Repository 'hicexplorer_hiccomparematrices'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccomparematrices

Changeset 4:6d2c4187805b (2019-12-16)
Previous changeset 3:b6c95ff7c3c3 (2018-06-09) Next changeset 5:55b4b8bc250d (2019-12-16)
Commit message:
"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"
modified:
hicCompareMatrices.xml
removed:
test-data/Li_chrX30-35_cool.png
test-data/Li_et_al_2015.cool
test-data/Li_et_al_2015.h5
test-data/bedgraph_chrx_2e6_5e6.bg
test-data/bigwig_chrx_2e6_5e6.bw
test-data/compare_matrices_log2ratio.h5
test-data/compare_matrices_pearson_ratio.cool
test-data/covariance_small_50kb.cool
test-data/covariance_small_50kb.h5
test-data/diagnostic_plot.png
test-data/distVsCounts.txt
test-data/dm3_genes.bed.gz
test-data/dm3_genes.bed6.gz
test-data/domains.bed
test-data/find_TADs/multiFDR_boundaries.bed
test-data/find_TADs/multiFDR_boundaries.gff
test-data/find_TADs/multiFDR_domains.bed
test-data/find_TADs/multiFDR_score.bedgraph
test-data/find_TADs/multiFDR_tad_score.bm
test-data/hicAggregateContacts_results1.png
test-data/hicCorrectMatrix_result1.npz.h5
test-data/hicCorrelate_heatmap_result1.png
test-data/hicCorrelate_scatter_result1.png
test-data/hicFindTADs_TAD_score.tabular
test-data/hicFindTADs_find_score.bedgraph
test-data/hicMergeMatrixBins_result1.npz.h5
test-data/hicPlotDistVsCounts_result1.png
test-data/hicPlotDistVsCounts_result2.png
test-data/hicPlotTADs_result1.svg
test-data/hicSumMatrices_result1.npz.h5
test-data/li_32-33mb_interactions.bedgraph
test-data/li_32mb_interactions.bedgraph
test-data/li_viewpoint_32-33Mb.png
test-data/li_viewpoint_32Mb.png
test-data/master_TADs_plot.png
test-data/master_matrix_plot.png
test-data/obs_exp_small_50kb.cool
test-data/obs_exp_small_50kb.h5
test-data/pca1.bedgraph
test-data/pca1.bw
test-data/pca2.bedgraph
test-data/pca2.bw
test-data/pearson_small_50kb.cool
test-data/pearson_small_50kb.h5
test-data/pearson_small_50kb_transform.cool
test-data/raw_qc_report
test-data/small_matrix_50kb_pearson_pca1_plot.png
test-data/small_matrix_50kb_pearson_pca1_plot.svg
test-data/small_test_R1_unsorted.bam
test-data/small_test_R1_unsorted.sam
test-data/small_test_R2_unsorted.bam
test-data/small_test_R2_unsorted.sam
test-data/small_test_matrix.h5
test-data/small_test_matrix_2.h5
test-data/small_test_matrix_50kb_res.h5
test-data/small_test_matrix_result_sorted.bam
test-data/tad_classification.bed
test-data/tad_score.gz
test-data/test_regions.bed
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diff -r b6c95ff7c3c3 -r 6d2c4187805b hicCompareMatrices.xml
--- a/hicCompareMatrices.xml Sat Jun 09 15:32:48 2018 -0400
+++ b/hicCompareMatrices.xml Mon Dec 16 08:39:14 2019 -0500
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@@ -44,7 +44,7 @@
             <param name="matrix2" value="small_test_matrix.h5"/>
             <param name="operation" value='log2ratio' />
             <param name="outputFormat" value="h5" />
-            <output name="outFileName" file="compare_matrices_log2ratio.h5" ftype="h5" compare="sim_size" delta='2000'/>
+            <output name="outFileName" file="compare_matrices_log2ratio.h5" ftype="h5" compare="sim_size" delta='10000'/>
         </test>
         <test>
             <param name="matrix1" value="pearson_small_50kb.cool"/>
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/Li_chrX30-35_cool.png
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/Li_et_al_2015.cool
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/Li_et_al_2015.h5
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/bedgraph_chrx_2e6_5e6.bg
--- a/test-data/bedgraph_chrx_2e6_5e6.bg Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/distVsCounts.txt
--- a/test-data/distVsCounts.txt Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,62 +0,0 @@
- Chromosome Contacts Distance Matrix
-0 all 2.673662429796039 0 small_test_matrix_50kb_res.h5
-1 all 1.6689429928741093 50000 small_test_matrix_50kb_res.h5
-2 all 0.7796660703637448 100000 small_test_matrix_50kb_res.h5
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-6 all 0.19278569263413156 300000 small_test_matrix_50kb_res.h5
-7 all 0.1475958612294583 350000 small_test_matrix_50kb_res.h5
-8 all 0.12736713500305435 400000 small_test_matrix_50kb_res.h5
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-10 all 0.09348093480934809 500000 small_test_matrix_50kb_res.h5
-11 all 0.08145634063560629 550000 small_test_matrix_50kb_res.h5
-12 all 0.07492260061919505 600000 small_test_matrix_50kb_res.h5
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-15 all 0.05411323115420707 750000 small_test_matrix_50kb_res.h5
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-18 all 0.04835651074589128 900000 small_test_matrix_50kb_res.h5
-19 all 0.04281636536631779 950000 small_test_matrix_50kb_res.h5
-20 all 0.04010184595798854 1000000 small_test_matrix_50kb_res.h5
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-27 all 0.026753670473083198 1350000 small_test_matrix_50kb_res.h5
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-29 all 0.028252299605781867 1450000 small_test_matrix_50kb_res.h5
-30 all 0.025379037574159526 1500000 small_test_matrix_50kb_res.h5
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-40 all 0.026244035446489435 2000000 small_test_matrix_50kb_res.h5
-41 all 0.024623803009575923 2050000 small_test_matrix_50kb_res.h5
-42 all 0.024365133836650652 2100000 small_test_matrix_50kb_res.h5
-43 all 0.01928374655647383 2150000 small_test_matrix_50kb_res.h5
-44 all 0.017622667588113337 2200000 small_test_matrix_50kb_res.h5
-45 all 0.015256588072122053 2250000 small_test_matrix_50kb_res.h5
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-53 all 0.020306376914855716 2650000 small_test_matrix_50kb_res.h5
-54 all 0.013576277241872096 2700000 small_test_matrix_50kb_res.h5
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-56 all 0.017966223499820338 2800000 small_test_matrix_50kb_res.h5
