056-6cc6-424c-9d5d-99bdce18a7e9.1\t\t8847\t2609\t1513\t1563\t3162\t34.77\t0\n+178\t3bfa7a5d-2aa7-40eb-a745-0d15d7a88cab.1\t\t12142\t4227\t2050\t2188\t3677\t34.90\t0\n+179\t062b0e2b-42c2-415a-93d5-944643d9e5e6.1\t\t1076\t328\t236\t232\t280\t43.49\t0\n+180\t652a78d6-b9bd-4fb3-869e-f33b2fb8a745.1\t\t6996\t1873\t1283\t1287\t2553\t36.74\t0\n+181\t97d47376-d56c-4447-9a92-a9a40b3da660.1\t\t4144\t1440\t769\t759\t1176\t36.87\t0\n+182\tcd1c1488-8997-40b6-b7ab-2366a8cf00a8.1\t\t7728\t2723\t1376\t1485\t2144\t37.02\t0\n+183\ta606d237-d887-4671-94d7-3e5a571cf34f.1\t\t2227\t767\t372\t394\t694\t34.40\t0\n+184\t75675f80-7982-4af2-9111-bd76d7325968.1\t\t6728\t2029\t1170\t1495\t2034\t39.61\t0\n+185\t29205a85-42bf-425f-b0c8-42a3603d2abc.1\t\t1472\t498\t240\t257\t477\t33.76\t0\n+186\t1f2f9610-80cf-4e4b-90f5-840c3ba90f35.1\t\t6074\t1662\t1089\t1140\t2183\t36.70\t0\n+187\t46f1d129-9f86-45c7-a9e2-1250ebbe5eed.1\t\t5700\t1546\t1022\t1075\t2057\t36.79\t0\n+188\tbe94d96b-0c90-4a78-beff-9575123f3f42.1\t\t7009\t2443\t1245\t1278\t2043\t36.00\t0\n+189\t0c6fc9d7-0385-46c5-8869-1b6f8e6a39d6.1\t\t4650\t1259\t888\t954\t1549\t39.61\t0\n+190\t94a9a3f9-b318-4cf9-a60d-11888856f2e5.1\t\t5557\t1984\t1015\t1035\t1523\t36.89\t0\n+191\t2ae01b26-de6a-4f64-ae9a-5bac19dfe8eb.1\t\t10752\t3023\t2001\t1932\t3796\t36.58\t0\n+192\tcf9094c2-11c2-4ed0-acee-68798a448c56.1\t\t3135\t884\t526\t564\t1161\t34.77\t0\n+193\td6ef2e66-9547-488c-aa53-554531f03cd8.1\t\t2970\t887\t545\t569\t969\t37.51\t0\n+194\t16faf9c6-9887-41e4-97d2-4b9433c4c6b5.1\t\t5256\t1862\t942\t968\t1484\t36.34\t0\n+195\t15e1d478-ee33-4a38-99f0-4fce40af07c2.1\t\t1103\t348\t191\t184\t380\t34.00\t0\n+196\t5aad2a5c-2896-419c-8aab-4bc1238fea95.1\t\t5515\t1489\t987\t1034\t2005\t36.65\t0\n+197\ta7d909b6-faa4-4bfa-bd82-3e2afd8d2185.1\t\t5784\t1823\t985\t999\t1977\t34.30\t0\n+198\tce713eb6-99b4-4dc3-83d3-056664bfcd99.1\t\t8283\t2271\t1489\t1481\t3042\t35.86\t0\n+199\t81f3e7bf-4e15-43f6-8a83-6bd617991df9.1\t\t8421\t3009\t1522\t1533\t2357\t36.28\t0\n+200\ta281deab-38f6-4e16-9129-a9dd00a14fcf.1\t\t5802\t1537\t1023\t1072\t2170\t36.11\t0\n+201\t325f1331-dec9-41b8-a69f-028b36681560.1\t\t5557\t1863\t1027\t1028\t1639\t36.98\t0\n+202\t140e6d68-cc21-4c3c-b854-de9594320be2.1\t\t4627\t1663\t865\t858\t1241\t37.24\t0\n+203\tbc025485-f152-4e18-ab61-740da71cc8a3.1\t\t2941\t812\t484\t542\t1103\t34.89\t0\n+204\t751f281c-c196-4257-9580-e203e4da2aeb.1\t\t5891\t1611\t1152