| Previous changeset 2:86526900cb8f (2015-10-12) Next changeset 4:cb0543909e83 (2015-11-20) |
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Commit message:
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty |
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modified:
fuma.xml test-data/refseq_genes_hg19.bed tool_dependencies.xml |
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added:
test-data/edgren_chimerascan.txt test-data/edgren_defuse.txt test-data/edgren_fusion-map.txt test-data/edgren_test_01_specifc_matching_output.txt test-data/edgren_test_02_unspecifc_matching_output.txt test-data/edgren_true_positives.txt |
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removed:
test-data/chimerascan.txt test-data/defuse.txt test-data/edgren_tp.txt test-data/fusion-map.txt test-data/output_test_1.txt test-data/output_test_2.txt |
| b |
| diff -r 86526900cb8f -r 4966079d474b fuma.xml --- a/fuma.xml Mon Oct 12 04:17:07 2015 -0400 +++ b/fuma.xml Tue Oct 20 10:12:08 2015 -0400 |
| b |
| @@ -113,22 +113,22 @@ <tests> <test> <!-- <repeat name="datasets"> --> - <param name="datasets_0|sample" value="chimerascan.txt" ftype="tabular" /> + <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" /> <param name="datasets_0|format" value="chimerascan" /> <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> <!-- </repeat> --> <!-- <repeat name="datasets"> --> - <param name="datasets_1|sample" value="defuse.txt" ftype="tabular" /> + <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" /> <param name="datasets_1|format" value="defuse" /> <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> <!-- </repeat> --> <!-- <repeat name="datasets"> --> - <param name="datasets_2|sample" value="fusion-map.txt" ftype="tabular" /> + <param name="datasets_2|sample" value="edgren_fusion-map.txt" ftype="tabular" /> <param name="datasets_2|format" value="fusionmap" /> <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> <!-- </repeat> --> <!-- <repeat name="datasets"> --> - <param name="datasets_3|sample" value="edgren_tp.txt" ftype="tabular" /> + <param name="datasets_3|sample" value="edgren_true_positives.txt" ftype="tabular" /> <param name="datasets_3|format" value="fusionmap" /> <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> <!-- </repeat> --> @@ -140,26 +140,26 @@ <param name="acceptor_donor_order_specific_matchig" value="--acceptor-donor-order-specific-matching" /> <param name="output_format" value="list_boolean" /> - <output name="fuma_overview" file="output_test_1.txt" /> + <output name="fuma_overview" file="edgren_test_01_specifc_matching_output.txt" /> </test> <test> <!-- <repeat name="datasets"> --> - <param name="datasets_0|sample" value="chimerascan.txt" ftype="tabular" /> + <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" /> <param name="datasets_0|format" value="chimerascan" /> <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> <!-- </repeat> --> <!-- <repeat name="datasets"> --> - <param name="datasets_1|sample" value="defuse.txt" ftype="tabular" /> + <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" /> <param name="datasets_1|format" value="defuse" /> <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> <!-- </repeat> --> <!-- <repeat name="datasets"> --> - <param name="datasets_2|sample" value="fusion-map.txt" ftype="tabular" /> + <param name="datasets_2|sample" value="edgren_fusion-map.txt" ftype="tabular" /> <param name="datasets_2|format" value="fusionmap" /> <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> <!-- </repeat> --> <!-- <repeat name="datasets"> --> - <param name="datasets_3|sample" value="edgren_tp.txt" ftype="tabular" /> + <param name="datasets_3|sample" value="edgren_true_positives.txt" ftype="tabular" /> <param name="datasets_3|format" value="fusionmap" /> <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> <!-- </repeat> --> @@ -171,7 +171,7 @@ <param name="acceptor_donor_order_specific_matchig" value="" /> <param name="output_format" value="list_boolean" /> - <output name="fuma_overview" file="output_test_2.txt" /> + <output name="fuma_overview" file="edgren_test_02_unspecifc_matching_output.txt" /> </test> </tests> |
| b |
| diff -r 86526900cb8f -r 4966079d474b test-data/chimerascan.txt --- a/test-data/chimerascan.txt Mon Oct 12 04:17:07 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,13347 +0,0 @@\n-#chrom5p\tstart5p\tend5p\tchrom3p\tstart3p\tend3p\tchimera_cluster_id\tscore\tstrand5p\tstrand3p\n-chr8\t125551265\t125551328\tchr17\t38060847\t38066176\tCLUSTER8432\t278\t-\t-\n-chr20\t49411466\t49411709\tchr17\t59445687\t59470198\tCLUSTER10677\t196\t+\t+\n-chr17\t35479452\t35562785\tchr17\t37366788\t37374425\tCLUSTER11520\t80\t-\t-\n-chr20\t56964174\t56964572\tchr17\t37921198\t37934019\tCLUSTER11559\t43\t+\t-\n-chr17\t57970442\t57970685\tchr17\t47007458\t47018423\tCLUSTER1046\t43\t+\t-\n-chr19\t571324\t580781\tchr19\t13135834\t13209609\tCLUSTER2159\t40\t+\t+\n-chr17\t76778283\t76778375\tchr8\t117657054\t117768035\tCLUSTER3062\t33\t-\t-\n-chr17\t48943418\t48943714\tchr17\t35874899\t35880750\tCLUSTER12009\t30\t-\t-\n-chr20\t45852969\t45905538\tchr20\t34078462\t34099802\tCLUSTER6163\t28\t-\t+\n-chrM\t15503\t15887\tchrM\t235\t367\tCLUSTER3998\t28\t-\t-\n-chr4\t76649459\t76649794\tchr4\t76567952\t76587232\tCLUSTER495\t21\t-\t-\n-chr20\t47538274\t47538546\tchr20\t46286149\t46365685\tCLUSTER6259\t21\t+\t-\n-chr21\t40665736\t40685711\tchr21\t9915249\t9916546\tCLUSTER3440\t19\t-\t-\n-chr1\t144340525\t144340772\tchr1\t145004780\t145005286\tCLUSTER301\t18\t-\t+\n-chr1\t143744200\t143744586\tchr1\t145004780\t145005286\tCLUSTER938\t18\t-\t+\n-chr1\t149576452\t149576699\tchr1\t145004780\t145005286\tCLUSTER2173\t18\t+\t+\n-chr1\t147931723\t147931979\tchr1\t145004780\t145005286\tCLUSTER2320\t18\t-\t+\n-chr8\t145064225\t145064478\tchr16\t22019455\t22098851\tCLUSTER3532\t34\t+\t+\n-chrM\t8366\t14148\tchrM\t235\t367\tCLUSTER8062\t19\t-\t-\n-chr17\t38465422\t38465537\tchr8\t79485045\t79517501\tCLUSTER96\t17\t+\t+\n-chr17\t37607290\t37607526\tchr17\t53218670\t53241448\tCLUSTER3673\t16\t-\t+\n-chr5\t139781398\t139825559\tchr5\t141232672\t141234000\tCLUSTER3292\t15\t+\t-\n-chr10\t5726800\t5727137\tchr10\t5751492\t5754479\tCLUSTER541\t14\t+\t+\n-chr16\t70024499\t70099850\tchr16\t21415197\t21426405\tCLUSTER959\t14\t-\t-\n-chr16\t70024499\t70099850\tchr16\t29497000\t29506927\tCLUSTER5884\t14\t-\t-\n-chr16\t70024499\t70099850\tchr16\t22535140\t22547840\tCLUSTER9215\t14\t-\t+\n-chr16\t70024499\t70099850\tchr16\t30234349\t30246899\tCLUSTER11103\t14\t-\t-\n-chr17\t37856253\t37856563\tchr17\t61509664\t61515530\tCLUSTER328\t13\t+\t-\n-chr20\t56884770\t56886177\tchr19\t17256206\t17324103\tCLUSTER9719\t11\t+\t+\n-chr20\t26189758\t26189868\tchr19\t16345223\t16346155\tCLUSTER9790\t11\t-\t+\n-chr2\t10262694\t10269280\tchr2\t10281980\t10350941\tCLUSTER5168\t10\t+\t+\n-chr3\t4418013\t4508965\tchr3\t37094116\t37170639\tCLUSTER8305\t11\t-\t-\n-chr20\t57226308\t57227142\tchr20\t55929087\t55953518\tCLUSTER10876\t9\t+\t+\n-chr17\t57232491\t57232799\tchr17\t34851598\t34863350\tCLUSTER7548\t9\t-\t-\n-chr4\t120375937\t120376287\tchr7\t56078743\t56088923\tCLUSTER3661\t9\t+\t-\n-chr17\t37595417\t37607526\tchr17\t48548388\t48552199\tCLUSTER7408\t8\t-\t+\n-chr17\t60556385\t60637486\tchr11\t141452\t169051\tCLUSTER7139\t8\t+\t-\n-chr17\t57183958\t57184951\tchr17\t57915655\t57917951\tCLUSTER9133\t8\t+\t+\n-chr17\t60556385\t60637486\tchr3\t197907625\t197907734\tCLUSTER11129\t8\t+\t+\n-chr17\t60556385\t60637486\tchr1\t243219615\t243260600\tCLUSTER11589\t8\t+\t-\n-chr17\t60556385\t60637486\tchr1\t700244\t709659\tCLUSTER13302\t8\t+\t-\n-chr2\t85804613\t85806289\tchr2\t85818847\t85820510\tCLUSTER2615\t8\t+\t+\n-chr17\t60129897\t60142642\tchr17\t59469337\t59470198\tCLUSTER2689\t8\t-\t+\n-chr9\t111754688\t111754848\tchr14\t74178485\t74181127\tCLUSTER598\t12\t-\t-\n-chr7\t45808258\t45808616\tchr7\t55840871\t55841375\tCLUSTER9736\t9\t-\t+\n-chr1\t153934695\t153935797\tchr1\t153920147\t153927641\tCLUSTER4216\t7\t-\t-\n-chr20\t62496580\t62500793\tchr20\t62559687\t62567383\tCLUSTER5323\t7\t+\t+\n-chr13\t32420919\t32520317\tchr13\t32652970\t32870775\tCLUSTER9025\t8\t+\t+\n-chr7\t64126510\t64139713\tchr7\t64144464\t64147263\tCLUSTER3026\t7\t+\t+\n-chr14\t96968712\t96968936\tchr14\t96904171\t96955111\tCLUSTER8583\t7\t+\t+\n-chr20\t61569147\t61569303\tchr20\t36611422\t36634798\tCLUSTER10444\t7\t-\t-\n-chr19\t15443100\t15443341\tchr19\t14072341\t14104706\tCLUSTER11451\t7\t-\t-\n-chr11\t61560108\t61560499\tchr11\t61605249\t61634824\tCLUSTER149\t7\t+\t+\n-chr2\t38829998\t38830177\tchr5\t77781037\t77806220\tCLUSTER7396\t26\t-\t-\n-chr9\t111754688\t111754848\tchr7\t150811764\t150820724\tCLUSTER378\t10\t-\t+\n-chr17\t60556385\t60637486\tchr16\t90196204\t90204398\tCLUSTER1148\t7\t+\t+\n-chr3\t158449928\t158450274\tchr3\t183821969\t183824782\tCLUSTER10641\t7\t-\t+\n-chr1\t114354331\t114355069\tchr1\t114442493\t114443858\tCLUSTER8735\t6\t-\t+\n-chr12\t80211173'..b'\t-\n-chr9\t131186320\t131196891\tchr16\t8946801\t8953191\tCLUSTER13277\t1\t+\t-\n-chr19\t45898693\t45908311\tchr6\t33383586\t33384229\tCLUSTER13278\t1\t-\t+\n-chr17\t62657946\t62658385\tchrM\t7586\t9207\tCLUSTER13279\t1\t-\t+\n-chr7\t75140252\t75157452\tchr7\t75046064\t75115567\tCLUSTER13281\t1\t-\t-\n-chrM\t8366\t14148\tchr20\t34236846\t34243265\tCLUSTER13282\t1\t-\t-\n-chr11\t111625703\t111637168\tchrM\t1755\t4263\tCLUSTER13283\t1\t-\t+\n-chr3\t148709194\t148745455\tchr17\t40465341\t40466879\tCLUSTER13284\t1\t+\t-\n-chr5\t140058646\t140070970\tchrM\t1755\t4263\tCLUSTER13285\t1\t-\t+\n-chr6\t24775158\t24775263\tchr19\t39138266\t39221170\tCLUSTER13286\t1\t+\t+\n-chr10\t27047990\t27150015\tchr17\t26864134\t26865174\tCLUSTER13287\t1\t-\t+\n-chrM\t10472\t12137\tchr7\t97920961\t97922907\tCLUSTER13288\t1\t+\t-\n-chr16\t1383605\t1399441\tchr8\t17827085\t17887456\tCLUSTER13289\t1\t+\t+\n-chr21\t37692486\t37734525\tchrX\t69510540\t69640773\tCLUSTER13290\t1\t+\t+\n-chr9\t117373705\t117373843\tchr16\t30418734\t30425929\tCLUSTER13291\t1\t+\t+\n-chr2\t201994451\t202014557\tchr14\t104200087\t104220580\tCLUSTER13293\t1\t+\t-\n-chr9\t139409934\t139440237\tchrM\t1755\t4263\tCLUSTER13294\t1\t-\t+\n-chr15\t102029696\t102030186\tchr6\t114257319\t114281181\tCLUSTER13295\t1\t-\t-\n-chrM\t8366\t14148\tchr6\t100956607\t101053575\tCLUSTER13296\t1\t-\t-\n-chr2\t120124503\t120130121\tchrX\t147018984\t147032155\tCLUSTER13297\t1\t+\t+\n-chr19\t55967002\t55973048\tchr12\t56552145\t56554578\tCLUSTER13298\t1\t-\t+\n-chr17\t35306174\t35346018\tchr3\t184019324\t184026839\tCLUSTER13299\t1\t+\t+\n-chr6\t32861952\t32862703\tchr1\t151261570\t151264380\tCLUSTER13300\t1\t+\t+\n-chr1\t116935486\t116961243\tchrM\t10059\t10404\tCLUSTER13301\t1\t-\t+\n-chr15\t40509628\t40532881\tchr8\t141668480\t141716303\tCLUSTER13303\t1\t+\t-\n-chr16\t29819965\t29823305\tchrM\t15998\t16570\tCLUSTER13304\t1\t-\t+\n-chr7\t39989958\t40102698\tchr11\t1213089\t1222365\tCLUSTER13305\t1\t+\t+\n-chr1\t9074739\t9086403\tchr2\t242192430\t242196220\tCLUSTER13306\t1\t-\t-\n-chr22\t21119872\t21213099\tchr21\t38123188\t38302732\tCLUSTER13307\t1\t-\t-\n-chr3\t183415605\t183446638\tchr8\t25158091\t25162808\tCLUSTER13308\t1\t+\t+\n-chr15\t44066793\t44068604\tchr8\t67474409\t67504778\tCLUSTER13310\t1\t-\t-\n-chr15\t58932975\t59042176\tchr9\t135766734\t135786075\tCLUSTER13311\t1\t-\t-\n-chr10\t95132686\t95141152\tchr17\t79860776\t79867477\tCLUSTER13312\t1\t-\t-\n-chr9\t35732071\t35732391\tchr14\t61184688\t61190764\tCLUSTER13313\t1\t-\t-\n-chr3\t49148382\t49158370\tchr1\t11166587\t11319479\tCLUSTER13314\t1\t-\t-\n-chr6\t170892144\t170893741\tchr14\t23344263\t23349585\tCLUSTER13315\t1\t-\t+\n-chr2\t99757806\t99757881\tchr9\t131314836\t131315614\tCLUSTER13316\t1\t-\t+\n-chr12\t132628992\t132636364\tchr7\t5566778\t5569293\tCLUSTER13317\t1\t+\t-\n-chr12\t64238540\t64410791\tchr17\t76987801\t76988839\tCLUSTER13318\t1\t+\t-\n-chr6\t44214848\t44221613\tchr10\t5029967\t5040938\tCLUSTER13320\t1\t+\t-\n-chr6\t30886540\t30890330\tchr7\t99661652\t99675055\tCLUSTER13321\t1\t+\t-\n-chr5\t10250281\t10250556\tchr10\t27035524\t27054246\tCLUSTER13322\t1\t+\t-\n-chr7\t26241323\t26246129\tchr10\t14938844\t14946303\tCLUSTER13324\t1\t+\t+\n-chr19\t15484596\t15484875\tchr19\t49458804\t49465054\tCLUSTER13326\t1\t-\t+\n-chr7\t20866916\t20867438\tchr22\t29723668\t29730338\tCLUSTER13327\t1\t+\t-\n-chr3\t49053251\t49058466\tchr9\t20978337\t20995953\tCLUSTER13328\t1\t-\t+\n-chr5\t150415142\t150443307\tchrX\t41206892\t41209523\tCLUSTER13329\t1\t-\t+\n-chr4\t190394298\t190395874\tchr20\t45838380\t45976669\tCLUSTER13330\t1\t+\t-\n-chr16\t55836763\t55867074\tchr2\t128934387\t128953248\tCLUSTER13331\t1\t-\t+\n-chrX\t37430821\t37536749\tchr17\t5289345\t5290429\tCLUSTER13332\t1\t+\t-\n-chr8\t91013579\t91064226\tchr4\t100820709\t100822308\tCLUSTER13333\t1\t+\t-\n-chr16\t2147728\t2153895\tchr16\t14849048\t14859286\tCLUSTER13334\t1\t-\t+\n-chr19\t33968951\t34012798\tchr7\t149576423\t149577786\tCLUSTER13335\t1\t-\t+\n-chr9\t123292255\t123342436\tchrX\t54566567\t54593719\tCLUSTER13337\t1\t-\t+\n-chr5\t1076808\t1112171\tchr22\t38169789\t38172562\tCLUSTER13338\t1\t-\t+\n-chr19\t44130935\t44143990\tchr19\t55602280\t55614935\tCLUSTER13339\t1\t-\t-\n-chr13\t41885340\t41891065\tchr10\t129894924\t129911865\tCLUSTER13341\t1\t+\t-\n-chr11\t47204554\t47207431\tchr6\t43164382\t43192324\tCLUSTER13342\t1\t-\t+\n-chr14\t24911551\t24912006\tchr2\t235401685\t235405692\tCLUSTER13343\t1\t-\t-\n-chr4\t154387497\t154542031\tchr19\t12786530\t12791138\tCLUSTER13344\t1\t+\t-\n-chr7\t102208456\t102213067\tchr19\t34818325\t34846470\tCLUSTER13345\t1\t-\t+\n' |
