| Previous changeset 9:c3ce472a315f (2017-09-26) Next changeset 11:3743fd602fa9 (2017-11-03) |
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Commit message:
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad |
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modified:
dr-disco_classify.xml dr-disco_integrate.xml macros.xml test-data/classify_test_16.in.dbed test-data/classify_test_16.test-01.out.dbed test-data/classify_test_16.test-02.out.dbed test-data/classify_test_16.test-03.out.dbed test-data/classify_test_16.test-04.out.dbed test-data/classify_test_16.test-05.out.dbed test-data/classify_test_16.test-06.out.dbed test-data/classify_test_16.test-07.out.dbed test-data/classify_test_16.test-08.out.dbed test-data/detect.txt test-data/fix_test-01.fixed.bam test-data/integrate_test_terg_s041.in.dbed test-data/integrate_test_terg_s041.out.no-gtf.txt test-data/integrate_test_terg_s041.out.txt |
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| diff -r c3ce472a315f -r f2c70d589596 dr-disco_classify.xml --- a/dr-disco_classify.xml Tue Sep 26 08:27:47 2017 -0400 +++ b/dr-disco_classify.xml Thu Nov 02 05:17:31 2017 -0400 |
| [ |
| @@ -22,6 +22,8 @@ --blacklist-junctions '${blacklist_junctions}' #end if + --min-chim-overhang '${min_chim_overhang}' + '${dr_disco_detect_output}' '${dr_disco_classify_output}' ]]></command> @@ -32,6 +34,8 @@ <param name="blacklist_regions" argument="--blacklist-regions" type="data" format="bed" optional="True" label="Blacklist Regions" help="List of regions known to be false positives (https://github.com/yhoogstrate/dr-disco/tree/master/share/)" /> <param name="blacklist_junctions" argument="--blacklist-junctions" type="data" format="tabular" optional="True" label="Blacklist Junctions" help="List of junctions know to be false positives (https://github.com/yhoogstrate/dr-disco/tree/master/share/)" /> + + <param name="min_chim_overhang" type="integer" min="-1" value="50" label="Minimum alignment length on each side of the junction." help="May need to be set to smaller values for read lengths smaller than 75bp." argument="--min-chim-overhang" /> </inputs> <outputs> @@ -45,6 +49,7 @@ <output name="dr_disco_classify_output" file="classify_test_16.test-01.out.dbed" ftype="tabular" /> </test> + <test> <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> <param name="only_valid" value="--only-valid" /> @@ -59,6 +64,7 @@ <output name="dr_disco_classify_output" file="classify_test_16.test-03.out.dbed" ftype="tabular" /> </test> + <test> <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> <param name="only_valid" /> @@ -81,7 +87,6 @@ <output name="dr_disco_classify_output" file="classify_test_16.test-06.out.dbed" /> </test> - <test> <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> <param name="only_valid" /> @@ -98,13 +103,14 @@ <output name="dr_disco_classify_output" file="classify_test_16.test-08.out.dbed" /> </test> + </tests> <help><![CDATA[ **What it does** - +It filters fusion events that are likely to be true or false based on a variety of parameters provided in the input table. **Attributions** |
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| diff -r c3ce472a315f -r f2c70d589596 dr-disco_integrate.xml --- a/dr-disco_integrate.xml Tue Sep 26 08:27:47 2017 -0400 +++ b/dr-disco_integrate.xml Thu Nov 02 05:17:31 2017 -0400 |
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| @@ -36,7 +36,9 @@ </test> <test> <param name="dr_disco_classify_output" value="integrate_test_terg_s041.in.dbed" /> + <!-- <param name="gtf" value="integrate_tmprss-erg.hg38.gtf" /> + --> <output name="dr_disco_integrate_output" file="integrate_test_terg_s041.out.no-gtf.txt" /> </test> |
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| diff -r c3ce472a315f -r f2c70d589596 macros.xml --- a/macros.xml Tue Sep 26 08:27:47 2017 -0400 +++ b/macros.xml Thu Nov 02 05:17:31 2017 -0400 |
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| @@ -1,12 +1,12 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.11.0=py27_0">dr-disco</requirement> + <requirement type="package" version="0.14.0">dr-disco</requirement> <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">0.11.0</token> + <token name="@TOOL_VERSION@">0.14.0</token> <xml name="version_command"> <version_command>dr-disco --version | head -n 1</version_command> |
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| diff -r c3ce472a315f -r f2c70d589596 test-data/classify_test_16.in.dbed --- a/test-data/classify_test_16.in.dbed Tue Sep 26 08:27:47 2017 -0400 +++ b/test-data/classify_test_16.in.dbed Thu Nov 02 05:17:31 2017 -0400 |
| b |
| b'@@ -1,37 +1,37 @@\n-chr-A\tpos-A\tdirection-A\tpos-A-acceptor\tpos-A-donor\tchr-B\tpos-B\tdirection-B\tpos-A-acceptor\tpos-A-donor\tgenomic-distance\tfilter-status\tcircRNA\tintronic/exonic\tscore\tsoft+hardclips\tn-split-reads\tn-discordant-reads\talignment-score\tmismatches\tn-edges\tn-nodes-A\tn-nodes-B\tn-splice-junc-A\tn-splice-junc-B\tentropy-bp-edge\tentropy-all-edges\tbp-pos-stddev\tentropy-disco-bps\tlr-A-slope\tlr-A-intercept\tlr-A-rvalue\tlr-A-pvalue\tlr-A-stderr\tlr-B-slope\tlr-B-intercept\tlr-B-rvalue\tlr-B-pvalue\tlr-B-stderr\tdisco/split\tclips/score\tnodes/edge\tdata-structure\n-chr21\t39817544\t-\t140\t0\tchr21\t42880007\t+\t0\t140\t3062463\tunclassified\tlinear\texonic\t253\t170\t85\t6\t10000\t0\t5\t2\t4\t1\t0\t0.8111\t0.8497\t0\t0.9535\t0.7247\t63.7843\t0.844\t0\t0.0559\t0.3651\t17.303\t0.8378\t0\t0.0289\t0.0706\t0.336\t1.2\tchr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:65,spanning_paired_2:65,spanning_singleton_1:2,spanning_singleton_1_r:3,spanning_singleton_2:2,spanning_singleton_2_r:3)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(discordant_mates:10,spanning_paired_1:6,spanning_paired_1_t:1,spanning_paired_2:6,spanning_paired_2_t:1,spanning_singleton_1_r:2,spanning_singleton_2_r:2)&chr21:39817544/39817545(-)->chr21:42878371/42878372(+):(discordant_mates:2,spanning_paired_1:1,spanning_paired_1_t:1,spanning_paired_2:1,spanning_paired_2_t:1,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:39846044/39846045(-)->chr21:42879876/42879877(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:39817544/39817545(-)->chr21:42876293/42876294(+):(spanning_paired_1:1,spanning_paired_2:1)\n-chr21\t39877811\t-\t98\t0\tchr21\t42873374\t+\t0\t98\t2995563\tunclassified\tlinear\tintronic\t91\t42\t21\t28\t10000\t0\t1\t1\t1\t0\t0\t0.9528\t0.9528\t0\t0.82\t2.9207\t17.3314\t0.9125\t0\t0.191\t1.588\t68.1747\t0.8769\t0\t0.1269\t1.3333\t0.2308\t2\tchr21:39877811/39877812(-)->chr21:42873374/42873375(+):(discordant_mates:56,spanning_paired_1:12,spanning_paired_1_t:9,spanning_paired_2:12,spanning_paired_2_t:9)\n-chr21\t42861433\t+\t6\t18\tchr21\t42866505\t-\t18\t6\t5072\tunclassified\tcircular\texonic\t41\t30\t14\t2\t10000\t0\t7\t5\t6\t1\t2\t1\t0.9375\t18.7474\t0.75\t26.9\t3\t0.9425\t0.0164\t5.5097\t20.1\t42.8\t0.8833\t0.047\t6.1587\t0.1429\t0.3659\t1.5714\tchr21:42861433/42861434(+)->chr21:42866505/42866506(-):(discordant_mates:2,spanning_paired_1:2,spanning_paired_1_t:1,spanning_paired_2:2,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42861433/42861434(+)->chr21:42870116/42870117(-):(spanning_paired_1:3,spanning_paired_2:3,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:42860568/42860569(+)->chr21:42867210/42867211(-):(spanning_paired_1_t:2,spanning_paired_2_t:2)&chr21:42860320/42860321(+)->chr21:42861520/42861521(-):(spanning_paired_1:1,spanning_paired_2:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42859986/42859987(+)->chr21:42863878/42863879(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:42860320/42860321(+)->chr21:42866505/42866506(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:42866446/42866447(+)->chr21:42870110/42870111(-):(discordant_mates:2)\n-chr21\t39836011\t+\t0\t8\tchr21\t39836545\t-\t8\t0\t534\tunclassified\tcircular\tintronic\t17\t12\t6\t0\t10000\t0\t2\t2\t2\t0\t0\t0.4056\t0.6934\t25.3065\t0\t1.5\t29.5\t0.7746\t0.2254\t0.866\t0\t93\t0\t1\t0\t0\t0.3529\t2\tchr21:39836011/39836012(+)->chr21:39836545/39836546(-):(spanning_paired_1_t:4,spanning_paired_2_t:4)&chr21:39835707/39835708(+)->chr21:39839850/39839851(-):(spanning_paired_1_t:1,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)\n-chr21\t39875880\t+\t0\t6\tchr21\t39876476\t-\t6\t0\t596\tunclassified\tcircular\tintronic\t12\t8\t4\t0\t10000\t0\t2\t2\t2\t0\t0\t0\t0.4056\t0\t0\t0\t68\t0\t1\t0\t0\t58\t0\t1\t0\t0\t0.3333\t2\tchr21:39875880/39875881(+)->chr21:39876476/39876477(-):(spanning_paired_1:3,spanning_paired_2:3)&chr21:39874280/39874281(+)->chr21:39876277/39876278(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n-chr21\t39851814\t+\t0\t6\tchr21\t39852667\t-\t6\t0\t853\tunclassified\tcircular\tintronic\t9\t6\t3\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t49\t0\t1\t0\t0\t77\t0\t1\t0\t0\t0.3333\t2\tchr21:39851814/39851815(+)->chr21:39852667/3'..b'7/39838728(+)->chr21:39863701/39863702(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t39849621\t+\t0\t2\tchr21\t39850505\t-\t2\t0\t884\tunclassified\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t52\t0\t1\t0\t0\t74\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39849621/39849622(+)->chr21:39850505/39850506(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t39858845\t+\t0\t2\tchr21\t39859592\t-\t2\t0\t747\tunclassified\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t41\t0\t1\t0\t0\t84\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39858845/39858846(+)->chr21:39859592/39859593(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t39863020\t+\t0\t2\tchr21\t39863629\t-\t2\t0\t609\tunclassified\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t101\t0\t1\t0\t0\t25\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39863020/39863021(+)->chr21:39863629/39863630(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t39871034\t+\t0\t2\tchr21\t39877568\t-\t2\t0\t6534\tunclassified\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t31\t0\t1\t0\t0\t66\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39871034/39871035(+)->chr21:39877568/39877569(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42836581\t+\t0\t2\tchr21\t42839672\t-\t2\t0\t3091\tunclassified\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t19\t0\t1\t0\t0\t107\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42836581/42836582(+)->chr21:42839672/42839673(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42853701\t+\t0\t2\tchr21\t42860029\t-\t2\t0\t6328\tunclassified\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t22\t0\t1\t0\t0\t31\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42853701/42853702(+)->chr21:42860029/42860030(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42866483\t-\t0\t2\tchr21\t42870116\t-\t2\t0\t3633\tunclassified\tlinear\tintronic\t3\t9\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t38\t0\t1\t0\t0\t88\t0\t1\t0\t0\t1.5\t2\t50\t50\t50\t50\tchr21:42866483/42866484(-)->chr21:42870116/42870117(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42839824\t+\t0\t4\tchr21\t42840323\t-\t4\t0\t499\tunclassified\tcircular\tintronic\t2\t2\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t1\t1\t0\t0.4056\t44\t82\t1\t0\t0\t0\t120\t0\t1\t0\t40\t0.5\t2\t50\t50\t50\t50\tchr21:42839824/42839825(+)->chr21:42840323/42840324(-):(discordant_mates:4)\n+chr21\t39770910\t+\t2\t0\tchr21\t39771416\t-\t0\t2\t506\tunclassified\tcircular\tintronic\t2\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t75\t0\t1\t0\t0\t48\t0\t1\t0\t0\t0.5\t2\t50\t50\t50\t50\tchr21:39770910/39770911(+)->chr21:39771416/39771417(-):(spanning_singleton_1_r:1,spanning_singleton_2_r:1)\n+chr21\t39860702\t-\t4\t0\tchr21\t42843890\t+\t0\t4\t2983188\tunclassified\tlinear\tintronic\t2\t0\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t40\t0\t2\t50\t50\t50\t50\tchr21:39860702/39860703(-)->chr21:42843890/42843891(+):(discordant_mates:4)\n+chr21\t39781087\t+\t0\t2\tchr21\t39782101\t-\t2\t0\t1014\tunclassified\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39781087/39781088(+)->chr21:39782101/39782102(-):(discordant_mates:2)\n+chr21\t39846131\t+\t0\t2\tchr21\t39846834\t-\t2\t0\t703\tunclassified\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t39\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39846131/39846132(+)->chr21:39846834/39846835(-):(discordant_mates:2)\n+chr21\t39853321\t-\t2\t0\tchr21\t42851610\t+\t0\t2\t2998289\tunclassified\tlinear\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39853321/39853322(-)->chr21:42851610/42851611(+):(discordant_mates:2)\n+chr21\t42840341\t+\t0\t2\tchr21\t42842586\t-\t2\t0\t2245\tunclassified\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t124\t0\t1\t0\t0\t124\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42840341/42840342(+)->chr21:42842586/42842587(-):(discordant_mates:2)\n+chr21\t42843861\t+\t2\t0\tchr21\t42845272\t-\t0\t2\t1411\tunclassified\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t65\t0\t1\t0\t0\t60\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42843861/42843862(+)->chr21:42845272/42845273(-):(discordant_mates:2)\n+chr21\t42863757\t+\t0\t2\tchr21\t42864220\t-\t2\t0\t463\tunclassified\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t123\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42863757/42863758(+)->chr21:42864220/42864221(-):(discordant_mates:2)\n' |