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-59 all 0.013773106197897789 2950000 small_test_matrix_50kb_res.h5
-60 all 0.01599418393311523 3000000 small_test_matrix_50kb_res.h5
b
diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/dm3_genes.bed.gz
b
Binary file test-data/dm3_genes.bed.gz has changed
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/dm3_genes.bed6.gz
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Binary file test-data/dm3_genes.bed6.gz has changed
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/domains.bed
--- a/test-data/domains.bed Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,498 +0,0 @@\n-X\t73624\t98011\tID_2159\t0.24484225\t.\t73624\t98011\t31,120,180\n-X\t98011\t163162\tID_2160\t0.078244125\t.\t98011\t163162\t51,160,44\n-X\t163162\t173032\tID_2161\t0.1488125\t.\t163162\t173032\t31,120,180\n-X\t173032\t245055\tID_2162\t0.10021325\t.\t173032\t245055\t51,160,44\n-X\t245055\t256176\tID_2163\t0.24866425\t.\t245055\t256176\t31,120,180\n-X\t256176\t370742\tID_2164\t0.218105125\t.\t256176\t370742\t51,160,44\n-X\t370742\t387797\tID_2165\t0.09920975\t.\t370742\t387797\t31,120,180\n-X\t387797\t425626\tID_2166\t0.1315695\t.\t387797\t425626\t51,160,44\n-X\t425626\t511958\tID_2167\t0.12402975\t.\t425626\t511958\t31,120,180\n-X\t511958\t549785\tID_2168\t0.093640125\t.\t511958\t549785\t51,160,44\n-X\t549785\t653272\tID_2169\t0.067879125\t.\t549785\t653272\t31,120,180\n-X\t653272\t659365\tID_2170\t0.14385325\t.\t653272\t659365\t51,160,44\n-X\t659365\t695160\tID_2171\t0.145119\t.\t659365\t695160\t31,120,180\n-X\t695160\t762046\tID_2172\t0.136754875\t.\t695160\t762046\t51,160,44\n-X\t762046\t811178\tID_2173\t0.25650025\t.\t762046\t811178\t31,120,180\n-X\t811178\t835720\tID_2174\t0.202794625\t.\t811178\t835720\t51,160,44\n-X\t835720\t920690\tID_2175\t0.201687125\t.\t835720\t920690\t31,120,180\n-X\t920690\t950857\tID_2176\t0.16776375\t.\t920690\t950857\t51,160,44\n-X\t950857\t1129676\tID_2177\t0.16578775\t.\t950857\t1129676\t31,120,180\n-X\t1129676\t1182377\tID_2178\t0.125434875\t.\t1129676\t1182377\t51,160,44\n-X\t1182377\t1215679\tID_2179\t0.127644875\t.\t1182377\t1215679\t31,120,180\n-X\t1215679\t1235538\tID_2180\t0.22391225\t.\t1215679\t1235538\t51,160,44\n-X\t1235538\t1269714\tID_2181\t0.14388225\t.\t1235538\t1269714\t31,120,180\n-X\t1269714\t1275302\tID_2182\t0.167577875\t.\t1269714\t1275302\t51,160,44\n-X\t1275302\t1293467\tID_2183\t0.175340125\t.\t1275302\t1293467\t31,120,180\n-X\t1293467\t1348185\tID_2184\t0.148177125\t.\t1293467\t1348185\t51,160,44\n-X\t1348185\t1378848\tID_2185\t0.104369375\t.\t1348185\t1378848\t31,120,180\n-X\t1378848\t1417785\tID_2186\t0.055848375\t.\t1378848\t1417785\t51,160,44\n-X\t1417785\t1509963\tID_2187\t0.1912035\t.\t1417785\t1509963\t31,120,180\n-X\t1509963\t1559576\tID_2188\t0.2622635\t.\t1509963\t1559576\t51,160,44\n-X\t1559576\t1590437\tID_2189\t0.1759295\t.\t1559576\t1590437\t31,120,180\n-X\t1590437\t1666959\tID_2190\t0.194465875\t.\t1590437\t1666959\t51,160,44\n-X\t1666959\t1721470\tID_2191\t0.22292475\t.\t1666959\t1721470\t31,120,180\n-X\t1721470\t1736471\tID_2192\t0.16601325\t.\t1721470\t1736471\t51,160,44\n-X\t1736471\t1753234\tID_2193\t0.208370375\t.\t1736471\t1753234\t31,120,180\n-X\t1753234\t1771304\tID_2194\t0.132250375\t.\t1753234\t1771304\t51,160,44\n-X\t1771304\t1784093\tID_2195\t0.180027625\t.\t1771304\t1784093\t31,120,180\n-X\t1784093\t1794340\tID_2196\t0.177347375\t.\t1784093\t1794340\t51,160,44\n-X\t1794340\t1847331\tID_2197\t0.155302\t.\t1794340\t1847331\t31,120,180\n-X\t1847331\t1904345\tID_2198\t0.091353\t.\t1847331\t1904345\t51,160,44\n-X\t1904345\t1935891\tID_2199\t0.144274625\t.\t1904345\t1935891\t31,120,180\n-X\t1935891\t1965737\tID_2200\t0.19876325\t.\t1935891\t1965737\t51,160,44\n-X\t1965737\t1988470\tID_2201\t0.0987945\t.\t1965737\t1988470\t31,120,180\n-X\t1988470\t2015677\tID_2202\t0.126307125\t.\t1988470\t2015677\t51,160,44\n-X\t2015677\t2039288\tID_2203\t0.11469475\t.\t2015677\t2039288\t31,120,180\n-X\t2039288\t2053111\tID_2204\t0.11339725\t.\t2039288\t2053111\t51,160,44\n-X\t2053111\t2066003\tID_2205\t0.092177375\t.\t2053111\t2066003\t31,120,180\n-X\t2066003\t2116316\tID_2206\t0.14135825\t.\t2066003\t2116316\t51,160,44\n-X\t2116316\t2136020\tID_2207\t0.13430075\t.\t2116316\t2136020\t31,120,180\n-X\t2136020\t2164365\tID_2208\t0.194079625\t.\t2136020\t2164365\t51,160,44\n-X\t2164365\t2169170\tID_2209\t0.11761975\t.\t2164365\t2169170\t31,120,180\n-X\t2169170\t2179239\tID_2210\t0.132970125\t.\t2169170\t2179239\t51,160,44\n-X\t2179239\t2234701\tID_2211\t0.159815375\t.\t2179239\t2234701\t31,120,180\n-X\t2234701\t2238520\tID_2212\t0.127241125\t.\t2234701\t2238520\t51,160,44\n-X\t2238520\t2280041\tID_2213\t0.125103375\t.\t2238520\t2280041\t31,120,180\n-X\t2280041\t2318567\tID_2214\t0.270983375\t.\t2280041\t2318567\t51,160,44\n-X\t2318567\t2338007\tID_2215\t0.167261375\t.\t2318567\t2338007\t31,120,180\n-X\t2338007\t2477307\tID_2216\t0.150055375\t.\t2338007\t2477307\t51,160,44\n-X\t2477307\t2508070\tID_2217\t0.103612\t.\t2477307\t2508070\t31,120,180\n-X\t2508070\t2528894\tID_2218\t0.156815\t.\t2508070\t2528894\t51,160,44\n-X\t2528894\t2557128\tID_2219\t0.0914065\t.\t2528894\t2557128\t31'..b'9416481\tID_2600\t0.21749325\t.\t19399952\t19416481\t51,160,44\n-X\t19416481\t19456185\tID_2601\t0.185489875\t.\t19416481\t19456185\t31,120,180\n-X\t19456185\t19473065\tID_2602\t0.188489875\t.\t19456185\t19473065\t51,160,44\n-X\t19473065\t19491987\tID_2603\t0.152931125\t.\t19473065\t19491987\t31,120,180\n-X\t19491987\t19507538\tID_2604\t0.12015975\t.\t19491987\t19507538\t51,160,44\n-X\t19507538\t19531934\tID_2605\t0.159455125\t.\t19507538\t1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b
diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/find_TADs/multiFDR_boundaries.bed
--- a/test-data/find_TADs/multiFDR_boundaries.bed Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,2 +0,0 @@
-chr2L 22922500 22927500 B09504 -0.0682563628914 .