| b |
| diff -r 86526900cb8f -r 4966079d474b test-data/defuse.txt --- a/test-data/defuse.txt Mon Oct 12 04:17:07 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,916 +0,0 @@\n-cluster_id\tsplitr_sequence\tsplitr_count\tsplitr_span_pvalue\tsplitr_pos_pvalue\tsplitr_min_pvalue\tadjacent\taltsplice\tbreak_adj_entropy1\tbreak_adj_entropy2\tbreak_adj_entropy_min\tbreakpoint_homology\tbreakseqs_estislands_percident\tcdna_breakseqs_percident\tconcordant_ratio\tdeletion\test_breakseqs_percident\teversion\texonboundaries\texpression1\texpression2\tgene1\tgene2\tgene_align_strand1\tgene_align_strand2\tgene_chromosome1\tgene_chromosome2\tgene_end1\tgene_end2\tgene_location1\tgene_location2\tgene_name1\tgene_name2\tgene_start1\tgene_start2\tgene_strand1\tgene_strand2\tgenome_breakseqs_percident\tgenomic_break_pos1\tgenomic_break_pos2\tgenomic_strand1\tgenomic_strand2\tinterchromosomal\tinterrupted_index1\tinterrupted_index2\tinversion\tlibrary_name\tmax_map_count\tmax_repeat_proportion\tmean_map_count\tmin_map_count\tnum_multi_map\tnum_splice_variants\torf\tread_through\n-23092\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t14006\t8407\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23115\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t11706\t5320\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-25612\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t12\t12\t\t\t\t\t\t\t\t\t\t\t\t6457893\t6443410\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tY\n-31848\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t8\t10\t\t\t\t\t\t\t\t\t\t\t\t43035551\t8925081\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23019\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t343\t7686\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-16995\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t14\t1\t\t\t\t\t\t\t\t\t\t\t\t43723013\t91853147\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-27652\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t14\t5\t\t\t\t\t\t\t\t\t\t\t\t102551038\t118309569\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-25508\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t12\t12\t\t\t\t\t\t\t\t\t\t\t\t52628954\t53298489\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-9682\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t17\t17\t\t\t\t\t\t\t\t\t\t\t\t37682566\t37700499\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tY\n-10165\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t17\tX\t\t\t\t\t\t\t\t\t\t\t\t33478116\t108297810\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-33747\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t4\t19\t\t\t\t\t\t\t\t\t\t\t\t38637596\t8451051\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-20438\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t16\t6\t\t\t\t\t\t\t\t\t\t\t\t33964132\t150665062\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-10624\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t17\t9\t\t\t\t\t\t\t\t\t\t\t\t80049211\t5684298\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23005\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t4000\t14769\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-33840\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t19\t19\t\t\t\t\t\t\t\t\t\t\t\t580782\t13135835\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-16823\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t12\t1\t\t\t\t\t\t\t\t\t\t\t\t52632491\t565697\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-16074\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t3\t1\t\t\t\t\t\t\t\t\t\t\t\t63898900\t106758926\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-13382\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t7\t1\t\t\t\t\t\t\t\t\t\t\t\t26235516\t566899\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-16017\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t1\tX\t\t\t\t\t\t\t\t\t\t\t\t91853147\t108297892\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-26187\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t12\t19\t\t\t\t\t\t\t\t\t\t\t\t46752889\t56299731\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-33085\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t9\t\t\t\t\t\t\t\t\t\t\t\t24184164\t79483765\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-13938\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t1\t2\t\t\t\t\t\t\t\t\t\t\t\t566950\t133012886\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-27355\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t14\t14\t\t\t\t\t\t\t\t\t\t\t\t75287839\t75321919\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tY\n-17825\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t1\t19\t\t\t\t\t\t\t\t\t\t\t\t565801\t11777312\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-8499\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t17\t21\t\t\t\t\t\t\t\t\t\t\t\t38151526\t9826993\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23047\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t3484\t14450\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-8015\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t5\t2\t\t\t\t\t\t\t\t\t\t\t\t71146755\t133038453\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23073\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t8586\t14763\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-25540\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t12\t12\t\t\t\t\t\t\t\t\t\t\t\t50506081\t50558806\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tY\n-19272\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t3\t13\t\t\t\t\t\t\t\t\t\t\t\t58551170\t72249657\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-17206\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t20\t1\t\t\t\t\t\t\t\t\t\t\t\t3765920\t565772\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23102\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t8931\t14449\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-2551\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t11\t12\t\t\t\t\t\t\t\t\t\t\t\t110167262\t34372608\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-34931\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t5\t5\t\t\t\t\t\t\t\t\t\t\t\t118309571\t170814948\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23113\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t12104\t5263\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-26300\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t12\t5\t\t\t\t\t\t\t\t\t\t\t\t53858625\t91139848\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23128\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t12103\t3340\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-15225\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t1\t1\t\t\t\t\t\t\t\t\t\t\t\t2473653'..b'\t\t\t\t\t\t\t\t33141546\t108113634\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-3168\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t5\t\t\t\t\t\t\t\t\t\t\t\t2019011\t134259999\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-12433\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t5\t17\t\t\t\t\t\t\t\t\t\t\t\t34955886\t29119901\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23330\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t9\t9\t\t\t\t\t\t\t\t\t\t\t\t139372139\t139378921\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tY\n-14232\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t1\t2\t\t\t\t\t\t\t\t\t\t\t\t569011\t207284336\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-31817\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t20\t10\t\t\t\t\t\t\t\t\t\t\t\t32664993\t21811145\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-17006\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t1\t14\t\t\t\t\t\t\t\t\t\t\t\t151738242\t50329313\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-16784\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t1\t12\t\t\t\t\t\t\t\t\t\t\t\t91852672\t127650989\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-3290\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t5\t\t\t\t\t\t\t\t\t\t\t\t2019030\t134263539\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-9360\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t17\t17\t\t\t\t\t\t\t\t\t\t\t\t37359262\t56769000\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-12747\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t1\t\t\t\t\t\t\t\t\t\t\t\t10830376\t569766\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-10164\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t17\tX\t\t\t\t\t\t\t\t\t\t\t\t33478114\t108297713\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23851\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t12\t2\t\t\t\t\t\t\t\t\t\t\t\t54677629\t88124624\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-33050\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t7\t\t\t\t\t\t\t\t\t\t\t\t9361819\t97599083\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-12227\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t17\t\t\t\t\t\t\t\t\t\t\t\t24184163\t60142706\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-12282\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t19\t17\t\t\t\t\t\t\t\t\t\t\t\t11945083\t37868701\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-8398\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t2\t5\t\t\t\t\t\t\t\t\t\t\t\t232576633\t134260383\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-14515\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t17\t1\t\t\t\t\t\t\t\t\t\t\t\t37828494\t569305\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-9626\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t17\t17\t\t\t\t\t\t\t\t\t\t\t\t57232492\t34863351\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-15768\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t1\tX\t\t\t\t\t\t\t\t\t\t\t\t568364\t108297446\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23135\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t6472\t10858\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-9691\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t17\t17\t\t\t\t\t\t\t\t\t\t\t\t37360941\t33478228\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-25777\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t20\t12\t\t\t\t\t\t\t\t\t\t\t\t2451398\t3560214\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-33699\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t4\t19\t\t\t\t\t\t\t\t\t\t\t\t38629661\t33185000\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-14138\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t2\t1\t\t\t\t\t\t\t\t\t\t\t\t232577176\t565851\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23083\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t13987\t6324\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-16016\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t1\tX\t\t\t\t\t\t\t\t\t\t\t\t91853050\t108297687\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-12950\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t1\t\t\t\t\t\t\t\t\t\t\t\t2017954\t568203\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-15652\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t6\t1\t\t\t\t\t\t\t\t\t\t\t\t75950980\t566931\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-15640\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t1\t6\t\t\t\t\t\t\t\t\t\t\t\t224548265\t937525\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-33433\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t2\t19\t\t\t\t\t\t\t\t\t\t\t\t204055493\t24184153\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23003\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t5490\t14115\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-33615\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t19\t8\t\t\t\t\t\t\t\t\t\t\t\t1478773\t145981626\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-4672\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t21\t2\t\t\t\t\t\t\t\t\t\t\t\t9827191\t88124672\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-33263\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t19\t2\t\t\t\t\t\t\t\t\t\t\t\t24184077\t230045634\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23075\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t7768\t14653\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-8397\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t2\t5\t\t\t\t\t\t\t\t\t\t\t\t232576639\t134263192\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-33953\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t5\t\t\t\t\t\t\t\t\t\t\t\t24184164\t139666182\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-18059\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t1\t5\t\t\t\t\t\t\t\t\t\t\t\t569446\t177482956\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-32486\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t3\t\t\t\t\t\t\t\t\t\t\t\t14606850\t129324128\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-2368\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t12\t11\t\t\t\t\t\t\t\t\t\t\t\t76443552\t125938478\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-1042\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t17\t\t\t\t\t\t\t\t\t\t\t\t810235\t33478232\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-7322\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t20\t2\t\t\t\t\t\t\t\t\t\t\t\t48807862\t133038722\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-17868\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t1\t\t\t\t\t\t\t\t\t\t\t\t13054352\t568203\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-30812\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t11\t10\t\t\t\t\t\t\t\t\t\t\t\t2018875\t69423263\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-34942\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t5\t5\t\t\t\t\t\t\t\t\t\t\t\t134260436\t177482849\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-14718\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t1\t17\t\t\t\t\t\t\t\t\t\t\t\t568222\t33478228\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n-23748\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t2\t12\t\t\t\t\t\t\t\t\t\t\t\t203500040\t124069216\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n' |