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| diff -r c3ce472a315f -r f2c70d589596 test-data/classify_test_16.test-01.out.dbed --- a/test-data/classify_test_16.test-01.out.dbed Tue Sep 26 08:27:47 2017 -0400 +++ b/test-data/classify_test_16.test-01.out.dbed Thu Nov 02 05:17:31 2017 -0400 |
| b |
| b'@@ -1,37 +1,37 @@\n-chr-A\tpos-A\tdirection-A\tpos-A-acceptor\tpos-A-donor\tchr-B\tpos-B\tdirection-B\tpos-A-acceptor\tpos-A-donor\tgenomic-distance\tfilter-status\tcircRNA\tintronic/exonic\tscore\tsoft+hardclips\tn-split-reads\tn-discordant-reads\talignment-score\tmismatches\tn-edges\tn-nodes-A\tn-nodes-B\tn-splice-junc-A\tn-splice-junc-B\tentropy-bp-edge\tentropy-all-edges\tbp-pos-stddev\tentropy-disco-bps\tlr-A-slope\tlr-A-intercept\tlr-A-rvalue\tlr-A-pvalue\tlr-A-stderr\tlr-B-slope\tlr-B-intercept\tlr-B-rvalue\tlr-B-pvalue\tlr-B-stderr\tdisco/split\tclips/score\tnodes/edge\tdata-structure\n-chr21\t39817544\t-\t140\t0\tchr21\t42880007\t+\t0\t140\t3062463\tvalid\tlinear\texonic\t253\t170\t85\t6\t10000\t0\t5\t2\t4\t1\t0\t0.8111\t0.8497\t0\t0.9535\t0.7247\t63.7843\t0.844\t0\t0.0559\t0.3651\t17.303\t0.8378\t0\t0.0289\t0.0706\t0.336\t1.2\tchr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:65,spanning_paired_2:65,spanning_singleton_1:2,spanning_singleton_1_r:3,spanning_singleton_2:2,spanning_singleton_2_r:3)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(discordant_mates:10,spanning_paired_1:6,spanning_paired_1_t:1,spanning_paired_2:6,spanning_paired_2_t:1,spanning_singleton_1_r:2,spanning_singleton_2_r:2)&chr21:39817544/39817545(-)->chr21:42878371/42878372(+):(discordant_mates:2,spanning_paired_1:1,spanning_paired_1_t:1,spanning_paired_2:1,spanning_paired_2_t:1,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:39846044/39846045(-)->chr21:42879876/42879877(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:39817544/39817545(-)->chr21:42876293/42876294(+):(spanning_paired_1:1,spanning_paired_2:1)\n-chr21\t39877811\t-\t98\t0\tchr21\t42873374\t+\t0\t98\t2995563\tvalid\tlinear\tintronic\t91\t42\t21\t28\t10000\t0\t1\t1\t1\t0\t0\t0.9528\t0.9528\t0\t0.82\t2.9207\t17.3314\t0.9125\t0\t0.191\t1.588\t68.1747\t0.8769\t0\t0.1269\t1.3333\t0.2308\t2\tchr21:39877811/39877812(-)->chr21:42873374/42873375(+):(discordant_mates:56,spanning_paired_1:12,spanning_paired_1_t:9,spanning_paired_2:12,spanning_paired_2_t:9)\n-chr21\t42861433\t+\t6\t18\tchr21\t42866505\t-\t18\t6\t5072\tn_discordant_reads=2<3\tcircular\texonic\t41\t30\t14\t2\t10000\t0\t7\t5\t6\t1\t2\t1\t0.9375\t18.7474\t0.75\t26.9\t3\t0.9425\t0.0164\t5.5097\t20.1\t42.8\t0.8833\t0.047\t6.1587\t0.1429\t0.3659\t1.5714\tchr21:42861433/42861434(+)->chr21:42866505/42866506(-):(discordant_mates:2,spanning_paired_1:2,spanning_paired_1_t:1,spanning_paired_2:2,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42861433/42861434(+)->chr21:42870116/42870117(-):(spanning_paired_1:3,spanning_paired_2:3,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:42860568/42860569(+)->chr21:42867210/42867211(-):(spanning_paired_1_t:2,spanning_paired_2_t:2)&chr21:42860320/42860321(+)->chr21:42861520/42861521(-):(spanning_paired_1:1,spanning_paired_2:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42859986/42859987(+)->chr21:42863878/42863879(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:42860320/42860321(+)->chr21:42866505/42866506(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:42866446/42866447(+)->chr21:42870110/42870111(-):(discordant_mates:2)\n-chr21\t39836011\t+\t0\t8\tchr21\t39836545\t-\t8\t0\t534\tn_support=6<8,bp_pos_stddev=25.3065>15.0,log_ratio_slope=9.62>1.8,log_ratio_rvalue=8.96>0.4\tcircular\tintronic\t17\t12\t6\t0\t10000\t0\t2\t2\t2\t0\t0\t0.4056\t0.6934\t25.3065\t0\t1.5\t29.5\t0.7746\t0.2254\t0.866\t0\t93\t0\t1\t0\t0\t0.3529\t2\tchr21:39836011/39836012(+)->chr21:39836545/39836546(-):(spanning_paired_1_t:4,spanning_paired_2_t:4)&chr21:39835707/39835708(+)->chr21:39839850/39839851(-):(spanning_paired_1_t:1,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)\n-chr21\t39875880\t+\t0\t6\tchr21\t39876476\t-\t6\t0\t596\tentropy=0.0<0.6839,n_support=4<8\tcircular\tintronic\t12\t8\t4\t0\t10000\t0\t2\t2\t2\t0\t0\t0\t0.4056\t0\t0\t0\t68\t0\t1\t0\t0\t58\t0\t1\t0\t0\t0.3333\t2\tchr21:39875880/39875881(+)->chr21:39876476/39876477(-):(spanning_paired_1:3,spanning_paired_2:3)&chr21:39874280/39874281(+)->chr21:39876277/39876278(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n-chr21\t39851814\t+\t0\t6\tchr21\t39852667\t-\t6\t0\t853\tentropy=0.0<0.6835,n_support=3<7\tcircular\tintro'..b'port=1<7,n_lr_symmetry=104.05>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t101\t0\t1\t0\t0\t25\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39863020/39863021(+)->chr21:39863629/39863630(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t39871034\t+\t0\t2\tchr21\t39877568\t-\t2\t0\t6534\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=72.92>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t31\t0\t1\t0\t0\t66\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39871034/39871035(+)->chr21:39877568/39877569(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42836581\t+\t0\t2\tchr21\t42839672\t-\t2\t0\t3091\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=108.67>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t19\t0\t1\t0\t0\t107\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42836581/42836582(+)->chr21:42839672/42839673(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42853701\t+\t0\t2\tchr21\t42860029\t-\t2\t0\t6328\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=38.01>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t22\t0\t1\t0\t0\t31\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42853701/42853702(+)->chr21:42860029/42860030(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42866483\t-\t0\t2\tchr21\t42870116\t-\t2\t0\t3633\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=95.85>=24.68\tlinear\tintronic\t3\t9\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t38\t0\t1\t0\t0\t88\t0\t1\t0\t0\t1.5\t2\t50\t50\t50\t50\tchr21:42866483/42866484(-)->chr21:42870116/42870117(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42839824\t+\t0\t4\tchr21\t42840323\t-\t4\t0\t499\tn_support=2<7,log_ratio_slope=12.99>1.8,log_ratio_rvalue=9.21>0.4\tcircular\tintronic\t2\t2\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t1\t1\t0\t0.4056\t44\t82\t1\t0\t0\t0\t120\t0\t1\t0\t40\t0.5\t2\t50\t50\t50\t50\tchr21:42839824/42839825(+)->chr21:42840323/42840324(-):(discordant_mates:4)\n+chr21\t39770910\t+\t2\t0\tchr21\t39771416\t-\t0\t2\t506\tentropy=0.0<0.6827,n_support=1<7,n_lr_symmetry=89.04>=28.44\tcircular\tintronic\t2\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t75\t0\t1\t0\t0\t48\t0\t1\t0\t0\t0.5\t2\t50\t50\t50\t50\tchr21:39770910/39770911(+)->chr21:39771416/39771417(-):(spanning_singleton_1_r:1,spanning_singleton_2_r:1)\n+chr21\t39860702\t-\t4\t0\tchr21\t42843890\t+\t0\t4\t2983188\tentropy=0.0<0.6827,n_support=2<7,n_lr_symmetry=178.19>=28.44\tlinear\tintronic\t2\t0\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t40\t0\t2\t50\t50\t50\t50\tchr21:39860702/39860703(-)->chr21:42843890/42843891(+):(discordant_mates:4)\n+chr21\t39781087\t+\t0\t2\tchr21\t39782101\t-\t2\t0\t1014\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39781087/39781088(+)->chr21:39782101/39782102(-):(discordant_mates:2)\n+chr21\t39846131\t+\t0\t2\tchr21\t39846834\t-\t2\t0\t703\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=131.9>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t39\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39846131/39846132(+)->chr21:39846834/39846835(-):(discordant_mates:2)\n+chr21\t39853321\t-\t2\t0\tchr21\t42851610\t+\t0\t2\t2998289\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tlinear\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39853321/39853322(-)->chr21:42851610/42851611(+):(discordant_mates:2)\n+chr21\t42840341\t+\t0\t2\tchr21\t42842586\t-\t2\t0\t2245\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=175.36>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t124\t0\t1\t0\t0\t124\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42840341/42840342(+)->chr21:42842586/42842587(-):(discordant_mates:2)\n+chr21\t42843861\t+\t2\t0\tchr21\t42845272\t-\t0\t2\t1411\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=88.46>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t65\t0\t1\t0\t0\t60\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42843861/42843862(+)->chr21:42845272/42845273(-):(discordant_mates:2)\n+chr21\t42863757\t+\t0\t2\tchr21\t42864220\t-\t2\t0\t463\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=176.08>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t123\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42863757/42863758(+)->chr21:42864220/42864221(-):(discordant_mates:2)\n' |
| b |
| diff -r c3ce472a315f -r f2c70d589596 test-data/classify_test_16.test-02.out.dbed --- a/test-data/classify_test_16.test-02.out.dbed Tue Sep 26 08:27:47 2017 -0400 +++ b/test-data/classify_test_16.test-02.out.dbed Thu Nov 02 05:17:31 2017 -0400 |
| b |
| @@ -1,3 +1,3 @@ -chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-A-acceptor pos-A-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge data-structure -chr21 39817544 - 140 0 chr21 42880007 + 0 140 3062463 valid linear exonic 253 170 85 6 10000 0 5 2 4 1 0 0.8111 0.8497 0 0.9535 0.7247 63.7843 0.844 0 0.0559 0.3651 17.303 0.8378 0 0.0289 0.0706 0.336 1.2 chr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:65,spanning_paired_2:65,spanning_singleton_1:2,spanning_singleton_1_r:3,spanning_singleton_2:2,spanning_singleton_2_r:3)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(discordant_mates:10,spanning_paired_1:6,spanning_paired_1_t:1,spanning_paired_2:6,spanning_paired_2_t:1,spanning_singleton_1_r:2,spanning_singleton_2_r:2)&chr21:39817544/39817545(-)->chr21:42878371/42878372(+):(discordant_mates:2,spanning_paired_1:1,spanning_paired_1_t:1,spanning_paired_2:1,spanning_paired_2_t:1,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:39846044/39846045(-)->chr21:42879876/42879877(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:39817544/39817545(-)->chr21:42876293/42876294(+):(spanning_paired_1:1,spanning_paired_2:1) -chr21 39877811 - 98 0 chr21 42873374 + 0 98 2995563 valid linear intronic 91 42 21 28 10000 0 1 1 1 0 0 0.9528 0.9528 0 0.82 2.9207 17.3314 0.9125 0 0.191 1.588 68.1747 0.8769 0 0.1269 1.3333 0.2308 2 chr21:39877811/39877812(-)->chr21:42873374/42873375(+):(discordant_mates:56,spanning_paired_1:12,spanning_paired_1_t:9,spanning_paired_2:12,spanning_paired_2_t:9) +chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-B-acceptor pos-B-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge median-AS-A median-AS-B max-AS-A max-AS-B data-structure +chr21 39817544 - 140 0 chr21 42880007 + 0 140 3062463 valid linear exonic 253 170 85 6 10000 0 5 2 4 1 0 0.8111 0.8497 0 0.9535 0.7247 63.7843 0.844 0 0.0559 0.3651 17.303 0.8378 0 0.0289 0.0706 0.336 1.2 50 50 50 50 chr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:65,spanning_paired_2:65,spanning_singleton_1:2,spanning_singleton_1_r:3,spanning_singleton_2:2,spanning_singleton_2_r:3)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(discordant_mates:10,spanning_paired_1:6,spanning_paired_1_t:1,spanning_paired_2:6,spanning_paired_2_t:1,spanning_singleton_1_r:2,spanning_singleton_2_r:2)&chr21:39817544/39817545(-)->chr21:42878371/42878372(+):(discordant_mates:2,spanning_paired_1:1,spanning_paired_1_t:1,spanning_paired_2:1,spanning_paired_2_t:1,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:39846044/39846045(-)->chr21:42879876/42879877(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:39817544/39817545(-)->chr21:42876293/42876294(+):(spanning_paired_1:1,spanning_paired_2:1) +chr21 39877811 - 98 0 chr21 42873374 + 0 98 2995563 valid linear intronic 91 42 21 28 10000 0 1 1 1 0 0 0.9528 0.9528 0 0.82 2.9207 17.3314 0.9125 0 0.191 1.588 68.1747 0.8769 0 0.1269 1.3333 0.2308 2 50 50 50 50 chr21:39877811/39877812(-)->chr21:42873374/42873375(+):(discordant_mates:56,spanning_paired_1:12,spanning_paired_1_t:9,spanning_paired_2:12,spanning_paired_2_t:9) |