-chrX 87500 92500 B09542 -0.0720204010166 .
b
diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/find_TADs/multiFDR_boundaries.gff
--- a/test-data/find_TADs/multiFDR_boundaries.gff Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,2 +0,0 @@
-chr2L HiCExplorer boundary 22922500 22927500 -0.0682563628914 . . ID=B09504;delta=0.0219548467205;pvalue=3.39647761363e-05;tad_sep=-0.0682563628914
-chrX HiCExplorer boundary 87500 92500 -0.0720204010166 . . ID=B09542;delta=0.0197999801036;pvalue=5.52234326074e-05;tad_sep=-0.0720204010166
b
diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/find_TADs/multiFDR_score.bedgraph
--- a/test-data/find_TADs/multiFDR_score.bedgraph Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,23814 +0,0 @@\n-chr2RHet\t2500\t3286880\t0.0\n-chr3RHet\t2500\t2516253\t0.0\n-chr2LHet\t2500\t366936\t0.0\n-chr4\t2500\t1350928\t0.0\n-chrYHet\t2500\t346019\t0.0\n-chr3L\t2500\t7500\t-0.159737358616\n-chr3L\t7500\t12500\t-0.155082487586\n-chr3L\t12500\t17500\t-0.151168327942\n-chr3L\t17500\t22500\t-0.147873215842\n-chr3L\t22500\t27500\t-0.144772772067\n-chr3L\t27500\t32500\t-0.141868972264\n-chr3L\t32500\t37500\t-0.139208396548\n-chr3L\t37500\t42500\t-0.136695519504\n-chr3L\t42500\t47500\t-0.13435784673\n-chr3L\t47500\t52500\t-0.132198322928\n-chr3L\t52500\t57500\t-0.130138647123\n-chr3L\t57500\t62500\t-0.094024059437\n-chr3L\t62500\t67500\t-0.0764270277659\n-chr3L\t67500\t72500\t-0.0418312780272\n-chr3L\t72500\t77500\t0.0197073538633\n-chr3L\t77500\t82500\t0.0705286553822\n-chr3L\t82500\t87500\t0.0728398203412\n-chr3L\t87500\t92500\t0.0704550755289\n-chr3L\t92500\t97500\t0.0683612984106\n-chr3L\t97500\t102500\t0.0699935523517\n-chr3L\t102500\t107500\t0.0683284920538\n-chr3L\t107500\t112500\t0.0668530433483\n-chr3L\t112500\t117500\t0.0655400239401\n-chr3L\t117500\t122500\t0.0643615010968\n-chr3L\t122500\t127500\t0.00960322899463\n-chr3L\t127500\t132500\t0.0122848570996\n-chr3L\t132500\t137500\t-0.00142777411793\n-chr3L\t137500\t142500\t-0.0603620960568\n-chr3L\t142500\t147500\t-0.0515625340117\n-chr3L\t147500\t152500\t-0.05521871309\n-chr3L\t152500\t157500\t-0.0666038885164\n-chr3L\t157500\t162500\t-0.0700877787653\n-chr3L\t162500\t167500\t-0.103166582026\n-chr3L\t167500\t172500\t-0.103166582026\n-chr3L\t172500\t177500\t-0.103166582026\n-chr3L\t177500\t182500\t-0.0892268305271\n-chr3L\t182500\t187500\t-0.0778912906571\n-chr3L\t187500\t192500\t-0.0547473455607\n-chr3L\t192500\t197500\t-0.0624074978774\n-chr3L\t197500\t202500\t-0.0402670995717\n-chr3L\t202500\t207500\t-0.0180889610265\n-chr3L\t207500\t212500\t-0.0180889610265\n-chr3L\t212500\t217500\t-0.0180889610265\n-chr3L\t217500\t222500\t0.0190634988953\n-chr3L\t222500\t227500\t0.0112223886772\n-chr3L\t227500\t232500\t-0.00338415767042\n-chr3L\t232500\t237500\t0.0186707022549\n-chr3L\t237500\t242500\t0.0157587330805\n-chr3L\t242500\t247500\t0.0157587330805\n-chr3L\t247500\t252500\t-0.00807602631835\n-chr3L\t252500\t257500\t-0.0104750989089\n-chr3L\t257500\t262500\t-0.0266548620056\n-chr3L\t262500\t267500\t-0.0146100294292\n-chr3L\t267500\t272500\t-0.0173923184009\n-chr3L\t272500\t277500\t0.00661604790157\n-chr3L\t277500\t282500\t0.0262671919612\n-chr3L\t282500\t287500\t0.0267167034717\n-chr3L\t287500\t292500\t0.0443137229877\n-chr3L\t292500\t297500\t0.0751279690126\n-chr3L\t297500\t302500\t0.0517535485658\n-chr3L\t302500\t307500\t0.0349828408048\n-chr3L\t307500\t312500\t0.0428087068076\n-chr3L\t312500\t317500\t-0.00566065878864\n-chr3L\t317500\t322500\t-0.00566065878864\n-chr3L\t322500\t327500\t-0.0169961986586\n-chr3L\t327500\t332500\t0.000157299660421\n-chr3L\t332500\t337500\t-0.0308482500837\n-chr3L\t337500\t342500\t-0.0226411965829\n-chr3L\t342500\t347500\t-0.0160718960842\n-chr3L\t347500\t352500\t-0.0300379106017\n-chr3L\t352500\t357500\t-0.0029144271306\n-chr3L\t357500\t362500\t-0.0580815967953\n-chr3L\t362500\t367500\t-0.0423382381668\n-chr3L\t367500\t372500\t-0.0243196018461\n-chr3L\t372500\t377500\t-0.0233236395501\n-chr3L\t377500\t382500\t0.0166536103463\n-chr3L\t382500\t387500\t0.0166536103463\n-chr3L\t387500\t392500\t0.0301338406883\n-chr3L\t392500\t397500\t0.019663316174\n-chr3L\t397500\t402500\t0.0270557022414\n-chr3L\t402500\t407500\t0.0371528801145\n-chr3L\t407500\t412500\t0.0321503361064\n-chr3L\t412500\t417500\t0.0071021124075\n-chr3L\t417500\t422500\t0.015319291476\n-chr3L\t422500\t427500\t0.0494427478616\n-chr3L\t427500\t432500\t0.0173949964846\n-chr3L\t432500\t437500\t0.0233486050163\n-chr3L\t437500\t442500\t0.0109350346776\n-chr3L\t442500\t447500\t0.0152410366959\n-chr3L\t447500\t452500\t-0.00172733084048\n-chr3L\t452500\t457500\t-0.00621496545075\n-chr3L\t457500\t462500\t-0.0121685739825\n-chr3L\t462500\t467500\t-0.00424252683144\n-chr3L\t467500\t472500\t0.000837611009745\n-chr3L\t472500\t477500\t-0.020134598244\n-chr3L\t477500\t482500\t-0.0582660019386\n-chr3L\t482500\t487500\t-0.0716979304628\n-chr3L\t487500\t492500\t-0.046010910774\n-chr3L\t492500\t497500\t-0.0233382831898\n-chr3L\t497500\t502500\t-0.00838723736395\n-chr3L\t502500\t507500\t-0.064184454726\n-chr3L\t507500\t512500\t-0.0674580254141\n-chr3L\t512500\t517500\t-0.0674580254141\n-chr3L\t517500\t522500\t-0.0992'..b'7432500\t-0.0366556086444\n-chr3R\t27432500\t27437500\t-0.0366556086444\n-chr3R\t27437500\t27442500\t-0.0474877411784\n-chr3R\t27442500\t27447500\t-0.0551103667922\n-chr3R\t27447500\t27452500\t-0.0573623591363\n-chr3R\t27452500\t27457500\t-0.0233204047703\n-chr3R\t27457500\t27462500\t-0.00202637276643\n-chr3R\t27462500\t27467500\t0.0250198151374\n-chr3R\t27467500\t27472500\t0.0363309617631\n-chr3R\t27472500\t27477500\t0.0363309617631\n-chr3R\t27477500\t27482500\t0.0363309617631\n-chr3R\t27482500\t27487500\t0.0672663093487\n-chr3R\t27487500\t27492500\t0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b
diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/find_TADs/multiFDR_tad_score.bm
--- a/test-data/find_TADs/multiFDR_tad_score.bm Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/hicFindTADs_TAD_score.tabular
--- a/test-data/hicFindTADs_TAD_score.tabular Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
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b
diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/hicFindTADs_find_score.bedgraph
--- a/test-data/hicFindTADs_find_score.bedgraph Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/hicPlotDistVsCounts_result1.png
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/hicPlotDistVsCounts_result2.png
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/hicPlotTADs_result1.svg
--- a/test-data/hicPlotTADs_result1.svg Sat Jun 09 15:32:48 2018 -0400
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/hicSumMatrices_result1.npz.h5
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/li_32-33mb_interactions.bedgraph
--- a/test-data/li_32-33mb_interactions.bedgraph Sat Jun 09 15:32:48 2018 -0400
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b
diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/li_32mb_interactions.bedgraph
--- a/test-data/li_32mb_interactions.bedgraph Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/pca1.bedgraph
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+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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b
diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/pca1.bw
b
Binary file test-data/pca1.bw has changed
b
diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/pca2.bedgraph
--- a/test-data/pca2.bedgraph Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,2717 +0,0 @@\n-chr2RHet\t0\t50000\t-0.177193350469\n-chr2RHet\t50000\t100000\t-0.032204538347\n-chr2RHet\t100000\t150000\t0.282387463612\n-chr2RHet\t150000\t200000\t-0.011825630271\n-chr2RHet\t200000\t250000\t-0.041231230909\n-chr2RHet\t300000\t350000\t-0.002926389428\n-chr2RHet\t350000\t400000\t0.254508542308\n-chr2RHet\t400000\t450000\t-0.026450269267\n-chr2RHet\t450000\t500000\t0.240952240415\n-chr2RHet\t500000\t550000\t-0.293599828712\n-chr2RHet\t550000\t600000\t-0.289808428461\n-chr2RHet\t600000\t650000\t0.303424484938\n-chr2RHet\t650000\t700000\t0.021093016199\n-chr2RHet\t700000\t750000\t0.010960418117\n-chr2RHet\t750000\t800000\t0.289273219599\n-chr2RHet\t800000\t850000\t-0.091930713152\n-chr2RHet\t850000\t900000\t0.128622195308\n-chr2RHet\t900000\t950000\t-0.002472300051\n-chr2RHet\t950000\t1000000\t0.114441574570\n-chr2RHet\t1000000\t1050000\t0.017909752708\n-chr2RHet\t1050000\t1100000\t-0.016855223244\n-chr2RHet\t1100000\t1150000\t0.000000000000\n-chr2RHet\t1250000\t1300000\t0.102697089188\n-chr2RHet\t1300000\t1350000\t0.075340309339\n-chr2RHet\t1350000\t1400000\t-0.035326054956\n-chr2RHet\t1400000\t1450000\t-0.141721952912\n-chr2RHet\t1450000\t1500000\t0.051213364907\n-chr2RHet\t1500000\t1550000\t0.000000000000\n-chr2RHet\t1550000\t1600000\t-0.288446354623\n-chr2RHet\t1600000\t1650000\t0.027506039012\n-chr2RHet\t1650000\t1700000\t0.050134411794\n-chr2RHet\t1700000\t1750000\t0.013977802418\n-chr2RHet\t1750000\t1800000\t0.000000000000\n-chr2RHet\t1850000\t1900000\t-0.062535524405\n-chr2RHet\t1900000\t1950000\t-0.102423419951\n-chr2RHet\t1950000\t2000000\t-0.000255452186\n-chr2RHet\t2000000\t2050000\t0.000000000000\n-chr2RHet\t2050000\t2100000\t0.226048172597\n-chr2RHet\t2100000\t2150000\t-0.009032181245\n-chr2RHet\t2150000\t2200000\t-0.156931793125\n-chr2RHet\t2200000\t2250000\t-0.076913071464\n-chr2RHet\t2250000\t2300000\t0.013015414891\n-chr2RHet\t2300000\t2350000\t0.260358373936\n-chr2RHet\t2350000\t2400000\t0.170971324927\n-chr2RHet\t2400000\t2450000\t-0.112722101985\n-chr2RHet\t2550000\t2600000\t0.012191890450\n-chr2RHet\t2600000\t2650000\t-0.022853015897\n-chr2RHet\t2750000\t2800000\t0.000000000000\n-chr2RHet\t2800000\t2850000\t-0.025282155888\n-chr2RHet\t2850000\t2900000\t-0.007270539302\n-chr2RHet\t2900000\t2950000\t-0.007270539302\n-chr2RHet\t3000000\t3050000\t0.000000000000\n-chr2RHet\t3050000\t3100000\t-0.018569899065\n-chr2RHet\t3100000\t3150000\t0.000000000000\n-chr2RHet\t3150000\t3200000\t-0.203490911545\n-chr2RHet\t3200000\t3250000\t0.032681603101\n-chr2RHet\t3250000\t3288761\t-0.011795145700\n-chr3RHet\t0\t50000\t0.284466569482\n-chr3RHet\t50000\t100000\t0.204455883661\n-chr3RHet\t100000\t150000\t0.143212426746\n-chr3RHet\t150000\t200000\t-0.119672115801\n-chr3RHet\t200000\t250000\t0.109167602607\n-chr3RHet\t250000\t300000\t0.272370238524\n-chr3RHet\t300000\t350000\t0.230075765445\n-chr3RHet\t350000\t400000\t0.005155204