| b |
| diff -r 86526900cb8f -r 4966079d474b test-data/edgren_chimerascan.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/edgren_chimerascan.txt Tue Oct 20 10:12:08 2015 -0400 |
| b |
| b'@@ -0,0 +1,13347 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tCLUSTER13283\t1\t-\t+\n+chr3\t148709194\t148745455\tchr17\t40465341\t40466879\tCLUSTER13284\t1\t+\t-\n+chr5\t140058646\t140070970\tchrM\t1755\t4263\tCLUSTER13285\t1\t-\t+\n+chr6\t24775158\t24775263\tchr19\t39138266\t39221170\tCLUSTER13286\t1\t+\t+\n+chr10\t27047990\t27150015\tchr17\t26864134\t26865174\tCLUSTER13287\t1\t-\t+\n+chrM\t10472\t12137\tchr7\t97920961\t97922907\tCLUSTER13288\t1\t+\t-\n+chr16\t1383605\t1399441\tchr8\t17827085\t17887456\tCLUSTER13289\t1\t+\t+\n+chr21\t37692486\t37734525\tchrX\t69510540\t69640773\tCLUSTER13290\t1\t+\t+\n+chr9\t117373705\t117373843\tchr16\t30418734\t30425929\tCLUSTER13291\t1\t+\t+\n+chr2\t201994451\t202014557\tchr14\t104200087\t104220580\tCLUSTER13293\t1\t+\t-\n+chr9\t139409934\t139440237\tchrM\t1755\t4263\tCLUSTER13294\t1\t-\t+\n+chr15\t102029696\t102030186\tchr6\t114257319\t114281181\tCLUSTER13295\t1\t-\t-\n+chrM\t8366\t14148\tchr6\t100956607\t101053575\tCLUSTER13296\t1\t-\t-\n+chr2\t120124503\t120130121\tchrX\t147018984\t147032155\tCLUSTER13297\t1\t+\t+\n+chr19\t55967002\t55973048\tchr12\t56552145\t56554578\tCLUSTER13298\t1\t-\t+\n+chr17\t35306174\t35346018\tchr3\t184019324\t184026839\tCLUSTER13299\t1\t+\t+\n+chr6\t32861952\t32862703\tchr1\t151261570\t151264380\tCLUSTER13300\t1\t+\t+\n+chr1\t116935486\t116961243\tchrM\t10059\t10404\tCLUSTER13301\t1\t-\t+\n+chr15\t40509628\t40532881\tchr8\t141668480\t141716303\tCLUSTER13303\t1\t+\t-\n+chr16\t29819965\t29823305\tchrM\t15998\t16570\tCLUSTER13304\t1\t-\t+\n+chr7\t39989958\t40102698\tchr11\t1213089\t1222365\tCLUSTER13305\t1\t+\t+\n+chr1\t9074739\t9086403\tchr2\t242192430\t242196220\tCLUSTER13306\t1\t-\t-\n+chr22\t21119872\t21213099\tchr21\t38123188\t38302732\tCLUSTER13307\t1\t-\t-\n+chr3\t183415605\t183446638\tchr8\t25158091\t25162808\tCLUSTER13308\t1\t+\t+\n+chr15\t44066793\t44068604\tchr8\t67474409\t67504778\tCLUSTER13310\t1\t-\t-\n+chr15\t58932975\t59042176\tchr9\t135766734\t135786075\tCLUSTER13311\t1\t-\t-\n+chr10\t95132686\t95141152\tchr17\t79860776\t79867477\tCLUSTER13312\t1\t-\t-\n+chr9\t35732071\t35732391\tchr14\t61184688\t61190764\tCLUSTER13313\t1\t-\t-\n+chr3\t49148382\t49158370\tchr1\t11166587\t11319479\tCLUSTER13314\t1\t-\t-\n+chr6\t170892144\t170893741\tchr14\t23344263\t23349585\tCLUSTER13315\t1\t-\t+\n+chr2\t99757806\t99757881\tchr9\t131314836\t131315614\tCLUSTER13316\t1\t-\t+\n+chr12\t132628992\t132636364\tchr7\t5566778\t5569293\tCLUSTER13317\t1\t+\t-\n+chr12\t64238540\t64410791\tchr17\t76987801\t76988839\tCLUSTER13318\t1\t+\t-\n+chr6\t44214848\t44221613\tchr10\t5029967\t5040938\tCLUSTER13320\t1\t+\t-\n+chr6\t30886540\t30890330\tchr7\t99661652\t99675055\tCLUSTER13321\t1\t+\t-\n+chr5\t10250281\t10250556\tchr10\t27035524\t27054246\tCLUSTER13322\t1\t+\t-\n+chr7\t26241323\t26246129\tchr10\t14938844\t14946303\tCLUSTER13324\t1\t+\t+\n+chr19\t15484596\t15484875\tchr19\t49458804\t49465054\tCLUSTER13326\t1\t-\t+\n+chr7\t20866916\t20867438\tchr22\t29723668\t29730338\tCLUSTER13327\t1\t+\t-\n+chr3\t49053251\t49058466\tchr9\t20978337\t20995953\tCLUSTER13328\t1\t-\t+\n+chr5\t150415142\t150443307\tchrX\t41206892\t41209523\tCLUSTER13329\t1\t-\t+\n+chr4\t190394298\t190395874\tchr20\t45838380\t45976669\tCLUSTER13330\t1\t+\t-\n+chr16\t55836763\t55867074\tchr2\t128934387\t128953248\tCLUSTER13331\t1\t-\t+\n+chrX\t37430821\t37536749\tchr17\t5289345\t5290429\tCLUSTER13332\t1\t+\t-\n+chr8\t91013579\t91064226\tchr4\t100820709\t100822308\tCLUSTER13333\t1\t+\t-\n+chr16\t2147728\t2153895\tchr16\t14849048\t14859286\tCLUSTER13334\t1\t-\t+\n+chr19\t33968951\t34012798\tchr7\t149576423\t149577786\tCLUSTER13335\t1\t-\t+\n+chr9\t123292255\t123342436\tchrX\t54566567\t54593719\tCLUSTER13337\t1\t-\t+\n+chr5\t1076808\t1112171\tchr22\t38169789\t38172562\tCLUSTER13338\t1\t-\t+\n+chr19\t44130935\t44143990\tchr19\t55602280\t55614935\tCLUSTER13339\t1\t-\t-\n+chr13\t41885340\t41891065\tchr10\t129894924\t129911865\tCLUSTER13341\t1\t+\t-\n+chr11\t47204554\t47207431\tchr6\t43164382\t43192324\tCLUSTER13342\t1\t-\t+\n+chr14\t24911551\t24912006\tchr2\t235401685\t235405692\tCLUSTER13343\t1\t-\t-\n+chr4\t154387497\t154542031\tchr19\t12786530\t12791138\tCLUSTER13344\t1\t+\t-\n+chr7\t102208456\t102213067\tchr19\t34818325\t34846470\tCLUSTER13345\t1\t-\t+\n' |
| b |
| diff -r 86526900cb8f -r 4966079d474b test-data/edgren_defuse.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/edgren_defuse.txt Tue Oct 20 10:12:08 2015 -0400 |
| b |
| b'@@ -0,0 +1,916 @@\n+cluster_id\tsplitr_sequence\tsplitr_count\tsplitr_span_pvalue\tsplitr_pos_pvalue\tsplitr_min_pvalue\tadjacent\taltsplice\tbreak_adj_entropy1\tbreak_adj_entropy2\tbreak_adj_entropy_min\tbreakpoint_homology\tbreakseqs_estislands_percident\tcdna_breakseqs_percident\tconcordant_ratio\tdeletion\test_breakseqs_percident\teversion\texonboundaries\texpression1\texpression2\tgene1\tgene2\tgene_align_strand1\tgene_align_strand2\tgene_chromosome1\tgene_chromosome2\tgene_end1\tgene_end2\tgene_location1\tgene_location2\tgene_name1\tgene_name2\tgene_start1\tgene_start2\tgene_strand1\tgene_strand2\tgenome_breakseqs_percident\tgenomic_break_pos1\tgenomic_break_pos2\tgenomic_strand1\tgenomic_strand2\tinterchromosomal\tinterrupted_index1\tinterrupted_index2\tinversion\tlibrary_name\tmax_map_count\tmax_repeat_proportion\tmean_map_count\tmin_map_count\tnum_multi_map\tnum_splice_variants\torf\tread_through\n+23092\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t14006\t8407\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23115\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t11706\t5320\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+25612\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t12\t12\t\t\t\t\t\t\t\t\t\t\t\t6457893\t6443410\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tY\n+31848\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t8\t10\t\t\t\t\t\t\t\t\t\t\t\t43035551\t8925081\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23019\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t343\t7686\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+16995\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t14\t1\t\t\t\t\t\t\t\t\t\t\t\t43723013\t91853147\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+27652\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t14\t5\t\t\t\t\t\t\t\t\t\t\t\t102551038\t118309569\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+25508\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t12\t12\t\t\t\t\t\t\t\t\t\t\t\t52628954\t53298489\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+9682\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t17\t17\t\t\t\t\t\t\t\t\t\t\t\t37682566\t37700499\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tY\n+10165\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t17\tX\t\t\t\t\t\t\t\t\t\t\t\t33478116\t108297810\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33747\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t4\t19\t\t\t\t\t\t\t\t\t\t\t\t38637596\t8451051\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+20438\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t16\t6\t\t\t\t\t\t\t\t\t\t\t\t33964132\t150665062\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+10624\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t17\t9\t\t\t\t\t\t\t\t\t\t\t\t80049211\t5684298\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23005\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t4000\t14769\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33840\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t19\t19\t\t\t\t\t\t\t\t\t\t\t\t580782\t13135835\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+16823\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t12\t1\t\t\t\t\t\t\t\t\t\t\t\t52632491\t565697\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+16074\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t3\t1\t\t\t\t\t\t\t\t\t\t\t\t63898900\t106758926\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+13382\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t7\t1\t\t\t\t\t\t\t\t\t\t\t\t26235516\t566899\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+16017\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t1\tX\t\t\t\t\t\t\t\t\t\t\t\t91853147\t108297892\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+26187\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t12\t19\t\t\t\t\t\t\t\t\t\t\t\t46752889\t56299731\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33085\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t9\t\t\t\t\t\t\t\t\t\t\t\t24184164\t79483765\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+13938\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t1\t2\t\t\t\t\t\t\t\t\t\t\t\t566950\t133012886\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+27355\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t14\t14\t\t\t\t\t\t\t\t\t\t\t\t75287839\t75321919\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tY\n+17825\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t1\t19\t\t\t\t\t\t\t\t\t\t\t\t565801\t11777312\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+8499\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t17\t21\t\t\t\t\t\t\t\t\t\t\t\t38151526\t9826993\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23047\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t3484\t14450\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+8015\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t5\t2\t\t\t\t\t\t\t\t\t\t\t\t71146755\t133038453\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23073\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t8586\t14763\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+25540\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t12\t12\t\t\t\t\t\t\t\t\t\t\t\t50506081\t50558806\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tY\n+19272\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t3\t13\t\t\t\t\t\t\t\t\t\t\t\t58551170\t72249657\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+17206\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t20\t1\t\t\t\t\t\t\t\t\t\t\t\t3765920\t565772\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23102\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t8931\t14449\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+2551\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t11\t12\t\t\t\t\t\t\t\t\t\t\t\t110167262\t34372608\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+34931\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t5\t5\t\t\t\t\t\t\t\t\t\t\t\t118309571\t170814948\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23113\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t12104\t5263\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+26300\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t12\t5\t\t\t\t\t\t\t\t\t\t\t\t53858625\t91139848\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23128\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t12103\t3340\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+15225\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t1\t1\t\t\t\t\t\t\t\t\t\t\t\t2473653'..b'\t\t\t\t\t\t\t\t33141546\t108113634\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+3168\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t5\t\t\t\t\t\t\t\t\t\t\t\t2019011\t134259999\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+12433\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t