| b |
| diff -r c3ce472a315f -r f2c70d589596 test-data/classify_test_16.test-03.out.dbed --- a/test-data/classify_test_16.test-03.out.dbed Tue Sep 26 08:27:47 2017 -0400 +++ b/test-data/classify_test_16.test-03.out.dbed Thu Nov 02 05:17:31 2017 -0400 |
| b |
| b'@@ -1,37 +1,37 @@\n-chr-A\tpos-A\tdirection-A\tpos-A-acceptor\tpos-A-donor\tchr-B\tpos-B\tdirection-B\tpos-A-acceptor\tpos-A-donor\tgenomic-distance\tfilter-status\tcircRNA\tintronic/exonic\tscore\tsoft+hardclips\tn-split-reads\tn-discordant-reads\talignment-score\tmismatches\tn-edges\tn-nodes-A\tn-nodes-B\tn-splice-junc-A\tn-splice-junc-B\tentropy-bp-edge\tentropy-all-edges\tbp-pos-stddev\tentropy-disco-bps\tlr-A-slope\tlr-A-intercept\tlr-A-rvalue\tlr-A-pvalue\tlr-A-stderr\tlr-B-slope\tlr-B-intercept\tlr-B-rvalue\tlr-B-pvalue\tlr-B-stderr\tdisco/split\tclips/score\tnodes/edge\tdata-structure\n-chr21\t39817544\t-\t140\t0\tchr21\t42880007\t+\t0\t140\t3062463\tvalid\tlinear\texonic\t253\t170\t85\t6\t10000\t0\t5\t2\t4\t1\t0\t0.8111\t0.8497\t0\t0.9535\t0.7247\t63.7843\t0.844\t0\t0.0559\t0.3651\t17.303\t0.8378\t0\t0.0289\t0.0706\t0.336\t1.2\tchr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:65,spanning_paired_2:65,spanning_singleton_1:2,spanning_singleton_1_r:3,spanning_singleton_2:2,spanning_singleton_2_r:3)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(discordant_mates:10,spanning_paired_1:6,spanning_paired_1_t:1,spanning_paired_2:6,spanning_paired_2_t:1,spanning_singleton_1_r:2,spanning_singleton_2_r:2)&chr21:39817544/39817545(-)->chr21:42878371/42878372(+):(discordant_mates:2,spanning_paired_1:1,spanning_paired_1_t:1,spanning_paired_2:1,spanning_paired_2_t:1,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:39846044/39846045(-)->chr21:42879876/42879877(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:39817544/39817545(-)->chr21:42876293/42876294(+):(spanning_paired_1:1,spanning_paired_2:1)\n-chr21\t39877811\t-\t98\t0\tchr21\t42873374\t+\t0\t98\t2995563\tvalid\tlinear\tintronic\t91\t42\t21\t28\t10000\t0\t1\t1\t1\t0\t0\t0.9528\t0.9528\t0\t0.82\t2.9207\t17.3314\t0.9125\t0\t0.191\t1.588\t68.1747\t0.8769\t0\t0.1269\t1.3333\t0.2308\t2\tchr21:39877811/39877812(-)->chr21:42873374/42873375(+):(discordant_mates:56,spanning_paired_1:12,spanning_paired_1_t:9,spanning_paired_2:12,spanning_paired_2_t:9)\n-chr21\t42861433\t+\t6\t18\tchr21\t42866505\t-\t18\t6\t5072\tn_discordant_reads=2<3\tcircular\texonic\t41\t30\t14\t2\t10000\t0\t7\t5\t6\t1\t2\t1\t0.9375\t18.7474\t0.75\t26.9\t3\t0.9425\t0.0164\t5.5097\t20.1\t42.8\t0.8833\t0.047\t6.1587\t0.1429\t0.3659\t1.5714\tchr21:42861433/42861434(+)->chr21:42866505/42866506(-):(discordant_mates:2,spanning_paired_1:2,spanning_paired_1_t:1,spanning_paired_2:2,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42861433/42861434(+)->chr21:42870116/42870117(-):(spanning_paired_1:3,spanning_paired_2:3,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:42860568/42860569(+)->chr21:42867210/42867211(-):(spanning_paired_1_t:2,spanning_paired_2_t:2)&chr21:42860320/42860321(+)->chr21:42861520/42861521(-):(spanning_paired_1:1,spanning_paired_2:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42859986/42859987(+)->chr21:42863878/42863879(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:42860320/42860321(+)->chr21:42866505/42866506(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:42866446/42866447(+)->chr21:42870110/42870111(-):(discordant_mates:2)\n-chr21\t39836011\t+\t0\t8\tchr21\t39836545\t-\t8\t0\t534\tn_support=6<8,bp_pos_stddev=25.3065>15.0,log_ratio_slope=9.62>1.8,log_ratio_rvalue=8.96>0.4\tcircular\tintronic\t17\t12\t6\t0\t10000\t0\t2\t2\t2\t0\t0\t0.4056\t0.6934\t25.3065\t0\t1.5\t29.5\t0.7746\t0.2254\t0.866\t0\t93\t0\t1\t0\t0\t0.3529\t2\tchr21:39836011/39836012(+)->chr21:39836545/39836546(-):(spanning_paired_1_t:4,spanning_paired_2_t:4)&chr21:39835707/39835708(+)->chr21:39839850/39839851(-):(spanning_paired_1_t:1,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)\n-chr21\t39875880\t+\t0\t6\tchr21\t39876476\t-\t6\t0\t596\tentropy=0.0<0.6839,n_support=4<8\tcircular\tintronic\t12\t8\t4\t0\t10000\t0\t2\t2\t2\t0\t0\t0\t0.4056\t0\t0\t0\t68\t0\t1\t0\t0\t58\t0\t1\t0\t0\t0.3333\t2\tchr21:39875880/39875881(+)->chr21:39876476/39876477(-):(spanning_paired_1:3,spanning_paired_2:3)&chr21:39874280/39874281(+)->chr21:39876277/39876278(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n-chr21\t39851814\t+\t0\t6\tchr21\t39852667\t-\t6\t0\t853\tentropy=0.0<0.6835,n_support=3<7\tcircular\tintro'..b'port=1<7,n_lr_symmetry=104.05>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t101\t0\t1\t0\t0\t25\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39863020/39863021(+)->chr21:39863629/39863630(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t39871034\t+\t0\t2\tchr21\t39877568\t-\t2\t0\t6534\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=72.92>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t31\t0\t1\t0\t0\t66\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39871034/39871035(+)->chr21:39877568/39877569(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42836581\t+\t0\t2\tchr21\t42839672\t-\t2\t0\t3091\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=108.67>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t19\t0\t1\t0\t0\t107\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42836581/42836582(+)->chr21:42839672/42839673(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42853701\t+\t0\t2\tchr21\t42860029\t-\t2\t0\t6328\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=38.01>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t22\t0\t1\t0\t0\t31\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42853701/42853702(+)->chr21:42860029/42860030(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42866483\t-\t0\t2\tchr21\t42870116\t-\t2\t0\t3633\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=95.85>=24.68\tlinear\tintronic\t3\t9\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t38\t0\t1\t0\t0\t88\t0\t1\t0\t0\t1.5\t2\t50\t50\t50\t50\tchr21:42866483/42866484(-)->chr21:42870116/42870117(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42839824\t+\t0\t4\tchr21\t42840323\t-\t4\t0\t499\tn_support=2<7,log_ratio_slope=12.99>1.8,log_ratio_rvalue=9.21>0.4\tcircular\tintronic\t2\t2\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t1\t1\t0\t0.4056\t44\t82\t1\t0\t0\t0\t120\t0\t1\t0\t40\t0.5\t2\t50\t50\t50\t50\tchr21:42839824/42839825(+)->chr21:42840323/42840324(-):(discordant_mates:4)\n+chr21\t39770910\t+\t2\t0\tchr21\t39771416\t-\t0\t2\t506\tentropy=0.0<0.6827,n_support=1<7,n_lr_symmetry=89.04>=28.44\tcircular\tintronic\t2\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t75\t0\t1\t0\t0\t48\t0\t1\t0\t0\t0.5\t2\t50\t50\t50\t50\tchr21:39770910/39770911(+)->chr21:39771416/39771417(-):(spanning_singleton_1_r:1,spanning_singleton_2_r:1)\n+chr21\t39860702\t-\t4\t0\tchr21\t42843890\t+\t0\t4\t2983188\tentropy=0.0<0.6827,n_support=2<7,n_lr_symmetry=178.19>=28.44\tlinear\tintronic\t2\t0\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t40\t0\t2\t50\t50\t50\t50\tchr21:39860702/39860703(-)->chr21:42843890/42843891(+):(discordant_mates:4)\n+chr21\t39781087\t+\t0\t2\tchr21\t39782101\t-\t2\t0\t1014\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39781087/39781088(+)->chr21:39782101/39782102(-):(discordant_mates:2)\n+chr21\t39846131\t+\t0\t2\tchr21\t39846834\t-\t2\t0\t703\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=131.9>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t39\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39846131/39846132(+)->chr21:39846834/39846835(-):(discordant_mates:2)\n+chr21\t39853321\t-\t2\t0\tchr21\t42851610\t+\t0\t2\t2998289\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tlinear\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39853321/39853322(-)->chr21:42851610/42851611(+):(discordant_mates:2)\n+chr21\t42840341\t+\t0\t2\tchr21\t42842586\t-\t2\t0\t2245\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=175.36>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t124\t0\t1\t0\t0\t124\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42840341/42840342(+)->chr21:42842586/42842587(-):(discordant_mates:2)\n+chr21\t42843861\t+\t2\t0\tchr21\t42845272\t-\t0\t2\t1411\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=88.46>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t65\t0\t1\t0\t0\t60\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42843861/42843862(+)->chr21:42845272/42845273(-):(discordant_mates:2)\n+chr21\t42863757\t+\t0\t2\tchr21\t42864220\t-\t2\t0\t463\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=176.08>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t123\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42863757/42863758(+)->chr21:42864220/42864221(-):(discordant_mates:2)\n' |
| b |
| diff -r c3ce472a315f -r f2c70d589596 test-data/classify_test_16.test-04.out.dbed --- a/test-data/classify_test_16.test-04.out.dbed Tue Sep 26 08:27:47 2017 -0400 +++ b/test-data/classify_test_16.test-04.out.dbed Thu Nov 02 05:17:31 2017 -0400 |
| b |
| b'@@ -1,37 +1,37 @@\n-chr-A\tpos-A\tdirection-A\tpos-A-acceptor\tpos-A-donor\tchr-B\tpos-B\tdirection-B\tpos-A-acceptor\tpos-A-donor\tgenomic-distance\tfilter-status\tcircRNA\tintronic/exonic\tscore\tsoft+hardclips\tn-split-reads\tn-discordant-reads\talignment-score\tmismatches\tn-edges\tn-nodes-A\tn-nodes-B\tn-splice-junc-A\tn-splice-junc-B\tentropy-bp-edge\tentropy-all-edges\tbp-pos-stddev\tentropy-disco-bps\tlr-A-slope\tlr-A-intercept\tlr-A-rvalue\tlr-A-pvalue\tlr-A-stderr\tlr-B-slope\tlr-B-intercept\tlr-B-rvalue\tlr-B-pvalue\tlr-B-stderr\tdisco/split\tclips/score\tnodes/edge\tdata-structure\n-chr21\t39817544\t-\t140\t0\tchr21\t42880007\t+\t0\t140\t3062463\tvalid\tlinear\texonic\t253\t170\t85\t6\t10000\t0\t5\t2\t4\t1\t0\t0.8111\t0.8497\t0\t0.9535\t0.7247\t63.7843\t0.844\t0\t0.0559\t0.3651\t17.303\t0.8378\t0\t0.0289\t0.0706\t0.336\t1.2\tchr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:65,spanning_paired_2:65,spanning_singleton_1:2,spanning_singleton_1_r:3,spanning_singleton_2:2,spanning_singleton_2_r:3)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(discordant_mates:10,spanning_paired_1:6,spanning_paired_1_t:1,spanning_paired_2:6,spanning_paired_2_t:1,spanning_singleton_1_r:2,spanning_singleton_2_r:2)&chr21:39817544/39817545(-)->chr21:42878371/42878372(+):(discordant_mates:2,spanning_paired_1:1,spanning_paired_1_t:1,spanning_paired_2:1,spanning_paired_2_t:1,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:39846044/39846045(-)->chr21:42879876/42879877(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:39817544/39817545(-)->chr21:42876293/42876294(+):(spanning_paired_1:1,spanning_paired_2:1)\n-chr21\t39877811\t-\t98\t0\tchr21\t42873374\t+\t0\t98\t2995563\tvalid\tlinear\tintronic\t91\t42\t21\t28\t10000\t0\t1\t1\t1\t0\t0\t0.9528\t0.9528\t0\t0.82\t2.9207\t17.3314\t0.9125\t0\t0.191\t1.588\t68.1747\t0.8769\t0\t0.1269\t1.3333\t0.2308\t2\tchr21:39877811/39877812(-)->chr21:42873374/42873375(+):(discordant_mates:56,spanning_paired_1:12,spanning_paired_1_t:9,spanning_paired_2:12,spanning_paired_2_t:9)\n-chr21\t42861433\t+\t6\t18\tchr21\t42866505\t-\t18\t6\t5072\tn_discordant_reads=2<3\tcircular\texonic\t41\t30\t14\t2\t10000\t0\t7\t5\t6\t1\t2\t1\t0.9375\t18.7474\t0.75\t26.9\t3\t0.9425\t0.0164\t5.5097\t20.1\t42.8\t0.8833\t0.047\t6.1587\t0.1429\t0.3659\t1.5714\tchr21:42861433/42861434(+)->chr21:42866505/42866506(-):(discordant_mates:2,spanning_paired_1:2,spanning_paired_1_t:1,spanning_paired_2:2,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42861433/42861434(+)->chr21:42870116/42870117(-):(spanning_paired_1:3,spanning_paired_2:3,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:42860568/42860569(+)->chr21:42867210/42867211(-):(spanning_paired_1_t:2,spanning_paired_2_t:2)&chr21:42860320/42860321(+)->chr21:42861520/42861521(-):(spanning_paired_1:1,spanning_paired_2:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42859986/42859987(+)->chr21:42863878/42863879(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:42860320/42860321(+)->chr21:42866505/42866506(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:42866446/42866447(+)->chr21:42870110/42870111(-):(discordant_mates:2)\n-chr21\t39836011\t+\t0\t8\tchr21\t39836545\t-\t8\t0\t534\tn_support=6<8,bp_pos_stddev=25.3065>15.0,log_ratio_slope=9.62>1.8,log_ratio_rvalue=8.96>0.4\tcircular\tintronic\t17\t12\t6\t0\t10000\t0\t2\t2\t2\t0\t0\t0.4056\t0.6934\t25.3065\t0\t1.5\t29.5\t0.7746\t0.2254\t0.866\t0\t93\t