417\n-chr3RHet\t400000\t450000\t-0.119414549611\n-chr3RHet\t500000\t550000\t0.019514024178\n-chr3RHet\t550000\t600000\t-0.328750388286\n-chr3RHet\t600000\t650000\t-0.090004795516\n-chr3RHet\t650000\t700000\t0.282771987696\n-chr3RHet\t700000\t750000\t-0.387972364344\n-chr3RHet\t750000\t800000\t-0.006440407038\n-chr3RHet\t800000\t850000\t0.111719040869\n-chr3RHet\t850000\t900000\t-0.319911282103\n-chr3RHet\t900000\t950000\t-0.098741582562\n-chr3RHet\t950000\t1000000\t0.000000000000\n-chr3RHet\t1000000\t1050000\t-0.006440407038\n-chr3RHet\t1100000\t1150000\t-0.390342708249\n-chr3RHet\t1150000\t1200000\t0.017617890478\n-chr3RHet\t1200000\t1250000\t0.011925436183\n-chr3RHet\t1250000\t1300000\t-0.017077678079\n-chr3RHet\t1300000\t1350000\t-0.134846013814\n-chr3RHet\t1350000\t1400000\t-0.000526086961\n-chr3RHet\t1400000\t1450000\t0.022215091223\n-chr3RHet\t1450000\t1500000\t0.060265355310\n-chr3RHet\t1500000\t1550000\t0.026499470821\n-chr3RHet\t1550000\t1600000\t0.060783329226\n-chr3RHet\t1600000\t1650000\t0.000000000000\n-chr3RHet\t1650000\t1700000\t-0.044362558029\n-chr3RHet\t1700000\t1750000\t0.033380758238\n-chr3RHet\t1750000\t1800000\t0.006383059364\n-chr3RHet\t1800000\t1850000\t0.039532252869\n-chr3RHet\t1850000\t1900000\t0.000000000000\n-chr3RHet\t1900000\t1950000\t0.071894526199\n-chr3RHet\t1950000\t2000000\t0.002187689061\n-chr3RHet\t2000000\t2050000\t0.039458725343\n-chr3RHet\t2050000\t2100000\t0.026268465670\n-chr3RHet\t2100000\t2150000\t-0.046248739349\n-chr3RH'..b'\t750000\t800000\t0.000000000000\n-chrUextra\t900000\t950000\t0.000000000000\n-chrUextra\t1000000\t1050000\t0.000000000000\n-chrUextra\t1150000\t1200000\t0.000000000000\n-chrUextra\t1250000\t1300000\t0.000000000000\n-chrUextra\t1400000\t1450000\t0.000000000000\n-chrUextra\t1450000\t1500000\t0.000000000000\n-chrUextra\t1500000\t1550000\t0.000000000000\n-chrUextra\t1550000\t1600000\t0.000000000000\n-chrUextra\t1750000\t1800000\t0.000000000000\n-chrUextra\t1850000\t1900000\t0.000000000000\n-chrUextra\t2150000\t2200000\t0.000000000000\n-chrUextra\t2300000\t2350000\t0.000000000000\n-chrUextra\t26500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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/pca2.bw
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/pearson_small_50kb.cool
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/pearson_small_50kb.h5
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/pearson_small_50kb_transform.cool
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/raw_qc_report
--- a/test-data/raw_qc_report Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -1,29 +0,0 @@
-
-File matrix.h5
-Pairs considered 983
-Min rest. site distance 300
-Max library insert size 1000
-
-# count (percentage w.r.t. total sequenced reads)
-Pairs mappable, unique and high quality 300 (30.52)
-Pairs used 215 (21.87)
-One mate unmapped 506 (51.48)
-One mate not unique 13 (1.32)
-One mate low quality 164 (16.68)
-
-# count (percentage w.r.t. mappable, unique and high quality pairs)
-dangling end 0 (0.00)
-self ligation (removed) 0 (0.00)
-One mate not close to rest site 0 (0.00)
-same fragment 85 (28.33)
-self circle 0 (0.00)
-duplicated pairs 0 (0.00)
-
-# count (percentage w.r.t. total valid pairs used)
-inter chromosomal 24 (11.16)
-short range < 20kb 61 (28.37)
-long range 130 (60.47)
-inward pairs 42 (19.53)
-outward pairs 66 (30.70)
-left pairs 48 (22.33)
-right pairs 35 (16.28)
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_matrix_50kb_pearson_pca1_plot.png
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_matrix_50kb_pearson_pca1_plot.svg
--- a/test-data/small_matrix_50kb_pearson_pca1_plot.svg Sat Jun 09 15:32:48 2018 -0400
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_test_R1_unsorted.bam
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Binary file test-data/small_test_R1_unsorted.bam has changed
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_test_R1_unsorted.sam
--- a/test-data/small_test_R1_unsorted.sam Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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b'@@ -1,1000 +0,0 @@\n-@HD\tVN:1.0\tSO:unsorted\n-@SQ\tSN:chr2L\tLN:23011544\n-@SQ\tSN:chr2LHet\tLN:368872\n-@SQ\tSN:chr2R\tLN:21146708\n-@SQ\tSN:chr2RHet\tLN:3288761\n-@SQ\tSN:chr3L\tLN:24543557\n-@SQ\tSN:chr3LHet\tLN:2555491\n-@SQ\tSN:chr3R\tLN:27905053\n-@SQ\tSN:chr3RHet\tLN:2517507\n-@SQ\tSN:chr4\tLN:1351857\n-@SQ\tSN:chrM\tLN:19517\n-@SQ\tSN:chrUextra\tLN:29004656\n-@SQ\tSN:chrU\tLN:10049037\n-@SQ\tSN:chrX\tLN:22422827\n-@SQ\tSN:chrXHet\tLN:204112\n-@SQ\tSN:chrYHet\tLN:347038\n-@PG\tID:bowtie2\tPN:bowtie2\tVN:2.0.5\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1121:2099\t4\t*\t0\t0\t*\t*\t0\t0\tTGTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t(8;@##############################################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1187:2101\t4\t*\t0\t0\t*\t*\t0\t0\tTTATNTGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t<<<@#2@?##########################################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1158:2104\t4\t*\t0\t0\t*\t*\t0\t0\tAAAANAGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t<<<?