5\t17\t\t\t\t\t\t\t\t\t\t\t\t34955886\t29119901\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23330\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t9\t9\t\t\t\t\t\t\t\t\t\t\t\t139372139\t139378921\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tY\n+14232\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t1\t2\t\t\t\t\t\t\t\t\t\t\t\t569011\t207284336\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+31817\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t20\t10\t\t\t\t\t\t\t\t\t\t\t\t32664993\t21811145\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+17006\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t1\t14\t\t\t\t\t\t\t\t\t\t\t\t151738242\t50329313\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+16784\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t1\t12\t\t\t\t\t\t\t\t\t\t\t\t91852672\t127650989\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+3290\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t5\t\t\t\t\t\t\t\t\t\t\t\t2019030\t134263539\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+9360\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t17\t17\t\t\t\t\t\t\t\t\t\t\t\t37359262\t56769000\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+12747\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t1\t\t\t\t\t\t\t\t\t\t\t\t10830376\t569766\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+10164\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t17\tX\t\t\t\t\t\t\t\t\t\t\t\t33478114\t108297713\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23851\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t12\t2\t\t\t\t\t\t\t\t\t\t\t\t54677629\t88124624\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33050\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t7\t\t\t\t\t\t\t\t\t\t\t\t9361819\t97599083\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+12227\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t17\t\t\t\t\t\t\t\t\t\t\t\t24184163\t60142706\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+12282\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t19\t17\t\t\t\t\t\t\t\t\t\t\t\t11945083\t37868701\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+8398\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t2\t5\t\t\t\t\t\t\t\t\t\t\t\t232576633\t134260383\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+14515\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t17\t1\t\t\t\t\t\t\t\t\t\t\t\t37828494\t569305\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+9626\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t17\t17\t\t\t\t\t\t\t\t\t\t\t\t57232492\t34863351\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+15768\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t1\tX\t\t\t\t\t\t\t\t\t\t\t\t568364\t108297446\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23135\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t6472\t10858\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+9691\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t17\t17\t\t\t\t\t\t\t\t\t\t\t\t37360941\t33478228\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+25777\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t20\t12\t\t\t\t\t\t\t\t\t\t\t\t2451398\t3560214\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33699\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t4\t19\t\t\t\t\t\t\t\t\t\t\t\t38629661\t33185000\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+14138\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t2\t1\t\t\t\t\t\t\t\t\t\t\t\t232577176\t565851\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23083\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t13987\t6324\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+16016\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t1\tX\t\t\t\t\t\t\t\t\t\t\t\t91853050\t108297687\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+12950\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t1\t\t\t\t\t\t\t\t\t\t\t\t2017954\t568203\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+15652\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t6\t1\t\t\t\t\t\t\t\t\t\t\t\t75950980\t566931\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+15640\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t1\t6\t\t\t\t\t\t\t\t\t\t\t\t224548265\t937525\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33433\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t2\t19\t\t\t\t\t\t\t\t\t\t\t\t204055493\t24184153\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23003\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t5490\t14115\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33615\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t19\t8\t\t\t\t\t\t\t\t\t\t\t\t1478773\t145981626\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+4672\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t21\t2\t\t\t\t\t\t\t\t\t\t\t\t9827191\t88124672\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33263\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t19\t2\t\t\t\t\t\t\t\t\t\t\t\t24184077\t230045634\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23075\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t7768\t14653\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+8397\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t2\t5\t\t\t\t\t\t\t\t\t\t\t\t232576639\t134263192\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33953\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t5\t\t\t\t\t\t\t\t\t\t\t\t24184164\t139666182\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+18059\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t1\t5\t\t\t\t\t\t\t\t\t\t\t\t569446\t177482956\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+32486\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t3\t\t\t\t\t\t\t\t\t\t\t\t14606850\t129324128\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+2368\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t12\t11\t\t\t\t\t\t\t\t\t\t\t\t76443552\t125938478\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+1042\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t17\t\t\t\t\t\t\t\t\t\t\t\t810235\t33478232\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+7322\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t20\t2\t\t\t\t\t\t\t\t\t\t\t\t48807862\t133038722\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+17868\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t1\t\t\t\t\t\t\t\t\t\t\t\t13054352\t568203\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+30812\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t11\t10\t\t\t\t\t\t\t\t\t\t\t\t2018875\t69423263\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+34942\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t5\t5\t\t\t\t\t\t\t\t\t\t\t\t134260436\t177482849\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+14718\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t1\t17\t\t\t\t\t\t\t\t\t\t\t\t568222\t33478228\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23748\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t2\t12\t\t\t\t\t\t\t\t\t\t\t\t203500040\t124069216\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n' |
| b |
| diff -r 86526900cb8f -r 4966079d474b test-data/edgren_fusion-map.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/edgren_fusion-map.txt Tue Oct 20 10:12:08 2015 -0400 |
| b |
| @@ -0,0 +1,70 @@ +FusionID all.UniqueCuttingPositionCount all.SeedCount all.RescuedCount Strand Chromosome1 Position1 Chromosome2 Position2 KnownGene1 KnownTranscript1 KnownExonNumber1 KnownTranscriptStrand1 KnownGene2 KnownTranscript2 KnownExonNumber2 KnownTranscriptStrand2 FusionJunctionSequence SplicePattern FusionGene FrameShift +FUS_26799002_2222102817(--) -- 1 26799003 12 56527458 +FUS_27652879_2794310094(-+) -+ 1 27652880 17 79477135 +FUS_27677421_1106763499(--) -- 1 27677422 6 44221420 +FUS_52818775_491865792(++) ++ 1 52818776 2 242615169 +FUS_109756747_2844503161(++) ++ 1 109756748 18 48474938 +FUS_162336993_162351680(++) ++ 1 162336994 1 162351681 +FUS_204162041_204183009(++) ++ 1 204162042 1 204183010 +FUS_260933576_260947203(++) ++ 2 11682953 2 11696580 +FUS_317729880_2671195661(--) -- 2 68479257 16 46717518 +FUS_431341885_488240973(++) ++ 2 182091262 2 238990350 +FUS_468401284_468407812(++) ++ 2 219150661 2 219157189 +FUS_481827274_1095808311(-+) -+ 2 232576651 6 33266232 +FUS_535356398_535379077(++) ++ 3 42906351 3 42929030 +FUS_564945819_2208207316(++) ++ 3 72495772 12 42631957 +FUS_622049449_622062384(++) ++ 3 129599402 3 129612337 +FUS_641333884_641344084(++) ++ 3 148883837 3 148894037 +FUS_642753372_2640297172(++) ++ 3 150303325 16 15819029 +FUS_650628845_650704928(++) ++ 3 158178798 3 158254881 +FUS_688959544_1831692166(-+) -+ 3 196509497 X 151302279 +FUS_690560141_1289758805(-+) -+ 4 87630 7 56101654 +FUS_844223288_2907008396(--) -- 4 153750777 19 32902925 +FUS_950027061_1496638003(+-) +- 5 68400246 8 103842164 +FUS_1021452375_1022860816(+-) +- 5 139825560 5 141234001 +FUS_1093233534_2218149952(-+) -+ 6 30691455 12 52574593 +FUS_1096426187_3038889284(--) -- 6 33884108 21 42629253 +FUS_1136770263_2286212600(++) ++ 6 74228184 12 120637241 +FUS_1136770312_2883379228(-+) -+ 6 74228233 19 9273757 +FUS_1136770987_1980946407(+-) +- 6 74228908 10 85912360 +FUS_1233435659_2723113969(--) -- 6 170893580 17 8281010 +FUS_1309258884_2298001199(++) ++ 7 75601733 12 132425840 +FUS_1325089044_1999508485(+-) +- 7 91431893 10 104474438 +FUS_1472280885_2753298497(--) -- 8 79485046 17 38465538 +FUS_1518347105_2752895197(--) -- 8 125551266 17 38062238 +FUS_1518347105_2752895483(--) -- 8 125551266 17 38062524 +FUS_1518347105_2752896199(--) -- 8 125551266 17 38063240 +FUS_1518347105_2752899136(--) -- 8 125551266 17 38066177 +FUS_1536899619_2586923912(++) ++ 8 144103780 15 64977161 +FUS_1625744006_2750144109(-+) -+ 9 86584135 17 35311150 +FUS_1654638612_1662879517(--) -- 9 115478741 9 123719646 +FUS_1669121216_1669132845(++) ++ 9 129961345 9 129972974 +FUS_1670521420_3062528544(++) ++ 9 131361549 22 18138593 +FUS_1799397243_2485431458(+-) +- X 119007356 14 70834275 +FUS_1900761185_1900785540(++) ++ 10 5727138 10 5751493 +FUS_1908751091_1908769529(++) ++ 10 13717044 10 13735482 +FUS_2018880080_2591692014(--) -- 10 123846033 15 69745263 +FUS_2041405408_2909026952(-+) -+ 11 10836577 19 34921481 +FUS_2088954897_2955778536(-+) -+ 11 58386066 20 22544041 +FUS_2123194535_2562850433(++) ++ 11 92625704 15 40903682 +FUS_2172555288_2751715570(--) -- 12 6979929 17 36882611 +FUS_2217352725_2217359993(++) ++ 12 51777366 12 51784634 +FUS_2220354100_2220360378(++) ++ 12 54778741 12 54785019 +FUS_2345398656_2640249892(-+) -+ 13 45971393 16 15771749 +FUS_2412983948_2413096340(++) ++ 13 113556685 13 113669077 +FUS_2439284820_2439298041(++) ++ 14 24687637 14 24700858 +FUS_2451742910_2913912193(-+) -+ 14 37145727 19 39806722 +FUS_2489891478_2508003573(+-) +- 14 75294295 14 93406390 +FUS_2749696310_2772065451(++) ++ 17 34863351 17 57232492 +FUS_2749696722_2772065451(++) ++ 17 34863763 17 57232492 +FUS_2750312412_2752207385(--) -- 17 35479453 17 37374426 +FUS_2752428377_2763381348(-+) -+ 17 37595418 17 48548389 +FUS_2758316408_2758339948(++) ++ 17 43483449 17 43506989 +FUS_2774302297_2774962857(-+) -+ 17 59469338 17 60129898 +FUS_2780655412_2781079288(++) ++ 17 65822453 17 66246329 +FUS_2788733755_2966381512(-+) -+ 17 73900796 20 33147017 +FUS_2792979986_2792985266(++) ++ 17 78147027 17 78152307 +FUS_2893652499_2893681620(++) ++ 19 19547028 19 19576149 +FUS_2914960146_2914976931(++) ++ 19 40854675 19 40871460 +FUS_2979600181_2980773042(+-) +- 20 46365686 20 47538547 +FUS_3006176578_3036925768(++) ++ 21 9916547 21 40665737 |
| b |
| diff -r 86526900cb8f -r 4966079d474b test-data/edgren_test_01_specifc_matching_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/edgren_test_01_specifc_matching_output.txt Tue Oct 20 10:12:08 2015 -0400 |
| b |