0\t1\t0\t0\t0.3529\t2\tchr21:39836011/39836012(+)->chr21:39836545/39836546(-):(spanning_paired_1_t:4,spanning_paired_2_t:4)&chr21:39835707/39835708(+)->chr21:39839850/39839851(-):(spanning_paired_1_t:1,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)\n-chr21\t39875880\t+\t0\t6\tchr21\t39876476\t-\t6\t0\t596\tentropy=0.0<0.6839,n_support=4<8\tcircular\tintronic\t12\t8\t4\t0\t10000\t0\t2\t2\t2\t0\t0\t0\t0.4056\t0\t0\t0\t68\t0\t1\t0\t0\t58\t0\t1\t0\t0\t0.3333\t2\tchr21:39875880/39875881(+)->chr21:39876476/39876477(-):(spanning_paired_1:3,spanning_paired_2:3)&chr21:39874280/39874281(+)->chr21:39876277/39876278(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n-chr21\t39851814\t+\t0\t6\tchr21\t39852667\t-\t6\t0\t853\tentropy=0.0<0.6835,n_support=3<7\tcircular\tintro'..b'port=1<7,n_lr_symmetry=104.05>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t101\t0\t1\t0\t0\t25\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39863020/39863021(+)->chr21:39863629/39863630(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t39871034\t+\t0\t2\tchr21\t39877568\t-\t2\t0\t6534\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=72.92>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t31\t0\t1\t0\t0\t66\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39871034/39871035(+)->chr21:39877568/39877569(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42836581\t+\t0\t2\tchr21\t42839672\t-\t2\t0\t3091\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=108.67>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t19\t0\t1\t0\t0\t107\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42836581/42836582(+)->chr21:42839672/42839673(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42853701\t+\t0\t2\tchr21\t42860029\t-\t2\t0\t6328\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=38.01>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t22\t0\t1\t0\t0\t31\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42853701/42853702(+)->chr21:42860029/42860030(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42866483\t-\t0\t2\tchr21\t42870116\t-\t2\t0\t3633\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=95.85>=24.68\tlinear\tintronic\t3\t9\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t38\t0\t1\t0\t0\t88\t0\t1\t0\t0\t1.5\t2\t50\t50\t50\t50\tchr21:42866483/42866484(-)->chr21:42870116/42870117(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42839824\t+\t0\t4\tchr21\t42840323\t-\t4\t0\t499\tn_support=2<7,log_ratio_slope=12.99>1.8,log_ratio_rvalue=9.21>0.4\tcircular\tintronic\t2\t2\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t1\t1\t0\t0.4056\t44\t82\t1\t0\t0\t0\t120\t0\t1\t0\t40\t0.5\t2\t50\t50\t50\t50\tchr21:42839824/42839825(+)->chr21:42840323/42840324(-):(discordant_mates:4)\n+chr21\t39770910\t+\t2\t0\tchr21\t39771416\t-\t0\t2\t506\tentropy=0.0<0.6827,n_support=1<7,n_lr_symmetry=89.04>=28.44\tcircular\tintronic\t2\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t75\t0\t1\t0\t0\t48\t0\t1\t0\t0\t0.5\t2\t50\t50\t50\t50\tchr21:39770910/39770911(+)->chr21:39771416/39771417(-):(spanning_singleton_1_r:1,spanning_singleton_2_r:1)\n+chr21\t39860702\t-\t4\t0\tchr21\t42843890\t+\t0\t4\t2983188\tentropy=0.0<0.6827,n_support=2<7,n_lr_symmetry=178.19>=28.44\tlinear\tintronic\t2\t0\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t40\t0\t2\t50\t50\t50\t50\tchr21:39860702/39860703(-)->chr21:42843890/42843891(+):(discordant_mates:4)\n+chr21\t39781087\t+\t0\t2\tchr21\t39782101\t-\t2\t0\t1014\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39781087/39781088(+)->chr21:39782101/39782102(-):(discordant_mates:2)\n+chr21\t39846131\t+\t0\t2\tchr21\t39846834\t-\t2\t0\t703\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=131.9>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t39\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39846131/39846132(+)->chr21:39846834/39846835(-):(discordant_mates:2)\n+chr21\t39853321\t-\t2\t0\tchr21\t42851610\t+\t0\t2\t2998289\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tlinear\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39853321/39853322(-)->chr21:42851610/42851611(+):(discordant_mates:2)\n+chr21\t42840341\t+\t0\t2\tchr21\t42842586\t-\t2\t0\t2245\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=175.36>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t124\t0\t1\t0\t0\t124\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42840341/42840342(+)->chr21:42842586/42842587(-):(discordant_mates:2)\n+chr21\t42843861\t+\t2\t0\tchr21\t42845272\t-\t0\t2\t1411\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=88.46>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t65\t0\t1\t0\t0\t60\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42843861/42843862(+)->chr21:42845272/42845273(-):(discordant_mates:2)\n+chr21\t42863757\t+\t0\t2\tchr21\t42864220\t-\t2\t0\t463\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=176.08>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t123\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42863757/42863758(+)->chr21:42864220/42864221(-):(discordant_mates:2)\n' |
| b |
| diff -r c3ce472a315f -r f2c70d589596 test-data/classify_test_16.test-05.out.dbed --- a/test-data/classify_test_16.test-05.out.dbed Tue Sep 26 08:27:47 2017 -0400 +++ b/test-data/classify_test_16.test-05.out.dbed Thu Nov 02 05:17:31 2017 -0400 |
| b |
| b'@@ -1,37 +1,37 @@\n-chr-A\tpos-A\tdirection-A\tpos-A-acceptor\tpos-A-donor\tchr-B\tpos-B\tdirection-B\tpos-A-acceptor\tpos-A-donor\tgenomic-distance\tfilter-status\tcircRNA\tintronic/exonic\tscore\tsoft+hardclips\tn-split-reads\tn-discordant-reads\talignment-score\tmismatches\tn-edges\tn-nodes-A\tn-nodes-B\tn-splice-junc-A\tn-splice-junc-B\tentropy-bp-edge\tentropy-all-edges\tbp-pos-stddev\tentropy-disco-bps\tlr-A-slope\tlr-A-intercept\tlr-A-rvalue\tlr-A-pvalue\tlr-A-stderr\tlr-B-slope\tlr-B-intercept\tlr-B-rvalue\tlr-B-pvalue\tlr-B-stderr\tdisco/split\tclips/score\tnodes/edge\tdata-structure\n-chr21\t39817544\t-\t140\t0\tchr21\t42880007\t+\t0\t140\t3062463\tvalid\tlinear\texonic\t253\t170\t85\t6\t10000\t0\t5\t2\t4\t1\t0\t0.8111\t0.8497\t0\t0.9535\t0.7247\t63.7843\t0.844\t0\t0.0559\t0.3651\t17.303\t0.8378\t0\t0.0289\t0.0706\t0.336\t1.2\tchr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:65,spanning_paired_2:65,spanning_singleton_1:2,spanning_singleton_1_r:3,spanning_singleton_2:2,spanning_singleton_2_r:3)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(discordant_mates:10,spanning_paired_1:6,spanning_paired_1_t:1,spanning_paired_2:6,spanning_paired_2_t:1,spanning_singleton_1_r:2,spanning_singleton_2_r:2)&chr21:39817544/39817545(-)->chr21:42878371/42878372(+):(discordant_mates:2,spanning_paired_1:1,spanning_paired_1_t:1,spanning_paired_2:1,spanning_paired_2_t:1,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:39846044/39846045(-)->chr21:42879876/42879877(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:39817544/39817545(-)->chr21:42876293/42876294(+):(spanning_paired_1:1,spanning_paired_2:1)\n-chr21\t39877811\t-\t98\t0\tchr21\t42873374\t+\t0\t98\t2995563\tvalid\tlinear\tintronic\t91\t42\t21\t28\t10000\t0\t1\t1\t1\t0\t0\t0.9528\t0.9528\t0\t0.82\t2.9207\t17.3314\t0.9125\t0\t0.191\t1.588\t68.1747\t0.8769\t0\t0.1269\t1.3333\t0.2308\t2\tchr21:39877811/39877812(-)->chr21:42873374/42873375(+):(discordant_mates:56,spanning_paired_1:12,spanning_paired_1_t:9,spanning_paired_2:12,spanning_paired_2_t:9)\n-chr21\t42861433\t+\t6\t18\tchr21\t42866505\t-\t18\t6\t5072\tn_discordant_reads=2<3\tcircular\texonic\t41\t30\t14\t2\t10000\t0\t7\t5\t6\t1\t2\t1\t0.9375\t18.7474\t0.75\t26.9\t3\t0.9425\t0.0164\t5.5097\t20.1\t42.8\t0.8833\t0.047\t6.1587\t0.1429\t0.3659\t1.5714\tchr21:42861433/42861434(+)->chr21:42866505/42866506(-):(discordant_mates:2,spanning_paired_1:2,spanning_paired_1_t:1,spanning_paired_2:2,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42861433/42861434(+)->chr21:42870116/42870117(-):(spanning_paired_1:3,spanning_paired_2:3,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:42860568/42860569(+)->chr21:42867210/42867211(-):(spanning_paired_1_t:2,spanning_paired_2_t:2)&chr21:42860320/42860321(+)->chr21:42861520/42861521(-):(spanning_paired_1:1,spanning_paired_2:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42859986/42859987(+)->chr21:42863878/42863879(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:42860320/42860321(+)->chr21:42866505/42866506(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:42866446/42866447(+)->chr21:42870110/42870111(-):(discordant_mates:2)\n-chr21\t39836011\t+\t0\t8\tchr21\t39836545\t-\t8\t0\t534\tn_support=6<8,bp_pos_stddev=25.3065>15.0,log_ratio_slope=9.62>1.8,log_ratio_rvalue=8.96>0.4\tcircular\tintronic\t17\t12\t6\t0\t10000\t0\t2\t2\t2\t0\t0\t0.4056\t0.6934\t25.3065\t0\t1.5\t29.5\t0.7746\t0.2254\t0.866\t0\t93\t0\t1\t0\t0\t0.3529\t2\tchr21:39836011/39836012(+)->chr21:39836545/39836546(-):(spanning_paired_1_t:4,spanning_paired_2_t:4)&chr21:39835707/39835708(+)->chr21:39839850/39839851(-):(spanning_paired_1_t:1,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)\n-chr21\t39875880\t+\t0\t6\tchr21\t39876476\t-\t6\t0\t596\tentropy=0.0<0.6839,n_support=4<8\tcircular\tintronic\t12\t8\t4\t0\t10000\t0\t2\t2\t2\t0\t0\t0\t0.4056\t0\t0\t0\t68\t0\t1\t0\t0\t58\t0\t1\t0\t0\t0.3333\t2\tchr21:39875880/39875881(+)->chr21:39876476/39876477(-):(spanning_paired_1:3,spanning_paired_2:3)&chr21:39874280/39874281(+)->chr21:39876277/39876278(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n-chr21\t39851814\t+\t0\t6\tchr21\t39852667\t-\t6\t0\t853\tentropy=0.0<0.6835,n_support=3<7\tcircular\tintro'..b'port=1<7,n_lr_symmetry=104.05>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t101\t0\t1\t0\t0\t25\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39863020/39863021(+)->chr21:39863629/39863630(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t39871034\t+\t0\t2\tchr21\t39877568\t-\t2\t0\t6534\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=72.92>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t31\t0\t1\t0\t0\t66\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39871034/39871035(+)->chr21:39877568/39877569(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42836581\t+\t0\t2\tchr21\t42839672\t-\t2\t0\t3091\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=108.67>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t19\t0\t1\t0\t0\t107\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42836581/42836582(+)->chr21:42839672/42839673(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42853701\t+\t0\t2\tchr21\t42860029\t-\t2\t0\t6328\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=38.01>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t22\t0\t1\t0\t0\t31\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42853701/42853702(+)->chr21:42860029/42860030(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42866483\t-\t0\t2\tchr21\t42870116\t-\t2\t0\t3633\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=95.85>=24.68\tlinear\tintronic\t3\t9\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t38\t0\t1\t0\t0\t88\t0\t1\t0\t0\t1.5\t2\t50\t50\t50\t50\tchr21:42866483/42866484(-)->chr21:42870116/42870117(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42839824\t+\t0\t4\tchr21\t42840323\t-\t4\t0\t499\tn_support=2<7,log_ratio_slope=12.99>1.8,log_ratio_rvalue=9.21>0.4\tcircular\tintronic\t2\t2\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t1\t1\t0\t0.4056\t44\t82\t1\t0\t0\t0\t120\t0\t1\t0\t40\t0.5\t2\t50\t50\t50\t50\tchr21:42839824/42839825(+)->chr21:42840323/42840324(-):(discordant_mates:4)\n+chr21\t39770910\t+\t2\t0\tchr21\t39771416\t-\t0\t2\t506\tentropy=0.0<0.6827,n_support=1<7,n_lr_symmetry=89.04>=28.44\tcircular\tintronic\t2\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t75\t0\t1\t0\t0\t48\t0\t1\t0\t0\t0.5\t2\t50\t50\t50\t50\tchr21:39770910/39770911(+)->chr21:39771416/39771417(-):(spanning_singleton_1_r:1,spanning_singleton_2_r:1)\n+chr21\t39860702\t-\t4\t0\tchr21\t42843890\t+\t0\t4\t2983188\tentropy=0.0<0.6827,n_support=2<7,n_lr_symmetry=178.19>=28.44\tlinear\tintronic\t2\t0\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t40\t0\t2\t50\t50\t50\t50\tchr21:39860702/39860703(-)->chr21:42843890/42843891(+):(discordant_mates:4)\n+chr21\t39781087\t+\t0\t2\tchr21\t39782101\t-\t2\t0\t1014\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39781087/39781088(+)->chr21:39782101/39782102(-):(discordant_mates:2)\n+chr21\t39846131\t+\t0\t2\tchr21\t39846834\t-\t2\t0\t703\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=131.9>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t39\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39846131/39846132(+)->chr21:39846834/39846835(-):(discordant_mates:2)\n+chr21\t39853321\t-\t2\t0\tchr21\t42851610\t+\t0\t2\t2998289\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tlinear\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39853321/39853322(-)->chr21:42851610/42851611(+):(discordant_mates:2)\n+chr21\t42840341\t+\t0\t2\tchr21\t42842586\t-\t2\t0\t2245\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=175.36>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t124\t0\t1\t0\t0\t124\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42840341/42840342(+)->chr21:42842586/42842587(-):(discordant_mates:2)\n+chr21\t42843861\t+\t2\t0\tchr21\t42845272\t-\t0\t2\t1411\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=88.46>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t65\t0\t1\t0\t0\t60\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42843861/42843862(+)->chr21:42845272/42845273(-):(discordant_mates:2)\n+chr21\t42863757\t+\t0\t2\tchr21\t42864220\t-\t2\t0\t463\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=176.08>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t123\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42863757/42863758(+)->chr21:42864220/42864221(-):(discordant_mates:2)\n' |