#2@###########################################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1087:2104\t4\t*\t0\t0\t*\t*\t0\t0\tCAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t<<<?##############################################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1164:2117\t4\t*\t0\t0\t*\t*\t0\t0\tAACANACATTATTNTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t<<<@#2-:<;@@@#####################################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1182:2118\t4\t*\t0\t0\t*\t*\t0\t0\tTCTANGGTAGCTTTGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t;;;?#2::<?>>?@??##################################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1242:2118\t4\t*\t0\t0\t*\t*\t0\t0\tGGCTNGCAACTGAACANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t<<<?#2=@?@??>?@?##################################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1122:2120\t4\t*\t0\t0\t*\t*\t0\t0\tCCCANANANNANNTNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t<<<?##############################################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1072:2126\t4\t*\t0\t0\t*\t*\t0\t0\tCNTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t<#0@##############################################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1214:2131\t4\t*\t0\t0\t*\t*\t0\t0\tTGCTTTAAGAGCGGAAGAGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t9;<???=@?#########################################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1188:2141\t4\t*\t0\t0\t*\t*\t0\t0\tAGAAGTTAAACTAAAGCTAAGCNNNNNNNTGTNNNNNNNNNNNNNNNNNN\t<<;;??@@?@???@?<:?@?##############################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1220:2147\t4\t*\t0\t0\t*\t*\t0\t0\tGGCTTGTTGCTTCATTTGTTGCACNTTAAACAAGNNNNNNNNNNNNNNCC\t>==AAAAABBCBACBBCB7AA=@B#2<??A<ABB################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1075:2148\t4\t*\t0\t0\t*\t*\t0\t0\tANTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t<#4<@#############################################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1175:2152\t4\t*\t0\t0\t*\t*\t0\t0\tATGTTCTCATAATAGCAGAAAGCANAGAAGATGCNNNNGTNNNNNNNCAG\t@@@DDDDDHHHFFIIAHIIIFGII#3AFHI@GGI################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1235:2156\t16\tchr2L\t17448552\t24\t9S30M11S\t*\t0\t0\tGTGNNNNNNAAAAATAAATAAATACAAGGGGCAAAAGCTATCTTACGCCG\t#########JJJIHGJIGIJIEGIGJJJIHDIJIJIIHFHHHFFFFF@C@\tAS:i:60\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:30\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1117:2156\t4\t*\t0\t0\t*\t*\t0\t0\tCGAGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t<<<@@@############################################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1052:2158\t4\t*\t0\t0\t*\t*\t0\t0\tANTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t<#0@##############################################\tYT:Z:UU\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1150:2167\t16\tchr2L\t20717028\t22\t26S24M\t*\t0\t0\tTNCAGCTGGTTNCGAGGTGGGAAGCTAGCTTTCTAGAAACCGCCTCCAAA\t##HGCEFGC;.#GIGIJIJJIIGGJIJIIIIJJIIHIHFHHHFFFFFCC@\tAS:i:48\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:24\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1212:2169\t4\t*\t0\t0\t*\t*\t0\t0\tAAAAAACAAAGCTAGCTTCGTGTTTGTTTAAATTATATTAATATTTTATG\t@@@DDDDBFHHFF?FGGGGIBACGG*)19:CF*:?BB9?9?#########\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:1082:2169\t4\t*\t0\t0\t*\t*\t0\t0\tACTTTNNNN'..b'\tYF:Z:NS\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6220:2160\t4\t*\t0\t0\t*\t*\t0\t0\tCTGAGTATCCTTTTTCAAGTAACTCGTCTTTATCGNATTTGNNNNNNTTA\t##################################################\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6080:2161\t16\tchr2L\t20418636\t42\t9S41M\t*\t0\t0\tCTTNNNNNNAATACTTTCGTGTACATTATTGCAAATTTTAGGCTTTGGAG\t#########JIHDJJIIJJIJIIJJJJJJJJJJJJJJHHHHHFFEFFCC@\tAS:i:82\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:41\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6107:2165\t0\tchr2R\t1793463\t0\t22M28S\t*\t0\t0\tTCCTGTCAGTCCAAGAAAAGCTAGCTTCAAGGAATGCGAACCNNNNNTGG\tCCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJIJ########\tAS:i:44\tXS:i:44\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:22\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6008:2166\t0\tchr3R\t7743490\t41\t50M\t*\t0\t0\tGACGGTCAGTCCGAGAAGCATCTGGAGCCGATGGCCAGTTTCNNNNNGCG\t@@@FFDDDHAHFFFHIJIGIJEIGGGGGHGHIHIFGHJEHDI########\tAS:i:77\tXN:i:0\tXM:i:6\tXO:i:0\tXG:i:0\tNM:i:6\tMD:Z:16G25G0G0G0G0C3\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6164:2167\t0\tchrU\t1886379\t2\t14S36M\t*\t0\t0\tCGCATTTGAAAGCTAGCTTTCTAGTTTCACTTGTTTGTTTTTNNNNGTTT\tB@CFFFFFHHHHGJHIIIJJJJIJIIJJJJIJIIIJIGIJJJ########\tAS:i:60\tXS:i:56\tXN:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tNM:i:4\tMD:Z:28T0T0T0T4\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6028:2168\t16\tchr3L\t23880171\t0\t27S23M\t*\t0\t0\tAGGAANNNGGACACTATCGAAAAAGCTAGCTTGCAAAGTTCAAATGACCG\t?B800###IIHC<GGFCIHIJJJJJJIJJJJJIJJIIHHGHGFFFDB@@B\tAS:i:46\tXS:i:46\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:23\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6130:2172\t0\tchr3L\t20041224\t44\t50M\t*\t0\t0\tCGAGGAAGCTGCAAATGGTACGGAGCTGCTGGCTGAGGACGTGTTTGTTG\t@@@BDDDDDFDDF9ABGH<CFFHHHGIIIIGIDEG@F)?FG6B8BB;B@@\tAS:i:96\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:37T12\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6218:2174\t16\tchr2R\t19978961\t44\t50M\t*\t0\t0\tAGGAGCGTTCGTACAAGCGAAGCTCGCCGGAGGACGACAAGCTGAGGCGC\t3>9;AEEE?G@=@@@/A:=<BDDGIFC:AGIGFCGHBDDFHDDDDDD@@@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6240:2175\t16\tchr2L\t8736543\t42\t50M\t*\t0\t0\tTTAAGTGGACTTCGTTAATGTTTTAAATTTGAAGAATATTTTACGAGTTA\tHIGIHEHFBGIIFJJJIGGJJIJJIJJJJJIIIJIJJHHHHHDFFFFB@@\tAS:i:85\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:4A25C19\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6080:2181\t0\tchr2L\t22737721\t44\t1S49M\t*\t0\t0\tACTCAGTATATATTAAAAGTTTGTTTATACAATATCCTTTTAATAGGTAT\t<@@FFFDDHAHHHJJIEGICHHGFHHEIJJJIIJJJJJIJJGIJIII?FI\tAS:i:98\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:49\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6184:2183\t16\tchr2L\t1627623\t44\t50M\t*\t0\t0\tTTTAGTTATTGGGCTTTAAAAAAATCTAAATTCTGTCATGATTGATTCTG\tJJJJJJIGIIIIIIJIJJJJJJJJJJJJJJIIJIJIJHHHHHFFFFFBCC\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6206:2186\t16\tchr3R\t5530104\t44\t50M\t*\t0\t0\tCACGACGGGACGCCCTAACGGTATCGTGTGTAATTGCAGTTGCACAAGCA\t<@GHCBJIHBJIJJJJJHIJJJIJJJJIGJIIIIGIGHHHGGFDFFFC@@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6022:2190\t0\tchr3R\t17305312\t36\t40M10S\t*\t0\t0\tACTATAGAAATCTATTAAAAGTATTCCATGTAAGCTAGCTTCTCCACTGT\t?@@BDDDFG?HHHEHIIIIIIHHIIIIFIGIIIIIIIIIGDDHGFFHDGD\tAS:i:72\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:36T3\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6130:2190\t0\tchr2R\t13131924\t36\t36M14S\t*\t0\t0\tATATTGAATTCGAGTCAGAAAAAATAAAACGAAGCTAGCTTATCTGTCAT\tCCCFFDFFGGGHDHHGEIHIIJEIJJJJIJJGIJJJJJJJJJJJJIIIJJ\tAS:i:72\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:36\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6163:2192\t16\tchr2L\t7371337\t2\t26M24S\t*\t0\t0\tGGGTTCTCCACCAGCCGGCAAAAGCTAGCTTAAATTAACTTTTAGTTTTA\tFB)B;B=HD9JJJJIJJJJJJJJJJJJJJJJJJJJJHFHHGHFFFFFCCC\tAS:i:52\tXS:i:48\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:26\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6060:2193\t16\tchr3R\t9331177\t44\t50M\t*\t0\t0\tGCTTACTCCTTTGCAGCACTAGTACTAATTTTTTATTTTTTCGAATTTTC\tGGHFCHFGGIJJIGIIHGIIEFGDIJJJIJJJJJIJIHHHHHFFFFFCC@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6038:2194\t0\tchrYHet\t283249\t2\t17S33M\t*\t0\t0\tAGGCAGTAAGGCAGTAAGCTAGCTTGCTATGGTATTTTTCCTTAAGTTCC\t@@@DDDDDHHHHHIIGIDC<<EEHICG@?<C>11?ECG<CCDHAAAFFGE\tAS:i:66\tXS:i:60\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:33\tYT:Z:UU\n'
b
diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_test_R2_unsorted.bam
b
Binary file test-data/small_test_R2_unsorted.bam has changed
b
diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_test_R2_unsorted.sam
--- a/test-data/small_test_R2_unsorted.sam Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_test_matrix.h5
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_test_matrix_50kb_res.h5
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_test_matrix_result_sorted.bam
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/tad_classification.bed
--- a/test-data/tad_classification.bed Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,2685 +0,0 @@\n-chr2L\t73103\t94543\tactive\t2\t.\t73103\t94543\t255,255,153\n-chr2L\t94543\t108120\tactive\t4\t.\t94543\t108120\t255,255,153\n-chr2L\t108120\t132269\tactive\t2\t.\t108120\t132269\t255,255,153\n-chr2L\t132269\t143461\tactive\t2\t.\t132269\t143461\t255,255,153\n-chr2L\t143461\t159101\tactive\t2\t.\t143461\t159101\t255,255,153\n-chr2L\t159101\t181297\tinactive\t1\t.\t159101\t181297\t0,0,0\n-chr2L\t181297\t207416\tactive\t4\t.\t181297\t207416\t255,255,153\n-chr2L\t207416\t248687\tactive\t4\t.\t207416\t248687\t255,255,153\n-chr2L\t248687\t271451\tinactive\t1\t.\t248687\t271451\t0,0,0\n-chr2L\t271451\t283072\tactive\t4\t.\t271451\t283072\t255,255,153\n-chr2L\t283072\t294919\tactive\t2\t.\t283072\t294919\t255,255,153\n-chr2L\t294919\t306028\tactive\t4\t.\t294919\t306028\t255,255,153\n-chr2L\t306028\t357775\tinactive\t1\t.\t306028\t357775\t0,0,0\n-chr2L\t357775\t403068\tinactive\t1\t.\t357775\t403068\t0,0,0\n-chr2L\t403068\t421370\tactive\t4\t.\t403068\t421370\t255,255,153\n-chr2L\t421370\t472506\tactive\t2\t.\t421370\t472506\t255,255,153\n-chr2L\t472506\t490303\tactive\t2\t.\t472506\t490303\t255,255,153\n-chr2L\t490303\t541886\tactive\t2\t.\t490303\t541886\t255,255,153\n-chr2L\t541886\t553339\tactive\t2\t.\t541886\t553339\t255,255,153\n-chr2L\t553339\t559789\tactive\t4\t.\t553339\t559789\t255,255,153\n-chr2L\t559789\t574511\tactive\t4\t.\t559789\t574511\t255,255,153\n-chr2L\t574511\t602435\tPcG\t0\t.\t574511\t602435\t56,108,176\n-chr2L\t602435\t810330\tinactive\t1\t.\t602435\t810330\t0,0,0\n-chr2L\t810330\t825970\tactive\t4\t.\t810330\t825970\t255,255,153\n-chr2L\t825970\t853278\tactive\t2\t.\t825970\t853278\t255,255,153\n-chr2L\t853278\t871106\tactive\t2\t.\t853278\t871106\t255,255,153\n-chr2L\t871106\t887664\tactive\t2\t.\t871106\t887664\t255,255,153\n-chr2L\t887664\t1006986\tinactive\t1\t.\t887664\t1006986\t0,0,0\n-chr2L\t1006986\t1077753\tinactive\t1\t.