\t1164\t1964\t39.31\t0\n+205\t9035679c-4e33-44f0-8f57-b4e7791d2616.1\t\t5428\t1864\t971\t1118\t1475\t38.49\t0\n+206\ta2d82a53-518c-4224-8f89-41723c3fa434.1\t\t4661\t1680\t847\t872\t1262\t36.88\t0\n+207\t48f635ff-a554-4baf-b00d-04b89da3c499.1\t\t855\t304\t156\t159\t236\t36.84\t0\n+208\t88a5ba1b-a388-48d1-964c-71f836904291.1\t\t1435\t432\t231\t238\t534\t32.68\t0\n+209\t5f3b0d4d-e80b-4ec9-bc9f-8f642acef345.1\t\t2360\t852\t419\t400\t689\t34.70\t0\n' 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| diff -r 5799092ffdff -r 2b8b4cacb83d test-data/test_04_stats.tabular --- a/test-data/test_04_stats.tabular Wed Mar 09 10:29:20 2022 +0000 +++ b/test-data/test_04_stats.tabular Mon Apr 25 09:38:18 2022 +0000 |
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| @@ -9,7 +9,6 @@ Scaffold auNG 290571.00 Scaffold LG50 1 Largest scaffold 417540 -# contigs 6 Total contig length 419573 Average contig length 69928.83 Contig N50 416949 @@ -19,16 +18,20 @@ Contig auNG 289747.19 Contig LG50 1 Largest contig 416949 -# gaps 3 -Total gap length 3 -Average gap length 1.00 -Gap N50 1 -Gap auN 1.00 -Gap L50 2 -Largest gap 1 -Base composition (ACGT) 102144, 112550, 104859, 100020 +# gaps in scaffolds 3 +Total gap length in scaffolds 3 +Average gap length in scaffolds 1.00 +Gap N50 in scaffolds 1 +Gap auN in scaffolds 1.00 +Gap L50 in scaffolds 2 +Largest gap in scaffolds 1 +Base composition (A:C:G:T) 102144:112550:104859:100020 GC content % 51.82 # soft-masked bases 0 +# segments 6 +Total segment length 419573 +Average segment length 69928.83 +# gaps 3 # paths 3 Scaffold N10 417540 Scaffold N20 417540 |
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| diff -r 5799092ffdff -r 2b8b4cacb83d test-data/test_05_stats.tabular --- a/test-data/test_05_stats.tabular Wed Mar 09 10:29:20 2022 +0000 +++ b/test-data/test_05_stats.tabular Mon Apr 25 09:38:18 2022 +0000 |
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| @@ -1,1 +1,1 @@ -edge_1 1 419576 1 W edge_1 1 419576 + +contig_1 1 419576 1 W edge_1 1 419576 + |
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| diff -r 5799092ffdff -r 2b8b4cacb83d test-data/test_07_stats.tabular --- a/test-data/test_07_stats.tabular Wed Mar 09 10:29:20 2022 +0000 +++ b/test-data/test_07_stats.tabular Mon Apr 25 09:38:18 2022 +0000 |
| b |