| b |
| diff -r c3ce472a315f -r f2c70d589596 test-data/classify_test_16.test-06.out.dbed --- a/test-data/classify_test_16.test-06.out.dbed Tue Sep 26 08:27:47 2017 -0400 +++ b/test-data/classify_test_16.test-06.out.dbed Thu Nov 02 05:17:31 2017 -0400 |
| b |
| b'@@ -1,37 +1,37 @@\n-chr-A\tpos-A\tdirection-A\tpos-A-acceptor\tpos-A-donor\tchr-B\tpos-B\tdirection-B\tpos-A-acceptor\tpos-A-donor\tgenomic-distance\tfilter-status\tcircRNA\tintronic/exonic\tscore\tsoft+hardclips\tn-split-reads\tn-discordant-reads\talignment-score\tmismatches\tn-edges\tn-nodes-A\tn-nodes-B\tn-splice-junc-A\tn-splice-junc-B\tentropy-bp-edge\tentropy-all-edges\tbp-pos-stddev\tentropy-disco-bps\tlr-A-slope\tlr-A-intercept\tlr-A-rvalue\tlr-A-pvalue\tlr-A-stderr\tlr-B-slope\tlr-B-intercept\tlr-B-rvalue\tlr-B-pvalue\tlr-B-stderr\tdisco/split\tclips/score\tnodes/edge\tdata-structure\n-chr21\t39817544\t-\t140\t0\tchr21\t42880007\t+\t0\t140\t3062463\tvalid\tlinear\texonic\t253\t170\t85\t6\t10000\t0\t5\t2\t4\t1\t0\t0.8111\t0.8497\t0\t0.9535\t0.7247\t63.7843\t0.844\t0\t0.0559\t0.3651\t17.303\t0.8378\t0\t0.0289\t0.0706\t0.336\t1.2\tchr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:65,spanning_paired_2:65,spanning_singleton_1:2,spanning_singleton_1_r:3,spanning_singleton_2:2,spanning_singleton_2_r:3)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(discordant_mates:10,spanning_paired_1:6,spanning_paired_1_t:1,spanning_paired_2:6,spanning_paired_2_t:1,spanning_singleton_1_r:2,spanning_singleton_2_r:2)&chr21:39817544/39817545(-)->chr21:42878371/42878372(+):(discordant_mates:2,spanning_paired_1:1,spanning_paired_1_t:1,spanning_paired_2:1,spanning_paired_2_t:1,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:39846044/39846045(-)->chr21:42879876/42879877(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:39817544/39817545(-)->chr21:42876293/42876294(+):(spanning_paired_1:1,spanning_paired_2:1)\n-chr21\t39877811\t-\t98\t0\tchr21\t42873374\t+\t0\t98\t2995563\tvalid\tlinear\tintronic\t91\t42\t21\t28\t10000\t0\t1\t1\t1\t0\t0\t0.9528\t0.9528\t0\t0.82\t2.9207\t17.3314\t0.9125\t0\t0.191\t1.588\t68.1747\t0.8769\t0\t0.1269\t1.3333\t0.2308\t2\tchr21:39877811/39877812(-)->chr21:42873374/42873375(+):(discordant_mates:56,spanning_paired_1:12,spanning_paired_1_t:9,spanning_paired_2:12,spanning_paired_2_t:9)\n-chr21\t42861433\t+\t6\t18\tchr21\t42866505\t-\t18\t6\t5072\tn_discordant_reads=2<3\tcircular\texonic\t41\t30\t14\t2\t10000\t0\t7\t5\t6\t1\t2\t1\t0.9375\t18.7474\t0.75\t26.9\t3\t0.9425\t0.0164\t5.5097\t20.1\t42.8\t0.8833\t0.047\t6.1587\t0.1429\t0.3659\t1.5714\tchr21:42861433/42861434(+)->chr21:42866505/42866506(-):(discordant_mates:2,spanning_paired_1:2,spanning_paired_1_t:1,spanning_paired_2:2,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42861433/42861434(+)->chr21:42870116/42870117(-):(spanning_paired_1:3,spanning_paired_2:3,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:42860568/42860569(+)->chr21:42867210/42867211(-):(spanning_paired_1_t:2,spanning_paired_2_t:2)&chr21:42860320/42860321(+)->chr21:42861520/42861521(-):(spanning_paired_1:1,spanning_paired_2:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42859986/42859987(+)->chr21:42863878/42863879(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:42860320/42860321(+)->chr21:42866505/42866506(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:42866446/42866447(+)->chr21:42870110/42870111(-):(discordant_mates:2)\n-chr21\t39836011\t+\t0\t8\tchr21\t39836545\t-\t8\t0\t534\tn_support=6<8,bp_pos_stddev=25.3065>15.0,log_ratio_slope=9.62>1.8,log_ratio_rvalue=8.96>0.4\tcircular\tintronic\t17\t12\t6\t0\t10000\t0\t2\t2\t2\t0\t0\t0.4056\t0.6934\t25.3065\t0\t1.5\t29.5\t0.7746\t0.2254\t0.866\t0\t93\t0\t1\t0\t0\t0.3529\t2\tchr21:39836011/39836012(+)->chr21:39836545/39836546(-):(spanning_paired_1_t:4,spanning_paired_2_t:4)&chr21:39835707/39835708(+)->chr21:39839850/39839851(-):(spanning_paired_1_t:1,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)\n-chr21\t39875880\t+\t0\t6\tchr21\t39876476\t-\t6\t0\t596\tentropy=0.0<0.6839,n_support=4<8\tcircular\tintronic\t12\t8\t4\t0\t10000\t0\t2\t2\t2\t0\t0\t0\t0.4056\t0\t0\t0\t68\t0\t1\t0\t0\t58\t0\t1\t0\t0\t0.3333\t2\tchr21:39875880/39875881(+)->chr21:39876476/39876477(-):(spanning_paired_1:3,spanning_paired_2:3)&chr21:39874280/39874281(+)->chr21:39876277/39876278(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n-chr21\t39851814\t+\t0\t6\tchr21\t39852667\t-\t6\t0\t853\tentropy=0.0<0.6835,n_support=3<7\tcircular\tintro'..b'port=1<7,n_lr_symmetry=104.05>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t101\t0\t1\t0\t0\t25\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39863020/39863021(+)->chr21:39863629/39863630(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t39871034\t+\t0\t2\tchr21\t39877568\t-\t2\t0\t6534\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=72.92>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t31\t0\t1\t0\t0\t66\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39871034/39871035(+)->chr21:39877568/39877569(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42836581\t+\t0\t2\tchr21\t42839672\t-\t2\t0\t3091\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=108.67>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t19\t0\t1\t0\t0\t107\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42836581/42836582(+)->chr21:42839672/42839673(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42853701\t+\t0\t2\tchr21\t42860029\t-\t2\t0\t6328\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=38.01>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t22\t0\t1\t0\t0\t31\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42853701/42853702(+)->chr21:42860029/42860030(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42866483\t-\t0\t2\tchr21\t42870116\t-\t2\t0\t3633\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=95.85>=24.68\tlinear\tintronic\t3\t9\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t38\t0\t1\t0\t0\t88\t0\t1\t0\t0\t1.5\t2\t50\t50\t50\t50\tchr21:42866483/42866484(-)->chr21:42870116/42870117(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42839824\t+\t0\t4\tchr21\t42840323\t-\t4\t0\t499\tn_support=2<7,log_ratio_slope=12.99>1.8,log_ratio_rvalue=9.21>0.4\tcircular\tintronic\t2\t2\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t1\t1\t0\t0.4056\t44\t82\t1\t0\t0\t0\t120\t0\t1\t0\t40\t0.5\t2\t50\t50\t50\t50\tchr21:42839824/42839825(+)->chr21:42840323/42840324(-):(discordant_mates:4)\n+chr21\t39770910\t+\t2\t0\tchr21\t39771416\t-\t0\t2\t506\tentropy=0.0<0.6827,n_support=1<7,n_lr_symmetry=89.04>=28.44\tcircular\tintronic\t2\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t75\t0\t1\t0\t0\t48\t0\t1\t0\t0\t0.5\t2\t50\t50\t50\t50\tchr21:39770910/39770911(+)->chr21:39771416/39771417(-):(spanning_singleton_1_r:1,spanning_singleton_2_r:1)\n+chr21\t39860702\t-\t4\t0\tchr21\t42843890\t+\t0\t4\t2983188\tentropy=0.0<0.6827,n_support=2<7,n_lr_symmetry=178.19>=28.44\tlinear\tintronic\t2\t0\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t40\t0\t2\t50\t50\t50\t50\tchr21:39860702/39860703(-)->chr21:42843890/42843891(+):(discordant_mates:4)\n+chr21\t39781087\t+\t0\t2\tchr21\t39782101\t-\t2\t0\t1014\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39781087/39781088(+)->chr21:39782101/39782102(-):(discordant_mates:2)\n+chr21\t39846131\t+\t0\t2\tchr21\t39846834\t-\t2\t0\t703\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=131.9>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t39\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39846131/39846132(+)->chr21:39846834/39846835(-):(discordant_mates:2)\n+chr21\t39853321\t-\t2\t0\tchr21\t42851610\t+\t0\t2\t2998289\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tlinear\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39853321/39853322(-)->chr21:42851610/42851611(+):(discordant_mates:2)\n+chr21\t42840341\t+\t0\t2\tchr21\t42842586\t-\t2\t0\t2245\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=175.36>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t124\t0\t1\t0\t0\t124\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42840341/42840342(+)->chr21:42842586/42842587(-):(discordant_mates:2)\n+chr21\t42843861\t+\t2\t0\tchr21\t42845272\t-\t0\t2\t1411\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=88.46>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t65\t0\t1\t0\t0\t60\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42843861/42843862(+)->chr21:42845272/42845273(-):(discordant_mates:2)\n+chr21\t42863757\t+\t0\t2\tchr21\t42864220\t-\t2\t0\t463\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=176.08>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t123\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42863757/42863758(+)->chr21:42864220/42864221(-):(discordant_mates:2)\n' |
| b |
| diff -r c3ce472a315f -r f2c70d589596 test-data/classify_test_16.test-07.out.dbed --- a/test-data/classify_test_16.test-07.out.dbed Tue Sep 26 08:27:47 2017 -0400 +++ b/test-data/classify_test_16.test-07.out.dbed Thu Nov 02 05:17:31 2017 -0400 |
| b |
| b'@@ -1,37 +1,37 @@\n-chr-A\tpos-A\tdirection-A\tpos-A-acceptor\tpos-A-donor\tchr-B\tpos-B\tdirection-B\tpos-A-acceptor\tpos-A-donor\tgenomic-distance\tfilter-status\tcircRNA\tintronic/exonic\tscore\tsoft+hardclips\tn-split-reads\tn-discordant-reads\talignment-score\tmismatches\tn-edges\tn-nodes-A\tn-nodes-B\tn-splice-junc-A\tn-splice-junc-B\tentropy-bp-edge\tentropy-all-edges\tbp-pos-stddev\tentropy-disco-bps\tlr-A-slope\tlr-A-intercept\tlr-A-rvalue\tlr-A-pvalue\tlr-A-stderr\tlr-B-slope\tlr-B-intercept\tlr-B-rvalue\tlr-B-pvalue\tlr-B-stderr\tdisco/split\tclips/score\tnodes/edge\tdata-structure\n-chr21\t39817544\t-\t140\t0\tchr21\t42880007\t+\t0\t140\t3062463\tvalid\tlinear\texonic\t253\t170\t85\t6\t10000\t0\t5\t2\t4\t1\t0\t0.8111\t0.8497\t0\t0.9535\t0.7247\t63.7843\t0.844\t0\t0.0559\t0.3651\t17.303\t0.8378\t0\t0.0289\t0.0706\t0.336\t1.2\tchr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:65,spanning_paired_2:65,spanning_singleton_1:2,spanning_singleton_1_r:3,spanning_singleton_2:2,spanning_singleton_2_r:3)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(discordant_mates:10,spanning_paired_1:6,spanning_paired_1_t:1,spanning_paired_2:6,spanning_paired_2_t:1,spanning_singleton_1_r:2,spanning_singleton_2_r:2)&chr21:39817544/39817545(-)->chr21:42878371/42878372(+):(discordant_mates:2,spanning_paired_1:1,spanning_paired_1_t:1,spanning_paired_2:1,spanning_paired_2_t:1,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:39846044/39846045(-)->chr21:42879876/42879877(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:39817544/39817545(-)->chr21:42876293/42876294(+):(spanning_paired_1:1,spanning_paired_2:1)\n-chr21\t39877811\t-\t98\t0\tchr21\t42873374\t+\t0\t98\t2995563\tvalid\tlinear\tintronic\t91\t42\t21\t28\t10000\t0\t1\t1\t1\t0\t0\t0.9528\t0.9528\t0\t0.82\t2.9207\t17.3314\t0.9125\t0\t0.191\t1.588\t68.1747\t0.8769\t0\t0.1269\t1.3333\t0.2308\t2\tchr21:39877811/39877812(-)->chr21:42873374/42873375(+):(discordant_mates:56,spanning_paired_1:12,spanning_paired_1_t:9,spanning_paired_2:12,spanning_paired_2_t:9)\n-chr21\t42861433\t+\t6\t18\tchr21\t42866505\t-\t18\t6\t5072\tn_discordant_reads=2<3\tcircular\texonic\t41\t30\t14\t2\t10000\t0\t7\t5\t6\t1\t2\t1\t0.9375\t18.7474\t0.75\t26.9\t3\t0.9425\t0.0164\t5.5097\t20.1\t42.8\t0.8833\t0.047\t6.1587\t0.1429\t0.3659\t1.5714\tchr21:42861433/42861434(+)->chr21:42866505/42866506(-):(discordant_mates:2,spanning_paired_1:2,spanning_paired