\t1006986\t1077753\t0,0,0\n-chr2L\t1077753\t1102940\tinactive\t1\t.\t1077753\t1102940\t0,0,0\n-chr2L\t1102940\t1108427\tactive\t4\t.\t1102940\t1108427\t255,255,153\n-chr2L\t1108427\t1142854\tactive\t2\t.\t1108427\t1142854\t255,255,153\n-chr2L\t1142854\t1157702\tactive\t4\t.\t1142854\t1157702\t255,255,153\n-chr2L\t1157702\t1185674\tactive\t4\t.\t1157702\t1185674\t255,255,153\n-chr2L\t1185674\t1246112\tinactive\t1\t.\t1185674\t1246112\t0,0,0\n-chr2L\t1246112\t1348267\tinactive\t1\t.\t1246112\t1348267\t0,0,0\n-chr2L\t1348267\t1492300\tinactive\t1\t.\t1348267\t1492300\t0,0,0\n-chr2L\t1492300\t1504156\tinactive\t1\t.\t1492300\t1504156\t0,0,0\n-chr2L\t1504156\t1614536\tinactive\t1\t.\t1504156\t1614536\t0,0,0\n-chr2L\t1614536\t1705229\tPcG\t0\t.\t1614536\t1705229\t56,108,176\n-chr2L\t1705229\t1728747\tactive\t2\t.\t1705229\t1728747\t255,255,153\n-chr2L\t1728747\t1818391\tinactive\t1\t.\t1728747\t1818391\t0,0,0\n-chr2L\t1818391\t1884683\tinactive\t1\t.\t1818391\t1884683\t0,0,0\n-chr2L\t1884683\t1909751\tinactive\t1\t.\t1884683\t1909751\t0,0,0\n-chr2L\t1909751\t1937585\tactive\t2\t.\t1909751\t1937585\t255,255,153\n-chr2L\t1937585\t1974067\tPcG\t0\t.\t1937585\t1974067\t56,108,176\n-chr2L\t1974067\t1987851\tactive\t4\t.\t1974067\t1987851\t255,255,153\n-chr2L\t1987851\t2037530\tinactive\t1\t.\t1987851\t2037530\t0,0,0\n-chr2L\t2037530\t2130843\tinactive\t1\t.\t2037530\t2130843\t0,0,0\n-chr2L\t2130843\t2151583\tactive\t4\t.\t2130843\t2151583\t255,255,153\n-chr2L\t2151583\t2193334\tactive\t2\t.\t2151583\t2193334\t255,255,153\n-chr2L\t2193334\t2216423\tactive\t2\t.\t2193334\t2216423\t255,255,153\n-chr2L\t2216423\t2221910\tactive\t4\t.\t2216423\t2221910\t255,255,153\n-chr2L\t2221910\t2237044\tactive\t4\t.\t2221910\t2237044\t255,255,153\n-chr2L\t2237044\t2362172\tinactive\t1\t.\t2237044\t2362172\t0,0,0\n-chr2L\t2362172\t2383056\tactive\t4\t.\t2362172\t2383056\t255,255,153\n-chr2L\t2383056\t2492696\tinactive\t1\t.\t2383056\t2492696\t0,0,0\n-chr2L\t2492696\t2561589\tinactive\t1\t.\t2492696\t2561589\t0,0,0\n-chr2L\t2561589\t2591551\tactive\t2\t.\t2561589\t2591551\t255,255,153\n-chr2L\t2591551\t2724465\tinactive\t1\t.\t2591551\t2724465\t0,0,0\n-chr2L\t2724465\t2740126\tactive\t2\t.\t2724465\t2740126\t255,255,153\n-chr2L\t2740126\t2750826\tactive\t4\t.\t2740126\t2750826\t255,255,153\n-chr2L\t2750826\t2770137\tactive\t4\t.\t2750826\t2770137\t255,255,153\n-chr2L\t2770137\t2809031\tactive\t2\t.\t2770137\t2809031\t255,255,153\n-chr2L\t2809031\t2855746\tinactive\t1\t.\t2809031\t2855746\t0,0,0\n-chr2L\t2855746\t2874843\tactive\t2\t.\t2855746\t2874843\t255,255,153\n-chr2L\t2874843\t2885455\tactive\t4\t.\t2874843\t2885455\t255,255,153\n-chr2L\t2885455\t2969305\tactive\t2\t.\t2885455\t2969'..b'9171063\t19201498\t255,255,153\n-chrX\t19201498\t19220554\tactive\t2\t.\t19201498\t19220554\t255,255,153\n-chrX\t19220554\t19242911\tinactive\t1\t.\t19220554\t19242911\t0,0,0\n-chrX\t19242911\t19366620\tinactive\t1\t.\t19242911\t19366620\t0,0,0\n-chrX\t19366620\t19374360\tactive\t4\t.\t19366620\t19374360\t255,255,153\n-chrX\t19374360\t19389270\tactive\t4\t.\t19374360\t19389270\t25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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/tad_score.gz
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Binary file test-data/tad_score.gz has changed
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diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/test_regions.bed
--- a/test-data/test_regions.bed Sat Jun 09 15:32:48 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,60 +0,0 @@
-2L 7998826 7998827 msl2_peak_350 17.17982
-2L 9895070 9895071 msl2_peak_415 6.67520
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-2R 5441451 5441452 msl2_peak_1532 9.54697
-2R 8291271 8291272 msl2_peak_1644 7.36770
-2R 14575573 14575574 msl2_peak_1947 4.41313
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-3R 2901523 2901524 msl2_peak_4559 2.22040
-3R 3932152 3932153 msl2_peak_4603 9.59945
-3R 11851634 11851635 msl2_peak_4969 8.43238
-3R 20545331 20545332 msl2_peak_5267 4.72876
-X 147841 147842 msl2_peak_22671 16.59036
-X 366894 366895 msl2_peak_22686 25.37647
-X 517100 517101 msl2_peak_22694 8.54298
-X 548547 548548 msl2_peak_22696 27.53758
-X 656427 656428 msl2_peak_22697 14.11897
-X 692287 692288 msl2_peak_22698 15.96065
-X 818016 818017 msl2_peak_22713 10.66184
-X 937135 937136 msl2_peak_22717 67.84654
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-X 2050114 2050115 msl2_peak_22805 47.23102
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-X 2126007 2126008 msl2_peak_22808 42.23372
-X 2162302 2162303 msl2_peak_22810 78.64520
-X 2237610 2237611 msl2_peak_22817 43.05813
-X 2340287 2340288 msl2_peak_22825 14.72497
-X 2493295 2493296 msl2_peak_22827 23.47760
-X 2503119 2503120 msl2_peak_22828 80.83590
-X 2520611 2520612 msl2_peak_22839 17.87077
-X 2521079 2521080 msl2_peak_22840 60.08352
-X 2613112 2613113 msl2_peak_22844 43.87985
-X 2628624 2628625 msl2_peak_22847 115.37079
-X 3382405 3382406 msl2_peak_22879 6.13203
-X 3593688 3593689 msl2_peak_22908 10.66184
-X 3596515 3596516 msl2_peak_22909 6.59200
-X 3755342 3755343 msl2_peak_22919 164.76546
-X 3848197 3848198 msl2_peak_22920 74.65739
-X 4021813 4021814 msl2_peak_22929 32.73601