| b'@@ -0,0 +1,11394 @@\n+Left-genes\tRight-genes\tedgren_chimerascan.txt\tedgren_defuse.txt\tedgren_fusion-map.txt\tedgren_true_positives.txt\n+NR_037945:STX16\tRAE1\tTRUE\tFALSE\tFALSE\tFALSE\n+TPD52L2\tDNAJC5\tTRUE\tFALSE\tFALSE\tFALSE\n+C20orf112\tC20orf112\tTRUE\tFALSE\tFALSE\tFALSE\n+PREX1\tCPNE1:NM_001198863:NR_037188\tTRUE\tFALSE\tFALSE\tFALSE\n+AP5S1\tMAVS:NR_037921\tTRUE\tFALSE\tFALSE\tFALSE\n+BCAS4\tNM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tTRUE\tFALSE\tFALSE\tFALSE\n+NR_036633:VAPB\tAPCDD1L-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+CSNK2A1\tFAM110A:NM_001289145:NM_001289146:NM_001289147\tTRUE\tFALSE\tFALSE\tFALSE\n+NR_109859\tAP5S1\tTRUE\tFALSE\tFALSE\tFALSE\n+FKBP1A:NR_037661:SDCBP2-AS1\tLOC284801\tTRUE\tFALSE\tFALSE\tFALSE\n+ADNP:NM_001282531\tRSPO4\tTRUE\tFALSE\tFALSE\tFALSE\n+LAMA5\tLOC284801\tTRUE\tFALSE\tFALSE\tFALSE\n+OSER1-AS1\tOSER1-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+ZFP64\tNM_001281507:PHACTR3\tTRUE\tFALSE\tFALSE\tFALSE\n+ARFGAP1:NM_001281482:NM_001281483:NM_001281484:NR_104022:NR_104023\tIFT52:NM_001303458:NM_001303459\tTRUE\tFALSE\tFALSE\tFALSE\n+RAD21L1\tHMGN1\tTRUE\tFALSE\tFALSE\tFALSE\n+VPS16\tPCP4\tTRUE\tFALSE\tFALSE\tFALSE\n+ATP5O\tKIF16B\tTRUE\tFALSE\tFALSE\tFALSE\n+PCNT\tADNP:NM_001282531:NM_001282532\tTRUE\tFALSE\tFALSE\tFALSE\n+SLC2A4RG\tBRWD1\tTRUE\tFALSE\tFALSE\tFALSE\n+LOC400927:NM_001289912\tNR_110051:ZNF217\tTRUE\tFALSE\tFALSE\tFALSE\n+LOC284801\tTUBGCP6\tTRUE\tFALSE\tFALSE\tFALSE\n+ELMO2\tJOSD1\tTRUE\tFALSE\tFALSE\tFALSE\n+RTCB\tSTMN3\tTRUE\tFALSE\tFALSE\tFALSE\n+HIRA\tNM_001282933:NM_001282935:NR_104259:NR_110623:ZNF341\tTRUE\tFALSE\tFALSE\tFALSE\n+DENND6B\tMTRNR2L3:RAE1\tTRUE\tFALSE\tFALSE\tFALSE\n+EWSR1\tNM_001278649:OSBPL2\tTRUE\tFALSE\tFALSE\tFALSE\n+CTSZ\tEP300\tTRUE\tFALSE\tFALSE\tFALSE\n+DYNLRB1:NM_001281727:NM_001281728:NM_001281729:NM_177953:NR_104032\tLARGE\tTRUE\tFALSE\tFALSE\tFALSE\n+ENTPD6\tNM_001287387:SLC25A1\tTRUE\tFALSE\tFALSE\tFALSE\n+SHANK3\tLAMA5\tTRUE\tFALSE\tFALSE\tFALSE\n+ATRN\tNM_001284277:NM_001284278:PITPNB\tTRUE\tFALSE\tFALSE\tFALSE\n+SULF2\tPRICKLE2:PRICKLE2-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+VPRBP\tNSFL1C\tTRUE\tFALSE\tFALSE\tFALSE\n+MFN1\tMAPRE1\tTRUE\tFALSE\tFALSE\tFALSE\n+PCMTD2\tPAK2\tTRUE\tFALSE\tFALSE\tFALSE\n+CEP63\tDNMT3B\tTRUE\tFALSE\tFALSE\tFALSE\n+RRP9\tCSE1L\tTRUE\tFALSE\tFALSE\tFALSE\n+CP:NR_046371\tCHD6\tTRUE\tFALSE\tFALSE\tFALSE\n+TMEM189:TMEM189-UBE2V1\tGLT8D1:GNL3:NM_001278280:NM_001278281\tTRUE\tFALSE\tFALSE\tFALSE\n+ST6GAL1\tNM_001278649:OSBPL2\tTRUE\tFALSE\tFALSE\tFALSE\n+OXSM\tMAP1LC3A\tTRUE\tFALSE\tFALSE\tFALSE\n+PHF20\tCDC25A\tTRUE\tFALSE\tFALSE\tFALSE\n+GOLIM4:NM_001308155\tGNAS:NM_001309840:NM_001309861\tTRUE\tFALSE\tFALSE\tFALSE\n+SLC25A38\tNM_001301188:NM_001301190:NM_001301193:NM_001301196:NM_001301201:TRIB3\tTRUE\tFALSE\tFALSE\tFALSE\n+ZNFX1\tIQCG\tTRUE\tFALSE\tFALSE\tFALSE\n+SNRK\tLAMA5\tTRUE\tFALSE\tFALSE\tFALSE\n+EYA2\tNR_103507:SLC6A6\tTRUE\tFALSE\tFALSE\tFALSE\n+KIF16B\tCACNA1D\tTRUE\tFALSE\tFALSE\tFALSE\n+SLC9A8\tTNIK\tTRUE\tFALSE\tFALSE\tFALSE\n+NCOA5\tMGLL\tTRUE\tFALSE\tFALSE\tFALSE\n+POLQ\tTGM2\tTRUE\tFALSE\tFALSE\tFALSE\n+FBLN2\tPOFUT1\tTRUE\tFALSE\tFALSE\tFALSE\n+FKBP1A:NR_037661\tATP11B\tTRUE\tFALSE\tFALSE\tFALSE\n+NRSN2\tNM_001195483:SLC12A8\tTRUE\tFALSE\tFALSE\tFALSE\n+FNDC3B\tSOGA1\tTRUE\tFALSE\tFALSE\tFALSE\n+CPNE1:NM_001198863:NR_037188:RBM12\tCHRD:NM_001304472:NM_001304473:NM_001304474:NR_130747\tTRUE\tFALSE\tFALSE\tFALSE\n+C3orf18:HEMK1\tPCNA:PCNA-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+RYBP\tLAMA5\tTRUE\tFALSE\tFALSE\tFALSE\n+USP19\tGNAS:NM_001309840:NM_001309861\tTRUE\tFALSE\tFALSE\tFALSE\n+SNRPB\tSEC61A1\tTRUE\tFALSE\tFALSE\tFALSE\n+MAVS:NR_037921\tKAT2B\tTRUE\tFALSE\tFALSE\tFALSE\n+GGT7\tCMC1\tTRUE\tFALSE\tFALSE\tFALSE\n+RPS21\tQRICH1\tTRUE\tFALSE\tFALSE\tFALSE\n+KIAA0226\tNM_001278649:OSBPL2\tTRUE\tFALSE\tFALSE\tFALSE\n+CDC25B:NM_001287516:NM_001287517:NM_001287518:NM_001287519:NM_001287520:NM_001287522:NM_001287524\tDNAJC19:NR_033721\tTRUE\tFALSE\tFALSE\tFALSE\n+C5orf34\tGNAS:NM_001309840:NM_001309861\tTRUE\tFALSE\tFALSE\tFALSE\n+DROSHA\tDLGAP4:NR_109939\tTRUE\tFALSE\tFALSE\tFALSE\n+SQSTM1\tEIF6\tTRUE\tFALSE\tFALSE\tFALSE\n+KDM3B\tDYNLRB1:NM_001281727:NM_001281728:NM_001281729:NM_177953:NR_104032\tTRUE\tFALSE\tFALSE\tFALSE\n+CYFIP2:NM_001291721:NM_001291722\tNR_037945:STX16\tTRUE\tFALSE\tFALSE\tFALSE\n+NPR3\t'..b'\tTRUE\tFALSE\tFALSE\n+SMAD2\tRPS23\tFALSE\tTRUE\tFALSE\tFALSE\n+NR_120540\tUBA2\tFALSE\tFALSE\tTRUE\tFALSE\n+NR_024091:ZFP91:ZFP91-CNTF\tLINC00261\tFALSE\tFALSE\tTRUE\tFALSE\n+FAT3\tCASC5\tFALSE\tFALSE\tTRUE\tFALSE\n+FRMD4A\tFRMD4A\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001291876:NM_001291877:TACC2\tRPLP1\tFALSE\tFALSE\tTRUE\tFALSE\n+EEF1A1\tGHITM\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001286806:NM_001286807:SLC25A30\tNDE1\tFALSE\tFALSE\tTRUE\tFALSE\n+RYBP\tYAF2\tFALSE\tFALSE\tTRUE\tFALSE\n+GALNT6\tGALNT6\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001290002:NM_001290004:NR_120486:NR_120487:ZNF385A\tNR_120486:NR_120487:ZNF385A\tFALSE\tFALSE\tTRUE\tFALSE\n+POR\tPUS1\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001159287:TPI1\tMLLT6\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001293212:NM_001293213:NM_001293214:NM_001293215:NM_001293216:NR_120608:TUBB\tKRT80\tFALSE\tFALSE\tTRUE\tFALSE\n+EEF1A1\tRPLP0\tFALSE\tFALSE\tTRUE\tFALSE\n+LY6E\tZNF609\tFALSE\tFALSE\tTRUE\tFALSE\n+TEKT4P2\tBRWD1\tFALSE\tFALSE\tTRUE\tFALSE\n+HNRNPK\tAATF\tFALSE\tFALSE\tTRUE\tFALSE\n+PKIA\tRARA\tFALSE\tFALSE\tTRUE\tFALSE\n+MRPL38\tMAP1LC3A\tFALSE\tFALSE\tTRUE\tFALSE\n+MYO19\tSKA2\tFALSE\tFALSE\tTRUE\tFALSE\n+ARHGAP27:NM_001282290\tARHGAP27:NM_001282290\tFALSE\tFALSE\tTRUE\tFALSE\n+BCAS3\tMED13\tFALSE\tFALSE\tTRUE\tFALSE\n+BPTF\tAMZ2:NM_001289054:NM_001289056\tFALSE\tFALSE\tTRUE\tFALSE\n+CARD14\tCARD14\tFALSE\tFALSE\tTRUE\tFALSE\n+PDCD2\tRPL26\tFALSE\tFALSE\tTRUE\tFALSE\n+EIF2A\tMYH11:NDE1\tFALSE\tFALSE\tTRUE\tFALSE\n+GATAD2A\tGATAD2A:NM_001300946\tFALSE\tFALSE\tTRUE\tFALSE\n+PLD3\tNM_001291311:PLD3\tFALSE\tFALSE\tTRUE\tFALSE\n+ARFIP1:NM_001287431:NM_001287432:NM_001287433\tDPY19L3\tFALSE\tFALSE\tTRUE\tFALSE\n+EEF1A1\tZNF317\tFALSE\tFALSE\tTRUE\tFALSE\n+NR_031672:SPTAN1\tBCL2L13:NR_073068:NR_073069\tFALSE\tFALSE\tTRUE\tFALSE\n+HMGN2\tESYT1\tFALSE\tFALSE\tTRUE\tFALSE\n+LOC644961:TMEM222\tACTG1:NR_037688\tFALSE\tFALSE\tTRUE\tFALSE\n+SARS\tME2\tFALSE\tFALSE\tTRUE\tFALSE\n+KISS1\tGOLT1A\tFALSE\tFALSE\tTRUE\tFALSE\n+CC2D1B\tDTYMK\tFALSE\tFALSE\tTRUE\tFALSE\n+SYTL1\tHSP90AB1\tFALSE\tFALSE\tTRUE\tFALSE\n+PAK2\tMAGEA10:MAGEA10-MAGEA5\tFALSE\tFALSE\tTRUE\tFALSE\n+TMCC1\tTMCC1\tFALSE\tFALSE\tTRUE\tFALSE\n+HPS3:NM_001308258:NR_046371\tCP:NR_046371\tFALSE\tFALSE\tTRUE\tFALSE\n+RSRC1\tRSRC1\tFALSE\tFALSE\tTRUE\tFALSE\n+GREB1\tGREB1\tFALSE\tFALSE\tTRUE\tFALSE\n+NR_130784\tNR_037904:SCLY\tFALSE\tFALSE\tTRUE\tFALSE\n+PNKD:TMBIM1\tPNKD:TMBIM1\tFALSE\tFALSE\tTRUE\tFALSE\n+PTMA\tRGL2\tFALSE\tFALSE\tTRUE\tFALSE\n+SLC30A5\tAZIN1:NM_001301668\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001286052:NM_001286053:NM_001286054:NM_001289931:NR_110527:ZNF595:ZNF718\tPSPH\tFALSE\tFALSE\tTRUE\tFALSE\n+RALGPS1\tRALGPS1\tFALSE\tFALSE\tTRUE\tFALSE\n+SULF2\tARFGEF2\tFALSE\tFALSE\tTRUE\tFALSE\n+NDUFA1\tSYNJ2BP:SYNJ2BP-COX16\tFALSE\tFALSE\tTRUE\tFALSE\n+NEDD8:NEDD8-MDP1\tNEDD8:NEDD8-MDP1\tFALSE\tFALSE\tTRUE\tFALSE\n+YLPM1\tITPK1\tFALSE\tFALSE\tTRUE\tFALSE\n+LAMP1\tMCF2L2\tFALSE\tFALSE\tFALSE\tTRUE\n+NFS1\tPREX1\tFALSE\tFALSE\tFALSE\tTRUE\n+STARD3\tDOK5:NM_177959\tFALSE\tFALSE\tFALSE\tTRUE\n+NM_001272060:RPS6KB1\tVMP1\tFALSE\tFALSE\tFALSE\tTRUE\n+NOS1AP\tC1orf226\tTRUE\tFALSE\tTRUE\tFALSE\n+INIP\tC5\tTRUE\tFALSE\tTRUE\tFALSE\n+FAM208B\tFAM208B\tTRUE\tFALSE\tTRUE\tFALSE\n+MED1\tACSF2:NM_001288968:NM_001288969:NM_001288970:NM_001288971:NM_001288972:NR_110232\tTRUE\tFALSE\tTRUE\tFALSE\n+PPP3R1\tVPS35\tTRUE\tFALSE\tTRUE\tFALSE\n+PPP1R12A\tSEPT10\tTRUE\tFALSE\tFALSE\tTRUE\n+NM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tCEP250\tTRUE\tFALSE\tFALSE\tTRUE\n+ARFGEF2\tSULF2\tTRUE\tFALSE\tFALSE\tTRUE\n+DIDO1\tNM_001303457:TTI1\tTRUE\tFALSE\tFALSE\tTRUE\n+DHX35\tITCH\tTRUE\tFALSE\tFALSE\tTRUE\n+CPNE1:NM_001198863:NR_037188\tPI3\tTRUE\tFALSE\tFALSE\tTRUE\n+CCDC85C\tSETD3\tTRUE\tFALSE\tFALSE\tTRUE\n+CYTH1\tEIF3H\tTRUE\tFALSE\tFALSE\tTRUE\n+RARA\tPKIA\tTRUE\tFALSE\tFALSE\tTRUE\n+BCAS4\tBCAS3\tTRUE\tFALSE\tFALSE\tTRUE\n+NR_036633:VAPB\tIKZF3:NM_001284514:NM_001284515\tTRUE\tFALSE\tFALSE\tTRUE\n+NM_001272060:RPS6KB1\tSNF8\tTRUE\tFALSE\tFALSE\tTRUE\n+SKA2\tMYO19\tTRUE\tFALSE\tFALSE\tTRUE\n+BSG\tNFIX\tTRUE\tFALSE\tFALSE\tTRUE\n+RAB22A\tMYO9B\tTRUE\tFALSE\tFALSE\tTRUE\n+GLB1\tCMTM7\tTRUE\tFALSE\tFALSE\tTRUE\n+NOTCH1\tNUP214\tTRUE\tFALSE\tFALSE\tTRUE\n+WDR67\tZNF704\tTRUE\tFALSE\tFALSE\tTRUE\n+ANKHD1:ANKHD1-EIF4EBP3\tPCDH1\tFALSE\tFALSE\tTRUE\tTRUE\n+TATDN1\tGSDMB\tTRUE\tFALSE\tTRUE\tTRUE\n+ACACA\tSTAC2\tTRUE\tFALSE\tTRUE\tTRUE\n' |
| b |
| diff -r 86526900cb8f -r 4966079d474b test-data/edgren_test_02_unspecifc_matching_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/edgren_test_02_unspecifc_matching_output.txt Tue Oct 20 10:12:08 2015 -0400 |
| b |
| b'@@ -0,0 +1,11248 @@\n+Left-genes\tRight-genes\tedgren_chimerascan.txt\tedgren_defuse.txt\tedgren_fusion-map.txt\tedgren_true_positives.txt\n+C20orf112\tC20orf112\tTRUE\tFALSE\tFALSE\tFALSE\n+AP5S1\tMAVS:NR_037921\tTRUE\tFALSE\tFALSE\tFALSE\n+NM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tBCAS4\tTRUE\tFALSE\tFALSE\tFALSE\n+NR_036633:VAPB\tAPCDD1L-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+CSNK2A1\tFAM110A:NM_001289145:NM_001289146:NM_001289147\tTRUE\tFALSE\tFALSE\tFALSE\n+NR_109859\tAP5S1\tTRUE\tFALSE\tFALSE\tFALSE\n+FKBP1A:NR_037661:SDCBP2-AS1\tLOC284801\tTRUE\tFALSE\tFALSE\tFALSE\n+RSPO4\tADNP:NM_001282531\tTRUE\tFALSE\tFALSE\tFALSE\n+LOC284801\tLAMA5\tTRUE\tFALSE\tFALSE\tFALSE\n+OSER1-AS1\tOSER1-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+ZFP64\tNM_001281507:PHACTR3\tTRUE\tFALSE\tFALSE\tFALSE\n+IFT52:NM_001303458:NM_001303459\tARFGAP1:NM_001281482:NM_001281483:NM_001281484:NR_104022:NR_104023\tTRUE\tFALSE\tFALSE\tFALSE\n+RAD21L1\tHMGN1\tTRUE\tFALSE\tFALSE\tFALSE\n+VPS16\tPCP4\tTRUE\tFALSE\tFALSE\tFALSE\n+KIF16B\tATP5O\tTRUE\tFALSE\tFALSE\tFALSE\n+ADNP:NM_001282531:NM_001282532\tPCNT\tTRUE\tFALSE\tFALSE\tFALSE\n+SLC2A4RG\tBRWD1\tTRUE\tFALSE\tFALSE\tFALSE\n+NR_110051:ZNF217\tLOC400927:NM_001289912\tTRUE\tFALSE\tFALSE\tFALSE\n+LOC284801\tTUBGCP6\tTRUE\tFALSE\tFALSE\tFALSE\n+ELMO2\tJOSD1\tTRUE\tFALSE\tFALSE\tFALSE\n+STMN3\tRTCB\tTRUE\tFALSE\tFALSE\tFALSE\n+NM_001282933:NM_001282935:NR_104259:NR_110623:ZNF341\tHIRA\tTRUE\tFALSE\tFALSE\tFALSE\n+MTRNR2L3:RAE1\tDENND6B\tTRUE\tFALSE\tFALSE\tFALSE\n+NM_001278649:OSBPL2\tEWSR1\tTRUE\tFALSE\tFALSE\tFALSE\n+CTSZ\tEP300\tTRUE\tFALSE\tFALSE\tFALSE\n+DYNLRB1:NM_001281727:NM_001281728:NM_001281729:NM_177953:NR_104032\tLARGE\tTRUE\tFALSE\tFALSE\tFALSE\n+ENTPD6\tNM_001287387:SLC25A1\tTRUE\tFALSE\tFALSE\tFALSE\n+LAMA5\tSHANK3\tTRUE\tFALSE\tFALSE\tFALSE\n+ATRN\tNM_001284277:NM_001284278:PITPNB\tTRUE\tFALSE\tFALSE\tFALSE\n+SULF2\tPRICKLE2:PRICKLE2-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+NSFL1C\tVPRBP\tTRUE\tFALSE\tFALSE\tFALSE\n+MAPRE1\tMFN1\tTRUE\tFALSE\tFALSE\tFALSE\n+PCMTD2\tPAK2\tTRUE\tFALSE\tFALSE\tFALSE\n+DNMT3B\tCEP63\tTRUE\tFALSE\tFALSE\tFALSE\n+CSE1L\tRRP9\tTRUE\tFALSE\tFALSE\tFALSE\n+CHD6\tCP:NR_046371\tTRUE\tFALSE\tFALSE\tFALSE\n+TMEM189:TMEM189-UBE2V1\tGLT8D1:GNL3:NM_001278280:NM_001278281\tTRUE\tFALSE\tFALSE\tFALSE\n+NM_001278649:OSBPL2\tST6GAL1\tTRUE\tFALSE\tFALSE\tFALSE\n+MAP1LC3A\tOXSM\tTRUE\tFALSE\tFALSE\tFALSE\n+PHF20\tCDC25A\tTRUE\tFALSE\tFALSE\tFALSE\n+GNAS:NM_001309840:NM_001309861\tGOLIM4:NM_001308155\tTRUE\tFALSE\tFALSE\tFALSE\n+NM_001301188:NM_001301190:NM_001301193:NM_001301196:NM_001301201:TRIB3\tSLC25A38\tTRUE\tFALSE\tFALSE\tFALSE\n+ZNFX1\tIQCG\tTRUE\tFALSE\tFALSE\tFALSE\n+LAMA5\tSNRK\tTRUE\tFALSE\tFALSE\tFALSE\n+EYA2\tNR_103507:SLC6A6\tTRUE\tFALSE\tFALSE\tFALSE\n+KIF16B\tCACNA1D\tTRUE\tFALSE\tFALSE\tFALSE\n+SLC9A8\tTNIK\tTRUE\tFALSE\tFALSE\tFALSE\n+NCOA5\tMGLL\tTRUE\tFALSE\tFALSE\tFALSE\n+TGM2\tPOLQ\tTRUE\tFALSE\tFALSE\tFALSE\n+POFUT1\tFBLN2\tTRUE\tFALSE\tFALSE\tFALSE\n+FKBP1A:NR_037661\tATP11B\tTRUE\tFALSE\tFALSE\tFALSE\n+NRSN2\tNM_001195483:SLC12A8\tTRUE\tFALSE\tFALSE\tFALSE\n+SOGA1\tFNDC3B\tTRUE\tFALSE\tFALSE\tFALSE\n+CPNE1:NM_001198863:NR_037188:RBM12\tCHRD:NM_001304472:NM_001304473:NM_001304474:NR_130747\tTRUE\tFALSE\tFALSE\tFALSE\n+PCNA:PCNA-AS1\tC3orf18:HEMK1\tTRUE\tFALSE\tFALSE\tFALSE\n+LAMA5\tRYBP\tTRUE\tFALSE\tFALSE\tFALSE\n+GNAS:NM_001309840:NM_001309861\tUSP19\tTRUE\tFALSE\tFALSE\tFALSE\n+SNRPB\tSEC61A1\tTRUE\tFALSE\tFALSE\tFALSE\n+MAVS:NR_037921\tKAT2B\tTRUE\tFALSE\tFALSE\tFALSE\n+GGT7\tCMC1\tTRUE\tFALSE\tFALSE\tFALSE\n+RPS21\tQRICH1\tTRUE\tFALSE\tFALSE\tFALSE\n+NM_001278649:OSBPL2\tKIAA0226\tTRUE\tFALSE\tFALSE\tFALSE\n+CDC25B:NM_001287516:NM_001287517:NM_001287518:NM_001287519:NM_001287520:NM_001287522:NM_001287524\tDNAJC19:NR_033721\tTRUE\tFALSE\tFALSE\tFALSE\n+GNAS:NM_001309840:NM_001309861\tC5orf34\tTRUE\tFALSE\tFALSE\tFALSE\n+DLGAP4:NR_109939\tDROSHA\tTRUE\tFALSE\tFALSE\tFALSE\n+EIF6\tSQSTM1\tTRUE\tFALSE\tFALSE\tFALSE\n+DYNLRB1:NM_001281727:NM_001281728:NM_001281729:NM_177953:NR_104032\tKDM3B\tTRUE\tFALSE\tFALSE\tFALSE\n+NR_037945:STX16\tCYFIP2:NM_001291721:NM_001291722\tTRUE\tFALSE\tFALSE\tFALSE\n+CPNE1:NM_001198863:NR_037188\tNPR3\tTRUE\tFALSE\tFALSE\tFALSE\n+ACSS2\tHMGCR\tTRUE\tFALSE\tFALSE\tFALSE\n+CTSZ\tCCT5:NM_001306153:NM_001306154:NM_001306155:NM_00'..b'0004:NR_120486:NR_120487:ZNF385A\tNR_120486:NR_120487:ZNF385A\tFALSE\tFALSE\tTRUE\tFALSE\n+PUS1\tPOR\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001159287:TPI1\tMLLT6\tFALSE\tFALSE\tTRUE\tFALSE\n+KRT80\tNM_001293212:NM_001293213:NM_001293214:NM_001293215:NM_001293216:NR_120608:TUBB\tFALSE\tFALSE\tTRUE\tFALSE\n+RPLP0\tEEF1A1\tFALSE\tFALSE\tTRUE\tFALSE\n+ZNF609\tLY6E\tFALSE\tFALSE\tTRUE\tFALSE\n+AATF\tHNRNPK\tFALSE\tFALSE\tTRUE\tFALSE\n+MRPL38\tMAP1LC3A\tFALSE\tFALSE\tTRUE\tFALSE\n+BPTF\tAMZ2:NM_001289054:NM_001289056\tFALSE\tFALSE\tTRUE\tFALSE\n+CARD14\tCARD14\tFALSE\tFALSE\tTRUE\tFALSE\n+RPL26\tPDCD2\tFALSE\tFALSE\tTRUE\tFALSE\n+MYH11:NDE1\tEIF2A\tFALSE\tFALSE\tTRUE\tFALSE\n+GATAD2A\tGATAD2A:NM_001300946\tFALSE\tFALSE\tTRUE\tFALSE\n+PLD3\tNM_001291311:PLD3\tFALSE\tFALSE\tTRUE\tFALSE\n+DPY19L3\tARFIP1:NM_001287431:NM_001287432:NM_001287433\tFALSE\tFALSE\tTRUE\tFALSE\n+ZNF317\tEEF1A1\tFALSE\tFALSE\tTRUE\tFALSE\n+BCL2L13:NR_073068:NR_073069\tNR_031672:SPTAN1\tFALSE\tFALSE\tTRUE\tFALSE\n+LOC644961:TMEM222\tACTG1:NR_037688\tFALSE\tFALSE\tTRUE\tFALSE\n+SARS\tME2\tFALSE\tFALSE\tTRUE\tFALSE\n+SYTL1\tHSP90AB1\tFALSE\tFALSE\tTRUE\tFALSE\n+PAK2\tMAGEA10:MAGEA10-MAGEA5\tFALSE\tFALSE\tTRUE\tFALSE\n+TMCC1\tTMCC1\tFALSE\tFALSE\tTRUE\tFALSE\n+HPS3:NM_001308258:NR_046371\tCP:NR_046371\tFALSE\tFALSE\tTRUE\tFALSE\n+RSRC1\tRSRC1\tFALSE\tFALSE\tTRUE\tFALSE\n+GREB1\tGREB1\tFALSE\tFALSE\tTRUE\tFALSE\n+NR_130784\tNR_037904:SCLY\tFALSE\tFALSE\tTRUE\tFALSE\n+PNKD:TMBIM1\tPNKD:TMBIM1\tFALSE\tFALSE\tTRUE\tFALSE\n+PTMA\tRGL2\tFALSE\tFALSE\tTRUE\tFALSE\n+SLC30A5\tAZIN1:NM_001301668\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001286052:NM_001286053:NM_001286054:NM_001289931:NR_110527:ZNF595:ZNF718\tPSPH\tFALSE\tFALSE\tTRUE\tFALSE\n+RALGPS1\tRALGPS1\tFALSE\tFALSE\tTRUE\tFALSE\n+SYNJ2BP:SYNJ2BP-COX16\tNDUFA1\tFALSE\tFALSE\tTRUE\tFALSE\n+NEDD8:NEDD8-MDP1\tNEDD8:NEDD8-MDP1\tFALSE\tFALSE\tTRUE\tFALSE\n+YLPM1\tITPK1\tFALSE\tFALSE\tTRUE\tFALSE\n+LAMP1\tMCF2L2\tFALSE\tFALSE\tFALSE\tTRUE\n+NFS1\tPREX1\tFALSE\tFALSE\tFALSE\tTRUE\n+VMP1\tNM_001272060:RPS6KB1\tFALSE\tFALSE\tFALSE\tTRUE\n+FEN1\tFADS2:NM_001281501:NM_001281502\tTRUE\tTRUE\tFALSE\tFALSE\n+MCF2L\tLAMP1\tTRUE\tTRUE\tFALSE\tFALSE\n+GCN1L1\tMSI1\tTRUE\tTRUE\tFALSE\tFALSE\n+TNFRSF1A\tSCNN1A\tTRUE\tTRUE\tFALSE\tFALSE\n+RAE1\tNR_037945:STX16\tTRUE\tTRUE\tFALSE\tFALSE\n+TPD52L2\tDNAJC5\tTRUE\tTRUE\tFALSE\tFALSE\n+CPNE1:NM_001198863:NR_037188\tPREX1\tTRUE\tTRUE\tFALSE\tFALSE\n+SYNRG\tTOB1\tTRUE\tTRUE\tFALSE\tFALSE\n+MED1\tSTXBP4\tTRUE\tTRUE\tFALSE\tFALSE\n+SUMF1\tLRRFIP2:NM_001282691\tTRUE\tTRUE\tFALSE\tFALSE\n+NM_001165931:RRM2\tC2orf48\tTRUE\tTRUE\tFALSE\tFALSE\n+VAMP8\tVAMP5\tTRUE\tTRUE\tFALSE\tFALSE\n+TMEM120A\tSTYXL1\tTRUE\tTRUE\tFALSE\tFALSE\n+NCOA2\tZNF704\tTRUE\tTRUE\tFALSE\tFALSE\n+FAM208B\tFAM208B\tTRUE\tFALSE\tTRUE\tFALSE\n+YAF2\tRYBP\tTRUE\tFALSE\tTRUE\tFALSE\n+ARHGAP27:NM_001282290\tARHGAP27:NM_001282290\tTRUE\tFALSE\tTRUE\tFALSE\n+VPS35\tPPP3R1\tTRUE\tFALSE\tTRUE\tFALSE\n+NOS1AP\tC1orf226\tTRUE\tFALSE\tTRUE\tFALSE\n+KISS1\tGOLT1A\tTRUE\tFALSE\tTRUE\tFALSE\n+CC2D1B\tDTYMK\tTRUE\tFALSE\tTRUE\tFALSE\n+HMGN2\tESYT1\tTRUE\tFALSE\tTRUE\tFALSE\n+INIP\tC5\tTRUE\tFALSE\tTRUE\tFALSE\n+PPP1R12A\tSEPT10\tTRUE\tFALSE\tFALSE\tTRUE\n+ITCH\tDHX35\tTRUE\tFALSE\tFALSE\tTRUE\n+CPNE1:NM_001198863:NR_037188\tPI3\tTRUE\tFALSE\tFALSE\tTRUE\n+SETD3\tCCDC85C\tTRUE\tFALSE\tFALSE\tTRUE\n+ZNF704\tWDR67\tTRUE\tFALSE\tFALSE\tTRUE\n+STARD3\tDOK5:NM_177959\tFALSE\tTRUE\tFALSE\tTRUE\n+TEKT4P2\tBRWD1\tTRUE\tTRUE\tTRUE\tFALSE\n+MED1\tACSF2:NM_001288968:NM_001288969:NM_001288970:NM_001288971:NM_001288972:NR_110232\tTRUE\tTRUE\tTRUE\tFALSE\n+BCAS3\tMED13\tTRUE\tTRUE\tTRUE\tFALSE\n+BSG\tNFIX\tTRUE\tTRUE\tFALSE\tTRUE\n+MYO9B\tRAB22A\tTRUE\tTRUE\tFALSE\tTRUE\n+NUP214\tNOTCH1\tTRUE\tTRUE\tFALSE\tTRUE\n+CMTM7\tGLB1\tTRUE\tTRUE\tFALSE\tTRUE\n+CEP250\tNM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tTRUE\tTRUE\tFALSE\tTRUE\n+NM_001303457:TTI1\tDIDO1\tTRUE\tTRUE\tFALSE\tTRUE\n+CYTH1\tEIF3H\tTRUE\tTRUE\tFALSE\tTRUE\n+BCAS3\tBCAS4\tTRUE\tTRUE\tFALSE\tTRUE\n+IKZF3:NM_001284514:NM_001284515\tNR_036633:VAPB\tTRUE\tTRUE\tFALSE\tTRUE\n+SNF8\tNM_001272060:RPS6KB1\tTRUE\tTRUE\tFALSE\tTRUE\n+ANKHD1:ANKHD1-EIF4EBP3\tPCDH1\tFALSE\tTRUE\tTRUE\tTRUE\n+SULF2\tARFGEF2\tTRUE\tTRUE\tTRUE\tTRUE\n+GSDMB\tTATDN1\tTRUE\tTRUE\tTRUE\tTRUE\n+RARA\tPKIA\tTRUE\tTRUE\tTRUE\tTRUE\n+ACACA\tSTAC2\tTRUE\tTRUE\tTRUE\tTRUE\n+MYO19\tSKA2\tTRUE\tTRUE\tTRUE\tTRUE\n' |
| b |
| diff -r 86526900cb8f -r 4966079d474b test-data/edgren_tp.txt --- a/test-data/edgren_tp.txt Mon Oct 12 04:17:07 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,28 +0,0 @@ -FusionID all.UniqueCuttingPositionCount all.SeedCount all.RescuedCount Strand Chromosome1 Position1 Chromosome2 Position2 KnownGene1 KnownTranscript1 KnownExonNumber1 KnownTranscriptStrand1 KnownGene2 KnownTranscript2 KnownExonNumber2 KnownTranscriptStrand2 FusionJunctionSequence SplicePattern FusionGene FrameShift -Edgren_ACACA_STAC2 -- chr17 35604416 chr17 37374457 -Edgren_ANKHD1_PCDH1 +- chr5 139855281 chr5 141245875 -Edgren_BSG_NFIX ++ chr19 577395 chr19 13158016 -Edgren_CCDC85C_SETD3 -- chr14 100023983 chr14 99905650 -Edgren_CPNE1_PI3 -+ chr20 34233416 chr20 43804351 -Edgren_CSE1L_ENSG00000236127 ++ chr20 47688169 chr20 47951036 -Edgren_CYTH1_EIF3H -- chr17 76724255 chr8 117716767 -Edgren_DHX35_ITCH ++ chr20 37629654 chr20 33025120 -Edgren_DIDO1_KIAA0406 -- chr20 61539197 chr20 36636628 -Edgren_GLB1_CMTM7 -+ chr3 33088411 chr3 32478861 -Edgren_LAMP1_MCF2L2 +- chr13 113964772 chr3 183021199 -Edgren_NFS1_PREX1 -- chr20 34271629 chr20 47342605 -Edgren_NOTCH1_NUP214 -+ chr9 139414605 chr9 134055503 -Edgren_PPP1R12A_SEPT10 -- chr12 80248292 chr2 110336171 -Edgren_RAB22A_MYO9B ++ chr20 56913658 chr19 17255969 -Edgren_RARA_PKIA ++ chr17 38489269 chr8 79472938 -Edgren_RPS6KB1_SNF8 +- chr17 57999186 chr17 47014579 -Edgren_SKA2_MYO19 -- chr17 57209971 chr17 34875381 -Edgren_STARD3_DOK5 ++ chr17 37806528 chr20 53179923 -Edgren_SUMF1_LRRFIP2 -- chr3 4125732 chr3 37159649 -Edgren_TATDN1_GSDMB -- chr8 125526213 chr17 38068478 -Edgren_VAPB_IKZF3 +- chr20 56995168 chr17 37970820 -Edgren_WDR67_ZNF704 +- chr8 124096521 chr8 81733797 -Edgren_ZMYND8_CEP250 -+ chr20 45911713 chr20 34071395 -Edgren_BCAS4_BCAS3 ++ chr20 49452573 chr17 59112507 -Edgren_ARFGEF2_SULF2 +- chr20 47595829 chr20 46350226 -Edgren_RPS6KB1_TMEM49 ++ chr17 57999186 chr17 57851408 |
| b |
| diff -r 86526900cb8f -r 4966079d474b test-data/edgren_true_positives.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/edgren_true_positives.txt Tue Oct 20 10:12:08 2015 -0400 |
| b |
| @@ -0,0 +1,28 @@ +FusionID all.UniqueCuttingPositionCount all.SeedCount all.RescuedCount Strand Chromosome1 Position1 Chromosome2 Position2 KnownGene1 KnownTranscript1 KnownExonNumber1 KnownTranscriptStrand1 KnownGene2 KnownTranscript2 KnownExonNumber2 KnownTranscriptStrand2 FusionJunctionSequence SplicePattern FusionGene FrameShift +Edgren_ACACA_STAC2 -- chr17 35604416 chr17 37374457 +Edgren_ANKHD1_PCDH1 +- chr5 139855281 chr5 141245875 +Edgren_BSG_NFIX ++ chr19 577395 chr19 13158016 +Edgren_CCDC85C_SETD3 -- chr14 100023983 chr14 99905650 +Edgren_CPNE1_PI3 -+ chr20 34233416 chr20 43804351 +Edgren_CSE1L_ENSG00000236127 ++ chr20 47688169 chr20 47951036 +Edgren_CYTH1_EIF3H -- chr17 76724255 chr8 117716767 +Edgren_DHX35_ITCH ++ chr20 37629654 chr20 33025120 +Edgren_DIDO1_KIAA0406 -- chr20 61539197 chr20 36636628 +Edgren_GLB1_CMTM7 -+ chr3 33088411 chr3 32478861 +Edgren_LAMP1_MCF2L2 +- chr13 113964772 chr3 183021199 +Edgren_NFS1_PREX1 -- chr20 34271629 chr20 47342605 +Edgren_NOTCH1_NUP214 -+ chr9 139414605 chr9 134055503 +Edgren_PPP1R12A_SEPT10 -- chr12 80248292 chr2 110336171 +Edgren_RAB22A_MYO9B ++ chr20 56913658 chr19 17255969 +Edgren_RARA_PKIA ++ chr17 38489269 chr8 79472938 +Edgren_RPS6KB1_SNF8 +- chr17 57999186 chr17 47014579 +Edgren_SKA2_MYO19 -- chr17 57209971 chr17 34875381 +Edgren_STARD3_DOK5 ++ chr17 37806528 chr20 53179923 +Edgren_SUMF1_LRRFIP2 -- chr3 4125732 chr3 37159649 +Edgren_TATDN1_GSDMB -- chr8 125526213 chr17 38068478 +Edgren_VAPB_IKZF3 +- chr20 56995168 chr17 37970820 +Edgren_WDR67_ZNF704 +- chr8 124096521 chr8 81733797 +Edgren_ZMYND8_CEP250 -+ chr20 45911713 chr20 34071395 +Edgren_BCAS4_BCAS3 ++ chr20 49452573 chr17 59112507 +Edgren_ARFGEF2_SULF2 +- chr20 47595829 chr20 46350226 +Edgren_RPS6KB1_TMEM49 ++ chr17 57999186 chr17 57851408 |
| b |
| diff -r 86526900cb8f -r 4966079d474b test-data/fusion-map.txt --- a/test-data/fusion-map.txt Mon Oct 12 04:17:07 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,70 +0,0 @@ -FusionID all.UniqueCuttingPositionCount all.SeedCount all.RescuedCount Strand Chromosome1 Position1 Chromosome2 Position2 KnownGene1 KnownTranscript1 KnownExonNumber1 KnownTranscriptStrand1 KnownGene2 KnownTranscript2 KnownExonNumber2 KnownTranscriptStrand2 FusionJunctionSequence SplicePattern FusionGene FrameShift -FUS_26799002_2222102817(--) -- 1 26799003 12 56527458 -FUS_27652879_2794310094(-+) -+ 1 27652880 17 79477135 -FUS_27677421_1106763499(--) -- 1 27677422 6 44221420 -FUS_52818775_491865792(++) ++ 1 52818776 2 242615169 -FUS_109756747_2844503161(++) ++ 1 109756748 18 48474938 -FUS_162336993_162351680(++) ++ 1 162336994 1 162351681 -FUS_204162041_204183009(++) ++ 1 204162042 1 204183010 -FUS_260933576_260947203(++) ++ 2 11682953 2 11696580 -FUS_317729880_2671195661(--) -- 2 68479257 16 46717518 -FUS_431341885_488240973(++) ++ 2 182091262 2 238990350 -FUS_468401284_468407812(++) ++ 2 219150661 2 219157189 -FUS_481827274_1095808311(-+) -+ 2 232576651 6 33266232 -FUS_535356398_535379077(++) ++ 3 42906351 3 42929030 -FUS_564945819_2208207316(++) ++ 3 72495772 12 42631957 -FUS_622049449_622062384(++) ++ 3 129599402 3 129612337 -FUS_641333884_641344084(++) ++ 3 148883837 3 148894037 -FUS_642753372_2640297172(++) ++ 3 150303325 16 15819029 -FUS_650628845_650704928(++) ++ 3 158178798 3 158254881 -FUS_688959544_1831692166(-+) -+ 3 196509497 X 151302279 -FUS_690560141_1289758805(-+) -+ 4 87630 7 56101654 -FUS_844223288_2907008396(--) -- 4 153750777 19 32902925 -FUS_950027061_1496638003(+-) +- 5 68400246 8 103842164 -FUS_1021452375_1022860816(+-) +- 5 139825560 5 141234001 -FUS_1093233534_2218149952(-+) -+ 6 30691455 12 52574593 -FUS_1096426187_3038889284(--) -- 6 33884108 21 42629253 -FUS_1136770263_2286212600(++) ++ 6 74228184 12 120637241 -FUS_1136770312_2883379228(-+) -+ 6 74228233 19 9273757 -FUS_1136770987_1980946407(+-) +- 6 74228908 10 85912360 -FUS_1233435659_2723113969(--) -- 6 170893580 17 8281010 -FUS_1309258884_2298001199(++) ++ 7 75601733 12 132425840 -FUS_1325089044_1999508485(+-) +- 7 91431893 10 104474438 -FUS_1472280885_2753298497(--) -- 8 79485046 17 38465538 -FUS_1518347105_2752895197(--) -- 8 125551266 17 38062238 -FUS_1518347105_2752895483(--) -- 8 125551266 17 38062524 -FUS_1518347105_2752896199(--) -- 8 125551266 17 38063240 -FUS_1518347105_2752899136(--) -- 8 125551266 17 38066177 -FUS_1536899619_2586923912(++) ++ 8 144103780 15 64977161 -FUS_1625744006_2750144109(-+) -+ 9 86584135 17 35311150 -FUS_1654638612_1662879517(--) -- 9 115478741 9 123719646 -FUS_1669121216_1669132845(++) ++ 9 129961345 9 129972974 -FUS_1670521420_3062528544(++) ++ 9 131361549 22 18138593 -FUS_1799397243_2485431458(+-) +- X 119007356 14 70834275 -FUS_1900761185_1900785540(++) ++ 10 5727138 10 5751493 -FUS_1908751091_1908769529(++) ++ 10 13717044 10 13735482 -FUS_2018880080_2591692014(--) -- 10 123846033 15 69745263 -FUS_2041405408_2909026952(-+) -+ 11 10836577 19 34921481 -FUS_2088954897_2955778536(-+) -+ 11 58386066 20 22544041 -FUS_2123194535_2562850433(++) ++ 11 92625704 15 40903682 -FUS_2172555288_2751715570(--) -- 12 6979929 17 36882611 -FUS_2217352725_2217359993(++) ++ 12 51777366 12 51784634 -FUS_2220354100_2220360378(++) ++ 12 54778741 12 54785019 -FUS_2345398656_2640249892(-+) -+ 13 45971393 16 15771749 -FUS_2412983948_2413096340(++) ++ 13 113556685 13 113669077 -FUS_2439284820_2439298041(++) ++ 14 24687637 14 24700858 -FUS_2451742910_2913912193(-+) -+ 14 37145727 19 39806722 -FUS_2489891478_2508003573(+-) +- 14 75294295 14 93406390 -FUS_2749696310_2772065451(++) ++ 17 34863351 17 57232492 -FUS_2749696722_2772065451(++) ++ 17 34863763 17 57232492 -FUS_2750312412_2752207385(--) -- 17 35479453 17 37374426 -FUS_2752428377_2763381348(-+) -+ 17 37595418 17 48548389 -FUS_2758316408_2758339948(++) ++ 17 43483449 17 43506989 -FUS_2774302297_2774962857(-+) -+ 17 59469338 17 60129898 -FUS_2780655412_2781079288(++) ++ 17 65822453 17 66246329 -FUS_2788733755_2966381512(-+) -+ 17 73900796 20 33147017 -FUS_2792979986_2792985266(++) ++ 17 78147027 17 78152307 -FUS_2893652499_2893681620(++) ++ 19 19547028 19 19576149 -FUS_2914960146_2914976931(++) ++ 19 40854675 19 40871460 -FUS_2979600181_2980773042(+-) +- 20 46365686 20 47538547 -FUS_3006176578_3036925768(++) ++ 21 9916547 21 40665737 |
| b |