_1_t:1,spanning_paired_2:2,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42861433/42861434(+)->chr21:42870116/42870117(-):(spanning_paired_1:3,spanning_paired_2:3,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:42860568/42860569(+)->chr21:42867210/42867211(-):(spanning_paired_1_t:2,spanning_paired_2_t:2)&chr21:42860320/42860321(+)->chr21:42861520/42861521(-):(spanning_paired_1:1,spanning_paired_2:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42859986/42859987(+)->chr21:42863878/42863879(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:42860320/42860321(+)->chr21:42866505/42866506(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:42866446/42866447(+)->chr21:42870110/42870111(-):(discordant_mates:2)\n-chr21\t39836011\t+\t0\t8\tchr21\t39836545\t-\t8\t0\t534\tn_support=6<8,bp_pos_stddev=25.3065>15.0,log_ratio_slope=9.62>1.8,log_ratio_rvalue=8.96>0.4\tcircular\tintronic\t17\t12\t6\t0\t10000\t0\t2\t2\t2\t0\t0\t0.4056\t0.6934\t25.3065\t0\t1.5\t29.5\t0.7746\t0.2254\t0.866\t0\t93\t0\t1\t0\t0\t0.3529\t2\tchr21:39836011/39836012(+)->chr21:39836545/39836546(-):(spanning_paired_1_t:4,spanning_paired_2_t:4)&chr21:39835707/39835708(+)->chr21:39839850/39839851(-):(spanning_paired_1_t:1,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)\n-chr21\t39875880\t+\t0\t6\tchr21\t39876476\t-\t6\t0\t596\tentropy=0.0<0.6839,n_support=4<8\tcircular\tintronic\t12\t8\t4\t0\t10000\t0\t2\t2\t2\t0\t0\t0\t0.4056\t0\t0\t0\t68\t0\t1\t0\t0\t58\t0\t1\t0\t0\t0.3333\t2\tchr21:39875880/39875881(+)->chr21:39876476/39876477(-):(spanning_paired_1:3,spanning_paired_2:3)&chr21:39874280/39874281(+)->chr21:39876277/39876278(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n-chr21\t39851814\t+\t0\t6\tchr21\t39852667\t-\t6\t0\t853\tentropy=0.0<0.6835,n_support=3<7\tcircular\tintro'..b'port=1<7,n_lr_symmetry=104.05>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t101\t0\t1\t0\t0\t25\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39863020/39863021(+)->chr21:39863629/39863630(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t39871034\t+\t0\t2\tchr21\t39877568\t-\t2\t0\t6534\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=72.92>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t31\t0\t1\t0\t0\t66\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39871034/39871035(+)->chr21:39877568/39877569(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42836581\t+\t0\t2\tchr21\t42839672\t-\t2\t0\t3091\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=108.67>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t19\t0\t1\t0\t0\t107\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42836581/42836582(+)->chr21:42839672/42839673(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42853701\t+\t0\t2\tchr21\t42860029\t-\t2\t0\t6328\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=38.01>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t22\t0\t1\t0\t0\t31\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42853701/42853702(+)->chr21:42860029/42860030(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42866483\t-\t0\t2\tchr21\t42870116\t-\t2\t0\t3633\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=95.85>=24.68\tlinear\tintronic\t3\t9\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t38\t0\t1\t0\t0\t88\t0\t1\t0\t0\t1.5\t2\t50\t50\t50\t50\tchr21:42866483/42866484(-)->chr21:42870116/42870117(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42839824\t+\t0\t4\tchr21\t42840323\t-\t4\t0\t499\tn_support=2<7,log_ratio_slope=12.99>1.8,log_ratio_rvalue=9.21>0.4\tcircular\tintronic\t2\t2\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t1\t1\t0\t0.4056\t44\t82\t1\t0\t0\t0\t120\t0\t1\t0\t40\t0.5\t2\t50\t50\t50\t50\tchr21:42839824/42839825(+)->chr21:42840323/42840324(-):(discordant_mates:4)\n+chr21\t39770910\t+\t2\t0\tchr21\t39771416\t-\t0\t2\t506\tentropy=0.0<0.6827,n_support=1<7,n_lr_symmetry=89.04>=28.44\tcircular\tintronic\t2\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t75\t0\t1\t0\t0\t48\t0\t1\t0\t0\t0.5\t2\t50\t50\t50\t50\tchr21:39770910/39770911(+)->chr21:39771416/39771417(-):(spanning_singleton_1_r:1,spanning_singleton_2_r:1)\n+chr21\t39860702\t-\t4\t0\tchr21\t42843890\t+\t0\t4\t2983188\tentropy=0.0<0.6827,n_support=2<7,n_lr_symmetry=178.19>=28.44\tlinear\tintronic\t2\t0\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t40\t0\t2\t50\t50\t50\t50\tchr21:39860702/39860703(-)->chr21:42843890/42843891(+):(discordant_mates:4)\n+chr21\t39781087\t+\t0\t2\tchr21\t39782101\t-\t2\t0\t1014\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39781087/39781088(+)->chr21:39782101/39782102(-):(discordant_mates:2)\n+chr21\t39846131\t+\t0\t2\tchr21\t39846834\t-\t2\t0\t703\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=131.9>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t39\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39846131/39846132(+)->chr21:39846834/39846835(-):(discordant_mates:2)\n+chr21\t39853321\t-\t2\t0\tchr21\t42851610\t+\t0\t2\t2998289\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tlinear\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39853321/39853322(-)->chr21:42851610/42851611(+):(discordant_mates:2)\n+chr21\t42840341\t+\t0\t2\tchr21\t42842586\t-\t2\t0\t2245\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=175.36>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t124\t0\t1\t0\t0\t124\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42840341/42840342(+)->chr21:42842586/42842587(-):(discordant_mates:2)\n+chr21\t42843861\t+\t2\t0\tchr21\t42845272\t-\t0\t2\t1411\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=88.46>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t65\t0\t1\t0\t0\t60\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42843861/42843862(+)->chr21:42845272/42845273(-):(discordant_mates:2)\n+chr21\t42863757\t+\t0\t2\tchr21\t42864220\t-\t2\t0\t463\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=176.08>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t123\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42863757/42863758(+)->chr21:42864220/42864221(-):(discordant_mates:2)\n' |
| b |
| diff -r c3ce472a315f -r f2c70d589596 test-data/classify_test_16.test-08.out.dbed --- a/test-data/classify_test_16.test-08.out.dbed Tue Sep 26 08:27:47 2017 -0400 +++ b/test-data/classify_test_16.test-08.out.dbed Thu Nov 02 05:17:31 2017 -0400 |
| b |
| b'@@ -1,37 +1,37 @@\n-chr-A\tpos-A\tdirection-A\tpos-A-acceptor\tpos-A-donor\tchr-B\tpos-B\tdirection-B\tpos-A-acceptor\tpos-A-donor\tgenomic-distance\tfilter-status\tcircRNA\tintronic/exonic\tscore\tsoft+hardclips\tn-split-reads\tn-discordant-reads\talignment-score\tmismatches\tn-edges\tn-nodes-A\tn-nodes-B\tn-splice-junc-A\tn-splice-junc-B\tentropy-bp-edge\tentropy-all-edges\tbp-pos-stddev\tentropy-disco-bps\tlr-A-slope\tlr-A-intercept\tlr-A-rvalue\tlr-A-pvalue\tlr-A-stderr\tlr-B-slope\tlr-B-intercept\tlr-B-rvalue\tlr-B-pvalue\tlr-B-stderr\tdisco/split\tclips/score\tnodes/edge\tdata-structure\n-chr21\t39817544\t-\t140\t0\tchr21\t42880007\t+\t0\t140\t3062463\tvalid\tlinear\texonic\t253\t170\t85\t6\t10000\t0\t5\t2\t4\t1\t0\t0.8111\t0.8497\t0\t0.9535\t0.7247\t63.7843\t0.844\t0\t0.0559\t0.3651\t17.303\t0.8378\t0\t0.0289\t0.0706\t0.336\t1.2\tchr21:39817544/39817545(-)->chr21:42880007/42880008(+):(spanning_paired_1:65,spanning_paired_2:65,spanning_singleton_1:2,spanning_singleton_1_r:3,spanning_singleton_2:2,spanning_singleton_2_r:3)&chr21:39817544/39817545(-)->chr21:42879876/42879877(+):(discordant_mates:10,spanning_paired_1:6,spanning_paired_1_t:1,spanning_paired_2:6,spanning_paired_2_t:1,spanning_singleton_1_r:2,spanning_singleton_2_r:2)&chr21:39817544/39817545(-)->chr21:42878371/42878372(+):(discordant_mates:2,spanning_paired_1:1,spanning_paired_1_t:1,spanning_paired_2:1,spanning_paired_2_t:1,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:39846044/39846045(-)->chr21:42879876/42879877(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:39817544/39817545(-)->chr21:42876293/42876294(+):(spanning_paired_1:1,spanning_paired_2:1)\n-chr21\t39877811\t-\t98\t0\tchr21\t42873374\t+\t0\t98\t2995563\tvalid\tlinear\tintronic\t91\t42\t21\t28\t10000\t0\t1\t1\t1\t0\t0\t0.9528\t0.9528\t0\t0.82\t2.9207\t17.3314\t0.9125\t0\t0.191\t1.588\t68.1747\t0.8769\t0\t0.1269\t1.3333\t0.2308\t2\tchr21:39877811/39877812(-)->chr21:42873374/42873375(+):(discordant_mates:56,spanning_paired_1:12,spanning_paired_1_t:9,spanning_paired_2:12,spanning_paired_2_t:9)\n-chr21\t42861433\t+\t6\t18\tchr21\t42866505\t-\t18\t6\t5072\tn_discordant_reads=2<3\tcircular\texonic\t41\t30\t14\t2\t10000\t0\t7\t5\t6\t1\t2\t1\t0.9375\t18.7474\t0.75\t26.9\t3\t0.9425\t0.0164\t5.5097\t20.1\t42.8\t0.8833\t0.047\t6.1587\t0.1429\t0.3659\t1.5714\tchr21:42861433/42861434(+)->chr21:42866505/42866506(-):(discordant_mates:2,spanning_paired_1:2,spanning_paired_1_t:1,spanning_paired_2:2,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42861433/42861434(+)->chr21:42870116/42870117(-):(spanning_paired_1:3,spanning_paired_2:3,spanning_singleton_1_r:1,spanning_singleton_2_r:1)&chr21:42860568/42860569(+)->chr21:42867210/42867211(-):(spanning_paired_1_t:2,spanning_paired_2_t:2)&chr21:42860320/42860321(+)->chr21:42861520/42861521(-):(spanning_paired_1:1,spanning_paired_2:1,spanning_singleton_1:1,spanning_singleton_2:1)&chr21:42859986/42859987(+)->chr21:42863878/42863879(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:42860320/42860321(+)->chr21:42866505/42866506(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:42866446/42866447(+)->chr21:42870110/42870111(-):(discordant_mates:2)\n-chr21\t39836011\t+\t0\t8\tchr21\t39836545\t-\t8\t0\t534\tn_support=6<8,bp_pos_stddev=25.3065>15.0,log_ratio_slope=9.62>1.8,log_ratio_rvalue=8.96>0.4\tcircular\tintronic\t17\t12\t6\t0\t10000\t0\t2\t2\t2\t0\t0\t0.4056\t0.6934\t25.3065\t0\t1.5\t29.5\t0.7746\t0.2254\t0.866\t0\t93\t0\t1\t0\t0\t0.3529\t2\tchr21:39836011/39836012(+)->chr21:39836545/39836546(-):(spanning_paired_1_t:4,spanning_paired_2_t:4)&chr21:39835707/39835708(+)->chr21:39839850/39839851(-):(spanning_paired_1_t:1,spanning_paired_2_t:1,spanning_singleton_1:1,spanning_singleton_2:1)\n-chr21\t39875880\t+\t0\t6\tchr21\t39876476\t-\t6\t0\t596\tentropy=0.0<0.6839,n_support=4<8\tcircular\tintronic\t12\t8\t4\t0\t10000\t0\t2\t2\t2\t0\t0\t0\t0.4056\t0\t0\t0\t68\t0\t1\t0\t0\t58\t0\t1\t0\t0\t0.3333\t2\tchr21:39875880/39875881(+)->chr21:39876476/39876477(-):(spanning_paired_1:3,spanning_paired_2:3)&chr21:39874280/39874281(+)->chr21:39876277/39876278(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n-chr21\t39851814\t+\t0\t6\tchr21\t39852667\t-\t6\t0\t853\tentropy=0.0<0.6835,n_support=3<7\tcircular\tintro'..b'port=1<7,n_lr_symmetry=104.05>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t101\t0\t1\t0\t0\t25\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39863020/39863021(+)->chr21:39863629/39863630(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t39871034\t+\t0\t2\tchr21\t39877568\t-\t2\t0\t6534\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=72.92>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t31\t0\t1\t0\t0\t66\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:39871034/39871035(+)->chr21:39877568/39877569(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42836581\t+\t0\t2\tchr21\t42839672\t-\t2\t0\t3091\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=108.67>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t19\t0\t1\t0\t0\t107\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42836581/42836582(+)->chr21:42839672/42839673(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)\n+chr21\t42853701\t+\t0\t2\tchr21\t42860029\t-\t2\t0\t6328\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=38.01>=24.68\tcircular\tintronic\t3\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t22\t0\t1\t0\t0\t31\t0\t1\t0\t0\t0.3333\t2\t50\t50\t50\t50\tchr21:42853701/42853702(+)->chr21:42860029/42860030(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42866483\t-\t0\t2\tchr21\t42870116\t-\t2\t0\t3633\tentropy=0.0<0.6828,n_support=1<7,n_lr_symmetry=95.85>=24.68\tlinear\tintronic\t3\t9\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t38\t0\t1\t0\t0\t88\t0\t1\t0\t0\t1.5\t2\t50\t50\t50\t50\tchr21:42866483/42866484(-)->chr21:42870116/42870117(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t42839824\t+\t0\t4\tchr21\t42840323\t-\t4\t0\t499\tn_support=2<7,log_ratio_slope=12.99>1.8,log_ratio_rvalue=9.21>0.4\tcircular\tintronic\t2\t2\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t1\t1\t0\t0.4056\t44\t82\t1\t0\t0\t0\t120\t0\t1\t0\t40\t0.5\t2\t50\t50\t50\t50\tchr21:42839824/42839825(+)->chr21:42840323/42840324(-):(discordant_mates:4)\n+chr21\t39770910\t+\t2\t0\tchr21\t39