| @@ -6,23 +6,26 @@ Scaffold auN: 415520.91 Scaffold L50: 1 Largest scaffold: 417540 -# contigs: 6 Total contig length: 419573 Average contig length: 69928.83 Contig N50: 416949 Contig auN: 414345.81 Contig L50: 1 Largest contig: 416949 -# gaps: 3 -Total gap length: 3 -Average gap length: 1.00 -Gap N50: 1 -Gap auN: 1.00 -Gap L50: 2 -Largest gap: 1 -Base composition (ACGT): 102144, 112550, 104859, 100020 +# gaps in scaffolds: 3 +Total gap length in scaffolds: 3 +Average gap length in scaffolds: 1.00 +Gap N50 in scaffolds: 1 +Gap auN in scaffolds: 1.00 +Gap L50 in scaffolds: 2 +Largest gap in scaffolds: 1 +Base composition (A:C:G:T): 102144:112550:104859:100020 GC content %: 51.82 # soft-masked bases: 0 +# segments: 6 +Total segment length: 419573 +Average segment length: 69928.83 +# gaps: 3 # paths: 3 Scaffold N10: 417540 Scaffold N20: 417540 |
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| diff -r 5799092ffdff -r 2b8b4cacb83d test-data/test_08.fasta.gz |
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| Binary file test-data/test_08.fasta.gz has changed |
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| diff -r 5799092ffdff -r 2b8b4cacb83d test-data/test_09.fasta.gz |
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| Binary file test-data/test_09.fasta.gz has changed |
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| diff -r 5799092ffdff -r 2b8b4cacb83d test-data/test_10.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_10.gfa Mon Apr 25 09:38:18 2022 +0000 |
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| b'@@ -0,0 +1,2 @@\n+H\tVN:Z:2.0\n+S\tedge_1\t419576\tTTTCCTTTTCCTACTGTACTTCTCAAATATTCCAGGCGACTTTCGTGATGATTCACAGCATGTTTCACGATTCGCTAACCCTAATCCGCTACCGCGGTTAGCCGGGAACCCCGCTTTATCAACGCGATAAAAACGCTTCGGTCAGGCCGCGGAATAATGCTCCGGTGCAATGCCCCGGGTCCGTTATCTTCAACGCTAAATTCGGCACCGTGCGGCACTCGCTGCCAGCGTACGGTGATATGCGTGCCCTTCCGGCGTATGGATTCACGCGTTATTAGACCAGGTTTGAAATCGCACTGCGGTAGCTGATCTTCGTTTGCCAGACACCTTGAGGCCGTTATCTATCTCAAAGGTAAATGTCTGTTTTTCTGACTCAGAGTCTGAGCCTCGCGCTCAACAACGCGCAGCATCATCGGCACAATCAACCTTTTCATTTGAGGAATGCGTCGGTGCGGCTTCTATTTTCGACAGCGTCAGCAAATGCTTCACCAGGTCCTTCCATCCCGCTGGGTCTGCTCGCGCATGGTGTGCAACGCTTTTTCGCGTACCGCGCCTTCCAGCGGCTGCTCAATTCATCATCTCCAGGTAACCCCTGTAACACGGTCCAATGGCGTACGTAACTCATGGCTCACCGTTGGCAAAAAAGTTACGCCGCGCCCCTTCCAGTTGATGCATTTGCGTGACATCACGCGCCACCATCAGCAACTGTTTGTGGGTATAAGGCATGACGCGAATTTCCAGATGCCGCCCGGTGGTTTGAGCACAGATTGAGCGGGCGAGAAAAATCACGCGTTTTCAGATATTGCGTAAACTCCGGGTAAACGCAGTAGTTAAGGATGTTCTGCCCGTTATCTTCCGGCCAGCGCAAACCAAGAAATTTGTTGCGCCAGACCGTTACACCAGAAAATACCGCCCTTTTCCTGGTCAGCACCACCGCGTCGGGCAGCGACTCCGCGCCGCTACGAAAAGCGTTTAATCAGATTGCCCACTGTTCACGGCGGGCGTTTTTTATTTCCGCAGCTGCATCTGGTGTAAGCCGTATAGTAGCGGTTCCCAGCTACCACCGCCCCGGTGGCGGGGTCATACTGCGATCCCACCCAACAGCCACCATGAAAAGGCGCAATAAATTCCAGAAATGCCAGATAAGCAGTCCTGTTACCGATGCCAGCAAAAACCAGGGCAGGTAACCAAAAAATGCACCCAAGGATGAAAGCCGGGAGGCAGCAAAGTAGCAGCTCCAGCACCAGGCCTTTCCACGACAGCCGTTCCAGCACCGTAAGATACTCCAGTTAAGAAAATCATAAGCCCTGCTCTGCGCCGGAGAGCAAGGCGTTAAAAGCGGGGTTGAAAAACGATTATCCTGTACCGCGCACGGTCTGCCACCATGCGGTCATGCCCGCCGGGCTCCAGAGCTTTACGCAGGCGACGAATGTGGACATCGACCGTGCGGTCTTCCACATACACGTTAGTTCCCAGACGTGTTTAACAGCTGCTCGCGCTGTACACGCGCTCAGGATGCGTCATAAAAAAGTGCAGCAGTTTTAAATTCTGTCGGCCCCATCTCCAGCGGCTCTTCGCCCGCCATCACTCGGTGAGATGTCGGGTCGAGACTTAATCCCTGCATCTTAATCACCTCTTCCACCGCCATTGGCGAAATACGGCGCATTACCGCTTTGATTCGCGCCACCAGCTCCTTCGGCGAAAACGGCTTGGTGATATAGTCATCCGCGCCGGTTTCAAGCCGCGCACGCGATCTTCTTCTTTCCCCTCTGGCGGTCAACATCACCACTGGGAATATCCCGGGGTCATCGACTCGCGCTTGAGGTGTTTGATGAACTGGATACCGGAGCCGCCAGGTAACATCCAGTCGAGGAGAATTAAAATCCGGCCAGGGTTCATTCAGTTTGATTCACAGCACTGTCATAATCTTCCGCTTCGACCGGCTGAAAGCCATTTTGTTCGAGCACGAAGAGAGACCAATTTCGGCGAATTGGAGCTTCATCTTCTACGACCAGAATACGTCTCGCCATGATTTGCCCTGTTGTAATAAATAGGTTGCGATCATTAATGCGACGTCATTATGCGTCAGATTTATGACAGATTTATGAAAAGCCTCGTCGCACAATATCTTCAGGTTATTGATTTCCGTGGCGCAGAAAAAAGCAAATGGCACCATCTGTTTGGGTATAATCGCGCCCATGCTTTTTCGCCAGGGAACCGTTATGCGCATCCTTCACACCTCAGACTGGCATCTCTGGCCAGAACTTCTACAGTAAAAGCCGCGAAGCTGAACAATAGGCTTTTCCTTGACTGGCTGCTGGAGACAGCACAAACCCATCAGGTGGATGCGATTATTGTTGCCGGTGATGTTTTCGATACCGGCTCGCCCGCCCAGTTACGCCCGCACGTTATACAACCGTTTTGTTGTCAATTTACAGCAAACTGGCTTTCATCTGGTGGTACTGGCAGGAAACCATGACTCGGTCGCCACGCTGAATGAATCGCGCGATATCATGGCGTCCTCAATACTACCGTGGTCGCCAGCGCCGGACATGCGCCGCAAATCTTGCCTCGTCGCGACGGGACGGCCAGGCGCAGTGCTGTGCCCCATTCCCGTTTTTACGTCCGCGTGACATTATTACCAGCCAGGCGGGGCTTAACGGTATTGAAAAACAGCAGCATTTACTGGCAGCGATTACCGATTATTACCAACAACACTATGCCGATGCCTGCAAACTGCGCGGCGATCAGCCTCTGCCCATCATCGCCACGGGACATTTAACGACCGTGGGGGCCAGTAAAAGTGACGCCGTGCGTGACCATTTATATTGGCACGCTGGACGCGTTTCCGGCACAAAACTTTCCACCAGCCGACTACATCGCGCTCGGGCATATTCACCGCGCACAGATTATTGGCGGCATGGAACATGTTCGCTATTGCGGCTCCCCCATTCCACTGAGTTTTGATGAATGCGGTAAGAGTAAATATGTCCATCTGGTGACATTTTCAAACGGCAAATTAGAGAGCGTGGAAAACCTGAACGTACCGGTAACGCAACCCATGGCAGTGCTGAAAGGCGATCTGGCGTCGATTACCGCACAGCTGGAACAGTGGCGCGATGTATCGCAGGAGCCACCTGTCTGGCTGGATATCGAAATCACTACTGATGAGTATCTGCATGATATTCAGCGCAAAATCCAGGCATTAACCGAATCATTGCCCTGTCGAAGTATTGCTGGTACGTCGGAGTCGTGAACAGCCCGAGCGTGTGTTAGCCAGCCAACAGCGTGAAACCCTCAGCGAACTCAGCGTCGAAGAGGGTGTTCAATCGCCGTCTGGCACTGGAAGAACTGGATGAATCGCAGCAGCAACGTCTGCAGCATCTTTTCACCACGACGTTGCATACCCTCGCCGGGAGAACACGAAGCATGAAAATTCTCAGCCTGCGCCTGAAAAACCTGAACTCATTAAAAGGCGAATGGAAGATTGATTTCACCCGCGAGCCGTTCGCCAGCAACGGCTGTTTGCTATTACCGGCCCAACAGGTGCGGGGAAAACCACCCTGCTGGACGCCATTTGTCTGGCGCTGTATCACGAAACTCCGCGTCTCTCTAACGTTTCACAATCGCAAAATGATCTCATGACCCGCGATACCGCCGAATGTCTGGCGGAGGTGGAGTTTGAAGTGAAAGGTGAAGCGTACCGTGCATTCTGGAGCCAGAATCGGGCGCGTAACCAACCCGACGGTAATTTGCAAGGGCCACGCGTAGAGCTGGCGCGCTGCGCCGACGGCAAAATTCTCGCCGACAAAGTGAAAGATAAGCTGGAACTGACAGCGCGGTTAACCGGGCTGGATTACGGGCGCTTCACCCGTTCGATGCTGCTTTCGCAGGGGCAATTTGCTGCCTTCCTGAATGCCAAACCCAAAGAACGCGCGGGAATTGCTCGAGGAG'..b'CTTCCAGGATTTTTCCTGTGGGATTTTCATCACCAATAAACGCCGAGAGGATCTCGCACTTGCGGGTGACAAAATCCAGCTTCAGCATCTCATCAATTTCAGTCAGGCTGAATTCCGGCAGGTCGTGCGGAAAAAACAGCCCCTGATTTTTGCCCAAACCCCTGGGTTACGCTTGCGCAAAGCTGACCTGCCTCGTTGTGATCTTTCAGATTGAGGTTTCATTTAGTTTTCCAGTACTCGTGCGCCCCCCGTATCCAGCCGGCAAATATGACAAAACCTTCCTGATTTTGCAGGTAGTTCTTACCCAACCAGTCGGCAACGCGCGGGGCGGTTTCCGGCTTGTCACACAGAGCGAACAAGGTCCGGGCCGGAGCCGGAGATACCGCTCGCTACCGCGCCATTTCCGCGACCGCCTGCCGCGCCTGCCGGAAGCCTGGCAGTAACCGTTCACGGTAGGTTCACGCGATAACATCTTTTCATACAGCGTTCGCGGCAAGCTCAGGCTGACGGGAATAGCAGGCGTGAATGAAGCCTGCCAGATGTCGCCCGTGCGCAATGCAATCCTGGCGCGATACTGCCCCGGTAAAATAGCCCTGGCTTTTCCGTCGAGACTTTAATCCCCGGATACGCCAGCACCCACAGCCACTCATCCAAACCTGGCACTTGCTGGCTGATGATGTCGTTTTCTTCGATCATCAACTGCATACCACCGAGAAAACACGGTGCCACGTTGTCGTAATGAATGCTGCCGGAGATACGGCCTTCCAGCTCGCCCATCAAAAGCCAGCGAACGAGTGTCATTAAGCGGCTTGCCGCAGTGTTCAATTTCATCCCATCAGCGCCGCGACCACGAAACAGGCACTGGAGCCTAAGCCCGAACCGATCGGCATATTCTTTTCCAGGGTCATCGCCACTGGAATTTGCTTACCCAGTTCCTGGCAAAAACGCCTCCCAGCACTGATAAACGATATTTTCCCGTGGTTTCTGACGGCAGCCTTATCCGGGCAAAGCGTCCGAGGTTGTTGAGACTGAATGTCTCTGCCGCCTCAACCGTGACTACATCTCCGAGCAATGCACCATCAACAGGTGTCACCGCCGCCCCGAGCACATCAAACCCGACGCTCATATTGGCACTGGAAGCCGGGGCATAAACTTTAACCATTTTCAGACTCCTAACTTCCATGAGAGGGTACGTAGCAGATCAGCAAAGACACCGGCAGCTGTAACCGTCAATTTGCCCGCACCATATCCGCGCAGTACCAAACGGCAAGCGGCTGATAATAGTGGCTTAAGAGCCAGGGCGTTTTCGCCATTTTTCACTTTGAACAGCGGATCATTACCATCCACTTCGGCAATCTTCACGCGGCAGACGCCATCTTCATCAATATTGCCAACATAGCGCAAAACCTTTCCCTTCATCACGGGCCTTCGCCACGCGCGCGGCAAAGAGATCGTCGAGTTGTGACAGATTCGCCATAAAAGCGGCAACATCACCCTCGGCGTTAACCTCTGCGGGGCAGCACAGGTTCAATTTCAATATCCGCCAGCTCCAGTTCACTCCCGTTTCACGAGCGAGAATCAATAGTTTACGCGCCACATCCATACCAGAAAGATCATCTCGCCGGGTCCGGTTCGGTATAACCCATTTCCCGACGCAGCGTGGTCGCCTCGGAGAAACTCATGCCTTCGTAAACTTGCCGAAGATATAAGAAAGCCGAACCAGACAAGAATGCCGGAGAACTTCATCAATTCATCACCTGCATTGAGCAGATTTTGCAGGTTCTCAATAACCGGTAATCCAGCCCCAACGTTGGTGTCATAGAGGAATTTACGCCGCGATTTTTCCGCCCGCATAACGCAACTGATGGTAGTAATCCATCGACGAGGTGTTTGCCTTTTTGTTCGGCGTGACAACGTGGAAACCTTCGCGCCAGGAAGTCGGCATATTGATCCGCCACCTGCCTGGCTGGAAGTGCAGTCAACAATGACCGGGTTTCAGCAGATGATATTCTTTTCACAAGGCGAGTTAGCGCCCGGGATAAACGGCTCTTGGCTTGCGCCAGTTCTTCCTGCCAGTTTTCCAGATTAAGGCCCATGTAATTGGTGAGCAGAGCCTTCGAGTTGGCAACACCGCAGACACGTAAGTCGATTATTTTATTCTTCAGCCCAGCTTTGCTGACGCGCTTCAGTTGCTCCAGCAGCGGCACCGCCAACGCCACCGACGCCAATCACAAACACTTCGATAACCTGATCGGTATTGAACAGGCATCTGATGAGTAACGCGCACGCCAGTGGTCGCATCATCGTTATTTACCACGACACGAGATTGAGCGTTCAGAAGATCCCTGAGCAATGGCGACAATGTTGATATTTGGCGCGGCCAGGCGGCAAAGAATTCTCGCCGAGATCCCACGCAAGGTGCGCATACCATCACCTCCCACGAGATAAATGGCCAGCCGTTCCGCACTGCCAGCGGCTCCCAGTAGCCTTCTTTCAGTTCCAGGTAGAACTCTCCTGGCATGCCCGTTCAGCTCGCACACAGTCGCTTTGTGGAACGCAGAAACTAATGCGTATTCGGAAAGATGATTGCGTAATCAGCCACACGGAAATACCGGGCGCGTGACATCGGCTGCAAAGCGCGCCGCCGCCATGCCGACCATCCTATCATCCCCGGACCAGAACGCTGAAACATGCCATGTTAATTCAGATTGGAAATGGTTCCCTTGACCGGTAATTCGTCTTCAACACGGCTGGCACCAATTAGCGTACCTGGTGCTTGAGGATTTCCGGTATTTTTTAATCAGGCAAAGGGATCTGGAACTGGGCGATGGGGGTAATGGTGCGGGTGAAGAACTTTAGCGCCGAAAGTAGGAAACCCATCGCTTCCTGGTAGGAACATCGACTTCAACAACCTCGCATCGGGGCCACCTGACGCGGGTCGCAGGTATAGACCCCCGTCAACGTCCGCCAAATCTCGCAACAATCGGGGCCCGTAAACAGGCAGCCAGCACCGCAGCAGAAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTTTTCATTACCGGCGGGGGAACCTGCCATCAGCACGCATGTGATCAGCCGGAATGCAGGGCTTGCCGCAATTAGGCGGGTGGACTCAGGAAATCGACGGTAGATTCGAGGTAATGCCCCACCGCCAGCAGTTTTTCGACCGGATCGATAACCTAAGTACTTGTGACGCCGGCGCCGTCTATACGCCGGCATAAATGGCGAGCGACATTTCTCGCCACGGCCAAAATCGAGCGCCAGCGTTTGATGCTAATCCGGCACTGCCCAACAAACTATTGCCATGGGCAGACATGTTTTATTGGGCCAAATTCCTGATCGACGAAAGTTTTCAATGCGCCAGCGGGAACCCCCGGCGGGGCGGCGGCGGTCTACCAGGTCAAAAGGTATCGGCAAAAAATACGTTGGCCATCGCGATTATTGGTAAAGCATCCTGGCCCCTAAATGGTATTTTGTCAATTCATCGACACCAAGGTGTTGGTGATTTTTGCGGGCGGGTCAGAGAGGGACGGTGGGCCTACCTGCCTCCTGCCTTCGGCTCGGCTTTCTAGAATATCGGCAAACACGCGAAAAAACGTTCTGCATTTGCCACTGATGATACCGCCCGAAACTTCAACACTCGCATGGTGTTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCCGCACTGTCTAAAGGTGGCGGGCTTTTATTACATGTGTTTCCGTACGCGTACGGCCCCGCTACCGATACCTGTGGTAATCGGTGAATGTGGGGGTATACGGTGGTGCTATCGTTTTCATGGATGTTGATGAATCTCTGGTATTTTTATCTGTCGGTGCGCTAGGCCTATATTGGTTAAAAATATTTGTGGTTCCGAGTCAATAAAATTTTTAATTTACCACGGGGCCCAAGGAAACCAGTTCAATAAACATGCTATCAGACACCTTTTTTTAGATCCACC\n' 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