| diff -r 86526900cb8f -r 4966079d474b test-data/output_test_1.txt --- a/test-data/output_test_1.txt Mon Oct 12 04:17:07 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,11394 +0,0 @@\n-Left-genes\tRight-genes\tchimerascan.txt\tdefuse.txt\tfusion-map.txt\tedgren_tp.txt\n-NR_037945:STX16\tRAE1\tTRUE\tFALSE\tFALSE\tFALSE\n-TPD52L2\tDNAJC5\tTRUE\tFALSE\tFALSE\tFALSE\n-C20orf112\tC20orf112\tTRUE\tFALSE\tFALSE\tFALSE\n-PREX1\tCPNE1:NM_001198863:NR_037188\tTRUE\tFALSE\tFALSE\tFALSE\n-AP5S1\tMAVS:NR_037921\tTRUE\tFALSE\tFALSE\tFALSE\n-BCAS4\tNM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tTRUE\tFALSE\tFALSE\tFALSE\n-NR_036633:VAPB\tAPCDD1L-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n-CSNK2A1\tFAM110A:NM_001289145:NM_001289146:NM_001289147\tTRUE\tFALSE\tFALSE\tFALSE\n-NR_109859\tAP5S1\tTRUE\tFALSE\tFALSE\tFALSE\n-FKBP1A:NR_037661:SDCBP2-AS1\tLOC284801\tTRUE\tFALSE\tFALSE\tFALSE\n-ADNP:NM_001282531\tRSPO4\tTRUE\tFALSE\tFALSE\tFALSE\n-LAMA5\tLOC284801\tTRUE\tFALSE\tFALSE\tFALSE\n-OSER1-AS1\tOSER1-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n-ZFP64\tNM_001281507:PHACTR3\tTRUE\tFALSE\tFALSE\tFALSE\n-ARFGAP1:NM_001281482:NM_001281483:NM_001281484:NR_104022:NR_104023\tIFT52:NM_001303458:NM_001303459\tTRUE\tFALSE\tFALSE\tFALSE\n-RAD21L1\tHMGN1\tTRUE\tFALSE\tFALSE\tFALSE\n-VPS16\tPCP4\tTRUE\tFALSE\tFALSE\tFALSE\n-ATP5O\tKIF16B\tTRUE\tFALSE\tFALSE\tFALSE\n-PCNT\tADNP:NM_001282531:NM_001282532\tTRUE\tFALSE\tFALSE\tFALSE\n-SLC2A4RG\tBRWD1\tTRUE\tFALSE\tFALSE\tFALSE\n-LOC400927:NM_001289912\tNR_110051:ZNF217\tTRUE\tFALSE\tFALSE\tFALSE\n-LOC284801\tTUBGCP6\tTRUE\tFALSE\tFALSE\tFALSE\n-ELMO2\tJOSD1\tTRUE\tFALSE\tFALSE\tFALSE\n-RTCB\tSTMN3\tTRUE\tFALSE\tFALSE\tFALSE\n-HIRA\tNM_001282933:NM_001282935:NR_104259:NR_110623:ZNF341\tTRUE\tFALSE\tFALSE\tFALSE\n-DENND6B\tMTRNR2L3:RAE1\tTRUE\tFALSE\tFALSE\tFALSE\n-EWSR1\tNM_001278649:OSBPL2\tTRUE\tFALSE\tFALSE\tFALSE\n-CTSZ\tEP300\tTRUE\tFALSE\tFALSE\tFALSE\n-DYNLRB1:NM_001281727:NM_001281728:NM_001281729:NM_177953:NR_104032\tLARGE\tTRUE\tFALSE\tFALSE\tFALSE\n-ENTPD6\tNM_001287387:SLC25A1\tTRUE\tFALSE\tFALSE\tFALSE\n-SHANK3\tLAMA5\tTRUE\tFALSE\tFALSE\tFALSE\n-ATRN\tNM_001284277:NM_001284278:PITPNB\tTRUE\tFALSE\tFALSE\tFALSE\n-SULF2\tPRICKLE2:PRICKLE2-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n-VPRBP\tNSFL1C\tTRUE\tFALSE\tFALSE\tFALSE\n-MFN1\tMAPRE1\tTRUE\tFALSE\tFALSE\tFALSE\n-PCMTD2\tPAK2\tTRUE\tFALSE\tFALSE\tFALSE\n-CEP63\tDNMT3B\tTRUE\tFALSE\tFALSE\tFALSE\n-RRP9\tCSE1L\tTRUE\tFALSE\tFALSE\tFALSE\n-CP:NR_046371\tCHD6\tTRUE\tFALSE\tFALSE\tFALSE\n-TMEM189:TMEM189-UBE2V1\tGLT8D1:GNL3:NM_001278280:NM_001278281\tTRUE\tFALSE\tFALSE\tFALSE\n-ST6GAL1\tNM_001278649:OSBPL2\tTRUE\tFALSE\tFALSE\tFALSE\n-OXSM\tMAP1LC3A\tTRUE\tFALSE\tFALSE\tFALSE\n-PHF20\tCDC25A\tTRUE\tFALSE\tFALSE\tFALSE\n-GOLIM4:NM_001308155\tGNAS:NM_001309840:NM_001309861\tTRUE\tFALSE\tFALSE\tFALSE\n-SLC25A38\tNM_001301188:NM_001301190:NM_001301193:NM_001301196:NM_001301201:TRIB3\tTRUE\tFALSE\tFALSE\tFALSE\n-ZNFX1\tIQCG\tTRUE\tFALSE\tFALSE\tFALSE\n-SNRK\tLAMA5\tTRUE\tFALSE\tFALSE\tFALSE\n-EYA2\tNR_103507:SLC6A6\tTRUE\tFALSE\tFALSE\tFALSE\n-KIF16B\tCACNA1D\tTRUE\tFALSE\tFALSE\tFALSE\n-SLC9A8\tTNIK\tTRUE\tFALSE\tFALSE\tFALSE\n-NCOA5\tMGLL\tTRUE\tFALSE\tFALSE\tFALSE\n-POLQ\tTGM2\tTRUE\tFALSE\tFALSE\tFALSE\n-FBLN2\tPOFUT1\tTRUE\tFALSE\tFALSE\tFALSE\n-FKBP1A:NR_037661\tATP11B\tTRUE\tFALSE\tFALSE\tFALSE\n-NRSN2\tNM_001195483:SLC12A8\tTRUE\tFALSE\tFALSE\tFALSE\n-FNDC3B\tSOGA1\tTRUE\tFALSE\tFALSE\tFALSE\n-CPNE1:NM_001198863:NR_037188:RBM12\tCHRD:NM_001304472:NM_001304473:NM_001304474:NR_130747\tTRUE\tFALSE\tFALSE\tFALSE\n-C3orf18:HEMK1\tPCNA:PCNA-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n-RYBP\tLAMA5\tTRUE\tFALSE\tFALSE\tFALSE\n-USP19\tGNAS:NM_001309840:NM_001309861\tTRUE\tFALSE\tFALSE\tFALSE\n-SNRPB\tSEC61A1\tTRUE\tFALSE\tFALSE\tFALSE\n-MAVS:NR_037921\tKAT2B\tTRUE\tFALSE\tFALSE\tFALSE\n-GGT7\tCMC1\tTRUE\tFALSE\tFALSE\tFALSE\n-RPS21\tQRICH1\tTRUE\tFALSE\tFALSE\tFALSE\n-KIAA0226\tNM_001278649:OSBPL2\tTRUE\tFALSE\tFALSE\tFALSE\n-CDC25B:NM_001287516:NM_001287517:NM_001287518:NM_001287519:NM_001287520:NM_001287522:NM_001287524\tDNAJC19:NR_033721\tTRUE\tFALSE\tFALSE\tFALSE\n-C5orf34\tGNAS:NM_001309840:NM_001309861\tTRUE\tFALSE\tFALSE\tFALSE\n-DROSHA\tDLGAP4:NR_109939\tTRUE\tFALSE\tFALSE\tFALSE\n-SQSTM1\tEIF6\tTRUE\tFALSE\tFALSE\tFALSE\n-KDM3B\tDYNLRB1:NM_001281727:NM_001281728:NM_001281729:NM_177953:NR_104032\tTRUE\tFALSE\tFALSE\tFALSE\n-CYFIP2:NM_001291721:NM_001291722\tNR_037945:STX16\tTRUE\tFALSE\tFALSE\tFALSE\n-NPR3\tCPNE1:NM_001198863:NR_037188\tTRUE'..b'\tTRUE\tFALSE\tFALSE\n-SMAD2\tRPS23\tFALSE\tTRUE\tFALSE\tFALSE\n-NR_120540\tUBA2\tFALSE\tFALSE\tTRUE\tFALSE\n-NR_024091:ZFP91:ZFP91-CNTF\tLINC00261\tFALSE\tFALSE\tTRUE\tFALSE\n-FAT3\tCASC5\tFALSE\tFALSE\tTRUE\tFALSE\n-FRMD4A\tFRMD4A\tFALSE\tFALSE\tTRUE\tFALSE\n-NM_001291876:NM_001291877:TACC2\tRPLP1\tFALSE\tFALSE\tTRUE\tFALSE\n-EEF1A1\tGHITM\tFALSE\tFALSE\tTRUE\tFALSE\n-NM_001286806:NM_001286807:SLC25A30\tNDE1\tFALSE\tFALSE\tTRUE\tFALSE\n-RYBP\tYAF2\tFALSE\tFALSE\tTRUE\tFALSE\n-GALNT6\tGALNT6\tFALSE\tFALSE\tTRUE\tFALSE\n-NM_001290002:NM_001290004:NR_120486:NR_120487:ZNF385A\tNR_120486:NR_120487:ZNF385A\tFALSE\tFALSE\tTRUE\tFALSE\n-POR\tPUS1\tFALSE\tFALSE\tTRUE\tFALSE\n-NM_001159287:TPI1\tMLLT6\tFALSE\tFALSE\tTRUE\tFALSE\n-NM_001293212:NM_001293213:NM_001293214:NM_001293215:NM_001293216:NR_120608:TUBB\tKRT80\tFALSE\tFALSE\tTRUE\tFALSE\n-EEF1A1\tRPLP0\tFALSE\tFALSE\tTRUE\tFALSE\n-LY6E\tZNF609\tFALSE\tFALSE\tTRUE\tFALSE\n-TEKT4P2\tBRWD1\tFALSE\tFALSE\tTRUE\tFALSE\n-HNRNPK\tAATF\tFALSE\tFALSE\tTRUE\tFALSE\n-PKIA\tRARA\tFALSE\tFALSE\tTRUE\tFALSE\n-MRPL38\tMAP1LC3A\tFALSE\tFALSE\tTRUE\tFALSE\n-MYO19\tSKA2\tFALSE\tFALSE\tTRUE\tFALSE\n-ARHGAP27:NM_001282290\tARHGAP27:NM_001282290\tFALSE\tFALSE\tTRUE\tFALSE\n-BCAS3\tMED13\tFALSE\tFALSE\tTRUE\tFALSE\n-BPTF\tAMZ2:NM_001289054:NM_001289056\tFALSE\tFALSE\tTRUE\tFALSE\n-CARD14\tCARD14\tFALSE\tFALSE\tTRUE\tFALSE\n-PDCD2\tRPL26\tFALSE\tFALSE\tTRUE\tFALSE\n-EIF2A\tMYH11:NDE1\tFALSE\tFALSE\tTRUE\tFALSE\n-GATAD2A\tGATAD2A:NM_001300946\tFALSE\tFALSE\tTRUE\tFALSE\n-PLD3\tNM_001291311:PLD3\tFALSE\tFALSE\tTRUE\tFALSE\n-ARFIP1:NM_001287431:NM_001287432:NM_001287433\tDPY19L3\tFALSE\tFALSE\tTRUE\tFALSE\n-EEF1A1\tZNF317\tFALSE\tFALSE\tTRUE\tFALSE\n-NR_031672:SPTAN1\tBCL2L13:NR_073068:NR_073069\tFALSE\tFALSE\tTRUE\tFALSE\n-HMGN2\tESYT1\tFALSE\tFALSE\tTRUE\tFALSE\n-LOC644961:TMEM222\tACTG1:NR_037688\tFALSE\tFALSE\tTRUE\tFALSE\n-SARS\tME2\tFALSE\tFALSE\tTRUE\tFALSE\n-KISS1\tGOLT1A\tFALSE\tFALSE\tTRUE\tFALSE\n-CC2D1B\tDTYMK\tFALSE\tFALSE\tTRUE\tFALSE\n-SYTL1\tHSP90AB1\tFALSE\tFALSE\tTRUE\tFALSE\n-PAK2\tMAGEA10:MAGEA10-MAGEA5\tFALSE\tFALSE\tTRUE\tFALSE\n-TMCC1\tTMCC1\tFALSE\tFALSE\tTRUE\tFALSE\n-HPS3:NM_001308258:NR_046371\tCP:NR_046371\tFALSE\tFALSE\tTRUE\tFALSE\n-RSRC1\tRSRC1\tFALSE\tFALSE\tTRUE\tFALSE\n-GREB1\tGREB1\tFALSE\tFALSE\tTRUE\tFALSE\n-NR_130784\tNR_037904:SCLY\tFALSE\tFALSE\tTRUE\tFALSE\n-PNKD:TMBIM1\tPNKD:TMBIM1\tFALSE\tFALSE\tTRUE\tFALSE\n-PTMA\tRGL2\tFALSE\tFALSE\tTRUE\tFALSE\n-SLC30A5\tAZIN1:NM_001301668\tFALSE\tFALSE\tTRUE\tFALSE\n-NM_001286052:NM_001286053:NM_001286054:NM_001289931:NR_110527:ZNF595:ZNF718\tPSPH\tFALSE\tFALSE\tTRUE\tFALSE\n-RALGPS1\tRALGPS1\tFALSE\tFALSE\tTRUE\tFALSE\n-SULF2\tARFGEF2\tFALSE\tFALSE\tTRUE\tFALSE\n-NDUFA1\tSYNJ2BP:SYNJ2BP-COX16\tFALSE\tFALSE\tTRUE\tFALSE\n-NEDD8:NEDD8-MDP1\tNEDD8:NEDD8-MDP1\tFALSE\tFALSE\tTRUE\tFALSE\n-YLPM1\tITPK1\tFALSE\tFALSE\tTRUE\tFALSE\n-LAMP1\tMCF2L2\tFALSE\tFALSE\tFALSE\tTRUE\n-NFS1\tPREX1\tFALSE\tFALSE\tFALSE\tTRUE\n-STARD3\tDOK5:NM_177959\tFALSE\tFALSE\tFALSE\tTRUE\n-NM_001272060:RPS6KB1\tVMP1\tFALSE\tFALSE\tFALSE\tTRUE\n-NOS1AP\tC1orf226\tTRUE\tFALSE\tTRUE\tFALSE\n-INIP\tC5\tTRUE\tFALSE\tTRUE\tFALSE\n-FAM208B\tFAM208B\tTRUE\tFALSE\tTRUE\tFALSE\n-MED1\tACSF2:NM_001288968:NM_001288969:NM_001288970:NM_001288971:NM_001288972:NR_110232\tTRUE\tFALSE\tTRUE\tFALSE\n-PPP3R1\tVPS35\tTRUE\tFALSE\tTRUE\tFALSE\n-PPP1R12A\tSEPT10\tTRUE\tFALSE\tFALSE\tTRUE\n-NM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tCEP250\tTRUE\tFALSE\tFALSE\tTRUE\n-ARFGEF2\tSULF2\tTRUE\tFALSE\tFALSE\tTRUE\n-DIDO1\tNM_001303457:TTI1\tTRUE\tFALSE\tFALSE\tTRUE\n-DHX35\tITCH\tTRUE\tFALSE\tFALSE\tTRUE\n-CPNE1:NM_001198863:NR_037188\tPI3\tTRUE\tFALSE\tFALSE\tTRUE\n-CCDC85C\tSETD3\tTRUE\tFALSE\tFALSE\tTRUE\n-CYTH1\tEIF3H\tTRUE\tFALSE\tFALSE\tTRUE\n-RARA\tPKIA\tTRUE\tFALSE\tFALSE\tTRUE\n-BCAS4\tBCAS3\tTRUE\tFALSE\tFALSE\tTRUE\n-NR_036633:VAPB\tIKZF3:NM_001284514:NM_001284515\tTRUE\tFALSE\tFALSE\tTRUE\n-NM_001272060:RPS6KB1\tSNF8\tTRUE\tFALSE\tFALSE\tTRUE\n-SKA2\tMYO19\tTRUE\tFALSE\tFALSE\tTRUE\n-BSG\tNFIX\tTRUE\tFALSE\tFALSE\tTRUE\n-RAB22A\tMYO9B\tTRUE\tFALSE\tFALSE\tTRUE\n-GLB1\tCMTM7\tTRUE\tFALSE\tFALSE\tTRUE\n-NOTCH1\tNUP214\tTRUE\tFALSE\tFALSE\tTRUE\n-WDR67\tZNF704\tTRUE\tFALSE\tFALSE\tTRUE\n-ANKHD1:ANKHD1-EIF4EBP3\tPCDH1\tFALSE\tFALSE\tTRUE\tTRUE\n-TATDN1\tGSDMB\tTRUE\tFALSE\tTRUE\tTRUE\n-ACACA\tSTAC2\tTRUE\tFALSE\tTRUE\tTRUE\n' |
| b |
| diff -r 86526900cb8f -r 4966079d474b test-data/output_test_2.txt --- a/test-data/output_test_2.txt Mon Oct 12 04:17:07 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,11248 +0,0 @@\n-Left-genes\tRight-genes\tchimerascan.txt\tdefuse.txt\tfusion-map.txt\tedgren_tp.txt\n-C20orf112\tC20orf112\tTRUE\tFALSE\tFALSE\tFALSE\n-AP5S1\tMAVS:NR_037921\tTRUE\tFALSE\tFALSE\tFALSE\n-NM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tBCAS4\tTRUE\tFALSE\tFALSE\tFALSE\n-NR_036633:VAPB\tAPCDD1L-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n-CSNK2A1\tFAM110A:NM_001289145:NM_001289146:NM_001289147\tTRUE\tFALSE\tFALSE\tFALSE\n-NR_109859\tAP5S1\tTRUE\tFALSE\tFALSE\tFALSE\n-FKBP1A:NR_037661:SDCBP2-AS1\tLOC284801\tTRUE\tFALSE\tFALSE\tFALSE\n-RSPO4\tADNP:NM_001282531\tTRUE\tFALSE\tFALSE\tFALSE\n-LOC284801\tLAMA5\tTRUE\tFALSE\tFALSE\tFALSE\n-OSER1-AS1\tOSER1-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n-ZFP64\tNM_001281507:PHACTR3\tTRUE\tFALSE\tFALSE\tFALSE\n-IFT52:NM_001303458:NM_001303459\tARFGAP1:NM_001281482:NM_001281483:NM_001281484:NR_104022:NR_104023\tTRUE\tFALSE\tFALSE\tFALSE\n-RAD21L1\tHMGN1\tTRUE\tFALSE\tFALSE\tFALSE\n-VPS16\tPCP4\tTRUE\tFALSE\tFALSE\tFALSE\n-KIF16B\tATP5O\tTRUE\tFALSE\tFALSE\tFALSE\n-ADNP:NM_001282531:NM_001282532\tPCNT\tTRUE\tFALSE\tFALSE\tFALSE\n-SLC2A4RG\tBRWD1\tTRUE\tFALSE\tFALSE\tFALSE\n-NR_110051:ZNF217\tLOC400927:NM_001289912\tTRUE\tFALSE\tFALSE\tFALSE\n-LOC284801\tTUBGCP6\tTRUE\tFALSE\tFALSE\tFALSE\n-ELMO2\tJOSD1\tTRUE\tFALSE\tFALSE\tFALSE\n-STMN3\tRTCB\tTRUE\tFALSE\tFALSE\tFALSE\n-NM_001282933:NM_001282935:NR_104259:NR_110623:ZNF341\tHIRA\tTRUE\tFALSE\tFALSE\tFALSE\n-MTRNR2L3:RAE1\tDENND6B\tTRUE\tFALSE\tFALSE\tFALSE\n-NM_001278649:OSBPL2\tEWSR1\tTRUE\tFALSE\tFALSE\tFALSE\n-CTSZ\tEP300\tTRUE\tFALSE\tFALSE\tFALSE\n-DYNLRB1:NM_001281727:NM_001281728:NM_001281729:NM_177953:NR_104032\tLARGE\tTRUE\tFALSE\tFALSE\tFALSE\n-ENTPD6\tNM_001287387:SLC25A1\tTRUE\tFALSE\tFALSE\tFALSE\n-LAMA5\tSHANK3\tTRUE\tFALSE\tFALSE\tFALSE\n-ATRN\tNM_001284277:NM_001284278:PITPNB\tTRUE\tFALSE\tFALSE\tFALSE\n-SULF2\tPRICKLE2:PRICKLE2-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n-NSFL1C\tVPRBP\tTRUE\tFALSE\tFALSE\tFALSE\n-MAPRE1\tMFN1\tTRUE\tFALSE\tFALSE\tFALSE\n-PCMTD2\tPAK2\tTRUE\tFALSE\tFALSE\tFALSE\n-DNMT3B\tCEP63\tTRUE\tFALSE\tFALSE\tFALSE\n-CSE1L\tRRP9\tTRUE\tFALSE\tFALSE\tFALSE\n-CHD6\tCP:NR_046371\tTRUE\tFALSE\tFALSE\tFALSE\n-TMEM189:TMEM189-UBE2V1\tGLT8D1:GNL3:NM_001278280:NM_001278281\tTRUE\tFALSE\tFALSE\tFALSE\n-NM_001278649:OSBPL2\tST6GAL1\tTRUE\tFALSE\tFALSE\tFALSE\n-MAP1LC3A\tOXSM\tTRUE\tFALSE\tFALSE\tFALSE\n-PHF20\tCDC25A\tTRUE\tFALSE\tFALSE\tFALSE\n-GNAS:NM_001309840:NM_001309861\tGOLIM4:NM_001308155\tTRUE\tFALSE\tFALSE\tFALSE\n-NM_001301188:NM_001301190:NM_001301193:NM_001301196:NM_001301201:TRIB3\tSLC25A38\tTRUE\tFALSE\tFALSE\tFALSE\n-ZNFX1\tIQCG\tTRUE\tFALSE\tFALSE\tFALSE\n-LAMA5\tSNRK\tTRUE\tFALSE\tFALSE\tFALSE\n-EYA2\tNR_103507:SLC6A6\tTRUE\tFALSE\tFALSE\tFALSE\n-KIF16B\tCACNA1D\tTRUE\tFALSE\tFALSE\tFALSE\n-SLC9A8\tTNIK\tTRUE\tFALSE\tFALSE\tFALSE\n-NCOA5\tMGLL\tTRUE\tFALSE\tFALSE\tFALSE\n-TGM2\tPOLQ\tTRUE\tFALSE\tFALSE\tFALSE\n-POFUT1\tFBLN2\tTRUE\tFALSE\tFALSE\tFALSE\n-FKBP1A:NR_037661\tATP11B\tTRUE\tFALSE\tFALSE\tFALSE\n-NRSN2\tNM_001195483:SLC12A8\tTRUE\tFALSE\tFALSE\tFALSE\n-SOGA1\tFNDC3B\tTRUE\tFALSE\tFALSE\tFALSE\n-CPNE1:NM_001198863:NR_037188:RBM12\tCHRD:NM_001304472:NM_001304473:NM_001304474:NR_130747\tTRUE\tFALSE\tFALSE\tFALSE\n-PCNA:PCNA-AS1\tC3orf18:HEMK1\tTRUE\tFALSE\tFALSE\tFALSE\n-LAMA5\tRYBP\tTRUE\tFALSE\tFALSE\tFALSE\n-GNAS:NM_001309840:NM_001309861\tUSP19\tTRUE\tFALSE\tFALSE\tFALSE\n-SNRPB\tSEC61A1\tTRUE\tFALSE\tFALSE\tFALSE\n-MAVS:NR_037921\tKAT2B\tTRUE\tFALSE\tFALSE\tFALSE\n-GGT7\tCMC1\tTRUE\tFALSE\tFALSE\tFALSE\n-RPS21\tQRICH1\tTRUE\tFALSE\tFALSE\tFALSE\n-NM_001278649:OSBPL2\tKIAA0226\tTRUE\tFALSE\tFALSE\tFALSE\n-CDC25B:NM_001287516:NM_001287517:NM_001287518:NM_001287519:NM_001287520:NM_001287522:NM_001287524\tDNAJC19:NR_033721\tTRUE\tFALSE\tFALSE\tFALSE\n-GNAS:NM_001309840:NM_001309861\tC5orf34\tTRUE\tFALSE\tFALSE\tFALSE\n-DLGAP4:NR_109939\tDROSHA\tTRUE\tFALSE\tFALSE\tFALSE\n-EIF6\tSQSTM1\tTRUE\tFALSE\tFALSE\tFALSE\n-DYNLRB1:NM_001281727:NM_001281728:NM_001281729:NM_177953:NR_104032\tKDM3B\tTRUE\tFALSE\tFALSE\tFALSE\n-NR_037945:STX16\tCYFIP2:NM_001291721:NM_001291722\tTRUE\tFALSE\tFALSE\tFALSE\n-CPNE1:NM_001198863:NR_037188\tNPR3\tTRUE\tFALSE\tFALSE\tFALSE\n-ACSS2\tHMGCR\tTRUE\tFALSE\tFALSE\tFALSE\n-CTSZ\tCCT5:NM_001306153:NM_001306154:NM_001306155:NM_001306156\tTRUE\tFALSE\tFALSE\tFALSE\n-L'..b'0004:NR_120486:NR_120487:ZNF385A\tNR_120486:NR_120487:ZNF385A\tFALSE\tFALSE\tTRUE\tFALSE\n-PUS1\tPOR\tFALSE\tFALSE\tTRUE\tFALSE\n-NM_001159287:TPI1\tMLLT6\tFALSE\tFALSE\tTRUE\tFALSE\n-KRT80\tNM_001293212:NM_001293213:NM_001293214:NM_001293215:NM_001293216:NR_120608:TUBB\tFALSE\tFALSE\tTRUE\tFALSE\n-RPLP0\tEEF1A1\tFALSE\tFALSE\tTRUE\tFALSE\n-ZNF609\tLY6E\tFALSE\tFALSE\tTRUE\tFALSE\n-AATF\tHNRNPK\tFALSE\tFALSE\tTRUE\tFALSE\n-MRPL38\tMAP1LC3A\tFALSE\tFALSE\tTRUE\tFALSE\n-BPTF\tAMZ2:NM_001289054:NM_001289056\tFALSE\tFALSE\tTRUE\tFALSE\n-CARD14\tCARD14\tFALSE\tFALSE\tTRUE\tFALSE\n-RPL26\tPDCD2\tFALSE\tFALSE\tTRUE\tFALSE\n-MYH11:NDE1\tEIF2A\tFALSE\tFALSE\tTRUE\tFALSE\n-GATAD2A\tGATAD2A:NM_001300946\tFALSE\tFALSE\tTRUE\tFALSE\n-PLD3\tNM_001291311:PLD3\tFALSE\tFALSE\tTRUE\tFALSE\n-DPY19L3\tARFIP1:NM_001287431:NM_001287432:NM_001287433\tFALSE\tFALSE\tTRUE\tFALSE\n-ZNF317\tEEF1A1\tFALSE\tFALSE\tTRUE\tFALSE\n-BCL2L13:NR_073068:NR_073069\tNR_031672:SPTAN1\tFALSE\tFALSE\tTRUE\tFALSE\n-LOC644961:TMEM222\tACTG1:NR_037688\tFALSE\tFALSE\tTRUE