771416\t-\t0\t2\t506\tentropy=0.0<0.6827,n_support=1<7,n_lr_symmetry=89.04>=28.44\tcircular\tintronic\t2\t2\t1\t0\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t75\t0\t1\t0\t0\t48\t0\t1\t0\t0\t0.5\t2\t50\t50\t50\t50\tchr21:39770910/39770911(+)->chr21:39771416/39771417(-):(spanning_singleton_1_r:1,spanning_singleton_2_r:1)\n+chr21\t39860702\t-\t4\t0\tchr21\t42843890\t+\t0\t4\t2983188\tentropy=0.0<0.6827,n_support=2<7,n_lr_symmetry=178.19>=28.44\tlinear\tintronic\t2\t0\t0\t2\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t40\t0\t2\t50\t50\t50\t50\tchr21:39860702/39860703(-)->chr21:42843890/42843891(+):(discordant_mates:4)\n+chr21\t39781087\t+\t0\t2\tchr21\t39782101\t-\t2\t0\t1014\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39781087/39781088(+)->chr21:39782101/39782102(-):(discordant_mates:2)\n+chr21\t39846131\t+\t0\t2\tchr21\t39846834\t-\t2\t0\t703\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=131.9>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t39\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39846131/39846132(+)->chr21:39846834/39846835(-):(discordant_mates:2)\n+chr21\t39853321\t-\t2\t0\tchr21\t42851610\t+\t0\t2\t2998289\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=178.19>=33.57\tlinear\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t126\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:39853321/39853322(-)->chr21:42851610/42851611(+):(discordant_mates:2)\n+chr21\t42840341\t+\t0\t2\tchr21\t42842586\t-\t2\t0\t2245\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=175.36>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t124\t0\t1\t0\t0\t124\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42840341/42840342(+)->chr21:42842586/42842587(-):(discordant_mates:2)\n+chr21\t42843861\t+\t2\t0\tchr21\t42845272\t-\t0\t2\t1411\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=88.46>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t65\t0\t1\t0\t0\t60\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42843861/42843862(+)->chr21:42845272/42845273(-):(discordant_mates:2)\n+chr21\t42863757\t+\t0\t2\tchr21\t42864220\t-\t2\t0\t463\tentropy=0.0<0.6826,n_support=1<7,n_lr_symmetry=176.08>=33.57\tcircular\tintronic\t1\t0\t0\t1\t10000\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t126\t0\t1\t0\t0\t123\t0\t1\t0\t20\t0\t2\t50\t50\t50\t50\tchr21:42863757/42863758(+)->chr21:42864220/42864221(-):(discordant_mates:2)\n' |
| b |
| diff -r c3ce472a315f -r f2c70d589596 test-data/detect.txt --- a/test-data/detect.txt Tue Sep 26 08:27:47 2017 -0400 +++ b/test-data/detect.txt Thu Nov 02 05:17:31 2017 -0400 |
| b |
| @@ -1,2 +1,2 @@ -chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-B-acceptor pos-B-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge data-structure -chr21 39877811 - 6 0 chr21 42873374 + 0 6 2995563 unclassified linear intronic 9 6 3 0 642 0 1 1 1 0 0 1.0000 1.0000 0.0000 0.0000 17.0000 37.3333 0.9994 0.0216 0.5774 24.0000 42.3333 0.9954 0.0611 2.3094 0.0000 0.3333 2.0000 chr21:39877811/39877812(-)->chr21:42873374/42873375(+):(spanning_paired_1_t:3,spanning_paired_2_t:3) +chr-A pos-A direction-A pos-A-acceptor pos-A-donor chr-B pos-B direction-B pos-B-acceptor pos-B-donor genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads alignment-score mismatches n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps lr-A-slope lr-A-intercept lr-A-rvalue lr-A-pvalue lr-A-stderr lr-B-slope lr-B-intercept lr-B-rvalue lr-B-pvalue lr-B-stderr disco/split clips/score nodes/edge median-AS-A median-AS-B max-AS-A max-AS-B data-structure +chr21 39877811 - 6 0 chr21 42873374 + 0 6 2995563 unclassified linear intronic 9 6 3 0 642 0 1 1 1 0 0 1.0000 1.0000 0.0000 0.0000 17.0000 37.3333 0.9994 0.0216 0.5774 24.0000 42.3333 0.9954 0.0611 2.3094 0.0000 0.3333 2.0000 55 69 71 89 chr21:39877811/39877812(-)->chr21:42873374/42873375(+):(spanning_paired_1_t:3,spanning_paired_2_t:3) |
| b |
| diff -r c3ce472a315f -r f2c70d589596 test-data/fix_test-01.fixed.bam |
| b |
| Binary file test-data/fix_test-01.fixed.bam has changed |
| b |
| diff -r c3ce472a315f -r f2c70d589596 test-data/integrate_test_terg_s041.in.dbed --- a/test-data/integrate_test_terg_s041.in.dbed Tue Sep 26 08:27:47 2017 -0400 +++ b/test-data/integrate_test_terg_s041.in.dbed Thu Nov 02 05:17:31 2017 -0400 |
| b |
| b'@@ -1,6 +1,6 @@\n-chr-A\tpos-A\tdirection-A\tpos-A-acceptor\tpos-A-donor\tchr-B\tpos-B\tdirection-B\tpos-A-acceptor\tpos-A-donor\tgenomic-distance\tfilter-status\tcircRNA\tintronic/exonic\tscore\tsoft+hardclips\tn-split-reads\tn-discordant-reads\talignment-score\tmismatches\tn-edges\tn-nodes-A\tn-nodes-B\tn-splice-junc-A\tn-splice-junc-B\tentropy-bp-edge\tentropy-all-edges\tbp-pos-stddev\tentropy-disco-bps\tlr-A-slope\tlr-A-intercept\tlr-A-rvalue\tlr-A-pvalue\tlr-A-stderr\tlr-B-slope\tlr-B-intercept\tlr-B-rvalue\tlr-B-pvalue\tlr-B-stderr\tdisco/split\tclips/score\tnodes/edge\tdata-structure\n-chr21\t38445621\t-\t200\t0\tchr21\t41498118\t+\t0\t200\t3052497\tvalid\tlinear\texonic\t588\t378\t189\t21\t10000\t0\t14\t7\t9\t2\t4\t0.7421\t0.8197\t0\t0.7162\t0.7344\t19.9882\t0.9657\t0\t0.0178\t0.7194\t21.976\t0.9648\t0\t0.0177\t0.1111\t0.3214\t1.1429\tchr21:38445621/38445622(-)->chr21:41498118/41498119(+):(discordant_mates:14,spanning_paired_1:114,spanning_paired_1_t:4,spanning_paired_2:114,spanning_paired_2_t:4)&chr21:38445621/38445622(-)->chr21:41508080/41508081(+):(spanning_paired_1:33,spanning_paired_2:33)&chr21:38445621/38445622(-)->chr21:41507949/41507950(+):(discordant_mates:8,spanning_paired_1:15,spanning_paired_2:15)&chr21:38474121/38474122(-)->chr21:41498118/41498119(+):(spanning_paired_1:14,spanning_paired_2:14)&chr21:38445621/38445622(-)->chr21:41480475/41480476(+):(discordant_mates:6,spanning_paired_1:2,spanning_paired_2:2)&chr21:38423561/38423562(-)->chr21:41498118/41498119(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:38445621/38445622(-)->chr21:41506444/41506445(+):(discordant_mates:6,spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:38445621/38445622(-)->chr21:41504366/41504367(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38446208/38446209(-)->chr21:41498118/41498119(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41480475/41480476(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41508080/41508081(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38423567/38423568(-)->chr21:41485824/41485825(+):(discordant_mates:4)&chr21:38445482/38445483(-)->chr21:41500346/41500347(+):(discordant_mates:2)&chr21:38474093/38474094(-)->chr21:41507966/41507967(+):(discordant_mates:2)\n-chr21\t38487350\t-\t200\t0\tchr21\t41479719\t+\t0\t200\t2992369\tvalid\tlinear\tintronic\t151\t96\t48\t7\t10000\t0\t1\t1\t1\t0\t0\t0.869\t0.869\t0.2887\t0.8124\t2.1465\t5.6435\t0.9817\t0\t0.0571\t1.9162\t26.2818\t0.99\t0\t0.0376\t0.1458\t0.3179\t2\tchr21:38487350/38487351(-)->chr21:41479719/41479720(+):(discordant_mates:14,spanning_paired_1:41,spanning_paired_1_t:7,spanning_paired_2:41,spanning_paired_2_t:7)\n-chr21\t36338771\t+\t0\t10\tchr21\t36344707\t-\t10\t0\t5936\tvalid\tcircular\texonic\t117\t58\t38\t3\t10000\t0\t2\t2\t2\t0\t0\t0.8536\t0.8591\t2.436\t0.871\t2.1714\t19.1829\t0.9605\t0\t0.1021\t2.0941\t32.6902\t0.9725\t0\t0.0814\t0.0789\t0.2479\t2\tchr21:36338771/36338772(+)->chr21:36344707/36344708(-):(discordant_mates:6,spanning_paired_1:14,spanning_paired_1_t:23,spanning_paired_2:14,spanning_paired_2_t:23)&chr21:36338841/36338842(+)->chr21:36341534/36341535(-):(spanning_paired_1:1,spanning_paired_2:1)\n-chr21\t29321220\t+\t10\t0\tchr21\t29329693\t-\t0\t10\t8473\tvalid\tcircular\texonic\t49\t35\t15\t4\t10000\t0\t4\t4\t3\t0\t0\t0.8605\t0.8018\t0\t0.6667\t8.3531\t34.3077\t0.9863\t0\t0.4412\t9.4685\t14.5897\t0.9701\t0\t0.749\t0.2667\t0.3571\t1.75\tchr21:29321220/29321221(+)->chr21:29329693/29329694(-):(discordant_mates:4,spanning_paired_1:9,spanning_paired_1_t:1,spanning_paired_2:9,spanning_paired_2_t:1)&chr21:29326058/29326059(+)->chr21:29329693/29329694(-):(spanning_paired_1:4,spanning_paired_2:4)&chr21:29327324/29327325(+)->chr21:29329704/29329705(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:29321216/29321217(+)->chr21:29329647/29329648(-):(discordant_mates:4)\n-chr21\t33414887\t+\t5\t5\tchr21\t33432871\t-\t5\t5\t17984\tvalid\tcircular\texonic\t20\t12\t6\t2\t10000\t0\t3\t3\t2\t1\t0\t0.8277\t0.9167\t0\t0.75\t12.6\t50.8\t0.7995\t0.1045\t5.4663\t12.8\t24.2\t0.8072\t0.0987\t5.4049\t0.3333\t0.3\t1.6667\tchr21:33414887/33414888(+)->chr21:33432871/33432872(-):(spanning_paired_1:2,spanning_paired_1_t:3,spanning_paired_2:2,spanni'..b'junc-A\tn-splice-junc-B\tentropy-bp-edge\tentropy-all-edges\tbp-pos-stddev\tentropy-disco-bps\tlr-A-slope\tlr-A-intercept\tlr-A-rvalue\tlr-A-pvalue\tlr-A-stderr\tlr-B-slope\tlr-B-intercept\tlr-B-rvalue\tlr-B-pvalue\tlr-B-stderr\tdisco/split\tclips/score\tnodes/edge\tmedian-AS-A\tmedian-AS-B\tmax-AS-A\tmax-AS-B\tdata-structure\n+chr21\t38445621\t-\t200\t0\tchr21\t41498118\t+\t0\t200\t3052497\tvalid\tlinear\texonic\t588\t378\t189\t21\t10000\t0\t14\t7\t9\t2\t4\t0.7421\t0.8197\t0\t0.7162\t0.7344\t19.9882\t0.9657\t0\t0.0178\t0.7194\t21.976\t0.9648\t0\t0.0177\t0.1111\t0.3214\t1.1429\t50\t50\t50\t50\tchr21:38445621/38445622(-)->chr21:41498118/41498119(+):(discordant_mates:14,spanning_paired_1:114,spanning_paired_1_t:4,spanning_paired_2:114,spanning_paired_2_t:4)&chr21:38445621/38445622(-)->chr21:41508080/41508081(+):(spanning_paired_1:33,spanning_paired_2:33)&chr21:38445621/38445622(-)->chr21:41507949/41507950(+):(discordant_mates:8,spanning_paired_1:15,spanning_paired_2:15)&chr21:38474121/38474122(-)->chr21:41498118/41498119(+):(spanning_paired_1:14,spanning_paired_2:14)&chr21:38445621/38445622(-)->chr21:41480475/41480476(+):(discordant_mates:6,spanning_paired_1:2,spanning_paired_2:2)&chr21:38423561/38423562(-)->chr21:41498118/41498119(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:38445621/38445622(-)->chr21:41506444/41506445(+):(discordant_mates:6,spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:38445621/38445622(-)->chr21:41504366/41504367(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38446208/38446209(-)->chr21:41498118/41498119(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41480475/41480476(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41508080/41508081(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38423567/38423568(-)->chr21:41485824/41485825(+):(discordant_mates:4)&chr21:38445482/38445483(-)->chr21:41500346/41500347(+):(discordant_mates:2)&chr21:38474093/38474094(-)->chr21:41507966/41507967(+):(discordant_mates:2)\n+chr21\t38487350\t-\t200\t0\tchr21\t41479719\t+\t0\t200\t2992369\tvalid\tlinear\tintronic\t151\t96\t48\t7\t10000\t0\t1\t1\t1\t0\t0\t0.869\t0.869\t0.2887\t0.8124\t2.1465\t5.6435\t0.9817\t0\t0.0571\t1.9162\t26.2818\t0.99\t0\t0.0376\t0.1458\t0.3179\t2\t50\t50\t50\t50\tchr21:38487350/38487351(-)->chr21:41479719/41479720(+):(discordant_mates:14,spanning_paired_1:41,spanning_paired_1_t:7,spanning_paired_2:41,spanning_paired_2_t:7)\n+chr21\t36338771\t+\t0\t10\tchr21\t36344707\t-\t10\t0\t5936\tvalid\tcircular\texonic\t117\t58\t38\t3\t10000\t0\t2\t2\t2\t0\t0\t0.8536\t0.8591\t2.436\t0.871\t2.1714\t19.1829\t0.9605\t0\t0.1021\t2.0941\t32.6902\t0.9725\t0\t0.0814\t0.0789\t0.2479\t2\t50\t50\t50\t50\tchr21:36338771/36338772(+)->chr21:36344707/36344708(-):(discordant_mates:6,spanning_paired_1:14,spanning_paired_1_t:23,spanning_paired_2:14,spanning_paired_2_t:23)&chr21:36338841/36338842(+)->chr21:36341534/36341535(-):(spanning_paired_1:1,spanning_paired_2:1)\n+chr21\t29321220\t+\t10\t0\tchr21\t29329693\t-\t0\t10\t8473\tvalid\tcircular\texonic\t49\t35\t15\t4\t10000\t0\t4\t4\t3\t0\t0\t0.8605\t0.8018\t0\t0.6667\t8.3531\t34.3077\t0.9863\t0\t0.4412\t9.4685\t14.5897\t0.9701\t0\t0.749\t0.2667\t0.3571\t1.75\t50\t50\t50\t50\tchr21:29321220/29321221(+)->chr21:29329693/29329694(-):(discordant_mates:4,spanning_paired_1:9,spanning_paired_1_t:1,spanning_paired_2:9,spanning_paired_2_t:1)&chr21:29326058/29326059(+)->chr21:29329693/29329694(-):(spanning_paired_1:4,spanning_paired_2:4)&chr21:29327324/29327325(+)->chr21:29329704/29329705(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:29321216/29321217(+)->chr21:29329647/29329648(-):(discordant_mates:4)\n+chr21\t33414887\t+\t5\t5\tchr21\t33432871\t-\t5\t5\t17984\tvalid\tcircular\texonic\t20\t12\t6\t2\t10000\t0\t3\t3\t2\t1\t0\t0.8277\t0.9167\t0\t0.75\t12.6\t50.8\t0.7995\t0.1045\t5.4663\t12.8\t24.2\t0.8072\t0.0987\t5.4049\t0.3333\t0.3\t1.6667\t50\t50\t50\t50\tchr21:33414887/33414888(+)->chr21:33432871/33432872(-):(spanning_paired_1:2,spanning_paired_1_t:3,spanning_paired_2:2,spanning_paired_2_t:3)&chr21:33426883/33426884(+)->chr21:33432871/33432872(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:33414915/33414916(+)->chr21:33421509/33421510(-):(discordant_mates:4)\n' |
| b |
| diff -r c3ce472a315f -r f2c70d589596 test-data/integrate_test_terg_s041.out.no-gtf.txt --- a/test-data/integrate_test_terg_s041.out.no-gtf.txt Tue Sep 26 08:27:47 2017 -0400 +++ b/test-data/integrate_test_terg_s041.out.no-gtf.txt Thu Nov 02 05:17:31 2017 -0400 |
| b |
| b'@@ -1,6 +1,6 @@\n-shared-id\tfusion\tchr-A\tpos-A\tdirection-A\tpos-A-acceptor\tpos-A-donor\tchr-B\tpos-B\tdirection-B\tpos-A-acceptor\tpos-A-donor\tgenomic-distance\tfilter-status\tcircRNA\tintronic/exonic\tscore\tsoft+hardclips\tn-split-reads\tn-discordant-reads\talignment-score\tmismatches\tn-edges\tn-nodes-A\tn-nodes-B\tn-splice-junc-A\tn-splice-junc-B\tentropy-bp-edge\tentropy-all-edges\tbp-pos-stddev\tentropy-disco-bps\tlr-A-slope\tlr-A-intercept\tlr-A-rvalue\tlr-A-pvalue\tlr-A-stderr\tlr-B-slope\tlr-B-intercept\tlr-B-rvalue\tlr-B-pvalue\tlr-B-stderr\tdisco/split\tclips/score\tnodes/edge\tfull-gene-disregulation\tframeshift=0\tframeshift=+1\tframeshift=+2\tdata-structure\n-1\tTMPRSS2->ERG\tchr21\t38487350\t-\t200\t0\tchr21\t41479719\t+\t0\t200\t2992369\tvalid\tlinear\tintronic\t151\t96\t48\t7\t10000\t0\t1\t1\t1\t0\t0\t0.869\t0.869\t0.2887\t0.8124\t2.1465\t5.6435\t0.9817\t0\t0.0571\t1.9162\t26.2818\t0.99\t0\t0.0376\t0.1458\t0.3179\t2\t\t\t\t\tchr21:38487350/38487351(-)->chr21:41479719/41479720(+):(discordant_mates:14,spanning_paired_1:41,spanning_paired_1_t:7,spanning_paired_2:41,spanning_paired_2_t:7)\n-1\tTMPRSS2->ERG\tchr21\t38445621\t-\t200\t0\tchr21\t41498118\t+\t0\t200\t3052497\tvalid\tlinear\texonic\t588\t378\t189\t21\t10000\t0\t14\t7\t9\t2\t4\t0.7421\t0.8197\t0\t0.7162\t0.7344\t19.9882\t0.9657\t0\t0.0178\t0.7194\t21.976\t0.9648\t0\t0.0177\t0.1111\t0.3214\t1.1429\tTMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000398897.5)-ensembl_havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000453032.6)-ensembl_havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000398897.5)-ensembl_havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000453032.6)-ensembl_havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000492833.5)-ensembl_havana\tTMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST000003'..b'l-gene-dysregulation\tframeshift=0\tframeshift=+1\tframeshift=+2\tmedian-AS-A\tmedian-AS-B\tmax-AS-A\tmax-AS-B\tdata-structure\n+1\tchr21:41479719->chr21:38487350\tchr21\t38487350\t-\t200\t0\tchr21\t41479719\t+\t0\t200\t2992369\tvalid\tlinear\tintronic\t151\t96\t48\t7\t10000\t0\t1\t1\t1\t0\t0\t0.869\t0.869\t0.2887\t0.8124\t2.1465\t5.6435\t0.9817\t0\t0.0571\t1.9162\t26.2818\t0.99\t0\t0.0376\t0.1458\t0.3179\t2\t\t\t\t\t50\t50\t50\t50\tchr21:38487350/38487351(-)->chr21:41479719/41479720(+):(discordant_mates:14,spanning_paired_1:41,spanning_paired_1_t:7,spanning_paired_2:41,spanning_paired_2_t:7)\n+1\tchr21:41498118->chr21:38445621\tchr21\t38445621\t-\t200\t0\tchr21\t41498118\t+\t0\t200\t3052497\tvalid\tlinear\texonic\t588\t378\t189\t21\t10000\t0\t14\t7\t9\t2\t4\t0.7421\t0.8197\t0\t0.7162\t0.7344\t19.9882\t0.9657\t0\t0.0178\t0.7194\t21.976\t0.9648\t0\t0.0177\t0.1111\t0.3214\t1.1429\t\t\t\t\t50\t50\t50\t50\tchr21:38445621/38445622(-)->chr21:41498118/41498119(+):(discordant_mates:14,spanning_paired_1:114,spanning_paired_1_t:4,spanning_paired_2:114,spanning_paired_2_t:4)&chr21:38445621/38445622(-)->chr21:41508080/41508081(+):(spanning_paired_1:33,spanning_paired_2:33)&chr21:38445621/38445622(-)->chr21:41507949/41507950(+):(discordant_mates:8,spanning_paired_1:15,spanning_paired_2:15)&chr21:38474121/38474122(-)->chr21:41498118/41498119(+):(spanning_paired_1:14,spanning_paired_2:14)&chr21:38445621/38445622(-)->chr21:41480475/41480476(+):(discordant_mates:6,spanning_paired_1:2,spanning_paired_2:2)&chr21:38423561/38423562(-)->chr21:41498118/41498119(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:38445621/38445622(-)->chr21:41506444/41506445(+):(discordant_mates:6,spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:38445621/38445622(-)->chr21:41504366/41504367(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38446208/38446209(-)->chr21:41498118/41498119(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41480475/41480476(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41508080/41508081(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38423567/38423568(-)->chr21:41485824/41485825(+):(discordant_mates:4)&chr21:38445482/38445483(-)->chr21:41500346/41500347(+):(discordant_mates:2)&chr21:38474093/38474094(-)->chr21:41507966/41507967(+):(discordant_mates:2)\n+2\tchr21:36338771->chr21:36344707\tchr21\t36338771\t+\t0\t10\tchr21\t36344707\t-\t10\t0\t5936\tvalid\tcircular\texonic\t117\t58\t38\t3\t10000\t0\t2\t2\t2\t0\t0\t0.8536\t0.8591\t2.436\t0.871\t2.1714\t19.1829\t0.9605\t0\t0.1021\t2.0941\t32.6902\t0.9725\t0\t0.0814\t0.0789\t0.2479\t2\t\t\t\t\t50\t50\t50\t50\tchr21:36338771/36338772(+)->chr21:36344707/36344708(-):(discordant_mates:6,spanning_paired_1:14,spanning_paired_1_t:23,spanning_paired_2:14,spanning_paired_2_t:23)&chr21:36338841/36338842(+)->chr21:36341534/36341535(-):(spanning_paired_1:1,spanning_paired_2:1)\n+3\tchr21:29329693->chr21:29321220\tchr21\t29321220\t+\t10\t0\tchr21\t29329693\t-\t0\t10\t8473\tvalid\tcircular\texonic\t49\t35\t15\t4\t10000\t0\t4\t4\t3\t0\t0\t0.8605\t0.8018\t0\t0.6667\t8.3531\t34.3077\t0.9863\t0\t0.4412\t9.4685\t14.5897\t0.9701\t0\t0.749\t0.2667\t0.3571\t1.75\t\t\t\t\t50\t50\t50\t50\tchr21:29321220/29321221(+)->chr21:29329693/29329694(-):(discordant_mates:4,spanning_paired_1:9,spanning_paired_1_t:1,spanning_paired_2:9,spanning_paired_2_t:1)&chr21:29326058/29326059(+)->chr21:29329693/29329694(-):(spanning_paired_1:4,spanning_paired_2:4)&chr21:29327324/29327325(+)->chr21:29329704/29329705(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:29321216/29321217(+)->chr21:29329647/29329648(-):(discordant_mates:4)\n+4\tchr21:33432871<->chr21:33414887\tchr21\t33414887\t+\t5\t5\tchr21\t33432871\t-\t5\t5\t17984\tvalid\tcircular\texonic\t20\t12\t6\t2\t10000\t0\t3\t3\t2\t1\t0\t0.8277\t0.9167\t0\t0.75\t12.6\t50.8\t0.7995\t0.1045\t5.4663\t12.8\t24.2\t0.8072\t0.0987\t5.4049\t0.3333\t0.3\t1.6667\t\t\t\t\t50\t50\t50\t50\tchr21:33414887/33414888(+)->chr21:33432871/33432872(-):(spanning_paired_1:2,spanning_paired_1_t:3,spanning_paired_2:2,spanning_paired_2_t:3)&chr21:33426883/33426884(+)->chr21:33432871/33432872(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:33414915/33414916(+)->chr21:33421509/33421510(-):(discordant_mates:4)\n' |
| b |
| diff -r c3ce472a315f -r f2c70d589596 test-data/integrate_test_terg_s041.out.txt --- a/test-data/integrate_test_terg_s041.out.txt Tue Sep 26 08:27:47 2017 -0400 +++ b/test-data/integrate_test_terg_s041.out.txt Thu Nov 02 05:17:31 2017 -0400 |
| b |
| b'@@ -1,6 +1,6 @@\n-shared-id\tfusion\tchr-A\tpos-A\tdirection-A\tpos-A-acceptor\tpos-A-donor\tchr-B\tpos-B\tdirection-B\tpos-A-acceptor\tpos-A-donor\tgenomic-distance\tfilter-status\tcircRNA\tintronic/exonic\tscore\tsoft+hardclips\tn-split-reads\tn-discordant-reads\talignment-score\tmismatches\tn-edges\tn-nodes-A\tn-nodes-B\tn-splice-junc-A\tn-splice-junc-B\tentropy-bp-edge\tentropy-all-edges\tbp-pos-stddev\tentropy-disco-bps\tlr-A-slope\tlr-A-intercept\tlr-A-rvalue\tlr-A-pvalue\tlr-A-stderr\tlr-B-slope\tlr-B-intercept\tlr-B-rvalue\tlr-B-pvalue\tlr-B-stderr\tdisco/split\tclips/score\tnodes/edge\tfull-gene-disregulation\tframeshift=0\tframeshift=+1\tframeshift=+2\tdata-structure\n-1\tTMPRSS2->ERG\tchr21\t38487350\t-\t200\t0\tchr21\t41479719\t+\t0\t200\t2992369\tvalid\tlinear\tintronic\t151\t96\t48\t7\t10000\t0\t1\t1\t1\t0\t0\t0.869\t0.869\t0.2887\t0.8124\t2.1465\t5.6435\t0.9817\t0\t0.0571\t1.9162\t26.2818\t0.99\t0\t0.0376\t0.1458\t0.3179\t2\t\t\t\t\tchr21:38487350/38487351(-)->chr21:41479719/41479720(+):(discordant_mates:14,spanning_paired_1:41,spanning_paired_1_t:7,spanning_paired_2:41,spanning_paired_2_t:7)\n-1\tTMPRSS2->ERG\tchr21\t38445621\t-\t200\t0\tchr21\t41498118\t+\t0\t200\t3052497\tvalid\tlinear\texonic\t588\t378\t189\t21\t10000\t0\t14\t7\t9\t2\t4\t0.7421\t0.8197\t0\t0.7162\t0.7344\t19.9882\t0.9657\t0\t0.0178\t0.7194\t21.976\t0.9648\t0\t0.0177\t0.1111\t0.3214\t1.1429\tTMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000458356.5)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000398897.5)-ensembl_havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000453032.6)-ensembl_havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000463138.1)-havana->ERG(ENST00000492833.5)-ensembl_havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000398897.5)-ensembl_havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000429727.6)-ensembl,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000453032.6)-ensembl_havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000468474.5)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000473107.1)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000481609.5)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000485493.1)-havana,TMPRSS2(ENST00000497881.5)-havana->ERG(ENST00000492833.5)-ensembl_havana\tTMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST000003'..b'19.6)-ensembl_havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000442448.5)-ensembl(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000442448.5)-ensembl(+0)\t50\t50\t50\t50\tchr21:38445621/38445622(-)->chr21:41498118/41498119(+):(discordant_mates:14,spanning_paired_1:114,spanning_paired_1_t:4,spanning_paired_2:114,spanning_paired_2_t:4)&chr21:38445621/38445622(-)->chr21:41508080/41508081(+):(spanning_paired_1:33,spanning_paired_2:33)&chr21:38445621/38445622(-)->chr21:41507949/41507950(+):(discordant_mates:8,spanning_paired_1:15,spanning_paired_2:15)&chr21:38474121/38474122(-)->chr21:41498118/41498119(+):(spanning_paired_1:14,spanning_paired_2:14)&chr21:38445621/38445622(-)->chr21:41480475/41480476(+):(discordant_mates:6,spanning_paired_1:2,spanning_paired_2:2)&chr21:38423561/38423562(-)->chr21:41498118/41498119(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:38445621/38445622(-)->chr21:41506444/41506445(+):(discordant_mates:6,spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:38445621/38445622(-)->chr21:41504366/41504367(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38446208/38446209(-)->chr21:41498118/41498119(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41480475/41480476(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41508080/41508081(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38423567/38423568(-)->chr21:41485824/41485825(+):(discordant_mates:4)&chr21:38445482/38445483(-)->chr21:41500346/41500347(+):(discordant_mates:2)&chr21:38474093/38474094(-)->chr21:41507966/41507967(+):(discordant_mates:2)\n+2\tchr21:36338771->chr21:36344707\tchr21\t36338771\t+\t0\t10\tchr21\t36344707\t-\t10\t0\t5936\tvalid\tcircular\texonic\t117\t58\t38\t3\t10000\t0\t2\t2\t2\t0\t0\t0.8536\t0.8591\t2.436\t0.871\t2.1714\t19.1829\t0.9605\t0\t0.1021\t2.0941\t32.6902\t0.9725\t0\t0.0814\t0.0789\t0.2479\t2\t\t\t\t\t50\t50\t50\t50\tchr21:36338771/36338772(+)->chr21:36344707/36344708(-):(discordant_mates:6,spanning_paired_1:14,spanning_paired_1_t:23,spanning_paired_2:14,spanning_paired_2_t:23)&chr21:36338841/36338842(+)->chr21:36341534/36341535(-):(spanning_paired_1:1,spanning_paired_2:1)\n+3\tchr21:29329693->chr21:29321220\tchr21\t29321220\t+\t10\t0\tchr21\t29329693\t-\t0\t10\t8473\tvalid\tcircular\texonic\t49\t35\t15\t4\t10000\t0\t4\t4\t3\t0\t0\t0.8605\t0.8018\t0\t0.6667\t8.3531\t34.3077\t0.9863\t0\t0.4412\t9.4685\t14.5897\t0.9701\t0\t0.749\t0.2667\t0.3571\t1.75\t\t\t\t\t50\t50\t50\t50\tchr21:29321220/29321221(+)->chr21:29329693/29329694(-):(discordant_mates:4,spanning_paired_1:9,spanning_paired_1_t:1,spanning_paired_2:9,spanning_paired_2_t:1)&chr21:29326058/29326059(+)->chr21:29329693/29329694(-):(spanning_paired_1:4,spanning_paired_2:4)&chr21:29327324/29327325(+)->chr21:29329704/29329705(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:29321216/29321217(+)->chr21:29329647/29329648(-):(discordant_mates:4)\n+4\tchr21:33432871<->chr21:33414887\tchr21\t33414887\t+\t5\t5\tchr21\t33432871\t-\t5\t5\t17984\tvalid\tcircular\texonic\t20\t12\t6\t2\t10000\t0\t3\t3\t2\t1\t0\t0.8277\t0.9167\t0\t0.75\t12.6\t50.8\t0.7995\t0.1045\t5.4663\t12.8\t24.2\t0.8072\t0.0987\t5.4049\t0.3333\t0.3\t1.6667\t\t\t\t\t50\t50\t50\t50\tchr21:33414887/33414888(+)->chr21:33432871/33432872(-):(spanning_paired_1:2,spanning_paired_1_t:3,spanning_paired_2:2,spanning_paired_2_t:3)&chr21:33426883/33426884(+)->chr21:33432871/33432872(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:33414915/33414916(+)->chr21:33421509/33421510(-):(discordant_mates:4)\n' 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