\tFALSE\n-SARS\tME2\tFALSE\tFALSE\tTRUE\tFALSE\n-SYTL1\tHSP90AB1\tFALSE\tFALSE\tTRUE\tFALSE\n-PAK2\tMAGEA10:MAGEA10-MAGEA5\tFALSE\tFALSE\tTRUE\tFALSE\n-TMCC1\tTMCC1\tFALSE\tFALSE\tTRUE\tFALSE\n-HPS3:NM_001308258:NR_046371\tCP:NR_046371\tFALSE\tFALSE\tTRUE\tFALSE\n-RSRC1\tRSRC1\tFALSE\tFALSE\tTRUE\tFALSE\n-GREB1\tGREB1\tFALSE\tFALSE\tTRUE\tFALSE\n-NR_130784\tNR_037904:SCLY\tFALSE\tFALSE\tTRUE\tFALSE\n-PNKD:TMBIM1\tPNKD:TMBIM1\tFALSE\tFALSE\tTRUE\tFALSE\n-PTMA\tRGL2\tFALSE\tFALSE\tTRUE\tFALSE\n-SLC30A5\tAZIN1:NM_001301668\tFALSE\tFALSE\tTRUE\tFALSE\n-NM_001286052:NM_001286053:NM_001286054:NM_001289931:NR_110527:ZNF595:ZNF718\tPSPH\tFALSE\tFALSE\tTRUE\tFALSE\n-RALGPS1\tRALGPS1\tFALSE\tFALSE\tTRUE\tFALSE\n-SYNJ2BP:SYNJ2BP-COX16\tNDUFA1\tFALSE\tFALSE\tTRUE\tFALSE\n-NEDD8:NEDD8-MDP1\tNEDD8:NEDD8-MDP1\tFALSE\tFALSE\tTRUE\tFALSE\n-YLPM1\tITPK1\tFALSE\tFALSE\tTRUE\tFALSE\n-LAMP1\tMCF2L2\tFALSE\tFALSE\tFALSE\tTRUE\n-NFS1\tPREX1\tFALSE\tFALSE\tFALSE\tTRUE\n-VMP1\tNM_001272060:RPS6KB1\tFALSE\tFALSE\tFALSE\tTRUE\n-FEN1\tFADS2:NM_001281501:NM_001281502\tTRUE\tTRUE\tFALSE\tFALSE\n-MCF2L\tLAMP1\tTRUE\tTRUE\tFALSE\tFALSE\n-GCN1L1\tMSI1\tTRUE\tTRUE\tFALSE\tFALSE\n-TNFRSF1A\tSCNN1A\tTRUE\tTRUE\tFALSE\tFALSE\n-RAE1\tNR_037945:STX16\tTRUE\tTRUE\tFALSE\tFALSE\n-TPD52L2\tDNAJC5\tTRUE\tTRUE\tFALSE\tFALSE\n-CPNE1:NM_001198863:NR_037188\tPREX1\tTRUE\tTRUE\tFALSE\tFALSE\n-SYNRG\tTOB1\tTRUE\tTRUE\tFALSE\tFALSE\n-MED1\tSTXBP4\tTRUE\tTRUE\tFALSE\tFALSE\n-SUMF1\tLRRFIP2:NM_001282691\tTRUE\tTRUE\tFALSE\tFALSE\n-NM_001165931:RRM2\tC2orf48\tTRUE\tTRUE\tFALSE\tFALSE\n-VAMP8\tVAMP5\tTRUE\tTRUE\tFALSE\tFALSE\n-TMEM120A\tSTYXL1\tTRUE\tTRUE\tFALSE\tFALSE\n-NCOA2\tZNF704\tTRUE\tTRUE\tFALSE\tFALSE\n-FAM208B\tFAM208B\tTRUE\tFALSE\tTRUE\tFALSE\n-YAF2\tRYBP\tTRUE\tFALSE\tTRUE\tFALSE\n-ARHGAP27:NM_001282290\tARHGAP27:NM_001282290\tTRUE\tFALSE\tTRUE\tFALSE\n-VPS35\tPPP3R1\tTRUE\tFALSE\tTRUE\tFALSE\n-NOS1AP\tC1orf226\tTRUE\tFALSE\tTRUE\tFALSE\n-KISS1\tGOLT1A\tTRUE\tFALSE\tTRUE\tFALSE\n-CC2D1B\tDTYMK\tTRUE\tFALSE\tTRUE\tFALSE\n-HMGN2\tESYT1\tTRUE\tFALSE\tTRUE\tFALSE\n-INIP\tC5\tTRUE\tFALSE\tTRUE\tFALSE\n-PPP1R12A\tSEPT10\tTRUE\tFALSE\tFALSE\tTRUE\n-ITCH\tDHX35\tTRUE\tFALSE\tFALSE\tTRUE\n-CPNE1:NM_001198863:NR_037188\tPI3\tTRUE\tFALSE\tFALSE\tTRUE\n-SETD3\tCCDC85C\tTRUE\tFALSE\tFALSE\tTRUE\n-ZNF704\tWDR67\tTRUE\tFALSE\tFALSE\tTRUE\n-STARD3\tDOK5:NM_177959\tFALSE\tTRUE\tFALSE\tTRUE\n-TEKT4P2\tBRWD1\tTRUE\tTRUE\tTRUE\tFALSE\n-MED1\tACSF2:NM_001288968:NM_001288969:NM_001288970:NM_001288971:NM_001288972:NR_110232\tTRUE\tTRUE\tTRUE\tFALSE\n-BCAS3\tMED13\tTRUE\tTRUE\tTRUE\tFALSE\n-BSG\tNFIX\tTRUE\tTRUE\tFALSE\tTRUE\n-MYO9B\tRAB22A\tTRUE\tTRUE\tFALSE\tTRUE\n-NUP214\tNOTCH1\tTRUE\tTRUE\tFALSE\tTRUE\n-CMTM7\tGLB1\tTRUE\tTRUE\tFALSE\tTRUE\n-CEP250\tNM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tTRUE\tTRUE\tFALSE\tTRUE\n-NM_001303457:TTI1\tDIDO1\tTRUE\tTRUE\tFALSE\tTRUE\n-CYTH1\tEIF3H\tTRUE\tTRUE\tFALSE\tTRUE\n-BCAS3\tBCAS4\tTRUE\tTRUE\tFALSE\tTRUE\n-IKZF3:NM_001284514:NM_001284515\tNR_036633:VAPB\tTRUE\tTRUE\tFALSE\tTRUE\n-SNF8\tNM_001272060:RPS6KB1\tTRUE\tTRUE\tFALSE\tTRUE\n-ANKHD1:ANKHD1-EIF4EBP3\tPCDH1\tFALSE\tTRUE\tTRUE\tTRUE\n-SULF2\tARFGEF2\tTRUE\tTRUE\tTRUE\tTRUE\n-GSDMB\tTATDN1\tTRUE\tTRUE\tTRUE\tTRUE\n-RARA\tPKIA\tTRUE\tTRUE\tTRUE\tTRUE\n-ACACA\tSTAC2\tTRUE\tTRUE\tTRUE\tTRUE\n-MYO19\tSKA2\tTRUE\tTRUE\tTRUE\tTRUE\n' |
| b |
| diff -r 86526900cb8f -r 4966079d474b test-data/refseq_genes_hg19.bed --- a/test-data/refseq_genes_hg19.bed Mon Oct 12 04:17:07 2015 -0400 +++ b/test-data/refseq_genes_hg19.bed Tue Oct 20 10:12:08 2015 -0400 |
| b |
| b'@@ -1,54143 +1,54143 @@\n-chr1\t66999638\t67216822\tSGIP1\n-chr1\t66999251\t67216822\tNM_001308203\n-chr1\t33547778\t33586132\tNM_001301825\n-chr1\t8378144\t8404227\tSLC45A1\n-chr1\t16767166\t16786584\tNECAP2\n-chr1\t16767166\t16786584\tNECAP2\n-chr1\t33547778\t33567493\tNR_126031\n-chr1\t16767166\t16786584\tNECAP2\n-chr1\t33546713\t33586132\tADC\n-chr1\t25071759\t25170815\tCLIC4\n-chr1\t33546713\t33586132\tNM_001293562\n-chr1\t33546729\t33586132\tNM_001301824\n-chr1\t33546729\t33586132\tNM_001301823\n-chr1\t33547778\t33567493\tNM_001301826\n-chr1\t48998526\t50489626\tAGBL4\n-chr1\t92145899\t92351836\tTGFBR3\n-chr1\t92145899\t92351836\tTGFBR3\n-chr1\t92145899\t92371559\tTGFBR3\n-chr1\t92145899\t92351836\tTGFBR3\n-chr1\t100652477\t100715409\tDBT\n-chr1\t175913961\t176176380\tRFWD2\n-chr1\t175913961\t176176380\tRFWD2\n-chr1\t150980866\t151008189\tNM_001303242\n-chr1\t175913961\t176176380\tNM_001286644\n-chr1\t150980866\t151008189\tPRUNE\n-chr1\t150980866\t151008189\tNM_001303243\n-chr1\t150980866\t151008189\tNM_001303229\n-chr1\t184356149\t184598155\tC1orf21\n-chr1\t150980866\t151008189\tNR_130132\n-chr1\t150980866\t151008189\tNR_130131\n-chr1\t150980866\t151008189\tNR_130130\n-chr1\t150980866\t151008189\tNR_130135\n-chr1\t226418849\t226497449\tLIN9\n-chr1\t226418849\t226497204\tLIN9\n-chr1\t226418849\t226497204\tLIN9\n-chr1\t1017197\t1051736\tC1orf159\n-chr1\t2036154\t2116834\tPRKCZ\n-chr1\t6845383\t7829766\tCAMTA1\n-chr1\t2005424\t2116834\tPRKCZ\n-chr1\t2985741\t3355185\tPRDM16\n-chr1\t2005085\t2116834\tPRKCZ\n-chr1\t6281252\t6296044\tICMT\n-chr1\t1981908\t2116834\tPRKCZ\n-chr1\t2985741\t3355185\tPRDM16\n-chr1\t13629924\t13635299\tPRAMEF10\n-chr1\t13328195\t13698405\tPRAMEF19\n-chr1\t13629931\t13635299\tNM_001291381\n-chr1\t20959947\t20978004\tPINK1\n-chr1\t23037330\t23247993\tEPHB2\n-chr1\t20969149\t20978686\tNR_046507\n-chr1\t22004791\t22109688\tUSP48\n-chr1\t23037330\t23247993\tEPHB2\n-chr1\t23037330\t23247993\tNM_001309193\n-chr1\t23037330\t23247993\tNM_001309192\n-chr1\t29213602\t29446558\tEPB41\n-chr1\t29241087\t29391733\tEPB41\n-chr1\t29213602\t29446558\tEPB41\n-chr1\t26210676\t26232993\tSTMN1\n-chr1\t31404352\t31538564\tPUM1\n-chr1\t28296854\t28415148\tNM_001282562\n-chr1\t28296854\t28415148\tNM_001282561\n-chr1\t28303783\t28415148\tNM_001282560\n-chr1\t28296854\t28415148\tEYA3\n-chr1\t31404352\t31538564\tPUM1\n-chr1\t32479294\t32526460\tNR_073499\n-chr1\t32479294\t32509482\tNR_073498\n-chr1\t32479294\t32509482\tKHDRBS1\n-chr1\t32479294\t32509482\tKHDRBS1\n-chr1\t27248212\t27273362\tNUDC\n-chr1\t29213602\t29446558\tEPB41\n-chr1\t29213602\t29446558\tEPB41\n-chr1\t29213602\t29446558\tEPB41\n-chr1\t39549838\t39952810\tMACF1\n-chr1\t36690016\t36770957\tTHRAP3\n-chr1\t33979598\t34630875\tNM_001281956\n-chr1\t35649200\t35658743\tSFPQ\n-chr1\t33979598\t34631443\tCSMD2\n-chr1\t46092975\t46152302\tGPBP1L1\n-chr1\t43996546\t44089343\tPTPRF\n-chr1\t48226199\t48462562\tTRABD2B\n-chr1\t43996546\t44089343\tPTPRF\n-chr1\t44870959\t45117396\tRNF220\n-chr1\t55532031\t55681039\tUSP24\n-chr1\t54519244\t54567321\tTCEANC2\n-chr1\t50906934\t51425936\tFAF1\n-chr1\t53392900\t53517289\tSCP2\n-chr1\t53392900\t53517289\tSCP2\n-chr1\t57463578\t58716211\tDAB1\n-chr1\t53392900\t53517289\tSCP2\n-chr1\t52373627\t52456436\tRAB3B\n-chr1\t53392900\t53517289\tSCP2\n-chr1\t54519244\t54578192\tNR_130900\n-chr1\t59762624\t60228402\tFGGY\n-chr1\t63906440\t63988944\tITGB3BP\n-chr1\t62901974\t62917475\tUSP1\n-chr1\t63906440\t63988944\tITGB3BP\n-chr1\t61547979\t61928460\tNFIA\n-chr1\t59762683\t60165066\tNR_103473\n-chr1\t64971596\t65158741\tNM_001293274\n-chr1\t61547979\t61928460\tNFIA\n-chr1\t64936475\t65158741\tCACHD1\n-chr1\t65991371\t66101111\tLEPR\n-chr1\t65991371\t66091917\tLEPR\n-chr1\t65991371\t66096095\tLEPR\n-chr1\t61542945\t61928460\tNFIA\n-chr1\t61547533\t61928460\tNFIA\n-chr1\t62902382\t62917475\tUSP1\n-chr1\t65886334\t66103176\tLEPR\n-chr1\t62901974\t62917475\tUSP1\n-chr1\t59762624\t60228402\tFGGY\n-chr1\t65886334\t66101111\tLEPR\n-chr1\t65886334\t66096095\tLEPR\n-chr1\t63906440\t63988944\tITGB3BP\n-chr1\t70225857\t70589171\tLRRC7\n-chr1\t71868624\t72748277\tNEGR1\n-chr1\t76540388\t77042892\tST6GALNAC3\n-chr1\t76540388\t77096669\tST6GALNAC3\n-chr1\t77554666\t77685132\tPIGK\n-chr1\t87012758\t87046432\tCLCA4\n-chr1\t89003195\t89150887\tNR_110682\n-chr1\t85784167\t86044046\tDDAH1\n-chr1\t90098643\t90185094\tLRRC8C\n-chr1\t87012758\t87046432\tCLCA4\n-chr1\t96457623\t96488436\tNR_125991\n-chr1\t94350755\t94375154\tGCLM\n-chr1\t94350755\t9437515'..b'4172\t50281\tNM_001300937\t0\t-\t37488\t50073\t0\t7\t3377,102,54,163,102,107,273,\t0,6998,7233,7510,10636,14372,15836,\n+chr1_gl000191_random\t34172\t50281\tNM_001300936\t0\t-\t37751\t50073\t0\t6\t3610,51,163,102,107,273,\t0,7233,7510,10636,14372,15836,\n+chr1_gl000192_random\t132568\t407510\tNR_103556\t0\t-\t407510\t407510\t0\t46\t1013,100,199,173,160,120,183,209,612,152,163,142,184,174,174,180,169,240,150,192,128,137,134,128,178,138,210,120,141,314,144,274,239,153,165,136,101,236,68,224,119,100,184,202,125,80,\t0,2445,7460,10376,10656,14094,14974,15375,27321,40251,42629,45294,48316,60392,64665,66977,69741,75593,78411,78897,79241,79602,80204,83980,86488,90288,93032,93501,97173,129300,131344,139102,143195,171991,173646,176182,178768,180746,191366,199776,205295,227269,241208,248406,264961,274862,\n+chr1_gl000192_random\t429709\t468683\tNR_120328\t0\t-\t468683\t468683\t0\t5\t562,194,128,82,443,\t0,8844,18401,19884,38531,\n+chr4_gl000193_random\t49162\t88375\tMGC39584\t0\t-\t88375\t88375\t0\t6\t456,58,88,240,188,176,\t0,1399,10706,25886,26325,39037,\n+chr4_gl000194_random\t61659\t115073\tMAFIP\t0\t-\t115073\t115073\t0\t3\t1290,59,88,\t0,51132,53326,\n+chr4_gl000194_random\t53588\t115073\tMAFIP\t0\t-\t115073\t115073\t0\t3\t2088,59,88,\t0,59203,61397,\n+chr4_gl000194_random\t53588\t115073\tMAFIP\t0\t-\t115073\t115073\t0\t8\t304,155,231,978,165,671,59,88,\t0,1089,1857,2433,3866,4739,59203,61397,\n+chr4_gl000194_random\t53588\t115073\tMAFIP\t0\t-\t115073\t115073\t0\t5\t304,155,231,59,88,\t0,1089,1857,59203,61397,\n+chr7_gl000195_random\t42937\t86719\tLOC389831\t0\t-\t44723\t49117\t0\t4\t1986,165,60,202,\t0,6017,31183,43580,\n+chr17_gl000205_random\t116622\t119732\tMGC70870\t0\t+\t119732\t119732\t0\t1\t3110,\t0,\n+chr19_gl000209_random\t86690\t96155\tNM_020535\t0\t+\t86745\t95742\t0\t8\t89,36,285,294,51,105,53,683,\t0,822,1620,2780,5246,8062,8629,8782,\n+chr19_gl000209_random\t98134\t112667\tKIR2DS5\t0\t+\t98145\t112480\t0\t8\t46,35,300,294,51,105,53,229,\t0,1522,4001,5829,9270,13586,14153,14304,\n+chr19_gl000209_random\t70070\t84658\tNM_001282170\t0\t+\t70107\t83979\t0\t8\t71,36,300,294,51,106,51,573,\t0,1070,3623,5503,8967,13298,13866,14015,\n+chr19_gl000209_random\t21910\t36449\tKIR2DL2\t0\t+\t21939\t35938\t0\t8\t63,36,300,294,51,102,53,688,\t0,971,3443,5257,8820,13136,13700,13851,\n+chr19_gl000209_random\t98111\t113132\tKIR2DS5\t0\t+\t98145\t112480\t0\t8\t68,36,300,294,51,105,53,694,\t0,1544,4024,5852,9293,13609,14176,14327,\n+chr19_gl000209_random\t57208\t68123\tLOC100287534\t0\t+\t57248\t67717\t0\t7\t80,36,285,294,51,53,676,\t0,279,1181,2345,5227,10087,10239,\n+chr19_gl000209_random\t57208\t68123\tKIR2DL4\t0\t+\t57248\t67717\t0\t8\t80,36,285,294,51,105,53,676,\t0,279,1181,2345,5227,9521,10087,10239,\n+chr19_gl000209_random\t57208\t68123\tLOC100287534\t0\t+\t57248\t67307\t0\t8\t80,36,285,294,51,104,53,676,\t0,279,1181,2345,5227,9521,10087,10239,\n+chr19_gl000209_random\t86745\t96246\tKIR2DL5B\t0\t+\t86745\t95742\t0\t8\t34,36,285,294,51,105,53,774,\t0,767,1565,2725,5191,8007,8574,8727,\n+chr19_gl000209_random\t115098\t129113\tKIR2DS1\t0\t+\t115111\t128940\t0\t8\t47,36,300,294,51,105,53,215,\t0,1011,3495,5320,8768,13082,13649,13800,\n+chr19_gl000209_random\t70070\t84658\tNM_001282171\t0\t+\t70107\t83979\t0\t7\t71,300,294,51,106,51,573,\t0,3623,5503,8967,13298,13866,14015,\n+chr19_gl000209_random\t70070\t84658\tKIR3DS1\t0\t+\t70107\t83979\t0\t9\t71,36,285,300,294,51,106,51,573,\t0,1070,1850,3623,5503,8967,13298,13866,14015,\n+chr19_gl000209_random\t21904\t129563\tNM_001291700\t0\t+\t21939\t128940\t0\t6\t69,36,51,105,53,665,\t0,977,101962,106276,106843,106994,\n+chr19_gl000209_random\t131432\t145743\tKIR2DS2\t0\t+\t131467\t145120\t0\t8\t69,36,300,294,51,105,53,665,\t0,861,3333,5151,8613,12928,13495,13646,\n+chr19_gl000209_random\t131432\t145743\tNM_001291695\t0\t+\t131467\t145288\t0\t8\t69,36,300,294,51,105,53,599,\t0,861,3333,5151,8613,12928,13495,13712,\n+chr19_gl000209_random\t131432\t145743\tNM_001291696\t0\t+\t131467\t145120\t0\t7\t69,36,294,51,105,53,665,\t0,861,5151,8613,12928,13495,13646,\n+chr19_gl000209_random\t131432\t145743\tNM_001291701\t0\t+\t131467\t145120\t0\t7\t69,36,300,294,105,53,665,\t0,861,3333,5151,12928,13495,13646,\n+chr19_gl000209_random\t131432\t145743\tNM_001291700\t0\t+\t131467\t145120\t0\t6\t69,36,51,105,53,665,\t0,861,8613,12928,13495,13646,\n' |
| b |
| diff -r 86526900cb8f -r 4966079d474b tool_dependencies.xml --- a/tool_dependencies.xml Mon Oct 12 04:17:07 2015 -0400 +++ b/tool_dependencies.xml Tue Oct 20 10:12:08 2015 -0400 |
| b |
| @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="python" version="2.7"> - <repository changeset_revision="ed2fa0e530f3" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="eb37ce21eef1" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="fuma" version="2.10.0"> - <repository changeset_revision="48783f711368" name="package_fuma_2_10_0" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="fuma" version="2.10.1"> + <repository changeset_revision="bd66bc0860db" name="package_fuma_2_10_1" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |