| Previous changeset 1:4a14714649b4 (2015-07-21) Next changeset 3:5c2cc3b58c7d (2020-10-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 4d5b98367b51a9e2f2711d1ccea9753a415d973a |
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modified:
sicer_wrapper.xml |
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added:
test-data/control-1-removed.bed test-data/test-1-removed.bed test-data/test-W200-G600-E0.01-islandfiltered-normalized.wig test-data/test-W200-G600-E0.01-islandfiltered.bed test-data/test-W200-G600-FDR0.01-islandfiltered-normalized.wig test-data/test-W200-G600-FDR0.01-islandfiltered.bed test-data/test-W200-normalized.wig test-data/test_1_output_log_file.contains test-data/test_1_test-W200-G600-E0.01.scoreisland test-data/test_1_test-W200.graph test-data/test_2_output_log_file.contains test-data/test_2_test-W200-G600-FDR0.01-island.bed test-data/test_2_test-W200-G600-islands-summary test-data/test_2_test-W200-G600-islands-summary-FDR0.01 test-data/test_2_test-W200-G600.scoreisland test-data/test_3_test-W200-G600-FDR0.01-island.bed test-data/test_3_test-W200-G600-islands-summary test-data/test_3_test-W200-G600-islands-summary-FDR0.01 test-data/test_3_test-W200-G600.scoreisland test-data/test_3_test-W200.graph test-data/test_4_test-W200-G600-E0.01.scoreisland |
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removed:
test-data/peakcalling_sicer/test_1/output_log_file.contains test-data/peakcalling_sicer/test_1/test-1-removed.bed test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01.scoreisland test-data/peakcalling_sicer/test_1/test-W200-normalized.wig test-data/peakcalling_sicer/test_1/test-W200.graph test-data/peakcalling_sicer/test_2/control-1-removed.bed test-data/peakcalling_sicer/test_2/output_log_file.contains test-data/peakcalling_sicer/test_2/test-1-removed.bed test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-island.bed test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01 test-data/peakcalling_sicer/test_2/test-W200-G600.scoreisland test-data/peakcalling_sicer/test_2/test-W200-normalized.wig test-data/peakcalling_sicer/test_2/test-W200.graph test-data/peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01 test-data/peakcalling_sicer/test_3/test-W200-G600.scoreisland test-data/peakcalling_sicer/test_3/test-W200.graph test-data/peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland test-data/peakcalling_sicer/test_4/test-W200.graph tool_dependencies.xml |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 sicer_wrapper.xml --- a/sicer_wrapper.xml Tue Jul 21 15:59:56 2015 -0400 +++ b/sicer_wrapper.xml Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -1,4 +1,4 @@\n-<tool id="peakcalling_sicer" name="SICER" version="0.0.1">\n+<tool id="peakcalling_sicer" name="SICER" version="0.0.2">\n <description>Statistical approach for the Identification of ChIP-Enriched Regions</description>\n <command interpreter="python">sicer_wrapper.py \n --bed_file \'${input_bed_file}\' \n@@ -78,13 +78,13 @@\n <param name="effective_genome_fraction" value="0.74" />\n <param name="gap_size" value="600" />\n <param name="error_cut_off" value="0.01" />\n- <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_1/test-1-removed.bed" />\n- <output name="summary_graph_output_file" file="peakcalling_sicer/test_1/test-W200.graph" />\n- <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-normalized.wig" />\n- <output name="island_filtered_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed" />\n- <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig" />\n- <output name="score_island_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01.scoreisland" />\n- <output name="output_log_file" file="peakcalling_sicer/test_1/output_log_file.contains" compare="contains"/>\n+ <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />\n+ <output name="summary_graph_output_file" file="test_1_test-W200.graph" />\n+ <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />\n+ <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />\n+ <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />\n+ <output name="score_island_output_file" file="test_1_test-W200-G600-E0.01.scoreisland" />\n+ <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>\n </test>\n <test>\n <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />\n@@ -96,17 +96,17 @@\n <param name="effective_genome_fraction" value="0.74" />\n <param name="gap_size" value="600" />\n <param name="error_cut_off" value="0.01" />\n- <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_2/test-1-removed.bed" />\n- <output name="redundancy_removed_control_bed_output_file" file="peakcalling_sicer/test_2/control-1-removed.bed" />\n- <output name="summary_graph_output_file" file="peakcalling_sicer/test_2/test-W200.graph" />\n- <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-normalized.wig" />\n- <output name="significant_islands_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-island.bed" />\n- <output name="island_filtered_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed" />\n- <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />\n- <output name="score_island_output_file" file="peakcalling_sicer/test_2/test-W200-G600.scoreisland" />\n- <output name="islands_summary_output_file" file="peakcalling_sicer/test_2/test-W200-G600-islands-summary" />\n- <output name="significant_islands_summary_output_file" file="peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01" />\n- <output name="output_log_file" file="peakcalling_sicer/test_2/output_log_file.contains" compare="contains"/>\n+ <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />\n+ <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />\n+ <output name="summary_graph_output_file" file="test_1_test-W200.graph" />\n+ <output name="test_normalized_wig_output_file" file="test-W200-normalized.w'..b'" file="peakcalling_sicer/test_3/test-W200.graph" />\n- <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-normalized.wig" />\n- <output name="significant_islands_output_file" file="peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed" />\n- <output name="island_filtered_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed" />\n- <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />\n- <output name="score_island_output_file" file="peakcalling_sicer/test_3/test-W200-G600.scoreisland" />\n- <output name="islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary" />\n- <output name="significant_islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01" />\n- <output name="output_log_file" file="peakcalling_sicer/test_2/output_log_file.contains" compare="contains"/>\n+ <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />\n+ <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />\n+ <output name="summary_graph_output_file" file="test_3_test-W200.graph" />\n+ <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />\n+ <output name="significant_islands_output_file" file="test_3_test-W200-G600-FDR0.01-island.bed" />\n+ <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />\n+ <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />\n+ <output name="score_island_output_file" file="test_3_test-W200-G600.scoreisland" />\n+ <output name="islands_summary_output_file" file="test_3_test-W200-G600-islands-summary" />\n+ <output name="significant_islands_summary_output_file" file="test_3_test-W200-G600-islands-summary-FDR0.01" />\n+ <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>\n </test>\n <test>\n <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />\n@@ -140,13 +140,13 @@\n <param name="effective_genome_fraction" value="0.74" />\n <param name="gap_size" value="600" />\n <param name="error_cut_off" value="0.01" />\n- <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_1/test-1-removed.bed" />\n- <output name="summary_graph_output_file" file="peakcalling_sicer/test_4/test-W200.graph" />\n- <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-normalized.wig" />\n- <output name="island_filtered_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed" />\n- <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig" />\n- <output name="score_island_output_file" file="peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland" />\n- <output name="output_log_file" file="peakcalling_sicer/test_1/output_log_file.contains" compare="contains"/>\n+ <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />\n+ <output name="summary_graph_output_file" file="test_3_test-W200.graph" />\n+ <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />\n+ <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />\n+ <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />\n+ <output name="score_island_output_file" file="test_4_test-W200-G600-E0.01.scoreisland" />\n+ <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>\n </test>\n </tests>\n <help>\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/control-1-removed.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/control-1-removed.bed Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,9896 @@\n+chr1\t3002334\t3002370\tregion_1\t0\t+\n+chr1\t3002376\t3002412\tregion_2\t0\t+\n+chr1\t3002409\t3002445\tregion_3\t0\t+\n+chr1\t3002773\t3002809\tregion_6\t0\t+\n+chr1\t3003136\t3003172\tregion_10\t0\t+\n+chr1\t3003183\t3003219\tregion_11\t0\t+\n+chr1\t3003699\t3003735\tregion_13\t0\t+\n+chr1\t3003700\t3003736\tregion_14\t0\t+\n+chr1\t3004263\t3004299\tregion_19\t0\t+\n+chr1\t3004503\t3004539\tregion_20\t0\t+\n+chr1\t3005109\t3005145\tregion_22\t0\t+\n+chr1\t3005814\t3005850\tregion_23\t0\t+\n+chr1\t3012338\t3012374\tregion_24\t0\t+\n+chr1\t3012362\t3012398\tregion_25\t0\t+\n+chr1\t3012639\t3012675\tregion_26\t0\t+\n+chr1\t3012924\t3012960\tregion_28\t0\t+\n+chr1\t3013931\t3013967\tregion_29\t0\t+\n+chr1\t3014180\t3014216\tregion_30\t0\t+\n+chr1\t3017021\t3017057\tregion_32\t0\t+\n+chr1\t3017070\t3017106\tregion_33\t0\t+\n+chr1\t3017705\t3017741\tregion_34\t0\t+\n+chr1\t3018651\t3018687\tregion_38\t0\t+\n+chr1\t3018685\t3018721\tregion_39\t0\t+\n+chr1\t3018749\t3018785\tregion_40\t0\t+\n+chr1\t3018845\t3018881\tregion_42\t0\t+\n+chr1\t3019016\t3019052\tregion_43\t0\t+\n+chr1\t3019424\t3019460\tregion_47\t0\t+\n+chr1\t3019503\t3019539\tregion_48\t0\t+\n+chr1\t3019573\t3019609\tregion_49\t0\t+\n+chr1\t3019649\t3019685\tregion_50\t0\t+\n+chr1\t3019842\t3019878\tregion_52\t0\t+\n+chr1\t3019908\t3019944\tregion_53\t0\t+\n+chr1\t3020099\t3020135\tregion_54\t0\t+\n+chr1\t3020410\t3020446\tregion_56\t0\t+\n+chr1\t3020436\t3020472\tregion_57\t0\t+\n+chr1\t3020632\t3020668\tregion_59\t0\t+\n+chr1\t3021163\t3021199\tregion_60\t0\t+\n+chr1\t3021171\t3021207\tregion_62\t0\t+\n+chr1\t3021200\t3021236\tregion_63\t0\t+\n+chr1\t3021769\t3021805\tregion_67\t0\t+\n+chr1\t3022609\t3022645\tregion_71\t0\t+\n+chr1\t3026253\t3026289\tregion_74\t0\t+\n+chr1\t3026835\t3026871\tregion_75\t0\t+\n+chr1\t3027203\t3027239\tregion_77\t0\t+\n+chr1\t3035392\t3035428\tregion_81\t0\t+\n+chr1\t3035417\t3035453\tregion_82\t0\t+\n+chr1\t3035631\t3035667\tregion_84\t0\t+\n+chr1\t3035745\t3035781\tregion_85\t0\t+\n+chr1\t3035953\t3035989\tregion_87\t0\t+\n+chr1\t3036879\t3036915\tregion_88\t0\t+\n+chr1\t3036895\t3036931\tregion_89\t0\t+\n+chr1\t3037005\t3037041\tregion_92\t0\t+\n+chr1\t3037056\t3037092\tregion_94\t0\t+\n+chr1\t3037424\t3037460\tregion_95\t0\t+\n+chr1\t3037433\t3037469\tregion_96\t0\t+\n+chr1\t3037588\t3037624\tregion_97\t0\t+\n+chr1\t3037807\t3037843\tregion_98\t0\t+\n+chr1\t3038447\t3038483\tregion_101\t0\t+\n+chr1\t3038631\t3038667\tregion_104\t0\t+\n+chr1\t3038670\t3038706\tregion_105\t0\t+\n+chr1\t3038775\t3038811\tregion_106\t0\t+\n+chr1\t3038786\t3038822\tregion_107\t0\t+\n+chr1\t3039016\t3039052\tregion_109\t0\t+\n+chr1\t3039031\t3039067\tregion_110\t0\t+\n+chr1\t3039101\t3039137\tregion_111\t0\t+\n+chr1\t3039489\t3039525\tregion_115\t0\t+\n+chr1\t3039820\t3039856\tregion_119\t0\t+\n+chr1\t3039864\t3039900\tregion_120\t0\t+\n+chr1\t3039975\t3040011\tregion_121\t0\t+\n+chr1\t3040082\t3040118\tregion_122\t0\t+\n+chr1\t3040771\t3040807\tregion_125\t0\t+\n+chr1\t3041069\t3041105\tregion_126\t0\t+\n+chr1\t3041907\t3041943\tregion_127\t0\t+\n+chr1\t3042500\t3042536\tregion_129\t0\t+\n+chr1\t3042997\t3043033\tregion_131\t0\t+\n+chr1\t3046741\t3046777\tregion_134\t0\t+\n+chr1\t3052164\t3052200\tregion_138\t0\t+\n+chr1\t3052236\t3052272\tregion_139\t0\t+\n+chr1\t3052291\t3052327\tregion_140\t0\t+\n+chr1\t3052367\t3052403\tregion_141\t0\t+\n+chr1\t3052377\t3052413\tregion_142\t0\t+\n+chr1\t3052420\t3052456\tregion_143\t0\t+\n+chr1\t3052495\t3052531\tregion_144\t0\t+\n+chr1\t3052915\t3052951\tregion_146\t0\t+\n+chr1\t3053000\t3053036\tregion_148\t0\t+\n+chr1\t3053127\t3053163\tregion_149\t0\t+\n+chr1\t3053826\t3053862\tregion_151\t0\t+\n+chr1\t3053951\t3053987\tregion_153\t0\t+\n+chr1\t3055234\t3055270\tregion_155\t0\t+\n+chr1\t3055845\t3055881\tregion_156\t0\t+\n+chr1\t3055879\t3055915\tregion_157\t0\t+\n+chr1\t3055905\t3055941\tregion_159\t0\t+\n+chr1\t3061917\t3061953\tregion_164\t0\t+\n+chr1\t3062806\t3062842\tregion_167\t0\t+\n+chr1\t3063436\t3063472\tregion_169\t0\t+\n+chr1\t3063698\t3063734\tregion_174\t0\t+\n+chr1\t3063875\t3063911\tregion_177\t0\t+\n+chr1\t3064025\t3064061\tregion_179\t0\t+\n+chr1\t3064052\t3064088\tregion_180\t0\t+\n+chr1\t3064225\t3064261\tregion_181\t0\t+\n+chr1\t3064331\t3064367\tregion_182\t0\t+\n+chr1\t3064622\t3064658\tregion_183\t0\t+\n+chr1\t3065905\t3065941\tregion_195\t0\t+\n+chr1\t3065957\t3065993\tregion_196\t0\t+\n+chr1\t3066232\t3066268\tregion_199\t0\t+\n+chr1\t3066934\t3066970\tregion_201\t0\t+\n+chr1\t3066965\t3067001\tregion_202\t0\t+\n+chr1\t3067022\t3067058\tregion_203\t0\t+\n+chr1\t3067151\t3067187\tregion_205\t0\t+\n+chr1\t30'..b'9800\t0\t-\n+chr1\t4635089\t4635125\tregion_9802\t0\t-\n+chr1\t4635363\t4635399\tregion_9806\t0\t-\n+chr1\t4636146\t4636182\tregion_9809\t0\t-\n+chr1\t4636163\t4636199\tregion_9810\t0\t-\n+chr1\t4636189\t4636225\tregion_9811\t0\t-\n+chr1\t4636190\t4636226\tregion_9812\t0\t-\n+chr1\t4636432\t4636468\tregion_9816\t0\t-\n+chr1\t4636510\t4636546\tregion_9817\t0\t-\n+chr1\t4636587\t4636623\tregion_9819\t0\t-\n+chr1\t4636746\t4636782\tregion_9820\t0\t-\n+chr1\t4636838\t4636874\tregion_9822\t0\t-\n+chr1\t4636902\t4636938\tregion_9825\t0\t-\n+chr1\t4637144\t4637180\tregion_9826\t0\t-\n+chr1\t4637146\t4637182\tregion_9827\t0\t-\n+chr1\t4637147\t4637183\tregion_9828\t0\t-\n+chr1\t4637203\t4637239\tregion_9829\t0\t-\n+chr1\t4637427\t4637463\tregion_9832\t0\t-\n+chr1\t4637457\t4637493\tregion_9834\t0\t-\n+chr1\t4638156\t4638192\tregion_9839\t0\t-\n+chr1\t4638493\t4638529\tregion_9840\t0\t-\n+chr1\t4638579\t4638615\tregion_9842\t0\t-\n+chr1\t4638640\t4638676\tregion_9843\t0\t-\n+chr1\t4638803\t4638839\tregion_9845\t0\t-\n+chr1\t4638946\t4638982\tregion_9846\t0\t-\n+chr1\t4638984\t4639020\tregion_9847\t0\t-\n+chr1\t4639170\t4639206\tregion_9848\t0\t-\n+chr1\t4639244\t4639280\tregion_9849\t0\t-\n+chr1\t4641241\t4641277\tregion_9852\t0\t-\n+chr1\t4641335\t4641371\tregion_9853\t0\t-\n+chr1\t4641663\t4641699\tregion_9855\t0\t-\n+chr1\t4641708\t4641744\tregion_9857\t0\t-\n+chr1\t4641729\t4641765\tregion_9858\t0\t-\n+chr1\t4641824\t4641860\tregion_9861\t0\t-\n+chr1\t4643866\t4643902\tregion_9863\t0\t-\n+chr1\t4644097\t4644133\tregion_9866\t0\t-\n+chr1\t4644105\t4644141\tregion_9867\t0\t-\n+chr1\t4644703\t4644739\tregion_9868\t0\t-\n+chr1\t4645149\t4645185\tregion_9872\t0\t-\n+chr1\t4645237\t4645273\tregion_9873\t0\t-\n+chr1\t4645497\t4645533\tregion_9875\t0\t-\n+chr1\t4645690\t4645726\tregion_9876\t0\t-\n+chr1\t4645789\t4645825\tregion_9877\t0\t-\n+chr1\t4645969\t4646005\tregion_9880\t0\t-\n+chr1\t4646298\t4646334\tregion_9884\t0\t-\n+chr1\t4646461\t4646497\tregion_9885\t0\t-\n+chr1\t4646550\t4646586\tregion_9887\t0\t-\n+chr1\t4646719\t4646755\tregion_9889\t0\t-\n+chr1\t4646807\t4646843\tregion_9891\t0\t-\n+chr1\t4646879\t4646915\tregion_9893\t0\t-\n+chr1\t4646916\t4646952\tregion_9894\t0\t-\n+chr1\t4646987\t4647023\tregion_9896\t0\t-\n+chr1\t4647088\t4647124\tregion_9898\t0\t-\n+chr1\t4647559\t4647595\tregion_9901\t0\t-\n+chr1\t4647582\t4647618\tregion_9902\t0\t-\n+chr1\t4647696\t4647732\tregion_9905\t0\t-\n+chr1\t4648124\t4648160\tregion_9908\t0\t-\n+chr1\t4648129\t4648165\tregion_9909\t0\t-\n+chr1\t4648179\t4648215\tregion_9910\t0\t-\n+chr1\t4648523\t4648559\tregion_9912\t0\t-\n+chr1\t4648554\t4648590\tregion_9914\t0\t-\n+chr1\t4650119\t4650155\tregion_9916\t0\t-\n+chr1\t4650645\t4650681\tregion_9917\t0\t-\n+chr1\t4652025\t4652061\tregion_9918\t0\t-\n+chr1\t4652368\t4652404\tregion_9921\t0\t-\n+chr1\t4652487\t4652523\tregion_9922\t0\t-\n+chr1\t4652701\t4652737\tregion_9924\t0\t-\n+chr1\t4653073\t4653109\tregion_9925\t0\t-\n+chr1\t4653175\t4653211\tregion_9926\t0\t-\n+chr1\t4653199\t4653235\tregion_9928\t0\t-\n+chr1\t4653387\t4653423\tregion_9931\t0\t-\n+chr1\t4653471\t4653507\tregion_9932\t0\t-\n+chr1\t4653503\t4653539\tregion_9933\t0\t-\n+chr1\t4653574\t4653610\tregion_9934\t0\t-\n+chr1\t4656708\t4656744\tregion_9938\t0\t-\n+chr1\t4656721\t4656757\tregion_9939\t0\t-\n+chr1\t4656810\t4656846\tregion_9941\t0\t-\n+chr1\t4657008\t4657044\tregion_9942\t0\t-\n+chr1\t4657224\t4657260\tregion_9943\t0\t-\n+chr1\t4657590\t4657626\tregion_9949\t0\t-\n+chr1\t4657717\t4657753\tregion_9950\t0\t-\n+chr1\t4657724\t4657760\tregion_9951\t0\t-\n+chr1\t4657836\t4657872\tregion_9953\t0\t-\n+chr1\t4657909\t4657945\tregion_9954\t0\t-\n+chr1\t4657928\t4657964\tregion_9956\t0\t-\n+chr1\t4658311\t4658347\tregion_9958\t0\t-\n+chr1\t4658664\t4658700\tregion_9963\t0\t-\n+chr1\t4658713\t4658749\tregion_9964\t0\t-\n+chr1\t4658824\t4658860\tregion_9965\t0\t-\n+chr1\t4658866\t4658902\tregion_9966\t0\t-\n+chr1\t4658971\t4659007\tregion_9969\t0\t-\n+chr1\t4659035\t4659071\tregion_9970\t0\t-\n+chr1\t4659244\t4659280\tregion_9971\t0\t-\n+chr1\t4659465\t4659501\tregion_9973\t0\t-\n+chr1\t4659470\t4659506\tregion_9974\t0\t-\n+chr1\t4659504\t4659540\tregion_9975\t0\t-\n+chr1\t4659511\t4659547\tregion_9977\t0\t-\n+chr1\t4659530\t4659566\tregion_9979\t0\t-\n+chr1\t4659563\t4659599\tregion_9980\t0\t-\n+chr1\t4659578\t4659614\tregion_9981\t0\t-\n+chr1\t4659880\t4659916\tregion_9986\t0\t-\n+chr1\t4660125\t4660161\tregion_9987\t0\t-\n+chr1\t4660431\t4660467\tregion_9991\t0\t-\n+chr1\t4661557\t4661593\tregion_9996\t0\t-\n+chr1\t4661619\t4661655\tregion_9997\t0\t-\n+chr1\t4662104\t4662140\tregion_9998\t0\t-\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_1/output_log_file.contains --- a/test-data/peakcalling_sicer/test_1/output_log_file.contains Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,190 +0,0 @@\n-#############################################\n-###### SICER v1.1 ######\n-#############################################\n-Input library directory:\n-ChIP library:\n-Output directory:\n-Species: mm8\n-Threshold for redundancy allowed for reads: 1\n-Window size: 200 bps\n-Fragment size: 150 bps. The shift for reads is half of 150\n-Effective genome size as a fraction of the reference genome of mm8: 0.740000\n-Gap size: 600 bps\n-Evalue for identification of significant islands: 0.01\n-Preprocess the raw input_bed_file file to remove redundancy with threshold 1...\n-chr1 \tPlus reads: 4989 \tRetained plus reads: 4935 ;\tMinus reads: 5011 \tRetained minus reads: 4963\n-chr2 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr3 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr4 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr5 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr6 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr7 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr8 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr9 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr10 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr11 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr12 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr13 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr14 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr15 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr16 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr17 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr18 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr19 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chrX \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chrY \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chrM \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-Partion the genome in windows ...\n-Generate summary files for input_bed_file...\n-total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0\n-total tag count in chr2.bed is: 0.0 = 0.0+0.0\n-total tag count in chr3.bed is: 0.0 = 0.0+0.0\n-total tag count in chr4.bed is: 0.0 = 0.0+0.0\n-total tag count in chr5.bed is: 0.0 = 0.0+0.0\n-total tag count in chr6.bed is: 0.0 = 0.0+0.0\n-total tag count in chr7.bed is: 0.0 = 0.0+0.0\n-total tag count in chr8.bed is: 0.0 = 0.0+0.0\n-total tag count in chr9.bed is: 0.0 = 0.0+0.0\n-total tag count in chr10.bed is: 0.0 = 0.0+0.0\n-total tag count in chr11.bed is: 0.0 = 0.0+0.0\n-total tag count in chr12.bed is: 0.0 = 0.0+0.0\n-total tag count in chr13.bed is: 0.0 = 0.0+0.0\n-total tag count in chr14.bed is: 0.0 = 0.0+0.0\n-total tag count in chr15.bed is: 0.0 = 0.0+0.0\n-total tag count in chr16.bed is: 0.0 = 0.0+0.0\n-total tag count in chr17.bed is: 0.0 = 0.0+0.0\n-total tag count in chr18.bed is: 0.0 = 0.0+0.0\n-total tag count in chr19.bed is: 0.0 = 0.0+0.0\n-total tag count in chrX.bed is: 0.0 = 0.0+0.0\n-total tag count in chrY.bed is: 0.0 = 0.0+0.0\n-total tag count in chrM.bed is: 0.0 = 0.0+0.0\n-Normalize summary graph by total redundancy-removed reads per million for input_bed_file ...\n-Convert the normalized summary graph into wig vstep format...\n-Find significant islands with E-value 0.01 for input_bed_file...\n-Species: mm8\n-Window_size: 200\n-Gap size: 600\n-E value is: 0.01\n-Total read count: 9898.0\n-Genome Length: '..b'ed is: 0.0 = 0.0+0.0\n-total tag count in chr12.bed is: 0.0 = 0.0+0.0\n-total tag count in chr13.bed is: 0.0 = 0.0+0.0\n-total tag count in chr14.bed is: 0.0 = 0.0+0.0\n-total tag count in chr15.bed is: 0.0 = 0.0+0.0\n-total tag count in chr16.bed is: 0.0 = 0.0+0.0\n-total tag count in chr17.bed is: 0.0 = 0.0+0.0\n-total tag count in chr18.bed is: 0.0 = 0.0+0.0\n-total tag count in chr19.bed is: 0.0 = 0.0+0.0\n-total tag count in chrX.bed is: 0.0 = 0.0+0.0\n-total tag count in chrY.bed is: 0.0 = 0.0+0.0\n-total tag count in chrM.bed is: 0.0 = 0.0+0.0\n-Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million...\n-Convert the summary graph made with the filtered reads into wig vstep format and normalize by total island-filtered read count per million...\n-Done!\n-Additionally, these warnings were reported:\n-Warning: chr2 reads do not exist in\n-Warning: chr3 reads do not exist in\n-Warning: chr4 reads do not exist in\n-Warning: chr5 reads do not exist in\n-Warning: chr6 reads do not exist in\n-Warning: chr7 reads do not exist in\n-Warning: chr8 reads do not exist in\n-Warning: chr9 reads do not exist in\n-Warning: chr10 reads do not exist in\n-Warning: chr11 reads do not exist in\n-Warning: chr12 reads do not exist in\n-Warning: chr13 reads do not exist in\n-Warning: chr14 reads do not exist in\n-Warning: chr15 reads do not exist in\n-Warning: chr16 reads do not exist in\n-Warning: chr17 reads do not exist in\n-Warning: chr18 reads do not exist in\n-Warning: chr19 reads do not exist in\n-Warning: chrX reads do not exist in\n-Warning: chrY reads do not exist in\n-Warning: chrM reads do not exist in\n-Warning: chr2 reads do not exist in\n-Warning: chr3 reads do not exist in\n-Warning: chr4 reads do not exist in\n-Warning: chr5 reads do not exist in\n-Warning: chr6 reads do not exist in\n-Warning: chr7 reads do not exist in\n-Warning: chr8 reads do not exist in\n-Warning: chr9 reads do not exist in\n-Warning: chr10 reads do not exist in\n-Warning: chr11 reads do not exist in\n-Warning: chr12 reads do not exist in\n-Warning: chr13 reads do not exist in\n-Warning: chr14 reads do not exist in\n-Warning: chr15 reads do not exist in\n-Warning: chr16 reads do not exist in\n-Warning: chr17 reads do not exist in\n-Warning: chr18 reads do not exist in\n-Warning: chr19 reads do not exist in\n-Warning: chrX reads do not exist in\n-Warning: chrY reads do not exist in\n-Warning: chrM reads do not exist in\n-Warning: chr2 reads do not exist in\n-Warning: chr3 reads do not exist in\n-Warning: chr4 reads do not exist in\n-Warning: chr5 reads do not exist in\n-Warning: chr6 reads do not exist in\n-Warning: chr7 reads do not exist in\n-Warning: chr8 reads do not exist in\n-Warning: chr9 reads do not exist in\n-Warning: chr10 reads do not exist in\n-Warning: chr11 reads do not exist in\n-Warning: chr12 reads do not exist in\n-Warning: chr13 reads do not exist in\n-Warning: chr14 reads do not exist in\n-Warning: chr15 reads do not exist in\n-Warning: chr16 reads do not exist in\n-Warning: chr17 reads do not exist in\n-Warning: chr18 reads do not exist in\n-Warning: chr19 reads do not exist in\n-Warning: chrX reads do not exist in\n-Warning: chrY reads do not exist in\n-Warning: chrM reads do not exist in\n-Warning: chr2 reads do not exist in\n-Warning: chr3 reads do not exist in\n-Warning: chr4 reads do not exist in\n-Warning: chr5 reads do not exist in\n-Warning: chr6 reads do not exist in\n-Warning: chr7 reads do not exist in\n-Warning: chr8 reads do not exist in\n-Warning: chr9 reads do not exist in\n-Warning: chr10 reads do not exist in\n-Warning: chr11 reads do not exist in\n-Warning: chr12 reads do not exist in\n-Warning: chr13 reads do not exist in\n-Warning: chr14 reads do not exist in\n-Warning: chr15 reads do not exist in\n-Warning: chr16 reads do not exist in\n-Warning: chr17 reads do not exist in\n-Warning: chr18 reads do not exist in\n-Warning: chr19 reads do not exist in\n-Warning: chrX reads do not exist in\n-Warning: chrY reads do not exist in\n-Warning: chrM reads do not exist in\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_1/test-1-removed.bed --- a/test-data/peakcalling_sicer/test_1/test-1-removed.bed Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,9898 +0,0 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\t0\t-\n-chr1\t5666894\t5666930\tregion_9805\t0\t-\n-chr1\t5667898\t5667934\tregion_9807\t0\t-\n-chr1\t5674133\t5674169\tregion_9808\t0\t-\n-chr1\t5675139\t5675175\tregion_9809\t0\t-\n-chr1\t5676675\t5676711\tregion_9811\t0\t-\n-chr1\t5677304\t5677340\tregion_9812\t0\t-\n-chr1\t5679098\t5679134\tregion_9814\t0\t-\n-chr1\t5679255\t5679291\tregion_9815\t0\t-\n-chr1\t5679303\t5679339\tregion_9817\t0\t-\n-chr1\t5679429\t5679465\tregion_9820\t0\t-\n-chr1\t5680276\t5680312\tregion_9824\t0\t-\n-chr1\t5680603\t5680639\tregion_9826\t0\t-\n-chr1\t5688108\t5688144\tregion_9830\t0\t-\n-chr1\t5688411\t5688447\tregion_9831\t0\t-\n-chr1\t5688571\t5688607\tregion_9834\t0\t-\n-chr1\t5689163\t5689199\tregion_9836\t0\t-\n-chr1\t5689312\t5689348\tregion_9837\t0\t-\n-chr1\t5689551\t5689587\tregion_9838\t0\t-\n-chr1\t5689847\t5689883\tregion_9839\t0\t-\n-chr1\t5694818\t5694854\tregion_9843\t0\t-\n-chr1\t5694996\t5695032\tregion_9844\t0\t-\n-chr1\t5695025\t5695061\tregion_9845\t0\t-\n-chr1\t5695144\t5695180\tregion_9846\t0\t-\n-chr1\t5695639\t5695675\tregion_9849\t0\t-\n-chr1\t5696688\t5696724\tregion_9851\t0\t-\n-chr1\t5696950\t5696986\tregion_9854\t0\t-\n-chr1\t5697092\t5697128\tregion_9855\t0\t-\n-chr1\t5698985\t5699021\tregion_9862\t0\t-\n-chr1\t5699555\t5699591\tregion_9863\t0\t-\n-chr1\t5700463\t5700499\tregion_9865\t0\t-\n-chr1\t5700467\t5700503\tregion_9866\t0\t-\n-chr1\t5703812\t5703848\tregion_9867\t0\t-\n-chr1\t5705804\t5705840\tregion_9872\t0\t-\n-chr1\t5706289\t5706325\tregion_9874\t0\t-\n-chr1\t5706307\t5706343\tregion_9875\t0\t-\n-chr1\t5706339\t5706375\tregion_9876\t0\t-\n-chr1\t5706399\t5706435\tregion_9877\t0\t-\n-chr1\t5706446\t5706482\tregion_9878\t0\t-\n-chr1\t5706955\t5706991\tregion_9879\t0\t-\n-chr1\t5707287\t5707323\tregion_9880\t0\t-\n-chr1\t5707378\t5707414\tregion_9881\t0\t-\n-chr1\t5709132\t5709168\tregion_9887\t0\t-\n-chr1\t5710251\t5710287\tregion_9889\t0\t-\n-chr1\t5711567\t5711603\tregion_9890\t0\t-\n-chr1\t5712819\t5712855\tregion_9894\t0\t-\n-chr1\t5714565\t5714601\tregion_9897\t0\t-\n-chr1\t5714689\t5714725\tregion_9898\t0\t-\n-chr1\t5715757\t5715793\tregion_9902\t0\t-\n-chr1\t5715995\t5716031\tregion_9903\t0\t-\n-chr1\t5716291\t5716327\tregion_9907\t0\t-\n-chr1\t5717567\t5717603\tregion_9911\t0\t-\n-chr1\t5717738\t5717774\tregion_9912\t0\t-\n-chr1\t5718495\t5718531\tregion_9915\t0\t-\n-chr1\t5718830\t5718866\tregion_9917\t0\t-\n-chr1\t5718966\t5719002\tregion_9919\t0\t-\n-chr1\t5719703\t5719739\tregion_9920\t0\t-\n-chr1\t5721599\t5721635\tregion_9922\t0\t-\n-chr1\t5721807\t5721843\tregion_9923\t0\t-\n-chr1\t5722297\t5722333\tregion_9925\t0\t-\n-chr1\t5722815\t5722851\tregion_9926\t0\t-\n-chr1\t5724418\t5724454\tregion_9930\t0\t-\n-chr1\t5725529\t5725565\tregion_9933\t0\t-\n-chr1\t5726039\t5726075\tregion_9935\t0\t-\n-chr1\t5726278\t5726314\tregion_9937\t0\t-\n-chr1\t5726381\t5726417\tregion_9939\t0\t-\n-chr1\t5726530\t5726566\tregion_9940\t0\t-\n-chr1\t5726534\t5726570\tregion_9941\t0\t-\n-chr1\t5726557\t5726593\tregion_9942\t0\t-\n-chr1\t5726561\t5726597\tregion_9943\t0\t-\n-chr1\t5726611\t5726647\tregion_9944\t0\t-\n-chr1\t5727379\t5727415\tregion_9946\t0\t-\n-chr1\t5727617\t5727653\tregion_9950\t0\t-\n-chr1\t5728091\t5728127\tregion_9951\t0\t-\n-chr1\t5728737\t5728773\tregion_9952\t0\t-\n-chr1\t5728886\t5728922\tregion_9953\t0\t-\n-chr1\t5729667\t5729703\tregion_9954\t0\t-\n-chr1\t5730047\t5730083\tregion_9956\t0\t-\n-chr1\t5738241\t5738277\tregion_9958\t0\t-\n-chr1\t5742298\t5742334\tregion_9962\t0\t-\n-chr1\t5742856\t5742892\tregion_9965\t0\t-\n-chr1\t5743555\t5743591\tregion_9966\t0\t-\n-chr1\t5743878\t5743914\tregion_9968\t0\t-\n-chr1\t5744403\t5744439\tregion_9969\t0\t-\n-chr1\t5744937\t5744973\tregion_9972\t0\t-\n-chr1\t5744965\t5745001\tregion_9973\t0\t-\n-chr1\t5745800\t5745836\tregion_9975\t0\t-\n-chr1\t5745885\t5745921\tregion_9976\t0\t-\n-chr1\t5745951\t5745987\tregion_9977\t0\t-\n-chr1\t5746138\t5746174\tregion_9979\t0\t-\n-chr1\t5746558\t5746594\tregion_9981\t0\t-\n-chr1\t5746574\t5746610\tregion_9982\t0\t-\n-chr1\t5746733\t5746769\tregion_9983\t0\t-\n-chr1\t5746922\t5746958\tregion_9984\t0\t-\n-chr1\t5751506\t5751542\tregion_9991\t0\t-\n-chr1\t5751966\t5752002\tregion_9995\t0\t-\n-chr1\t5752456\t5752492\tregion_9996\t0\t-\n-chr1\t5752543\t5752579\tregion_9997\t0\t-\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig --- a/test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5454 +0,0 @@\n-track type=wiggle_0 name=input_bed_file-islandfiltered\n-variableStep chrom=chr1 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed --- a/test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,9654 +0,0 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\t0\t-\n-chr1\t5660451\t5660487\tregion_9787\t0\t-\n-chr1\t5660539\t5660575\tregion_9788\t0\t-\n-chr1\t5663767\t5663803\tregion_9795\t0\t-\n-chr1\t5664658\t5664694\tregion_9798\t0\t-\n-chr1\t5665152\t5665188\tregion_9799\t0\t-\n-chr1\t5665971\t5666007\tregion_9800\t0\t-\n-chr1\t5666823\t5666859\tregion_9804\t0\t-\n-chr1\t5666894\t5666930\tregion_9805\t0\t-\n-chr1\t5676675\t5676711\tregion_9811\t0\t-\n-chr1\t5677304\t5677340\tregion_9812\t0\t-\n-chr1\t5679098\t5679134\tregion_9814\t0\t-\n-chr1\t5679255\t5679291\tregion_9815\t0\t-\n-chr1\t5679303\t5679339\tregion_9817\t0\t-\n-chr1\t5679429\t5679465\tregion_9820\t0\t-\n-chr1\t5680276\t5680312\tregion_9824\t0\t-\n-chr1\t5680603\t5680639\tregion_9826\t0\t-\n-chr1\t5688108\t5688144\tregion_9830\t0\t-\n-chr1\t5688411\t5688447\tregion_9831\t0\t-\n-chr1\t5688571\t5688607\tregion_9834\t0\t-\n-chr1\t5689163\t5689199\tregion_9836\t0\t-\n-chr1\t5689312\t5689348\tregion_9837\t0\t-\n-chr1\t5689551\t5689587\tregion_9838\t0\t-\n-chr1\t5689847\t5689883\tregion_9839\t0\t-\n-chr1\t5694818\t5694854\tregion_9843\t0\t-\n-chr1\t5694996\t5695032\tregion_9844\t0\t-\n-chr1\t5695025\t5695061\tregion_9845\t0\t-\n-chr1\t5695144\t5695180\tregion_9846\t0\t-\n-chr1\t5695639\t5695675\tregion_9849\t0\t-\n-chr1\t5696688\t5696724\tregion_9851\t0\t-\n-chr1\t5696950\t5696986\tregion_9854\t0\t-\n-chr1\t5697092\t5697128\tregion_9855\t0\t-\n-chr1\t5698985\t5699021\tregion_9862\t0\t-\n-chr1\t5699555\t5699591\tregion_9863\t0\t-\n-chr1\t5700463\t5700499\tregion_9865\t0\t-\n-chr1\t5700467\t5700503\tregion_9866\t0\t-\n-chr1\t5705804\t5705840\tregion_9872\t0\t-\n-chr1\t5706289\t5706325\tregion_9874\t0\t-\n-chr1\t5706307\t5706343\tregion_9875\t0\t-\n-chr1\t5706339\t5706375\tregion_9876\t0\t-\n-chr1\t5706399\t5706435\tregion_9877\t0\t-\n-chr1\t5706446\t5706482\tregion_9878\t0\t-\n-chr1\t5706955\t5706991\tregion_9879\t0\t-\n-chr1\t5707287\t5707323\tregion_9880\t0\t-\n-chr1\t5707378\t5707414\tregion_9881\t0\t-\n-chr1\t5709132\t5709168\tregion_9887\t0\t-\n-chr1\t5710251\t5710287\tregion_9889\t0\t-\n-chr1\t5712819\t5712855\tregion_9894\t0\t-\n-chr1\t5714565\t5714601\tregion_9897\t0\t-\n-chr1\t5714689\t5714725\tregion_9898\t0\t-\n-chr1\t5715757\t5715793\tregion_9902\t0\t-\n-chr1\t5715995\t5716031\tregion_9903\t0\t-\n-chr1\t5716291\t5716327\tregion_9907\t0\t-\n-chr1\t5717567\t5717603\tregion_9911\t0\t-\n-chr1\t5717738\t5717774\tregion_9912\t0\t-\n-chr1\t5718495\t5718531\tregion_9915\t0\t-\n-chr1\t5718830\t5718866\tregion_9917\t0\t-\n-chr1\t5718966\t5719002\tregion_9919\t0\t-\n-chr1\t5719703\t5719739\tregion_9920\t0\t-\n-chr1\t5721599\t5721635\tregion_9922\t0\t-\n-chr1\t5721807\t5721843\tregion_9923\t0\t-\n-chr1\t5722297\t5722333\tregion_9925\t0\t-\n-chr1\t5722815\t5722851\tregion_9926\t0\t-\n-chr1\t5725529\t5725565\tregion_9933\t0\t-\n-chr1\t5726039\t5726075\tregion_9935\t0\t-\n-chr1\t5726278\t5726314\tregion_9937\t0\t-\n-chr1\t5726381\t5726417\tregion_9939\t0\t-\n-chr1\t5726530\t5726566\tregion_9940\t0\t-\n-chr1\t5726534\t5726570\tregion_9941\t0\t-\n-chr1\t5726557\t5726593\tregion_9942\t0\t-\n-chr1\t5726561\t5726597\tregion_9943\t0\t-\n-chr1\t5726611\t5726647\tregion_9944\t0\t-\n-chr1\t5727379\t5727415\tregion_9946\t0\t-\n-chr1\t5727617\t5727653\tregion_9950\t0\t-\n-chr1\t5728091\t5728127\tregion_9951\t0\t-\n-chr1\t5728737\t5728773\tregion_9952\t0\t-\n-chr1\t5728886\t5728922\tregion_9953\t0\t-\n-chr1\t5729667\t5729703\tregion_9954\t0\t-\n-chr1\t5730047\t5730083\tregion_9956\t0\t-\n-chr1\t5742298\t5742334\tregion_9962\t0\t-\n-chr1\t5742856\t5742892\tregion_9965\t0\t-\n-chr1\t5743555\t5743591\tregion_9966\t0\t-\n-chr1\t5743878\t5743914\tregion_9968\t0\t-\n-chr1\t5744403\t5744439\tregion_9969\t0\t-\n-chr1\t5744937\t5744973\tregion_9972\t0\t-\n-chr1\t5744965\t5745001\tregion_9973\t0\t-\n-chr1\t5745800\t5745836\tregion_9975\t0\t-\n-chr1\t5745885\t5745921\tregion_9976\t0\t-\n-chr1\t5745951\t5745987\tregion_9977\t0\t-\n-chr1\t5746138\t5746174\tregion_9979\t0\t-\n-chr1\t5746558\t5746594\tregion_9981\t0\t-\n-chr1\t5746574\t5746610\tregion_9982\t0\t-\n-chr1\t5746733\t5746769\tregion_9983\t0\t-\n-chr1\t5746922\t5746958\tregion_9984\t0\t-\n-chr1\t5751506\t5751542\tregion_9991\t0\t-\n-chr1\t5751966\t5752002\tregion_9995\t0\t-\n-chr1\t5752456\t5752492\tregion_9996\t0\t-\n-chr1\t5752543\t5752579\tregion_9997\t0\t-\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01.scoreisland --- a/test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01.scoreisland Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,352 +0,0 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_1/test-W200-normalized.wig --- a/test-data/peakcalling_sicer/test_1/test-W200-normalized.wig Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_1/test-W200.graph --- a/test-data/peakcalling_sicer/test_1/test-W200.graph Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5667 +0,0 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\t2\n-chr1\t5652800\t5652999\t3\n-chr1\t5653400\t5653599\t6\n-chr1\t5653600\t5653799\t2\n-chr1\t5653800\t5653999\t1\n-chr1\t5654200\t5654399\t1\n-chr1\t5654600\t5654799\t1\n-chr1\t5654800\t5654999\t1\n-chr1\t5655800\t5655999\t4\n-chr1\t5656000\t5656199\t1\n-chr1\t5656200\t5656399\t1\n-chr1\t5657200\t5657399\t1\n-chr1\t5657600\t5657799\t3\n-chr1\t5657800\t5657999\t1\n-chr1\t5658400\t5658599\t1\n-chr1\t5659200\t5659399\t2\n-chr1\t5660400\t5660599\t3\n-chr1\t5660800\t5660999\t1\n-chr1\t5661400\t5661599\t1\n-chr1\t5662400\t5662599\t2\n-chr1\t5662600\t5662799\t1\n-chr1\t5663600\t5663799\t2\n-chr1\t5663800\t5663999\t1\n-chr1\t5664600\t5664799\t2\n-chr1\t5665000\t5665199\t1\n-chr1\t5665800\t5665999\t1\n-chr1\t5666400\t5666599\t1\n-chr1\t5666600\t5666799\t3\n-chr1\t5666800\t5666999\t1\n-chr1\t5667800\t5667999\t2\n-chr1\t5674000\t5674199\t1\n-chr1\t5675000\t5675199\t1\n-chr1\t5676200\t5676399\t1\n-chr1\t5676600\t5676799\t1\n-chr1\t5677200\t5677399\t1\n-chr1\t5677800\t5677999\t1\n-chr1\t5679000\t5679199\t1\n-chr1\t5679200\t5679399\t4\n-chr1\t5679400\t5679599\t2\n-chr1\t5679600\t5679799\t1\n-chr1\t5680000\t5680199\t1\n-chr1\t5680200\t5680399\t2\n-chr1\t5680400\t5680599\t2\n-chr1\t5680800\t5680999\t2\n-chr1\t5682800\t5682999\t1\n-chr1\t5688000\t5688199\t1\n-chr1\t5688200\t5688399\t1\n-chr1\t5688400\t5688599\t1\n-chr1\t5688600\t5688799\t1\n-chr1\t5688800\t5688999\t1\n-chr1\t5689000\t5689199\t1\n-chr1\t5689200\t5689399\t1\n-chr1\t5689400\t5689599\t1\n-chr1\t5689800\t5689999\t1\n-chr1\t5690200\t5690399\t1\n-chr1\t5690800\t5690999\t2\n-chr1\t5694600\t5694799\t1\n-chr1\t5694800\t5694999\t2\n-chr1\t5695000\t5695199\t1\n-chr1\t5695400\t5695599\t3\n-chr1\t5696000\t5696199\t1\n-chr1\t5696600\t5696799\t1\n-chr1\t5696800\t5696999\t3\n-chr1\t5697000\t5697199\t1\n-chr1\t5697200\t5697399\t2\n-chr1\t5698000\t5698199\t1\n-chr1\t5698200\t5698399\t2\n-chr1\t5698800\t5698999\t2\n-chr1\t5699400\t5699599\t1\n-chr1\t5700000\t5700199\t1\n-chr1\t5700400\t5700599\t2\n-chr1\t5703600\t5703799\t1\n-chr1\t5704600\t5704799\t1\n-chr1\t5705000\t5705199\t3\n-chr1\t5705600\t5705799\t1\n-chr1\t5706200\t5706399\t5\n-chr1\t5706400\t5706599\t1\n-chr1\t5706800\t5706999\t1\n-chr1\t5707200\t5707399\t2\n-chr1\t5707800\t5707999\t2\n-chr1\t5708400\t5708599\t1\n-chr1\t5708600\t5708799\t1\n-chr1\t5709000\t5709199\t2\n-chr1\t5709600\t5709799\t1\n-chr1\t5710200\t5710399\t1\n-chr1\t5711400\t5711599\t1\n-chr1\t5712400\t5712599\t1\n-chr1\t5712600\t5712799\t2\n-chr1\t5712800\t5712999\t1\n-chr1\t5713600\t5713799\t1\n-chr1\t5714200\t5714399\t1\n-chr1\t5714400\t5714599\t1\n-chr1\t5714600\t5714799\t3\n-chr1\t5715600\t5715799\t2\n-chr1\t5715800\t5715999\t1\n-chr1\t5716200\t5716399\t4\n-chr1\t5717000\t5717199\t1\n-chr1\t5717400\t5717599\t2\n-chr1\t5717600\t5717799\t1\n-chr1\t5718200\t5718399\t1\n-chr1\t5718400\t5718599\t2\n-chr1\t5718600\t5718799\t1\n-chr1\t5718800\t5718999\t3\n-chr1\t5719600\t5719799\t1\n-chr1\t5720600\t5720799\t1\n-chr1\t5721400\t5721599\t1\n-chr1\t5721600\t5721799\t1\n-chr1\t5722200\t5722399\t2\n-chr1\t5722600\t5722799\t1\n-chr1\t5723200\t5723399\t3\n-chr1\t5724200\t5724399\t1\n-chr1\t5724400\t5724599\t1\n-chr1\t5725400\t5725599\t2\n-chr1\t5725800\t5725999\t1\n-chr1\t5726000\t5726199\t1\n-chr1\t5726200\t5726399\t3\n-chr1\t5726400\t5726599\t5\n-chr1\t5726800\t5726999\t1\n-chr1\t5727200\t5727399\t1\n-chr1\t5727400\t5727599\t1\n-chr1\t5727600\t5727799\t3\n-chr1\t5728000\t5728199\t1\n-chr1\t5728600\t5728799\t1\n-chr1\t5728800\t5728999\t1\n-chr1\t5729600\t5729799\t1\n-chr1\t5730000\t5730199\t2\n-chr1\t5735000\t5735199\t1\n-chr1\t5738200\t5738399\t1\n-chr1\t5741800\t5741999\t2\n-chr1\t5742200\t5742399\t2\n-chr1\t5742400\t5742599\t1\n-chr1\t5742600\t5742799\t1\n-chr1\t5742800\t5742999\t1\n-chr1\t5743400\t5743599\t1\n-chr1\t5743800\t5743999\t2\n-chr1\t5744200\t5744399\t1\n-chr1\t5744600\t5744799\t2\n-chr1\t5744800\t5744999\t2\n-chr1\t5745600\t5745799\t2\n-chr1\t5745800\t5745999\t2\n-chr1\t5746000\t5746199\t2\n-chr1\t5746400\t5746599\t2\n-chr1\t5746600\t5746799\t2\n-chr1\t5746800\t5746999\t1\n-chr1\t5747000\t5747199\t1\n-chr1\t5747800\t5747999\t1\n-chr1\t5749400\t5749599\t1\n-chr1\t5750000\t5750199\t1\n-chr1\t5750400\t5750599\t1\n-chr1\t5751400\t5751599\t2\n-chr1\t5751600\t5751799\t2\n-chr1\t5751800\t5751999\t2\n-chr1\t5752400\t5752599\t2\n-chr1\t5753000\t5753199\t1\n-chr1\t5754400\t5754599\t1\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_2/control-1-removed.bed --- a/test-data/peakcalling_sicer/test_2/control-1-removed.bed Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,9896 +0,0 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\t0\t-\n-chr1\t4636587\t4636623\tregion_9819\t0\t-\n-chr1\t4636746\t4636782\tregion_9820\t0\t-\n-chr1\t4636838\t4636874\tregion_9822\t0\t-\n-chr1\t4636902\t4636938\tregion_9825\t0\t-\n-chr1\t4637144\t4637180\tregion_9826\t0\t-\n-chr1\t4637146\t4637182\tregion_9827\t0\t-\n-chr1\t4637147\t4637183\tregion_9828\t0\t-\n-chr1\t4637203\t4637239\tregion_9829\t0\t-\n-chr1\t4637427\t4637463\tregion_9832\t0\t-\n-chr1\t4637457\t4637493\tregion_9834\t0\t-\n-chr1\t4638156\t4638192\tregion_9839\t0\t-\n-chr1\t4638493\t4638529\tregion_9840\t0\t-\n-chr1\t4638579\t4638615\tregion_9842\t0\t-\n-chr1\t4638640\t4638676\tregion_9843\t0\t-\n-chr1\t4638803\t4638839\tregion_9845\t0\t-\n-chr1\t4638946\t4638982\tregion_9846\t0\t-\n-chr1\t4638984\t4639020\tregion_9847\t0\t-\n-chr1\t4639170\t4639206\tregion_9848\t0\t-\n-chr1\t4639244\t4639280\tregion_9849\t0\t-\n-chr1\t4641241\t4641277\tregion_9852\t0\t-\n-chr1\t4641335\t4641371\tregion_9853\t0\t-\n-chr1\t4641663\t4641699\tregion_9855\t0\t-\n-chr1\t4641708\t4641744\tregion_9857\t0\t-\n-chr1\t4641729\t4641765\tregion_9858\t0\t-\n-chr1\t4641824\t4641860\tregion_9861\t0\t-\n-chr1\t4643866\t4643902\tregion_9863\t0\t-\n-chr1\t4644097\t4644133\tregion_9866\t0\t-\n-chr1\t4644105\t4644141\tregion_9867\t0\t-\n-chr1\t4644703\t4644739\tregion_9868\t0\t-\n-chr1\t4645149\t4645185\tregion_9872\t0\t-\n-chr1\t4645237\t4645273\tregion_9873\t0\t-\n-chr1\t4645497\t4645533\tregion_9875\t0\t-\n-chr1\t4645690\t4645726\tregion_9876\t0\t-\n-chr1\t4645789\t4645825\tregion_9877\t0\t-\n-chr1\t4645969\t4646005\tregion_9880\t0\t-\n-chr1\t4646298\t4646334\tregion_9884\t0\t-\n-chr1\t4646461\t4646497\tregion_9885\t0\t-\n-chr1\t4646550\t4646586\tregion_9887\t0\t-\n-chr1\t4646719\t4646755\tregion_9889\t0\t-\n-chr1\t4646807\t4646843\tregion_9891\t0\t-\n-chr1\t4646879\t4646915\tregion_9893\t0\t-\n-chr1\t4646916\t4646952\tregion_9894\t0\t-\n-chr1\t4646987\t4647023\tregion_9896\t0\t-\n-chr1\t4647088\t4647124\tregion_9898\t0\t-\n-chr1\t4647559\t4647595\tregion_9901\t0\t-\n-chr1\t4647582\t4647618\tregion_9902\t0\t-\n-chr1\t4647696\t4647732\tregion_9905\t0\t-\n-chr1\t4648124\t4648160\tregion_9908\t0\t-\n-chr1\t4648129\t4648165\tregion_9909\t0\t-\n-chr1\t4648179\t4648215\tregion_9910\t0\t-\n-chr1\t4648523\t4648559\tregion_9912\t0\t-\n-chr1\t4648554\t4648590\tregion_9914\t0\t-\n-chr1\t4650119\t4650155\tregion_9916\t0\t-\n-chr1\t4650645\t4650681\tregion_9917\t0\t-\n-chr1\t4652025\t4652061\tregion_9918\t0\t-\n-chr1\t4652368\t4652404\tregion_9921\t0\t-\n-chr1\t4652487\t4652523\tregion_9922\t0\t-\n-chr1\t4652701\t4652737\tregion_9924\t0\t-\n-chr1\t4653073\t4653109\tregion_9925\t0\t-\n-chr1\t4653175\t4653211\tregion_9926\t0\t-\n-chr1\t4653199\t4653235\tregion_9928\t0\t-\n-chr1\t4653387\t4653423\tregion_9931\t0\t-\n-chr1\t4653471\t4653507\tregion_9932\t0\t-\n-chr1\t4653503\t4653539\tregion_9933\t0\t-\n-chr1\t4653574\t4653610\tregion_9934\t0\t-\n-chr1\t4656708\t4656744\tregion_9938\t0\t-\n-chr1\t4656721\t4656757\tregion_9939\t0\t-\n-chr1\t4656810\t4656846\tregion_9941\t0\t-\n-chr1\t4657008\t4657044\tregion_9942\t0\t-\n-chr1\t4657224\t4657260\tregion_9943\t0\t-\n-chr1\t4657590\t4657626\tregion_9949\t0\t-\n-chr1\t4657717\t4657753\tregion_9950\t0\t-\n-chr1\t4657724\t4657760\tregion_9951\t0\t-\n-chr1\t4657836\t4657872\tregion_9953\t0\t-\n-chr1\t4657909\t4657945\tregion_9954\t0\t-\n-chr1\t4657928\t4657964\tregion_9956\t0\t-\n-chr1\t4658311\t4658347\tregion_9958\t0\t-\n-chr1\t4658664\t4658700\tregion_9963\t0\t-\n-chr1\t4658713\t4658749\tregion_9964\t0\t-\n-chr1\t4658824\t4658860\tregion_9965\t0\t-\n-chr1\t4658866\t4658902\tregion_9966\t0\t-\n-chr1\t4658971\t4659007\tregion_9969\t0\t-\n-chr1\t4659035\t4659071\tregion_9970\t0\t-\n-chr1\t4659244\t4659280\tregion_9971\t0\t-\n-chr1\t4659465\t4659501\tregion_9973\t0\t-\n-chr1\t4659470\t4659506\tregion_9974\t0\t-\n-chr1\t4659504\t4659540\tregion_9975\t0\t-\n-chr1\t4659511\t4659547\tregion_9977\t0\t-\n-chr1\t4659530\t4659566\tregion_9979\t0\t-\n-chr1\t4659563\t4659599\tregion_9980\t0\t-\n-chr1\t4659578\t4659614\tregion_9981\t0\t-\n-chr1\t4659880\t4659916\tregion_9986\t0\t-\n-chr1\t4660125\t4660161\tregion_9987\t0\t-\n-chr1\t4660431\t4660467\tregion_9991\t0\t-\n-chr1\t4661557\t4661593\tregion_9996\t0\t-\n-chr1\t4661619\t4661655\tregion_9997\t0\t-\n-chr1\t4662104\t4662140\tregion_9998\t0\t-\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_2/output_log_file.contains --- a/test-data/peakcalling_sicer/test_2/output_log_file.contains Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,287 +0,0 @@\n-#############################################\n-###### SICER v1.1 ######\n-#############################################\n-Input library directory:\n-ChIP library: input_bed_file.bed\n-Control library: input_control_file.bed\n-Output directory:\n-Species: mm8\n-Threshold for redundancy allowed for chip reads: 1\n-Threshold for redundancy allowed for control reads: 1\n-Window size: 200 bps\n-Fragment size: 150 bps. The shift for reads is half of 150\n-Effective genome size as a fraction of the reference genome of mm8: 0.740000\n-Gap size: 600 bps\n-Evalue for identification of candidate islands that exhibit clustering: 1000\n-False discovery rate controlling significance: 0.01\n-Preprocess the raw input_bed_file file to remove redundancy with threshold 1...\n-chr1 \tPlus reads: 4989 \tRetained plus reads: 4935 ;\tMinus reads: 5011 \tRetained minus reads: 4963\n-chr2 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr3 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr4 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr5 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr6 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr7 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr8 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr9 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr10 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr11 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr12 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr13 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr14 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr15 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr16 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr17 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr18 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr19 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chrX \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chrY \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chrM \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-Preprocess the raw input_control_file file to remove redundancy with threshold 1...\n-chr1 \tPlus reads: 4980 \tRetained plus reads: 4937 ;\tMinus reads: 5020 \tRetained minus reads: 4959\n-chr2 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr3 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr4 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr5 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr6 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr7 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr8 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr9 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr10 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr11 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr12 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr13 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n-chr14 \tPlus reads: 0 \tRetained plus rea'..b'chrY reads do not exist in\n-Warning: chrM reads do not exist in\n-Warning: chr2 reads do not exist in\n-Warning: chr3 reads do not exist in\n-Warning: chr4 reads do not exist in\n-Warning: chr5 reads do not exist in\n-Warning: chr6 reads do not exist in\n-Warning: chr7 reads do not exist in\n-Warning: chr8 reads do not exist in\n-Warning: chr9 reads do not exist in\n-Warning: chr10 reads do not exist in\n-Warning: chr11 reads do not exist in\n-Warning: chr12 reads do not exist in\n-Warning: chr13 reads do not exist in\n-Warning: chr14 reads do not exist in\n-Warning: chr15 reads do not exist in\n-Warning: chr16 reads do not exist in\n-Warning: chr17 reads do not exist in\n-Warning: chr18 reads do not exist in\n-Warning: chr19 reads do not exist in\n-Warning: chrX reads do not exist in\n-Warning: chrY reads do not exist in\n-Warning: chrM reads do not exist in\n-Warning: chr2 reads do not exist in\n-Warning: chr3 reads do not exist in\n-Warning: chr4 reads do not exist in\n-Warning: chr5 reads do not exist in\n-Warning: chr6 reads do not exist in\n-Warning: chr7 reads do not exist in\n-Warning: chr8 reads do not exist in\n-Warning: chr9 reads do not exist in\n-Warning: chr10 reads do not exist in\n-Warning: chr11 reads do not exist in\n-Warning: chr12 reads do not exist in\n-Warning: chr13 reads do not exist in\n-Warning: chr14 reads do not exist in\n-Warning: chr15 reads do not exist in\n-Warning: chr16 reads do not exist in\n-Warning: chr17 reads do not exist in\n-Warning: chr18 reads do not exist in\n-Warning: chr19 reads do not exist in\n-Warning: chrX reads do not exist in\n-Warning: chrY reads do not exist in\n-Warning: chrM reads do not exist in\n-Warning: chr2 reads do not exist in\n-Warning: chr3 reads do not exist in\n-Warning: chr4 reads do not exist in\n-Warning: chr5 reads do not exist in\n-Warning: chr6 reads do not exist in\n-Warning: chr7 reads do not exist in\n-Warning: chr8 reads do not exist in\n-Warning: chr9 reads do not exist in\n-Warning: chr10 reads do not exist in\n-Warning: chr11 reads do not exist in\n-Warning: chr12 reads do not exist in\n-Warning: chr13 reads do not exist in\n-Warning: chr14 reads do not exist in\n-Warning: chr15 reads do not exist in\n-Warning: chr16 reads do not exist in\n-Warning: chr17 reads do not exist in\n-Warning: chr18 reads do not exist in\n-Warning: chr19 reads do not exist in\n-Warning: chrX reads do not exist in\n-Warning: chrY reads do not exist in\n-Warning: chrM reads do not exist in\n-Warning: chr2 reads do not exist in\n-Warning: chr3 reads do not exist in\n-Warning: chr4 reads do not exist in\n-Warning: chr5 reads do not exist in\n-Warning: chr6 reads do not exist in\n-Warning: chr7 reads do not exist in\n-Warning: chr8 reads do not exist in\n-Warning: chr9 reads do not exist in\n-Warning: chr10 reads do not exist in\n-Warning: chr11 reads do not exist in\n-Warning: chr12 reads do not exist in\n-Warning: chr13 reads do not exist in\n-Warning: chr14 reads do not exist in\n-Warning: chr15 reads do not exist in\n-Warning: chr16 reads do not exist in\n-Warning: chr17 reads do not exist in\n-Warning: chr18 reads do not exist in\n-Warning: chr19 reads do not exist in\n-Warning: chrX reads do not exist in\n-Warning: chrY reads do not exist in\n-Warning: chrM reads do not exist in\n-Warning: chr2 reads do not exist in\n-Warning: chr3 reads do not exist in\n-Warning: chr4 reads do not exist in\n-Warning: chr5 reads do not exist in\n-Warning: chr6 reads do not exist in\n-Warning: chr7 reads do not exist in\n-Warning: chr8 reads do not exist in\n-Warning: chr9 reads do not exist in\n-Warning: chr10 reads do not exist in\n-Warning: chr11 reads do not exist in\n-Warning: chr12 reads do not exist in\n-Warning: chr13 reads do not exist in\n-Warning: chr14 reads do not exist in\n-Warning: chr15 reads do not exist in\n-Warning: chr16 reads do not exist in\n-Warning: chr17 reads do not exist in\n-Warning: chr18 reads do not exist in\n-Warning: chr19 reads do not exist in\n-Warning: chrX reads do not exist in\n-Warning: chrY reads do not exist in\n-Warning: chrM reads do not exist in\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_2/test-1-removed.bed --- a/test-data/peakcalling_sicer/test_2/test-1-removed.bed Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,9898 +0,0 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\t0\t-\n-chr1\t5666894\t5666930\tregion_9805\t0\t-\n-chr1\t5667898\t5667934\tregion_9807\t0\t-\n-chr1\t5674133\t5674169\tregion_9808\t0\t-\n-chr1\t5675139\t5675175\tregion_9809\t0\t-\n-chr1\t5676675\t5676711\tregion_9811\t0\t-\n-chr1\t5677304\t5677340\tregion_9812\t0\t-\n-chr1\t5679098\t5679134\tregion_9814\t0\t-\n-chr1\t5679255\t5679291\tregion_9815\t0\t-\n-chr1\t5679303\t5679339\tregion_9817\t0\t-\n-chr1\t5679429\t5679465\tregion_9820\t0\t-\n-chr1\t5680276\t5680312\tregion_9824\t0\t-\n-chr1\t5680603\t5680639\tregion_9826\t0\t-\n-chr1\t5688108\t5688144\tregion_9830\t0\t-\n-chr1\t5688411\t5688447\tregion_9831\t0\t-\n-chr1\t5688571\t5688607\tregion_9834\t0\t-\n-chr1\t5689163\t5689199\tregion_9836\t0\t-\n-chr1\t5689312\t5689348\tregion_9837\t0\t-\n-chr1\t5689551\t5689587\tregion_9838\t0\t-\n-chr1\t5689847\t5689883\tregion_9839\t0\t-\n-chr1\t5694818\t5694854\tregion_9843\t0\t-\n-chr1\t5694996\t5695032\tregion_9844\t0\t-\n-chr1\t5695025\t5695061\tregion_9845\t0\t-\n-chr1\t5695144\t5695180\tregion_9846\t0\t-\n-chr1\t5695639\t5695675\tregion_9849\t0\t-\n-chr1\t5696688\t5696724\tregion_9851\t0\t-\n-chr1\t5696950\t5696986\tregion_9854\t0\t-\n-chr1\t5697092\t5697128\tregion_9855\t0\t-\n-chr1\t5698985\t5699021\tregion_9862\t0\t-\n-chr1\t5699555\t5699591\tregion_9863\t0\t-\n-chr1\t5700463\t5700499\tregion_9865\t0\t-\n-chr1\t5700467\t5700503\tregion_9866\t0\t-\n-chr1\t5703812\t5703848\tregion_9867\t0\t-\n-chr1\t5705804\t5705840\tregion_9872\t0\t-\n-chr1\t5706289\t5706325\tregion_9874\t0\t-\n-chr1\t5706307\t5706343\tregion_9875\t0\t-\n-chr1\t5706339\t5706375\tregion_9876\t0\t-\n-chr1\t5706399\t5706435\tregion_9877\t0\t-\n-chr1\t5706446\t5706482\tregion_9878\t0\t-\n-chr1\t5706955\t5706991\tregion_9879\t0\t-\n-chr1\t5707287\t5707323\tregion_9880\t0\t-\n-chr1\t5707378\t5707414\tregion_9881\t0\t-\n-chr1\t5709132\t5709168\tregion_9887\t0\t-\n-chr1\t5710251\t5710287\tregion_9889\t0\t-\n-chr1\t5711567\t5711603\tregion_9890\t0\t-\n-chr1\t5712819\t5712855\tregion_9894\t0\t-\n-chr1\t5714565\t5714601\tregion_9897\t0\t-\n-chr1\t5714689\t5714725\tregion_9898\t0\t-\n-chr1\t5715757\t5715793\tregion_9902\t0\t-\n-chr1\t5715995\t5716031\tregion_9903\t0\t-\n-chr1\t5716291\t5716327\tregion_9907\t0\t-\n-chr1\t5717567\t5717603\tregion_9911\t0\t-\n-chr1\t5717738\t5717774\tregion_9912\t0\t-\n-chr1\t5718495\t5718531\tregion_9915\t0\t-\n-chr1\t5718830\t5718866\tregion_9917\t0\t-\n-chr1\t5718966\t5719002\tregion_9919\t0\t-\n-chr1\t5719703\t5719739\tregion_9920\t0\t-\n-chr1\t5721599\t5721635\tregion_9922\t0\t-\n-chr1\t5721807\t5721843\tregion_9923\t0\t-\n-chr1\t5722297\t5722333\tregion_9925\t0\t-\n-chr1\t5722815\t5722851\tregion_9926\t0\t-\n-chr1\t5724418\t5724454\tregion_9930\t0\t-\n-chr1\t5725529\t5725565\tregion_9933\t0\t-\n-chr1\t5726039\t5726075\tregion_9935\t0\t-\n-chr1\t5726278\t5726314\tregion_9937\t0\t-\n-chr1\t5726381\t5726417\tregion_9939\t0\t-\n-chr1\t5726530\t5726566\tregion_9940\t0\t-\n-chr1\t5726534\t5726570\tregion_9941\t0\t-\n-chr1\t5726557\t5726593\tregion_9942\t0\t-\n-chr1\t5726561\t5726597\tregion_9943\t0\t-\n-chr1\t5726611\t5726647\tregion_9944\t0\t-\n-chr1\t5727379\t5727415\tregion_9946\t0\t-\n-chr1\t5727617\t5727653\tregion_9950\t0\t-\n-chr1\t5728091\t5728127\tregion_9951\t0\t-\n-chr1\t5728737\t5728773\tregion_9952\t0\t-\n-chr1\t5728886\t5728922\tregion_9953\t0\t-\n-chr1\t5729667\t5729703\tregion_9954\t0\t-\n-chr1\t5730047\t5730083\tregion_9956\t0\t-\n-chr1\t5738241\t5738277\tregion_9958\t0\t-\n-chr1\t5742298\t5742334\tregion_9962\t0\t-\n-chr1\t5742856\t5742892\tregion_9965\t0\t-\n-chr1\t5743555\t5743591\tregion_9966\t0\t-\n-chr1\t5743878\t5743914\tregion_9968\t0\t-\n-chr1\t5744403\t5744439\tregion_9969\t0\t-\n-chr1\t5744937\t5744973\tregion_9972\t0\t-\n-chr1\t5744965\t5745001\tregion_9973\t0\t-\n-chr1\t5745800\t5745836\tregion_9975\t0\t-\n-chr1\t5745885\t5745921\tregion_9976\t0\t-\n-chr1\t5745951\t5745987\tregion_9977\t0\t-\n-chr1\t5746138\t5746174\tregion_9979\t0\t-\n-chr1\t5746558\t5746594\tregion_9981\t0\t-\n-chr1\t5746574\t5746610\tregion_9982\t0\t-\n-chr1\t5746733\t5746769\tregion_9983\t0\t-\n-chr1\t5746922\t5746958\tregion_9984\t0\t-\n-chr1\t5751506\t5751542\tregion_9991\t0\t-\n-chr1\t5751966\t5752002\tregion_9995\t0\t-\n-chr1\t5752456\t5752492\tregion_9996\t0\t-\n-chr1\t5752543\t5752579\tregion_9997\t0\t-\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-island.bed --- a/test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-island.bed Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,184 +0,0 @@ -chr1 3023200 3023999 4 -chr1 3088400 3088599 3 -chr1 3138800 3139399 5 -chr1 3165800 3165999 2 -chr1 3273000 3273399 2 -chr1 3294800 3295199 2 -chr1 3672800 3672999 4 -chr1 3810800 3811199 2 -chr1 3872600 3873599 2 -chr1 3976600 3976799 2 -chr1 4122200 4122399 2 -chr1 4232600 4232799 2 -chr1 4278600 4279199 6 -chr1 4323600 4327199 59 -chr1 4334200 4339399 83 -chr1 4392400 4392599 3 -chr1 4456400 4456799 2 -chr1 4625200 4625599 3 -chr1 4627200 4627399 2 -chr1 4668600 4670399 15 -chr1 4673800 4675199 7 -chr1 4676200 4700999 114 -chr1 4708400 4718199 71 -chr1 4719000 4722399 8 -chr1 4726200 4727999 12 -chr1 4729000 4746399 127 -chr1 4747200 4755999 66 -chr1 4756800 4762199 264 -chr1 4763200 4779399 145 -chr1 4780800 4781799 5 -chr1 4784200 4785599 6 -chr1 4786800 4787799 7 -chr1 4789400 4793399 31 -chr1 4794400 4797999 18 -chr1 4799000 4808199 50 -chr1 4809600 4818399 58 -chr1 4819600 4825999 35 -chr1 4827000 4827799 3 -chr1 4828600 4839599 64 -chr1 4840400 4853599 67 -chr1 4854400 4863599 49 -chr1 4864800 4866599 10 -chr1 4867600 4867799 2 -chr1 4868600 4869799 4 -chr1 4872000 4875199 25 -chr1 4876600 4887799 51 -chr1 4889400 4895799 50 -chr1 4896600 4907399 66 -chr1 4908200 4910999 22 -chr1 4912200 4912399 2 -chr1 4913400 4923799 64 -chr1 4924800 4931599 50 -chr1 4932400 4934999 22 -chr1 4935800 4937999 15 -chr1 4944800 4948799 22 -chr1 4952400 4963999 86 -chr1 4965800 4970599 31 -chr1 4975200 4975999 6 -chr1 4979800 4981999 16 -chr1 4982800 4982999 2 -chr1 4984400 4986199 6 -chr1 4991200 5000799 56 -chr1 5002000 5025799 121 -chr1 5032600 5035199 7 -chr1 5038800 5040199 6 -chr1 5044400 5048399 21 -chr1 5054200 5057799 24 -chr1 5058800 5063399 34 -chr1 5064200 5067599 19 -chr1 5074000 5079799 35 -chr1 5081600 5098199 89 -chr1 5099000 5100799 4 -chr1 5106000 5112799 37 -chr1 5113600 5117199 17 -chr1 5118800 5120799 10 -chr1 5122400 5123199 9 -chr1 5124200 5127599 14 -chr1 5128400 5136199 56 -chr1 5137200 5139599 11 -chr1 5140400 5144599 14 -chr1 5145400 5145599 3 -chr1 5146800 5147399 2 -chr1 5148400 5156199 45 -chr1 5160000 5162599 9 -chr1 5164200 5164799 6 -chr1 5166000 5169399 22 -chr1 5170200 5171599 4 -chr1 5172600 5175199 24 -chr1 5176200 5180599 41 -chr1 5187000 5187599 3 -chr1 5193800 5205999 83 -chr1 5206800 5219199 78 -chr1 5220000 5227799 55 -chr1 5229400 5231599 13 -chr1 5232400 5233199 5 -chr1 5234200 5238399 17 -chr1 5239800 5241199 10 -chr1 5247800 5251999 28 -chr1 5253200 5258199 25 -chr1 5264400 5265399 8 -chr1 5266200 5266399 2 -chr1 5267200 5268199 10 -chr1 5269800 5278799 43 -chr1 5279600 5280999 8 -chr1 5282800 5284599 7 -chr1 5285600 5287199 14 -chr1 5288200 5299399 47 -chr1 5301600 5302599 4 -chr1 5303400 5308999 36 -chr1 5310000 5311599 15 -chr1 5312400 5318599 29 -chr1 5323400 5333999 41 -chr1 5336200 5336799 3 -chr1 5338400 5338999 3 -chr1 5348600 5349199 6 -chr1 5353800 5356999 16 -chr1 5358400 5362799 15 -chr1 5363800 5365599 12 -chr1 5369400 5375799 29 -chr1 5376600 5378999 6 -chr1 5379800 5383199 11 -chr1 5384000 5384999 8 -chr1 5385800 5388799 15 -chr1 5391800 5398399 20 -chr1 5399600 5399799 2 -chr1 5400600 5404399 16 -chr1 5405200 5405799 2 -chr1 5407400 5413799 32 -chr1 5420800 5421199 3 -chr1 5428000 5433199 24 -chr1 5434000 5434599 4 -chr1 5439600 5440599 6 -chr1 5442000 5444999 15 -chr1 5446200 5446999 3 -chr1 5447800 5449199 11 -chr1 5451000 5458199 27 -chr1 5470600 5470999 3 -chr1 5475400 5475799 5 -chr1 5476600 5476799 2 -chr1 5478200 5478999 3 -chr1 5480800 5482199 3 -chr1 5483400 5483799 3 -chr1 5484800 5488999 13 -chr1 5492600 5493999 5 -chr1 5496000 5498999 15 -chr1 5501800 5512799 52 -chr1 5514400 5516599 11 -chr1 5522400 5524599 8 -chr1 5525800 5531199 18 -chr1 5532200 5535999 21 -chr1 5539400 5541799 11 -chr1 5548200 5551399 17 -chr1 5560800 5561599 3 -chr1 5563400 5565399 6 -chr1 5568400 5573599 33 -chr1 5576200 5590399 71 -chr1 5591200 5592399 5 -chr1 5593200 5613599 89 -chr1 5614400 5617799 22 -chr1 5619800 5620599 3 -chr1 5621400 5621999 6 -chr1 5624600 5625399 2 -chr1 5632000 5637799 20 -chr1 5643200 5643399 2 -chr1 5646400 5654999 60 -chr1 5655800 5656399 6 -chr1 5657200 5659399 8 -chr1 5660400 5661599 5 -chr1 5662400 5662799 3 -chr1 5663600 5666999 12 -chr1 5667800 5667999 2 -chr1 5676200 5677999 4 -chr1 5679000 5680999 15 -chr1 5688000 5690999 12 -chr1 5694600 5700599 24 -chr1 5704600 5710399 22 -chr1 5712400 5714799 10 -chr1 5715600 5719799 19 -chr1 5720600 5723399 9 -chr1 5724200 5724599 2 -chr1 5725400 5730199 24 -chr1 5741800 5747999 28 -chr1 5749400 5750599 3 -chr1 5751400 5753199 9 |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig --- a/test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2296 +0,0 @@\n-track type=wiggle_0 name=input_bed_file-islandfiltered\n-variableStep chrom=chr1 span=200\n-3023201\t232.396\n-3023401\t232.396\n-3023801\t464.792\n-3088401\t697.188\n-3138801\t464.792\n-3139001\t464.792\n-3139201\t232.396\n-3165801\t464.792\n-3273001\t232.396\n-3273201\t232.396\n-3294801\t232.396\n-3295001\t232.396\n-3672801\t929.584\n-3810801\t232.396\n-3811001\t232.396\n-3872601\t232.396\n-3873401\t232.396\n-3976601\t464.792\n-4122201\t464.792\n-4232601\t464.792\n-4278601\t464.792\n-4278801\t697.188\n-4279001\t232.396\n-4323601\t232.396\n-4323801\t7436.67\n-4324001\t3253.54\n-4324201\t232.396\n-4325001\t232.396\n-4325201\t232.396\n-4326001\t464.792\n-4326201\t697.188\n-4326401\t464.792\n-4326601\t232.396\n-4327001\t232.396\n-4334201\t232.396\n-4334401\t232.396\n-4334801\t232.396\n-4335201\t232.396\n-4335401\t232.396\n-4335601\t232.396\n-4336401\t232.396\n-4336601\t929.584\n-4336801\t464.792\n-4337001\t697.188\n-4337201\t232.396\n-4337401\t1859.17\n-4337601\t9760.63\n-4337801\t697.188\n-4338201\t1161.98\n-4338401\t929.584\n-4338601\t232.396\n-4339001\t464.792\n-4339201\t232.396\n-4392401\t697.188\n-4456401\t232.396\n-4456601\t232.396\n-4625201\t232.396\n-4625401\t464.792\n-4627201\t464.792\n-4668601\t232.396\n-4668801\t697.188\n-4669001\t232.396\n-4669401\t232.396\n-4669601\t697.188\n-4670001\t232.396\n-4670201\t1161.98\n-4673801\t464.792\n-4674001\t232.396\n-4674201\t232.396\n-4674401\t232.396\n-4675001\t464.792\n-4676201\t232.396\n-4676401\t232.396\n-4676801\t232.396\n-4677001\t232.396\n-4677601\t232.396\n-4678201\t232.396\n-4678601\t232.396\n-4678801\t464.792\n-4679001\t697.188\n-4679401\t232.396\n-4680001\t232.396\n-4680201\t464.792\n-4680401\t232.396\n-4680801\t232.396\n-4681001\t232.396\n-4681201\t232.396\n-4681401\t232.396\n-4681601\t232.396\n-4681801\t464.792\n-4682001\t232.396\n-4682201\t464.792\n-4682601\t232.396\n-4683001\t232.396\n-4683401\t232.396\n-4683801\t232.396\n-4684601\t464.792\n-4685201\t232.396\n-4685801\t232.396\n-4686001\t464.792\n-4686401\t232.396\n-4686801\t232.396\n-4687401\t232.396\n-4687601\t464.792\n-4687801\t464.792\n-4688201\t929.584\n-4688401\t464.792\n-4688601\t232.396\n-4689001\t232.396\n-4689201\t929.584\n-4689401\t232.396\n-4690001\t232.396\n-4690201\t232.396\n-4690801\t464.792\n-4691401\t232.396\n-4691601\t464.792\n-4691801\t464.792\n-4692001\t464.792\n-4692201\t464.792\n-4692401\t464.792\n-4692601\t232.396\n-4693201\t232.396\n-4693401\t697.188\n-4693601\t464.792\n-4694201\t232.396\n-4694601\t232.396\n-4694801\t697.188\n-4695201\t464.792\n-4695401\t232.396\n-4695601\t232.396\n-4695801\t464.792\n-4696001\t464.792\n-4696201\t464.792\n-4696401\t697.188\n-4696801\t232.396\n-4697601\t929.584\n-4697801\t464.792\n-4698201\t464.792\n-4698801\t464.792\n-4699201\t697.188\n-4699601\t232.396\n-4700401\t232.396\n-4700801\t232.396\n-4708401\t232.396\n-4708601\t232.396\n-4708801\t232.396\n-4709401\t697.188\n-4709601\t232.396\n-4709801\t232.396\n-4710001\t464.792\n-4710401\t232.396\n-4710801\t464.792\n-4711001\t464.792\n-4711201\t232.396\n-4711401\t232.396\n-4711601\t464.792\n-4712201\t232.396\n-4712401\t232.396\n-4712601\t697.188\n-4712801\t464.792\n-4713001\t929.584\n-4713601\t232.396\n-4713801\t697.188\n-4714001\t697.188\n-4714401\t1161.98\n-4714801\t464.792\n-4715001\t464.792\n-4715201\t232.396\n-4715401\t232.396\n-4715601\t232.396\n-4715801\t232.396\n-4716001\t464.792\n-4716201\t1161.98\n-4716401\t232.396\n-4716601\t1394.38\n-4717201\t232.396\n-4717801\t1161.98\n-4718001\t232.396\n-4719001\t464.792\n-4719601\t232.396\n-4720201\t232.396\n-4721001\t232.396\n-4721601\t464.792\n-4722201\t232.396\n-4726201\t232.396\n-4726401\t464.792\n-4726601\t232.396\n-4726801\t232.396\n-4727001\t232.396\n-4727201\t464.792\n-4727401\t464.792\n-4727601\t232.396\n-4727801\t232.396\n-4729001\t232.396\n-4729401\t464.792\n-4729801\t232.396\n-4730001\t232.396\n-4730601\t464.792\n-4730801\t232.396\n-4731001\t464.792\n-4731201\t232.396\n-4731801\t232.396\n-4732001\t929.584\n-4732201\t929.584\n-4732401\t232.396\n-4733201\t232.396\n-4733601\t464.792\n-4734001\t697.188\n-4734201\t232.396\n-4734401\t464.792\n-4734601\t697.188\n-4734801\t232.396\n-4735001\t464.792\n-4735201\t232.396\n-4735401\t232.396\n-4735601\t464.792\n-4735801\t464.792\n-4736001\t232.396\n-4736401\t697.188\n-4736601\t232.396\n-4736801\t697.188\n-4737001\t697.188\n-4737401\t697.188\n-4738001\t697.188\n-4738201\t697.188\n-4738801\t464.792\n-4739001\t697.188\n-4739401\t232.396\n-4739601\t697.1'..b'396\n-5601601\t232.396\n-5602401\t232.396\n-5602601\t232.396\n-5603001\t232.396\n-5603401\t464.792\n-5603601\t232.396\n-5603801\t232.396\n-5604601\t232.396\n-5604801\t232.396\n-5605001\t232.396\n-5605601\t232.396\n-5605801\t232.396\n-5606401\t464.792\n-5606601\t697.188\n-5607201\t232.396\n-5607601\t232.396\n-5608001\t232.396\n-5608201\t232.396\n-5609001\t464.792\n-5609601\t232.396\n-5610401\t232.396\n-5611001\t464.792\n-5611201\t232.396\n-5611601\t464.792\n-5611801\t232.396\n-5612001\t232.396\n-5612201\t232.396\n-5612601\t697.188\n-5612801\t232.396\n-5613001\t464.792\n-5613401\t232.396\n-5614401\t232.396\n-5614601\t464.792\n-5614801\t464.792\n-5615001\t464.792\n-5615201\t232.396\n-5615601\t232.396\n-5616201\t232.396\n-5616401\t232.396\n-5616601\t929.584\n-5616801\t697.188\n-5617001\t464.792\n-5617401\t232.396\n-5617601\t232.396\n-5619801\t232.396\n-5620001\t232.396\n-5620401\t232.396\n-5621401\t464.792\n-5621601\t464.792\n-5621801\t464.792\n-5624601\t232.396\n-5625201\t232.396\n-5632001\t232.396\n-5632401\t697.188\n-5632601\t232.396\n-5633201\t232.396\n-5633401\t464.792\n-5633601\t232.396\n-5633801\t232.396\n-5634401\t232.396\n-5634601\t232.396\n-5635001\t232.396\n-5635201\t232.396\n-5635401\t232.396\n-5635801\t232.396\n-5636601\t464.792\n-5637001\t232.396\n-5637601\t232.396\n-5643201\t464.792\n-5646401\t464.792\n-5646601\t232.396\n-5646801\t697.188\n-5647001\t232.396\n-5647401\t232.396\n-5647601\t464.792\n-5648401\t1161.98\n-5648601\t464.792\n-5648801\t464.792\n-5649001\t232.396\n-5649401\t697.188\n-5649601\t464.792\n-5649801\t1394.38\n-5650001\t464.792\n-5650601\t464.792\n-5650801\t232.396\n-5651401\t232.396\n-5651601\t929.584\n-5652001\t464.792\n-5652201\t464.792\n-5652801\t697.188\n-5653401\t1394.38\n-5653601\t464.792\n-5653801\t232.396\n-5654201\t232.396\n-5654601\t232.396\n-5654801\t232.396\n-5655801\t929.584\n-5656001\t232.396\n-5656201\t232.396\n-5657201\t232.396\n-5657601\t697.188\n-5657801\t232.396\n-5658401\t232.396\n-5659201\t464.792\n-5660401\t697.188\n-5660801\t232.396\n-5661401\t232.396\n-5662401\t464.792\n-5662601\t232.396\n-5663601\t464.792\n-5663801\t232.396\n-5664601\t464.792\n-5665001\t232.396\n-5665801\t232.396\n-5666401\t232.396\n-5666601\t697.188\n-5666801\t232.396\n-5667801\t464.792\n-5676201\t232.396\n-5676601\t232.396\n-5677201\t232.396\n-5677801\t232.396\n-5679001\t232.396\n-5679201\t929.584\n-5679401\t464.792\n-5679601\t232.396\n-5680001\t232.396\n-5680201\t464.792\n-5680401\t464.792\n-5680801\t464.792\n-5688001\t232.396\n-5688201\t232.396\n-5688401\t232.396\n-5688601\t232.396\n-5688801\t232.396\n-5689001\t232.396\n-5689201\t232.396\n-5689401\t232.396\n-5689801\t232.396\n-5690201\t232.396\n-5690801\t464.792\n-5694601\t232.396\n-5694801\t464.792\n-5695001\t232.396\n-5695401\t697.188\n-5696001\t232.396\n-5696601\t232.396\n-5696801\t697.188\n-5697001\t232.396\n-5697201\t464.792\n-5698001\t232.396\n-5698201\t464.792\n-5698801\t464.792\n-5699401\t232.396\n-5700001\t232.396\n-5700401\t464.792\n-5704601\t232.396\n-5705001\t697.188\n-5705601\t232.396\n-5706201\t1161.98\n-5706401\t232.396\n-5706801\t232.396\n-5707201\t464.792\n-5707801\t464.792\n-5708401\t232.396\n-5708601\t232.396\n-5709001\t464.792\n-5709601\t232.396\n-5710201\t232.396\n-5712401\t232.396\n-5712601\t464.792\n-5712801\t232.396\n-5713601\t232.396\n-5714201\t232.396\n-5714401\t232.396\n-5714601\t697.188\n-5715601\t464.792\n-5715801\t232.396\n-5716201\t929.584\n-5717001\t232.396\n-5717401\t464.792\n-5717601\t232.396\n-5718201\t232.396\n-5718401\t464.792\n-5718601\t232.396\n-5718801\t697.188\n-5719601\t232.396\n-5720601\t232.396\n-5721401\t232.396\n-5721601\t232.396\n-5722201\t464.792\n-5722601\t232.396\n-5723201\t697.188\n-5724201\t232.396\n-5724401\t232.396\n-5725401\t464.792\n-5725801\t232.396\n-5726001\t232.396\n-5726201\t697.188\n-5726401\t1161.98\n-5726801\t232.396\n-5727201\t232.396\n-5727401\t232.396\n-5727601\t697.188\n-5728001\t232.396\n-5728601\t232.396\n-5728801\t232.396\n-5729601\t232.396\n-5730001\t464.792\n-5741801\t464.792\n-5742201\t464.792\n-5742401\t232.396\n-5742601\t232.396\n-5742801\t232.396\n-5743401\t232.396\n-5743801\t464.792\n-5744201\t232.396\n-5744601\t464.792\n-5744801\t464.792\n-5745601\t464.792\n-5745801\t464.792\n-5746001\t464.792\n-5746401\t464.792\n-5746601\t464.792\n-5746801\t232.396\n-5747001\t232.396\n-5747801\t232.396\n-5749401\t232.396\n-5750001\t232.396\n-5750401\t232.396\n-5751401\t464.792\n-5751601\t464.792\n-5751801\t464.792\n-5752401\t464.792\n-5753001\t232.396\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed --- a/test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,4303 +0,0 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary --- a/test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,417 +0,0 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01 --- a/test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01 Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,184 +0,0 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_2/test-W200-G600.scoreisland --- a/test-data/peakcalling_sicer/test_2/test-W200-G600.scoreisland Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,417 +0,0 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_2/test-W200-normalized.wig --- a/test-data/peakcalling_sicer/test_2/test-W200-normalized.wig Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_2/test-W200.graph --- a/test-data/peakcalling_sicer/test_2/test-W200.graph Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5667 +0,0 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed --- a/test-data/peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,184 +0,0 @@ -chr1 3023200 3024000 4 -chr1 3088400 3088600 3 -chr1 3138800 3139400 5 -chr1 3165800 3166000 2 -chr1 3273000 3273400 2 -chr1 3294800 3295200 2 -chr1 3672800 3673000 4 -chr1 3810800 3811200 2 -chr1 3872600 3873600 2 -chr1 3976600 3976800 2 -chr1 4122200 4122400 2 -chr1 4232600 4232800 2 -chr1 4278600 4279200 6 -chr1 4323600 4327200 59 -chr1 4334200 4339400 83 -chr1 4392400 4392600 3 -chr1 4456400 4456800 2 -chr1 4625200 4625600 3 -chr1 4627200 4627400 2 -chr1 4668600 4670400 15 -chr1 4673800 4675200 7 -chr1 4676200 4701000 114 -chr1 4708400 4718200 71 -chr1 4719000 4722400 8 -chr1 4726200 4728000 12 -chr1 4729000 4746400 127 -chr1 4747200 4756000 66 -chr1 4756800 4762200 264 -chr1 4763200 4779400 145 -chr1 4780800 4781800 5 -chr1 4784200 4785600 6 -chr1 4786800 4787800 7 -chr1 4789400 4793400 31 -chr1 4794400 4798000 18 -chr1 4799000 4808200 50 -chr1 4809600 4818400 58 -chr1 4819600 4826000 35 -chr1 4827000 4827800 3 -chr1 4828600 4839600 64 -chr1 4840400 4853600 67 -chr1 4854400 4863600 49 -chr1 4864800 4866600 10 -chr1 4867600 4867800 2 -chr1 4868600 4869800 4 -chr1 4872000 4875200 25 -chr1 4876600 4887800 51 -chr1 4889400 4895800 50 -chr1 4896600 4907400 66 -chr1 4908200 4911000 22 -chr1 4912200 4912400 2 -chr1 4913400 4923800 64 -chr1 4924800 4931600 50 -chr1 4932400 4935000 22 -chr1 4935800 4938000 15 -chr1 4944800 4948800 22 -chr1 4952400 4964000 86 -chr1 4965800 4970600 31 -chr1 4975200 4976000 6 -chr1 4979800 4982000 16 -chr1 4982800 4983000 2 -chr1 4984400 4986200 6 -chr1 4991200 5000800 56 -chr1 5002000 5025800 121 -chr1 5032600 5035200 7 -chr1 5038800 5040200 6 -chr1 5044400 5048400 21 -chr1 5054200 5057800 24 -chr1 5058800 5063400 34 -chr1 5064200 5067600 19 -chr1 5074000 5079800 35 -chr1 5081600 5098200 89 -chr1 5099000 5100800 4 -chr1 5106000 5112800 37 -chr1 5113600 5117200 17 -chr1 5118800 5120800 10 -chr1 5122400 5123200 9 -chr1 5124200 5127600 14 -chr1 5128400 5136200 56 -chr1 5137200 5139600 11 -chr1 5140400 5144600 14 -chr1 5145400 5145600 3 -chr1 5146800 5147400 2 -chr1 5148400 5156200 45 -chr1 5160000 5162600 9 -chr1 5164200 5164800 6 -chr1 5166000 5169400 22 -chr1 5170200 5171600 4 -chr1 5172600 5175200 24 -chr1 5176200 5180600 41 -chr1 5187000 5187600 3 -chr1 5193800 5206000 83 -chr1 5206800 5219200 78 -chr1 5220000 5227800 55 -chr1 5229400 5231600 13 -chr1 5232400 5233200 5 -chr1 5234200 5238400 17 -chr1 5239800 5241200 10 -chr1 5247800 5252000 28 -chr1 5253200 5258200 25 -chr1 5264400 5265400 8 -chr1 5266200 5266400 2 -chr1 5267200 5268200 10 -chr1 5269800 5278800 43 -chr1 5279600 5281000 8 -chr1 5282800 5284600 7 -chr1 5285600 5287200 14 -chr1 5288200 5299400 47 -chr1 5301600 5302600 4 -chr1 5303400 5309000 36 -chr1 5310000 5311600 15 -chr1 5312400 5318600 29 -chr1 5323400 5334000 41 -chr1 5336200 5336800 3 -chr1 5338400 5339000 3 -chr1 5348600 5349200 6 -chr1 5353800 5357000 16 -chr1 5358400 5362800 15 -chr1 5363800 5365600 12 -chr1 5369400 5375800 29 -chr1 5376600 5379000 6 -chr1 5379800 5383200 11 -chr1 5384000 5385000 8 -chr1 5385800 5388800 15 -chr1 5391800 5398400 20 -chr1 5399600 5399800 2 -chr1 5400600 5404400 16 -chr1 5405200 5405800 2 -chr1 5407400 5413800 32 -chr1 5420800 5421200 3 -chr1 5428000 5433200 24 -chr1 5434000 5434600 4 -chr1 5439600 5440600 6 -chr1 5442000 5445000 15 -chr1 5446200 5447000 3 -chr1 5447800 5449200 11 -chr1 5451000 5458200 27 -chr1 5470600 5471000 3 -chr1 5475400 5475800 5 -chr1 5476600 5476800 2 -chr1 5478200 5479000 3 -chr1 5480800 5482200 3 -chr1 5483400 5483800 3 -chr1 5484800 5489000 13 -chr1 5492600 5494000 5 -chr1 5496000 5499000 15 -chr1 5501800 5512800 52 -chr1 5514400 5516600 11 -chr1 5522400 5524600 8 -chr1 5525800 5531200 18 -chr1 5532200 5536000 21 -chr1 5539400 5541800 11 -chr1 5548200 5551400 17 -chr1 5560800 5561600 3 -chr1 5563400 5565400 6 -chr1 5568400 5573600 33 -chr1 5576200 5590400 71 -chr1 5591200 5592400 5 -chr1 5593200 5613600 89 -chr1 5614400 5617800 22 -chr1 5619800 5620600 3 -chr1 5621400 5622000 6 -chr1 5624600 5625400 2 -chr1 5632000 5637800 20 -chr1 5643200 5643400 2 -chr1 5646400 5655000 60 -chr1 5655800 5656400 6 -chr1 5657200 5659400 8 -chr1 5660400 5661600 5 -chr1 5662400 5662800 3 -chr1 5663600 5667000 12 -chr1 5667800 5668000 2 -chr1 5676200 5678000 4 -chr1 5679000 5681000 15 -chr1 5688000 5691000 12 -chr1 5694600 5700600 24 -chr1 5704600 5710400 22 -chr1 5712400 5714800 10 -chr1 5715600 5719800 19 -chr1 5720600 5723400 9 -chr1 5724200 5724600 2 -chr1 5725400 5730200 24 -chr1 5741800 5748000 28 -chr1 5749400 5750600 3 -chr1 5751400 5753200 9 |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary --- a/test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,417 +0,0 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01 --- a/test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01 Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,184 +0,0 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_3/test-W200-G600.scoreisland --- a/test-data/peakcalling_sicer/test_3/test-W200-G600.scoreisland Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,417 +0,0 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_3/test-W200.graph --- a/test-data/peakcalling_sicer/test_3/test-W200.graph Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland --- a/test-data/peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,352 +0,0 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/peakcalling_sicer/test_4/test-W200.graph --- a/test-data/peakcalling_sicer/test_4/test-W200.graph Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test-1-removed.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-1-removed.bed Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,9898 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\t0\t-\n+chr1\t5666894\t5666930\tregion_9805\t0\t-\n+chr1\t5667898\t5667934\tregion_9807\t0\t-\n+chr1\t5674133\t5674169\tregion_9808\t0\t-\n+chr1\t5675139\t5675175\tregion_9809\t0\t-\n+chr1\t5676675\t5676711\tregion_9811\t0\t-\n+chr1\t5677304\t5677340\tregion_9812\t0\t-\n+chr1\t5679098\t5679134\tregion_9814\t0\t-\n+chr1\t5679255\t5679291\tregion_9815\t0\t-\n+chr1\t5679303\t5679339\tregion_9817\t0\t-\n+chr1\t5679429\t5679465\tregion_9820\t0\t-\n+chr1\t5680276\t5680312\tregion_9824\t0\t-\n+chr1\t5680603\t5680639\tregion_9826\t0\t-\n+chr1\t5688108\t5688144\tregion_9830\t0\t-\n+chr1\t5688411\t5688447\tregion_9831\t0\t-\n+chr1\t5688571\t5688607\tregion_9834\t0\t-\n+chr1\t5689163\t5689199\tregion_9836\t0\t-\n+chr1\t5689312\t5689348\tregion_9837\t0\t-\n+chr1\t5689551\t5689587\tregion_9838\t0\t-\n+chr1\t5689847\t5689883\tregion_9839\t0\t-\n+chr1\t5694818\t5694854\tregion_9843\t0\t-\n+chr1\t5694996\t5695032\tregion_9844\t0\t-\n+chr1\t5695025\t5695061\tregion_9845\t0\t-\n+chr1\t5695144\t5695180\tregion_9846\t0\t-\n+chr1\t5695639\t5695675\tregion_9849\t0\t-\n+chr1\t5696688\t5696724\tregion_9851\t0\t-\n+chr1\t5696950\t5696986\tregion_9854\t0\t-\n+chr1\t5697092\t5697128\tregion_9855\t0\t-\n+chr1\t5698985\t5699021\tregion_9862\t0\t-\n+chr1\t5699555\t5699591\tregion_9863\t0\t-\n+chr1\t5700463\t5700499\tregion_9865\t0\t-\n+chr1\t5700467\t5700503\tregion_9866\t0\t-\n+chr1\t5703812\t5703848\tregion_9867\t0\t-\n+chr1\t5705804\t5705840\tregion_9872\t0\t-\n+chr1\t5706289\t5706325\tregion_9874\t0\t-\n+chr1\t5706307\t5706343\tregion_9875\t0\t-\n+chr1\t5706339\t5706375\tregion_9876\t0\t-\n+chr1\t5706399\t5706435\tregion_9877\t0\t-\n+chr1\t5706446\t5706482\tregion_9878\t0\t-\n+chr1\t5706955\t5706991\tregion_9879\t0\t-\n+chr1\t5707287\t5707323\tregion_9880\t0\t-\n+chr1\t5707378\t5707414\tregion_9881\t0\t-\n+chr1\t5709132\t5709168\tregion_9887\t0\t-\n+chr1\t5710251\t5710287\tregion_9889\t0\t-\n+chr1\t5711567\t5711603\tregion_9890\t0\t-\n+chr1\t5712819\t5712855\tregion_9894\t0\t-\n+chr1\t5714565\t5714601\tregion_9897\t0\t-\n+chr1\t5714689\t5714725\tregion_9898\t0\t-\n+chr1\t5715757\t5715793\tregion_9902\t0\t-\n+chr1\t5715995\t5716031\tregion_9903\t0\t-\n+chr1\t5716291\t5716327\tregion_9907\t0\t-\n+chr1\t5717567\t5717603\tregion_9911\t0\t-\n+chr1\t5717738\t5717774\tregion_9912\t0\t-\n+chr1\t5718495\t5718531\tregion_9915\t0\t-\n+chr1\t5718830\t5718866\tregion_9917\t0\t-\n+chr1\t5718966\t5719002\tregion_9919\t0\t-\n+chr1\t5719703\t5719739\tregion_9920\t0\t-\n+chr1\t5721599\t5721635\tregion_9922\t0\t-\n+chr1\t5721807\t5721843\tregion_9923\t0\t-\n+chr1\t5722297\t5722333\tregion_9925\t0\t-\n+chr1\t5722815\t5722851\tregion_9926\t0\t-\n+chr1\t5724418\t5724454\tregion_9930\t0\t-\n+chr1\t5725529\t5725565\tregion_9933\t0\t-\n+chr1\t5726039\t5726075\tregion_9935\t0\t-\n+chr1\t5726278\t5726314\tregion_9937\t0\t-\n+chr1\t5726381\t5726417\tregion_9939\t0\t-\n+chr1\t5726530\t5726566\tregion_9940\t0\t-\n+chr1\t5726534\t5726570\tregion_9941\t0\t-\n+chr1\t5726557\t5726593\tregion_9942\t0\t-\n+chr1\t5726561\t5726597\tregion_9943\t0\t-\n+chr1\t5726611\t5726647\tregion_9944\t0\t-\n+chr1\t5727379\t5727415\tregion_9946\t0\t-\n+chr1\t5727617\t5727653\tregion_9950\t0\t-\n+chr1\t5728091\t5728127\tregion_9951\t0\t-\n+chr1\t5728737\t5728773\tregion_9952\t0\t-\n+chr1\t5728886\t5728922\tregion_9953\t0\t-\n+chr1\t5729667\t5729703\tregion_9954\t0\t-\n+chr1\t5730047\t5730083\tregion_9956\t0\t-\n+chr1\t5738241\t5738277\tregion_9958\t0\t-\n+chr1\t5742298\t5742334\tregion_9962\t0\t-\n+chr1\t5742856\t5742892\tregion_9965\t0\t-\n+chr1\t5743555\t5743591\tregion_9966\t0\t-\n+chr1\t5743878\t5743914\tregion_9968\t0\t-\n+chr1\t5744403\t5744439\tregion_9969\t0\t-\n+chr1\t5744937\t5744973\tregion_9972\t0\t-\n+chr1\t5744965\t5745001\tregion_9973\t0\t-\n+chr1\t5745800\t5745836\tregion_9975\t0\t-\n+chr1\t5745885\t5745921\tregion_9976\t0\t-\n+chr1\t5745951\t5745987\tregion_9977\t0\t-\n+chr1\t5746138\t5746174\tregion_9979\t0\t-\n+chr1\t5746558\t5746594\tregion_9981\t0\t-\n+chr1\t5746574\t5746610\tregion_9982\t0\t-\n+chr1\t5746733\t5746769\tregion_9983\t0\t-\n+chr1\t5746922\t5746958\tregion_9984\t0\t-\n+chr1\t5751506\t5751542\tregion_9991\t0\t-\n+chr1\t5751966\t5752002\tregion_9995\t0\t-\n+chr1\t5752456\t5752492\tregion_9996\t0\t-\n+chr1\t5752543\t5752579\tregion_9997\t0\t-\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test-W200-G600-E0.01-islandfiltered-normalized.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-W200-G600-E0.01-islandfiltered-normalized.wig Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,5454 @@\n+track type=wiggle_0 name=input_bed_file-islandfiltered\n+variableStep chrom=chr1 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test-W200-G600-E0.01-islandfiltered.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-W200-G600-E0.01-islandfiltered.bed Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,9654 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\t0\t-\n+chr1\t5660451\t5660487\tregion_9787\t0\t-\n+chr1\t5660539\t5660575\tregion_9788\t0\t-\n+chr1\t5663767\t5663803\tregion_9795\t0\t-\n+chr1\t5664658\t5664694\tregion_9798\t0\t-\n+chr1\t5665152\t5665188\tregion_9799\t0\t-\n+chr1\t5665971\t5666007\tregion_9800\t0\t-\n+chr1\t5666823\t5666859\tregion_9804\t0\t-\n+chr1\t5666894\t5666930\tregion_9805\t0\t-\n+chr1\t5676675\t5676711\tregion_9811\t0\t-\n+chr1\t5677304\t5677340\tregion_9812\t0\t-\n+chr1\t5679098\t5679134\tregion_9814\t0\t-\n+chr1\t5679255\t5679291\tregion_9815\t0\t-\n+chr1\t5679303\t5679339\tregion_9817\t0\t-\n+chr1\t5679429\t5679465\tregion_9820\t0\t-\n+chr1\t5680276\t5680312\tregion_9824\t0\t-\n+chr1\t5680603\t5680639\tregion_9826\t0\t-\n+chr1\t5688108\t5688144\tregion_9830\t0\t-\n+chr1\t5688411\t5688447\tregion_9831\t0\t-\n+chr1\t5688571\t5688607\tregion_9834\t0\t-\n+chr1\t5689163\t5689199\tregion_9836\t0\t-\n+chr1\t5689312\t5689348\tregion_9837\t0\t-\n+chr1\t5689551\t5689587\tregion_9838\t0\t-\n+chr1\t5689847\t5689883\tregion_9839\t0\t-\n+chr1\t5694818\t5694854\tregion_9843\t0\t-\n+chr1\t5694996\t5695032\tregion_9844\t0\t-\n+chr1\t5695025\t5695061\tregion_9845\t0\t-\n+chr1\t5695144\t5695180\tregion_9846\t0\t-\n+chr1\t5695639\t5695675\tregion_9849\t0\t-\n+chr1\t5696688\t5696724\tregion_9851\t0\t-\n+chr1\t5696950\t5696986\tregion_9854\t0\t-\n+chr1\t5697092\t5697128\tregion_9855\t0\t-\n+chr1\t5698985\t5699021\tregion_9862\t0\t-\n+chr1\t5699555\t5699591\tregion_9863\t0\t-\n+chr1\t5700463\t5700499\tregion_9865\t0\t-\n+chr1\t5700467\t5700503\tregion_9866\t0\t-\n+chr1\t5705804\t5705840\tregion_9872\t0\t-\n+chr1\t5706289\t5706325\tregion_9874\t0\t-\n+chr1\t5706307\t5706343\tregion_9875\t0\t-\n+chr1\t5706339\t5706375\tregion_9876\t0\t-\n+chr1\t5706399\t5706435\tregion_9877\t0\t-\n+chr1\t5706446\t5706482\tregion_9878\t0\t-\n+chr1\t5706955\t5706991\tregion_9879\t0\t-\n+chr1\t5707287\t5707323\tregion_9880\t0\t-\n+chr1\t5707378\t5707414\tregion_9881\t0\t-\n+chr1\t5709132\t5709168\tregion_9887\t0\t-\n+chr1\t5710251\t5710287\tregion_9889\t0\t-\n+chr1\t5712819\t5712855\tregion_9894\t0\t-\n+chr1\t5714565\t5714601\tregion_9897\t0\t-\n+chr1\t5714689\t5714725\tregion_9898\t0\t-\n+chr1\t5715757\t5715793\tregion_9902\t0\t-\n+chr1\t5715995\t5716031\tregion_9903\t0\t-\n+chr1\t5716291\t5716327\tregion_9907\t0\t-\n+chr1\t5717567\t5717603\tregion_9911\t0\t-\n+chr1\t5717738\t5717774\tregion_9912\t0\t-\n+chr1\t5718495\t5718531\tregion_9915\t0\t-\n+chr1\t5718830\t5718866\tregion_9917\t0\t-\n+chr1\t5718966\t5719002\tregion_9919\t0\t-\n+chr1\t5719703\t5719739\tregion_9920\t0\t-\n+chr1\t5721599\t5721635\tregion_9922\t0\t-\n+chr1\t5721807\t5721843\tregion_9923\t0\t-\n+chr1\t5722297\t5722333\tregion_9925\t0\t-\n+chr1\t5722815\t5722851\tregion_9926\t0\t-\n+chr1\t5725529\t5725565\tregion_9933\t0\t-\n+chr1\t5726039\t5726075\tregion_9935\t0\t-\n+chr1\t5726278\t5726314\tregion_9937\t0\t-\n+chr1\t5726381\t5726417\tregion_9939\t0\t-\n+chr1\t5726530\t5726566\tregion_9940\t0\t-\n+chr1\t5726534\t5726570\tregion_9941\t0\t-\n+chr1\t5726557\t5726593\tregion_9942\t0\t-\n+chr1\t5726561\t5726597\tregion_9943\t0\t-\n+chr1\t5726611\t5726647\tregion_9944\t0\t-\n+chr1\t5727379\t5727415\tregion_9946\t0\t-\n+chr1\t5727617\t5727653\tregion_9950\t0\t-\n+chr1\t5728091\t5728127\tregion_9951\t0\t-\n+chr1\t5728737\t5728773\tregion_9952\t0\t-\n+chr1\t5728886\t5728922\tregion_9953\t0\t-\n+chr1\t5729667\t5729703\tregion_9954\t0\t-\n+chr1\t5730047\t5730083\tregion_9956\t0\t-\n+chr1\t5742298\t5742334\tregion_9962\t0\t-\n+chr1\t5742856\t5742892\tregion_9965\t0\t-\n+chr1\t5743555\t5743591\tregion_9966\t0\t-\n+chr1\t5743878\t5743914\tregion_9968\t0\t-\n+chr1\t5744403\t5744439\tregion_9969\t0\t-\n+chr1\t5744937\t5744973\tregion_9972\t0\t-\n+chr1\t5744965\t5745001\tregion_9973\t0\t-\n+chr1\t5745800\t5745836\tregion_9975\t0\t-\n+chr1\t5745885\t5745921\tregion_9976\t0\t-\n+chr1\t5745951\t5745987\tregion_9977\t0\t-\n+chr1\t5746138\t5746174\tregion_9979\t0\t-\n+chr1\t5746558\t5746594\tregion_9981\t0\t-\n+chr1\t5746574\t5746610\tregion_9982\t0\t-\n+chr1\t5746733\t5746769\tregion_9983\t0\t-\n+chr1\t5746922\t5746958\tregion_9984\t0\t-\n+chr1\t5751506\t5751542\tregion_9991\t0\t-\n+chr1\t5751966\t5752002\tregion_9995\t0\t-\n+chr1\t5752456\t5752492\tregion_9996\t0\t-\n+chr1\t5752543\t5752579\tregion_9997\t0\t-\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test-W200-G600-FDR0.01-islandfiltered-normalized.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-W200-G600-FDR0.01-islandfiltered-normalized.wig Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,2296 @@\n+track type=wiggle_0 name=input_bed_file-islandfiltered\n+variableStep chrom=chr1 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test-W200-G600-FDR0.01-islandfiltered.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-W200-G600-FDR0.01-islandfiltered.bed Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,4303 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663803\tregion_9795\t0\t-\n+chr1\t5664658\t5664694\tregion_9798\t0\t-\n+chr1\t5665152\t5665188\tregion_9799\t0\t-\n+chr1\t5665971\t5666007\tregion_9800\t0\t-\n+chr1\t5666823\t5666859\tregion_9804\t0\t-\n+chr1\t5666894\t5666930\tregion_9805\t0\t-\n+chr1\t5667898\t5667934\tregion_9807\t0\t-\n+chr1\t5676675\t5676711\tregion_9811\t0\t-\n+chr1\t5677304\t5677340\tregion_9812\t0\t-\n+chr1\t5679098\t5679134\tregion_9814\t0\t-\n+chr1\t5679255\t5679291\tregion_9815\t0\t-\n+chr1\t5679303\t5679339\tregion_9817\t0\t-\n+chr1\t5679429\t5679465\tregion_9820\t0\t-\n+chr1\t5680276\t5680312\tregion_9824\t0\t-\n+chr1\t5680603\t5680639\tregion_9826\t0\t-\n+chr1\t5688108\t5688144\tregion_9830\t0\t-\n+chr1\t5688411\t5688447\tregion_9831\t0\t-\n+chr1\t5688571\t5688607\tregion_9834\t0\t-\n+chr1\t5689163\t5689199\tregion_9836\t0\t-\n+chr1\t5689312\t5689348\tregion_9837\t0\t-\n+chr1\t5689551\t5689587\tregion_9838\t0\t-\n+chr1\t5689847\t5689883\tregion_9839\t0\t-\n+chr1\t5694818\t5694854\tregion_9843\t0\t-\n+chr1\t5694996\t5695032\tregion_9844\t0\t-\n+chr1\t5695025\t5695061\tregion_9845\t0\t-\n+chr1\t5695144\t5695180\tregion_9846\t0\t-\n+chr1\t5695639\t5695675\tregion_9849\t0\t-\n+chr1\t5696688\t5696724\tregion_9851\t0\t-\n+chr1\t5696950\t5696986\tregion_9854\t0\t-\n+chr1\t5697092\t5697128\tregion_9855\t0\t-\n+chr1\t5698985\t5699021\tregion_9862\t0\t-\n+chr1\t5699555\t5699591\tregion_9863\t0\t-\n+chr1\t5700463\t5700499\tregion_9865\t0\t-\n+chr1\t5700467\t5700503\tregion_9866\t0\t-\n+chr1\t5705804\t5705840\tregion_9872\t0\t-\n+chr1\t5706289\t5706325\tregion_9874\t0\t-\n+chr1\t5706307\t5706343\tregion_9875\t0\t-\n+chr1\t5706339\t5706375\tregion_9876\t0\t-\n+chr1\t5706399\t5706435\tregion_9877\t0\t-\n+chr1\t5706446\t5706482\tregion_9878\t0\t-\n+chr1\t5706955\t5706991\tregion_9879\t0\t-\n+chr1\t5707287\t5707323\tregion_9880\t0\t-\n+chr1\t5707378\t5707414\tregion_9881\t0\t-\n+chr1\t5709132\t5709168\tregion_9887\t0\t-\n+chr1\t5710251\t5710287\tregion_9889\t0\t-\n+chr1\t5712819\t5712855\tregion_9894\t0\t-\n+chr1\t5714565\t5714601\tregion_9897\t0\t-\n+chr1\t5714689\t5714725\tregion_9898\t0\t-\n+chr1\t5715757\t5715793\tregion_9902\t0\t-\n+chr1\t5715995\t5716031\tregion_9903\t0\t-\n+chr1\t5716291\t5716327\tregion_9907\t0\t-\n+chr1\t5717567\t5717603\tregion_9911\t0\t-\n+chr1\t5717738\t5717774\tregion_9912\t0\t-\n+chr1\t5718495\t5718531\tregion_9915\t0\t-\n+chr1\t5718830\t5718866\tregion_9917\t0\t-\n+chr1\t5718966\t5719002\tregion_9919\t0\t-\n+chr1\t5719703\t5719739\tregion_9920\t0\t-\n+chr1\t5721599\t5721635\tregion_9922\t0\t-\n+chr1\t5721807\t5721843\tregion_9923\t0\t-\n+chr1\t5722297\t5722333\tregion_9925\t0\t-\n+chr1\t5722815\t5722851\tregion_9926\t0\t-\n+chr1\t5724418\t5724454\tregion_9930\t0\t-\n+chr1\t5725529\t5725565\tregion_9933\t0\t-\n+chr1\t5726039\t5726075\tregion_9935\t0\t-\n+chr1\t5726278\t5726314\tregion_9937\t0\t-\n+chr1\t5726381\t5726417\tregion_9939\t0\t-\n+chr1\t5726530\t5726566\tregion_9940\t0\t-\n+chr1\t5726534\t5726570\tregion_9941\t0\t-\n+chr1\t5726557\t5726593\tregion_9942\t0\t-\n+chr1\t5726561\t5726597\tregion_9943\t0\t-\n+chr1\t5726611\t5726647\tregion_9944\t0\t-\n+chr1\t5727379\t5727415\tregion_9946\t0\t-\n+chr1\t5727617\t5727653\tregion_9950\t0\t-\n+chr1\t5728091\t5728127\tregion_9951\t0\t-\n+chr1\t5728737\t5728773\tregion_9952\t0\t-\n+chr1\t5728886\t5728922\tregion_9953\t0\t-\n+chr1\t5729667\t5729703\tregion_9954\t0\t-\n+chr1\t5730047\t5730083\tregion_9956\t0\t-\n+chr1\t5742298\t5742334\tregion_9962\t0\t-\n+chr1\t5742856\t5742892\tregion_9965\t0\t-\n+chr1\t5743555\t5743591\tregion_9966\t0\t-\n+chr1\t5743878\t5743914\tregion_9968\t0\t-\n+chr1\t5744403\t5744439\tregion_9969\t0\t-\n+chr1\t5744937\t5744973\tregion_9972\t0\t-\n+chr1\t5744965\t5745001\tregion_9973\t0\t-\n+chr1\t5745800\t5745836\tregion_9975\t0\t-\n+chr1\t5745885\t5745921\tregion_9976\t0\t-\n+chr1\t5745951\t5745987\tregion_9977\t0\t-\n+chr1\t5746138\t5746174\tregion_9979\t0\t-\n+chr1\t5746558\t5746594\tregion_9981\t0\t-\n+chr1\t5746574\t5746610\tregion_9982\t0\t-\n+chr1\t5746733\t5746769\tregion_9983\t0\t-\n+chr1\t5746922\t5746958\tregion_9984\t0\t-\n+chr1\t5751506\t5751542\tregion_9991\t0\t-\n+chr1\t5751966\t5752002\tregion_9995\t0\t-\n+chr1\t5752456\t5752492\tregion_9996\t0\t-\n+chr1\t5752543\t5752579\tregion_9997\t0\t-\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test-W200-normalized.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-W200-normalized.wig Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,5669 @@\n+track type=wiggle_0 name=input_bed_file\n+variableStep chrom=chr1 span=200\n+3002001\t101.031\n+3002201\t202.061\n+3002801\t202.061\n+3003001\t202.061\n+3003401\t202.061\n+3004001\t101.031\n+3004201\t101.031\n+3005001\t101.031\n+3005801\t101.031\n+3016401\t101.031\n+3017801\t101.031\n+3018401\t202.061\n+3018601\t101.031\n+3018801\t101.031\n+3019001\t101.031\n+3019201\t101.031\n+3019401\t101.031\n+3019601\t202.061\n+3019801\t101.031\n+3020201\t303.092\n+3021001\t303.092\n+3021201\t101.031\n+3021401\t404.122\n+3021801\t202.061\n+3022001\t101.031\n+3022201\t101.031\n+3023201\t101.031\n+3023401\t101.031\n+3023801\t202.061\n+3025001\t101.031\n+3026801\t202.061\n+3027001\t202.061\n+3027801\t101.031\n+3028401\t101.031\n+3028601\t101.031\n+3028801\t101.031\n+3029001\t101.031\n+3035401\t101.031\n+3035601\t303.092\n+3036001\t101.031\n+3036801\t101.031\n+3037001\t101.031\n+3037201\t202.061\n+3037601\t101.031\n+3038401\t101.031\n+3038601\t303.092\n+3038801\t202.061\n+3039001\t101.031\n+3039401\t101.031\n+3039601\t202.061\n+3040801\t101.031\n+3041001\t303.092\n+3041801\t202.061\n+3051601\t101.031\n+3051801\t101.031\n+3052001\t101.031\n+3052401\t202.061\n+3052801\t101.031\n+3053001\t101.031\n+3053801\t101.031\n+3054801\t404.122\n+3055001\t101.031\n+3055201\t101.031\n+3055801\t101.031\n+3062201\t101.031\n+3062401\t101.031\n+3062601\t202.061\n+3063001\t101.031\n+3063201\t202.061\n+3063401\t101.031\n+3063601\t101.031\n+3063801\t101.031\n+3064801\t101.031\n+3065201\t101.031\n+3066001\t303.092\n+3066201\t101.031\n+3066801\t101.031\n+3067001\t101.031\n+3068801\t101.031\n+3069801\t101.031\n+3071001\t101.031\n+3071201\t303.092\n+3072001\t101.031\n+3073401\t101.031\n+3073601\t101.031\n+3073801\t101.031\n+3074001\t101.031\n+3077401\t202.061\n+3078401\t101.031\n+3085601\t101.031\n+3086201\t505.153\n+3086401\t404.122\n+3086601\t303.092\n+3086801\t101.031\n+3087001\t202.061\n+3088401\t303.092\n+3089401\t303.092\n+3089601\t101.031\n+3089801\t101.031\n+3091601\t101.031\n+3091801\t101.031\n+3092801\t101.031\n+3093001\t101.031\n+3093601\t202.061\n+3094801\t202.061\n+3095201\t303.092\n+3095401\t202.061\n+3095601\t202.061\n+3097001\t101.031\n+3104201\t101.031\n+3104801\t303.092\n+3105001\t202.061\n+3105801\t202.061\n+3106801\t404.122\n+3107001\t101.031\n+3107201\t101.031\n+3107401\t202.061\n+3107601\t101.031\n+3108001\t101.031\n+3108201\t101.031\n+3108401\t202.061\n+3108601\t101.031\n+3109201\t202.061\n+3109401\t101.031\n+3110201\t303.092\n+3110401\t606.183\n+3110601\t101.031\n+3110801\t202.061\n+3111001\t101.031\n+3111201\t101.031\n+3111401\t101.031\n+3111601\t101.031\n+3111801\t202.061\n+3112001\t101.031\n+3112201\t101.031\n+3112401\t101.031\n+3112601\t202.061\n+3112801\t101.031\n+3113201\t202.061\n+3113401\t202.061\n+3114401\t101.031\n+3114801\t101.031\n+3115001\t101.031\n+3115201\t101.031\n+3117801\t202.061\n+3118001\t101.031\n+3118201\t101.031\n+3119001\t101.031\n+3119401\t101.031\n+3119601\t303.092\n+3119801\t101.031\n+3120001\t101.031\n+3120201\t101.031\n+3120601\t202.061\n+3121401\t101.031\n+3121601\t101.031\n+3122201\t101.031\n+3122401\t202.061\n+3122601\t202.061\n+3123201\t202.061\n+3123801\t101.031\n+3124201\t101.031\n+3124601\t303.092\n+3124801\t101.031\n+3125801\t101.031\n+3126401\t101.031\n+3126801\t101.031\n+3127201\t202.061\n+3131001\t101.031\n+3131801\t202.061\n+3132601\t101.031\n+3138801\t202.061\n+3139001\t202.061\n+3139201\t101.031\n+3155601\t101.031\n+3155801\t202.061\n+3156001\t101.031\n+3156201\t303.092\n+3156401\t101.031\n+3156601\t101.031\n+3156801\t101.031\n+3157201\t202.061\n+3157601\t202.061\n+3157801\t202.061\n+3158001\t101.031\n+3158201\t101.031\n+3158601\t101.031\n+3159201\t101.031\n+3159401\t101.031\n+3159801\t101.031\n+3160801\t202.061\n+3161401\t202.061\n+3161601\t101.031\n+3161801\t404.122\n+3162601\t101.031\n+3162801\t101.031\n+3163001\t101.031\n+3163201\t101.031\n+3164601\t101.031\n+3165801\t202.061\n+3168601\t303.092\n+3168801\t101.031\n+3169001\t202.061\n+3169201\t101.031\n+3172601\t101.031\n+3173401\t101.031\n+3173601\t202.061\n+3173801\t101.031\n+3174001\t101.031\n+3174601\t101.031\n+3174801\t202.061\n+3175401\t101.031\n+3176601\t101.031\n+3179601\t202.061\n+3179801\t101.031\n+3180401\t202.061\n+3180601\t101.031\n+3180801\t101.031\n+3181001\t101.031\n+3181201\t101.031\n+3181801\t202.061\n+3182201\t101.031\n+3182401\t202.061\n+3183401\t101.031\n+3185601\t101.031\n+3185801\t101.031\n+3186201\t202.061\n+3186801\t101.031\n+3187001\t202.061\n+3187201\t202'..b'031\n+5605801\t101.031\n+5606401\t202.061\n+5606601\t303.092\n+5607201\t101.031\n+5607601\t101.031\n+5608001\t101.031\n+5608201\t101.031\n+5609001\t202.061\n+5609601\t101.031\n+5610401\t101.031\n+5611001\t202.061\n+5611201\t101.031\n+5611601\t202.061\n+5611801\t101.031\n+5612001\t101.031\n+5612201\t101.031\n+5612601\t303.092\n+5612801\t101.031\n+5613001\t202.061\n+5613401\t101.031\n+5614401\t101.031\n+5614601\t202.061\n+5614801\t202.061\n+5615001\t202.061\n+5615201\t101.031\n+5615601\t101.031\n+5616201\t101.031\n+5616401\t101.031\n+5616601\t404.122\n+5616801\t303.092\n+5617001\t202.061\n+5617401\t101.031\n+5617601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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_1_output_log_file.contains --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1_output_log_file.contains Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,190 @@\n+#############################################\n+###### SICER v1.1 ######\n+#############################################\n+Input library directory:\n+ChIP library:\n+Output directory:\n+Species: mm8\n+Threshold for redundancy allowed for reads: 1\n+Window size: 200 bps\n+Fragment size: 150 bps. The shift for reads is half of 150\n+Effective genome size as a fraction of the reference genome of mm8: 0.740000\n+Gap size: 600 bps\n+Evalue for identification of significant islands: 0.01\n+Preprocess the raw input_bed_file file to remove redundancy with threshold 1...\n+chr1 \tPlus reads: 4989 \tRetained plus reads: 4935 ;\tMinus reads: 5011 \tRetained minus reads: 4963\n+chr2 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr3 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr4 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr5 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr6 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr7 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr8 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr9 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr10 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr11 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr12 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr13 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr14 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr15 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr16 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr17 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr18 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr19 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chrX \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chrY \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chrM \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+Partion the genome in windows ...\n+Generate summary files for input_bed_file...\n+total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0\n+total tag count in chr2.bed is: 0.0 = 0.0+0.0\n+total tag count in chr3.bed is: 0.0 = 0.0+0.0\n+total tag count in chr4.bed is: 0.0 = 0.0+0.0\n+total tag count in chr5.bed is: 0.0 = 0.0+0.0\n+total tag count in chr6.bed is: 0.0 = 0.0+0.0\n+total tag count in chr7.bed is: 0.0 = 0.0+0.0\n+total tag count in chr8.bed is: 0.0 = 0.0+0.0\n+total tag count in chr9.bed is: 0.0 = 0.0+0.0\n+total tag count in chr10.bed is: 0.0 = 0.0+0.0\n+total tag count in chr11.bed is: 0.0 = 0.0+0.0\n+total tag count in chr12.bed is: 0.0 = 0.0+0.0\n+total tag count in chr13.bed is: 0.0 = 0.0+0.0\n+total tag count in chr14.bed is: 0.0 = 0.0+0.0\n+total tag count in chr15.bed is: 0.0 = 0.0+0.0\n+total tag count in chr16.bed is: 0.0 = 0.0+0.0\n+total tag count in chr17.bed is: 0.0 = 0.0+0.0\n+total tag count in chr18.bed is: 0.0 = 0.0+0.0\n+total tag count in chr19.bed is: 0.0 = 0.0+0.0\n+total tag count in chrX.bed is: 0.0 = 0.0+0.0\n+total tag count in chrY.bed is: 0.0 = 0.0+0.0\n+total tag count in chrM.bed is: 0.0 = 0.0+0.0\n+Normalize summary graph by total redundancy-removed reads per million for input_bed_file ...\n+Convert the normalized summary graph into wig vstep format...\n+Find significant islands with E-value 0.01 for input_bed_file...\n+Species: mm8\n+Window_size: 200\n+Gap size: 600\n+E value is: 0.01\n+Total read count: 9898.0\n+Genome Length: '..b'ed is: 0.0 = 0.0+0.0\n+total tag count in chr12.bed is: 0.0 = 0.0+0.0\n+total tag count in chr13.bed is: 0.0 = 0.0+0.0\n+total tag count in chr14.bed is: 0.0 = 0.0+0.0\n+total tag count in chr15.bed is: 0.0 = 0.0+0.0\n+total tag count in chr16.bed is: 0.0 = 0.0+0.0\n+total tag count in chr17.bed is: 0.0 = 0.0+0.0\n+total tag count in chr18.bed is: 0.0 = 0.0+0.0\n+total tag count in chr19.bed is: 0.0 = 0.0+0.0\n+total tag count in chrX.bed is: 0.0 = 0.0+0.0\n+total tag count in chrY.bed is: 0.0 = 0.0+0.0\n+total tag count in chrM.bed is: 0.0 = 0.0+0.0\n+Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million...\n+Convert the summary graph made with the filtered reads into wig vstep format and normalize by total island-filtered read count per million...\n+Done!\n+Additionally, these warnings were reported:\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_1_test-W200-G600-E0.01.scoreisland --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1_test-W200-G600-E0.01.scoreisland Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,352 @@\n+chr1\t3002000\t3005999\t92.4307844442\n+chr1\t3017800\t3022399\t188.155382275\n+chr1\t3023200\t3023999\t28.2805178042\n+chr1\t3026800\t3029199\t63.4581311992\n+chr1\t3035400\t3039799\t143.597790119\n+chr1\t3040800\t3041999\t43.8644449755\n+chr1\t3051600\t3053999\t55.8689001676\n+chr1\t3054800\t3055999\t51.4546877469\n+chr1\t3062200\t3063999\t70.3552267901\n+chr1\t3064800\t3067199\t56.9665007165\n+chr1\t3071000\t3072199\t36.2752139439\n+chr1\t3073400\t3074199\t27.5883823634\n+chr1\t3085600\t3087199\t120.793864279\n+chr1\t3088400\t3088599\t22.4810227622\n+chr1\t3089400\t3089999\t36.2752139439\n+chr1\t3092800\t3093799\t28.2805178042\n+chr1\t3094800\t3095799\t65.9400026296\n+chr1\t3104200\t3105999\t58.350771598\n+chr1\t3106800\t3113599\t327.445332228\n+chr1\t3114400\t3115399\t27.5883823634\n+chr1\t3117800\t3124999\t207.055921318\n+chr1\t3125800\t3127399\t35.177613395\n+chr1\t3131000\t3132799\t28.2805178042\n+chr1\t3138800\t3139399\t35.8697488358\n+chr1\t3155600\t3159999\t156.294380752\n+chr1\t3160800\t3163399\t94.2215321736\n+chr1\t3168600\t3169399\t50.7615405664\n+chr1\t3172600\t3175599\t70.3552267901\n+chr1\t3179600\t3182599\t99.327880035\n+chr1\t3185600\t3189799\t182.461247748\n+chr1\t3191200\t3193399\t79.7352055511\n+chr1\t3194200\t3199599\t156.987527932\n+chr1\t3201600\t3216199\t615.108892615\n+chr1\t3217000\t3220599\t189.134188048\n+chr1\t3236800\t3249399\t477.832833942\n+chr1\t3254400\t3260799\t231.027587217\n+chr1\t3274600\t3275199\t36.2752139439\n+chr1\t3276600\t3277999\t35.177613395\n+chr1\t3279800\t3281399\t90.031475044\n+chr1\t3283600\t3292999\t278.103283549\n+chr1\t3301600\t3302799\t50.7615405664\n+chr1\t3309000\t3318399\t370.10479266\n+chr1\t3322200\t3327199\t216.029423231\n+chr1\t3334400\t3335399\t27.5883823634\n+chr1\t3342000\t3347799\t156.69984586\n+chr1\t3348600\t3362399\t557.349485192\n+chr1\t3363400\t3367599\t98.6357445943\n+chr1\t3368600\t3380399\t328.578153783\n+chr1\t3381200\t3392799\t373.82686964\n+chr1\t3395000\t3397799\t107.728041283\n+chr1\t3398600\t3400599\t55.8689001676\n+chr1\t3401800\t3403799\t101.524092873\n+chr1\t3404600\t3410999\t236.720710004\n+chr1\t3411800\t3413999\t94.2205204338\n+chr1\t3415200\t3420799\t165.674359513\n+chr1\t3421600\t3433999\t355.761071038\n+chr1\t3435400\t3437199\t72.1449627797\n+chr1\t3438000\t3439999\t107.000684837\n+chr1\t3440800\t3459399\t599.239306851\n+chr1\t3460800\t3462999\t148.382246642\n+chr1\t3465200\t3466599\t42.7668444267\n+chr1\t3467400\t3475599\t224.859871552\n+chr1\t3477800\t3485399\t259.202744506\n+chr1\t3486800\t3490799\t141.808054129\n+chr1\t3493600\t3503799\t286.790115129\n+chr1\t3504600\t3509999\t317.231624766\n+chr1\t3514400\t3516999\t84.8415534126\n+chr1\t3517800\t3519199\t34.4854779543\n+chr1\t3522000\t3524199\t56.5610356084\n+chr1\t3529400\t3530599\t50.7615405664\n+chr1\t3531800\t3548199\t588.724483056\n+chr1\t3550600\t3557399\t176.580202416\n+chr1\t3558200\t3563599\t196.149066675\n+chr1\t3565000\t3567599\t109.112312164\n+chr1\t3568400\t3576199\t415.971718136\n+chr1\t3577000\t3578799\t79.0420583706\n+chr1\t3579800\t3583599\t112.835400884\n+chr1\t3585000\t3590599\t177.391132632\n+chr1\t3592200\t3597799\t166.771960061\n+chr1\t3599000\t3604199\t181.662740052\n+chr1\t3614200\t3617999\t90.3543781219\n+chr1\t3619600\t3620199\t29.3781183531\n+chr1\t3621000\t3627199\t234.790392493\n+chr1\t3628000\t3628399\t44.9620455244\n+chr1\t3629200\t3658799\t1022.26213636\n+chr1\t3659600\t3671999\t413.38347445\n+chr1\t3672800\t3672999\t30.7634009744\n+chr1\t3674000\t3678399\t149.397285161\n+chr1\t3679800\t3680999\t89.8073197529\n+chr1\t3682000\t3684599\t114.219671766\n+chr1\t3686200\t3687799\t35.177613395\n+chr1\t3698200\t3698799\t43.4589798674\n+chr1\t3700000\t3708999\t266.505305205\n+chr1\t3710800\t3718799\t250.920366293\n+chr1\t3720000\t3723599\t159.063934254\n+chr1\t3724400\t3726399\t49.6639400175\n+chr1\t3732400\t3738599\t171.472842815\n+chr1\t3742600\t3748799\t230.740916884\n+chr1\t3749600\t3752599\t100.425480584\n+chr1\t3754200\t3757399\t63.4581311992\n+chr1\t3763400\t3766199\t84.1494179718\n+chr1\t3767800\t3772599\t126.916262398\n+chr1\t3774000\t3783199\t361.417961079\n+chr1\t3784000\t3790199\t209.251122416\n+chr1\t3803000\t3806399\t136.29522942\n+chr1\t3812000\t3814799\t85.2470185207\n+chr1\t3823600\t3834199\t366.643103716\n+chr1\t3846800\t3853399\t153.812509321\n+chr1\t3855400\t3861399\t247.604766161\n+chr1\t3864400\t3866399\t64.15026664\n+chr1\t3868800\t3870599\t48.971804576'..b'999\t161.66460046\n+chr1\t4913400\t4923799\t465.019472014\n+chr1\t4924800\t4931599\t368.173463409\n+chr1\t4932400\t4934999\t162.356735901\n+chr1\t4935800\t4937999\t110.721750077\n+chr1\t4944800\t4948799\t161.077825535\n+chr1\t4952400\t4963999\t635.887330667\n+chr1\t4965800\t4970599\t224.717266551\n+chr1\t4975200\t4975999\t43.8644449755\n+chr1\t4979800\t4981999\t116.701543196\n+chr1\t4984400\t4986199\t42.7668444267\n+chr1\t4991200\t5000799\t411.13831573\n+chr1\t5002000\t5025799\t871.422277103\n+chr1\t5032600\t5035199\t48.9718045768\n+chr1\t5038800\t5040199\t43.1723095348\n+chr1\t5044400\t5048399\t151.18702115\n+chr1\t5054200\t5057799\t174.466551609\n+chr1\t5058800\t5063399\t256.991357651\n+chr1\t5064200\t5067599\t138.085977149\n+chr1\t5074000\t5079799\t254.606210528\n+chr1\t5081600\t5098199\t656.182132241\n+chr1\t5099000\t5100799\t27.5883823634\n+chr1\t5106000\t5112799\t270.373470996\n+chr1\t5113600\t5117199\t125.209088439\n+chr1\t5118800\t5120799\t70.7606918982\n+chr1\t5122400\t5123199\t67.549440542\n+chr1\t5124200\t5127599\t99.327880035\n+chr1\t5128400\t5136199\t413.646334557\n+chr1\t5137200\t5139599\t79.4475234787\n+chr1\t5140400\t5144599\t100.425480584\n+chr1\t5145400\t5145599\t22.4810227622\n+chr1\t5148400\t5156199\t326.059037867\n+chr1\t5160000\t5162599\t62.7659957585\n+chr1\t5164200\t5164799\t43.8644449755\n+chr1\t5166000\t5169399\t162.356735901\n+chr1\t5170200\t5171599\t28.2805178042\n+chr1\t5172600\t5175199\t185.589343956\n+chr1\t5176200\t5180599\t301.826983932\n+chr1\t5193800\t5205999\t612.253148745\n+chr1\t5206800\t5219199\t570.633862489\n+chr1\t5220000\t5227799\t405.652650157\n+chr1\t5229400\t5231599\t95.3191327225\n+chr1\t5232400\t5233199\t36.2752139439\n+chr1\t5234200\t5238399\t120.711302248\n+chr1\t5239800\t5241199\t73.2425633286\n+chr1\t5247800\t5251999\t206.040882799\n+chr1\t5253200\t5258199\t181.258286684\n+chr1\t5264400\t5265399\t57.2531710491\n+chr1\t5267200\t5268199\t73.530245401\n+chr1\t5269800\t5278799\t309.559831704\n+chr1\t5279600\t5280999\t57.6586361572\n+chr1\t5282800\t5284599\t48.279669136\n+chr1\t5285600\t5287199\t104.922255035\n+chr1\t5288200\t5299399\t337.148214067\n+chr1\t5301600\t5302599\t28.2805178042\n+chr1\t5303400\t5308999\t264.67933647\n+chr1\t5310000\t5311599\t113.896768688\n+chr1\t5312400\t5318599\t210.92307537\n+chr1\t5323400\t5333999\t292.996087019\n+chr1\t5348600\t5349199\t44.5575921561\n+chr1\t5353800\t5356999\t113.122071217\n+chr1\t5358400\t5362799\t106.224975626\n+chr1\t5363800\t5365599\t86.6312894022\n+chr1\t5369400\t5375799\t206.65045621\n+chr1\t5376600\t5378999\t41.3825735452\n+chr1\t5379800\t5383199\t76.5601869402\n+chr1\t5384000\t5384999\t59.9602095104\n+chr1\t5385800\t5388799\t110.722761817\n+chr1\t5391800\t5398399\t140.71045358\n+chr1\t5400600\t5404399\t114.625136874\n+chr1\t5407400\t5413799\t230.515749854\n+chr1\t5428000\t5433199\t173.263590544\n+chr1\t5434000\t5434599\t28.2805178042\n+chr1\t5439600\t5440599\t42.7668444267\n+chr1\t5442000\t5444999\t108.015723355\n+chr1\t5447800\t5449199\t81.1194764326\n+chr1\t5451000\t5458199\t190.779858706\n+chr1\t5475400\t5475799\t37.6604965652\n+chr1\t5484800\t5488999\t92.4307844442\n+chr1\t5492600\t5493999\t35.177613395\n+chr1\t5496000\t5498999\t108.014711616\n+chr1\t5501800\t5512799\t376.534919841\n+chr1\t5514400\t5516599\t78.3499229298\n+chr1\t5522400\t5524599\t55.8689001676\n+chr1\t5525800\t5531199\t126.916262398\n+chr1\t5532200\t5535999\t154.363051501\n+chr1\t5539400\t5541799\t79.0420583706\n+chr1\t5548200\t5551399\t121.403437689\n+chr1\t5563400\t5565399\t41.3825735452\n+chr1\t5568400\t5573599\t244.260995152\n+chr1\t5576200\t5590399\t509.02449851\n+chr1\t5591200\t5592399\t35.177613395\n+chr1\t5593200\t5613599\t640.725217432\n+chr1\t5614400\t5617799\t159.469399362\n+chr1\t5621400\t5621999\t43.4589798674\n+chr1\t5632000\t5637799\t141.115918688\n+chr1\t5646400\t5654999\t447.223146248\n+chr1\t5655800\t5656399\t44.5575921561\n+chr1\t5657200\t5659399\t57.6586361572\n+chr1\t5660400\t5661599\t36.2752139439\n+chr1\t5663600\t5666999\t85.9391539614\n+chr1\t5676200\t5677999\t27.5883823634\n+chr1\t5679000\t5680999\t109.399994237\n+chr1\t5688000\t5690999\t83.4572825311\n+chr1\t5694600\t5700599\t172.570443364\n+chr1\t5704600\t5710399\t160.385690094\n+chr1\t5712400\t5714799\t71.452827339\n+chr1\t5715600\t5719799\t138.085977149\n+chr1\t5720600\t5723399\t64.5557317481\n+chr1\t5725400\t5730199\t175.277481825\n+chr1\t5741800\t5747999\t200.040030952\n+chr1\t5751400\t5753199\t64.8424020807\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_1_test-W200.graph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1_test-W200.graph Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,5667 @@\n+chr1\t3002000\t3002199\t1\n+chr1\t3002200\t3002399\t2\n+chr1\t3002800\t3002999\t2\n+chr1\t3003000\t3003199\t2\n+chr1\t3003400\t3003599\t2\n+chr1\t3004000\t3004199\t1\n+chr1\t3004200\t3004399\t1\n+chr1\t3005000\t3005199\t1\n+chr1\t3005800\t3005999\t1\n+chr1\t3016400\t3016599\t1\n+chr1\t3017800\t3017999\t1\n+chr1\t3018400\t3018599\t2\n+chr1\t3018600\t3018799\t1\n+chr1\t3018800\t3018999\t1\n+chr1\t3019000\t3019199\t1\n+chr1\t3019200\t3019399\t1\n+chr1\t3019400\t3019599\t1\n+chr1\t3019600\t3019799\t2\n+chr1\t3019800\t3019999\t1\n+chr1\t3020200\t3020399\t3\n+chr1\t3021000\t3021199\t3\n+chr1\t3021200\t3021399\t1\n+chr1\t3021400\t3021599\t4\n+chr1\t3021800\t3021999\t2\n+chr1\t3022000\t3022199\t1\n+chr1\t3022200\t3022399\t1\n+chr1\t3023200\t3023399\t1\n+chr1\t3023400\t3023599\t1\n+chr1\t3023800\t3023999\t2\n+chr1\t3025000\t3025199\t1\n+chr1\t3026800\t3026999\t2\n+chr1\t3027000\t3027199\t2\n+chr1\t3027800\t3027999\t1\n+chr1\t3028400\t3028599\t1\n+chr1\t3028600\t3028799\t1\n+chr1\t3028800\t3028999\t1\n+chr1\t3029000\t3029199\t1\n+chr1\t3035400\t3035599\t1\n+chr1\t3035600\t3035799\t3\n+chr1\t3036000\t3036199\t1\n+chr1\t3036800\t3036999\t1\n+chr1\t3037000\t3037199\t1\n+chr1\t3037200\t3037399\t2\n+chr1\t3037600\t3037799\t1\n+chr1\t3038400\t3038599\t1\n+chr1\t3038600\t3038799\t3\n+chr1\t3038800\t3038999\t2\n+chr1\t3039000\t3039199\t1\n+chr1\t3039400\t3039599\t1\n+chr1\t3039600\t3039799\t2\n+chr1\t3040800\t3040999\t1\n+chr1\t3041000\t3041199\t3\n+chr1\t3041800\t3041999\t2\n+chr1\t3051600\t3051799\t1\n+chr1\t3051800\t3051999\t1\n+chr1\t3052000\t3052199\t1\n+chr1\t3052400\t3052599\t2\n+chr1\t3052800\t3052999\t1\n+chr1\t3053000\t3053199\t1\n+chr1\t3053800\t3053999\t1\n+chr1\t3054800\t3054999\t4\n+chr1\t3055000\t3055199\t1\n+chr1\t3055200\t3055399\t1\n+chr1\t3055800\t3055999\t1\n+chr1\t3062200\t3062399\t1\n+chr1\t3062400\t3062599\t1\n+chr1\t3062600\t3062799\t2\n+chr1\t3063000\t3063199\t1\n+chr1\t3063200\t3063399\t2\n+chr1\t3063400\t3063599\t1\n+chr1\t3063600\t3063799\t1\n+chr1\t3063800\t3063999\t1\n+chr1\t3064800\t3064999\t1\n+chr1\t3065200\t3065399\t1\n+chr1\t3066000\t3066199\t3\n+chr1\t3066200\t3066399\t1\n+chr1\t3066800\t3066999\t1\n+chr1\t3067000\t3067199\t1\n+chr1\t3068800\t3068999\t1\n+chr1\t3069800\t3069999\t1\n+chr1\t3071000\t3071199\t1\n+chr1\t3071200\t3071399\t3\n+chr1\t3072000\t3072199\t1\n+chr1\t3073400\t3073599\t1\n+chr1\t3073600\t3073799\t1\n+chr1\t3073800\t3073999\t1\n+chr1\t3074000\t3074199\t1\n+chr1\t3077400\t3077599\t2\n+chr1\t3078400\t3078599\t1\n+chr1\t3085600\t3085799\t1\n+chr1\t3086200\t3086399\t5\n+chr1\t3086400\t3086599\t4\n+chr1\t3086600\t3086799\t3\n+chr1\t3086800\t3086999\t1\n+chr1\t3087000\t3087199\t2\n+chr1\t3088400\t3088599\t3\n+chr1\t3089400\t3089599\t3\n+chr1\t3089600\t3089799\t1\n+chr1\t3089800\t3089999\t1\n+chr1\t3091600\t3091799\t1\n+chr1\t3091800\t3091999\t1\n+chr1\t3092800\t3092999\t1\n+chr1\t3093000\t3093199\t1\n+chr1\t3093600\t3093799\t2\n+chr1\t3094800\t3094999\t2\n+chr1\t3095200\t3095399\t3\n+chr1\t3095400\t3095599\t2\n+chr1\t3095600\t3095799\t2\n+chr1\t3097000\t3097199\t1\n+chr1\t3104200\t3104399\t1\n+chr1\t3104800\t3104999\t3\n+chr1\t3105000\t3105199\t2\n+chr1\t3105800\t3105999\t2\n+chr1\t3106800\t3106999\t4\n+chr1\t3107000\t3107199\t1\n+chr1\t3107200\t3107399\t1\n+chr1\t3107400\t3107599\t2\n+chr1\t3107600\t3107799\t1\n+chr1\t3108000\t3108199\t1\n+chr1\t3108200\t3108399\t1\n+chr1\t3108400\t3108599\t2\n+chr1\t3108600\t3108799\t1\n+chr1\t3109200\t3109399\t2\n+chr1\t3109400\t3109599\t1\n+chr1\t3110200\t3110399\t3\n+chr1\t3110400\t3110599\t6\n+chr1\t3110600\t3110799\t1\n+chr1\t3110800\t3110999\t2\n+chr1\t3111000\t3111199\t1\n+chr1\t3111200\t3111399\t1\n+chr1\t3111400\t3111599\t1\n+chr1\t3111600\t3111799\t1\n+chr1\t3111800\t3111999\t2\n+chr1\t3112000\t3112199\t1\n+chr1\t3112200\t3112399\t1\n+chr1\t3112400\t3112599\t1\n+chr1\t3112600\t3112799\t2\n+chr1\t3112800\t3112999\t1\n+chr1\t3113200\t3113399\t2\n+chr1\t3113400\t3113599\t2\n+chr1\t3114400\t3114599\t1\n+chr1\t3114800\t3114999\t1\n+chr1\t3115000\t3115199\t1\n+chr1\t3115200\t3115399\t1\n+chr1\t3117800\t3117999\t2\n+chr1\t3118000\t3118199\t1\n+chr1\t3118200\t3118399\t1\n+chr1\t3119000\t3119199\t1\n+chr1\t3119400\t3119599\t1\n+chr1\t3119600\t3119799\t3\n+chr1\t3119800\t3119999\t1\n+chr1\t3120000\t3120199\t1\n+chr1\t3120200\t3120399\t1\n+chr1\t3120600\t3120799\t2\n+chr1\t3121400\t3121599\t1\n+chr1\t3121600\t3121799\t1\n+chr1\t3122200\t3122399\t1\n+chr1\t3122400\t3122599\t2\n+chr1\t3122600\t3122799\t2\n+chr1\t3123200\t3123399\t2\n+chr1\t3123800\t3123999\t1\n+chr1\t3124200\t3124399\t1\n+chr1\t3124600\t3124799\t3\n+chr1\t3124800\t3124999\t1\n+chr1\t3125800\t3125999\t1\n+chr1\t3126400\t312659'..b'8600\t5648799\t2\n+chr1\t5648800\t5648999\t2\n+chr1\t5649000\t5649199\t1\n+chr1\t5649400\t5649599\t3\n+chr1\t5649600\t5649799\t2\n+chr1\t5649800\t5649999\t6\n+chr1\t5650000\t5650199\t2\n+chr1\t5650600\t5650799\t2\n+chr1\t5650800\t5650999\t1\n+chr1\t5651400\t5651599\t1\n+chr1\t5651600\t5651799\t4\n+chr1\t5652000\t5652199\t2\n+chr1\t5652200\t5652399\t2\n+chr1\t5652800\t5652999\t3\n+chr1\t5653400\t5653599\t6\n+chr1\t5653600\t5653799\t2\n+chr1\t5653800\t5653999\t1\n+chr1\t5654200\t5654399\t1\n+chr1\t5654600\t5654799\t1\n+chr1\t5654800\t5654999\t1\n+chr1\t5655800\t5655999\t4\n+chr1\t5656000\t5656199\t1\n+chr1\t5656200\t5656399\t1\n+chr1\t5657200\t5657399\t1\n+chr1\t5657600\t5657799\t3\n+chr1\t5657800\t5657999\t1\n+chr1\t5658400\t5658599\t1\n+chr1\t5659200\t5659399\t2\n+chr1\t5660400\t5660599\t3\n+chr1\t5660800\t5660999\t1\n+chr1\t5661400\t5661599\t1\n+chr1\t5662400\t5662599\t2\n+chr1\t5662600\t5662799\t1\n+chr1\t5663600\t5663799\t2\n+chr1\t5663800\t5663999\t1\n+chr1\t5664600\t5664799\t2\n+chr1\t5665000\t5665199\t1\n+chr1\t5665800\t5665999\t1\n+chr1\t5666400\t5666599\t1\n+chr1\t5666600\t5666799\t3\n+chr1\t5666800\t5666999\t1\n+chr1\t5667800\t5667999\t2\n+chr1\t5674000\t5674199\t1\n+chr1\t5675000\t5675199\t1\n+chr1\t5676200\t5676399\t1\n+chr1\t5676600\t5676799\t1\n+chr1\t5677200\t5677399\t1\n+chr1\t5677800\t5677999\t1\n+chr1\t5679000\t5679199\t1\n+chr1\t5679200\t5679399\t4\n+chr1\t5679400\t5679599\t2\n+chr1\t5679600\t5679799\t1\n+chr1\t5680000\t5680199\t1\n+chr1\t5680200\t5680399\t2\n+chr1\t5680400\t5680599\t2\n+chr1\t5680800\t5680999\t2\n+chr1\t5682800\t5682999\t1\n+chr1\t5688000\t5688199\t1\n+chr1\t5688200\t5688399\t1\n+chr1\t5688400\t5688599\t1\n+chr1\t5688600\t5688799\t1\n+chr1\t5688800\t5688999\t1\n+chr1\t5689000\t5689199\t1\n+chr1\t5689200\t5689399\t1\n+chr1\t5689400\t5689599\t1\n+chr1\t5689800\t5689999\t1\n+chr1\t5690200\t5690399\t1\n+chr1\t5690800\t5690999\t2\n+chr1\t5694600\t5694799\t1\n+chr1\t5694800\t5694999\t2\n+chr1\t5695000\t5695199\t1\n+chr1\t5695400\t5695599\t3\n+chr1\t5696000\t5696199\t1\n+chr1\t5696600\t5696799\t1\n+chr1\t5696800\t5696999\t3\n+chr1\t5697000\t5697199\t1\n+chr1\t5697200\t5697399\t2\n+chr1\t5698000\t5698199\t1\n+chr1\t5698200\t5698399\t2\n+chr1\t5698800\t5698999\t2\n+chr1\t5699400\t5699599\t1\n+chr1\t5700000\t5700199\t1\n+chr1\t5700400\t5700599\t2\n+chr1\t5703600\t5703799\t1\n+chr1\t5704600\t5704799\t1\n+chr1\t5705000\t5705199\t3\n+chr1\t5705600\t5705799\t1\n+chr1\t5706200\t5706399\t5\n+chr1\t5706400\t5706599\t1\n+chr1\t5706800\t5706999\t1\n+chr1\t5707200\t5707399\t2\n+chr1\t5707800\t5707999\t2\n+chr1\t5708400\t5708599\t1\n+chr1\t5708600\t5708799\t1\n+chr1\t5709000\t5709199\t2\n+chr1\t5709600\t5709799\t1\n+chr1\t5710200\t5710399\t1\n+chr1\t5711400\t5711599\t1\n+chr1\t5712400\t5712599\t1\n+chr1\t5712600\t5712799\t2\n+chr1\t5712800\t5712999\t1\n+chr1\t5713600\t5713799\t1\n+chr1\t5714200\t5714399\t1\n+chr1\t5714400\t5714599\t1\n+chr1\t5714600\t5714799\t3\n+chr1\t5715600\t5715799\t2\n+chr1\t5715800\t5715999\t1\n+chr1\t5716200\t5716399\t4\n+chr1\t5717000\t5717199\t1\n+chr1\t5717400\t5717599\t2\n+chr1\t5717600\t5717799\t1\n+chr1\t5718200\t5718399\t1\n+chr1\t5718400\t5718599\t2\n+chr1\t5718600\t5718799\t1\n+chr1\t5718800\t5718999\t3\n+chr1\t5719600\t5719799\t1\n+chr1\t5720600\t5720799\t1\n+chr1\t5721400\t5721599\t1\n+chr1\t5721600\t5721799\t1\n+chr1\t5722200\t5722399\t2\n+chr1\t5722600\t5722799\t1\n+chr1\t5723200\t5723399\t3\n+chr1\t5724200\t5724399\t1\n+chr1\t5724400\t5724599\t1\n+chr1\t5725400\t5725599\t2\n+chr1\t5725800\t5725999\t1\n+chr1\t5726000\t5726199\t1\n+chr1\t5726200\t5726399\t3\n+chr1\t5726400\t5726599\t5\n+chr1\t5726800\t5726999\t1\n+chr1\t5727200\t5727399\t1\n+chr1\t5727400\t5727599\t1\n+chr1\t5727600\t5727799\t3\n+chr1\t5728000\t5728199\t1\n+chr1\t5728600\t5728799\t1\n+chr1\t5728800\t5728999\t1\n+chr1\t5729600\t5729799\t1\n+chr1\t5730000\t5730199\t2\n+chr1\t5735000\t5735199\t1\n+chr1\t5738200\t5738399\t1\n+chr1\t5741800\t5741999\t2\n+chr1\t5742200\t5742399\t2\n+chr1\t5742400\t5742599\t1\n+chr1\t5742600\t5742799\t1\n+chr1\t5742800\t5742999\t1\n+chr1\t5743400\t5743599\t1\n+chr1\t5743800\t5743999\t2\n+chr1\t5744200\t5744399\t1\n+chr1\t5744600\t5744799\t2\n+chr1\t5744800\t5744999\t2\n+chr1\t5745600\t5745799\t2\n+chr1\t5745800\t5745999\t2\n+chr1\t5746000\t5746199\t2\n+chr1\t5746400\t5746599\t2\n+chr1\t5746600\t5746799\t2\n+chr1\t5746800\t5746999\t1\n+chr1\t5747000\t5747199\t1\n+chr1\t5747800\t5747999\t1\n+chr1\t5749400\t5749599\t1\n+chr1\t5750000\t5750199\t1\n+chr1\t5750400\t5750599\t1\n+chr1\t5751400\t5751599\t2\n+chr1\t5751600\t5751799\t2\n+chr1\t5751800\t5751999\t2\n+chr1\t5752400\t5752599\t2\n+chr1\t5753000\t5753199\t1\n+chr1\t5754400\t5754599\t1\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_2_output_log_file.contains --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_output_log_file.contains Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,287 @@\n+#############################################\n+###### SICER v1.1 ######\n+#############################################\n+Input library directory:\n+ChIP library: input_bed_file.bed\n+Control library: input_control_file.bed\n+Output directory:\n+Species: mm8\n+Threshold for redundancy allowed for chip reads: 1\n+Threshold for redundancy allowed for control reads: 1\n+Window size: 200 bps\n+Fragment size: 150 bps. The shift for reads is half of 150\n+Effective genome size as a fraction of the reference genome of mm8: 0.740000\n+Gap size: 600 bps\n+Evalue for identification of candidate islands that exhibit clustering: 1000\n+False discovery rate controlling significance: 0.01\n+Preprocess the raw input_bed_file file to remove redundancy with threshold 1...\n+chr1 \tPlus reads: 4989 \tRetained plus reads: 4935 ;\tMinus reads: 5011 \tRetained minus reads: 4963\n+chr2 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr3 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr4 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr5 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr6 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr7 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr8 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr9 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr10 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr11 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr12 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr13 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr14 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr15 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr16 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr17 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr18 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr19 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chrX \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chrY \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chrM \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+Preprocess the raw input_control_file file to remove redundancy with threshold 1...\n+chr1 \tPlus reads: 4980 \tRetained plus reads: 4937 ;\tMinus reads: 5020 \tRetained minus reads: 4959\n+chr2 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr3 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr4 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr5 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr6 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr7 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr8 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr9 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr10 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr11 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr12 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr13 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr14 \tPlus reads: 0 \tRetained plus rea'..b'chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_2_test-W200-G600-FDR0.01-island.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_test-W200-G600-FDR0.01-island.bed Wed Oct 24 11:31:03 2018 -0400 |
| b |
| @@ -0,0 +1,184 @@ +chr1 3023200 3023999 4 +chr1 3088400 3088599 3 +chr1 3138800 3139399 5 +chr1 3165800 3165999 2 +chr1 3273000 3273399 2 +chr1 3294800 3295199 2 +chr1 3672800 3672999 4 +chr1 3810800 3811199 2 +chr1 3872600 3873599 2 +chr1 3976600 3976799 2 +chr1 4122200 4122399 2 +chr1 4232600 4232799 2 +chr1 4278600 4279199 6 +chr1 4323600 4327199 59 +chr1 4334200 4339399 83 +chr1 4392400 4392599 3 +chr1 4456400 4456799 2 +chr1 4625200 4625599 3 +chr1 4627200 4627399 2 +chr1 4668600 4670399 15 +chr1 4673800 4675199 7 +chr1 4676200 4700999 114 +chr1 4708400 4718199 71 +chr1 4719000 4722399 8 +chr1 4726200 4727999 12 +chr1 4729000 4746399 127 +chr1 4747200 4755999 66 +chr1 4756800 4762199 264 +chr1 4763200 4779399 145 +chr1 4780800 4781799 5 +chr1 4784200 4785599 6 +chr1 4786800 4787799 7 +chr1 4789400 4793399 31 +chr1 4794400 4797999 18 +chr1 4799000 4808199 50 +chr1 4809600 4818399 58 +chr1 4819600 4825999 35 +chr1 4827000 4827799 3 +chr1 4828600 4839599 64 +chr1 4840400 4853599 67 +chr1 4854400 4863599 49 +chr1 4864800 4866599 10 +chr1 4867600 4867799 2 +chr1 4868600 4869799 4 +chr1 4872000 4875199 25 +chr1 4876600 4887799 51 +chr1 4889400 4895799 50 +chr1 4896600 4907399 66 +chr1 4908200 4910999 22 +chr1 4912200 4912399 2 +chr1 4913400 4923799 64 +chr1 4924800 4931599 50 +chr1 4932400 4934999 22 +chr1 4935800 4937999 15 +chr1 4944800 4948799 22 +chr1 4952400 4963999 86 +chr1 4965800 4970599 31 +chr1 4975200 4975999 6 +chr1 4979800 4981999 16 +chr1 4982800 4982999 2 +chr1 4984400 4986199 6 +chr1 4991200 5000799 56 +chr1 5002000 5025799 121 +chr1 5032600 5035199 7 +chr1 5038800 5040199 6 +chr1 5044400 5048399 21 +chr1 5054200 5057799 24 +chr1 5058800 5063399 34 +chr1 5064200 5067599 19 +chr1 5074000 5079799 35 +chr1 5081600 5098199 89 +chr1 5099000 5100799 4 +chr1 5106000 5112799 37 +chr1 5113600 5117199 17 +chr1 5118800 5120799 10 +chr1 5122400 5123199 9 +chr1 5124200 5127599 14 +chr1 5128400 5136199 56 +chr1 5137200 5139599 11 +chr1 5140400 5144599 14 +chr1 5145400 5145599 3 +chr1 5146800 5147399 2 +chr1 5148400 5156199 45 +chr1 5160000 5162599 9 +chr1 5164200 5164799 6 +chr1 5166000 5169399 22 +chr1 5170200 5171599 4 +chr1 5172600 5175199 24 +chr1 5176200 5180599 41 +chr1 5187000 5187599 3 +chr1 5193800 5205999 83 +chr1 5206800 5219199 78 +chr1 5220000 5227799 55 +chr1 5229400 5231599 13 +chr1 5232400 5233199 5 +chr1 5234200 5238399 17 +chr1 5239800 5241199 10 +chr1 5247800 5251999 28 +chr1 5253200 5258199 25 +chr1 5264400 5265399 8 +chr1 5266200 5266399 2 +chr1 5267200 5268199 10 +chr1 5269800 5278799 43 +chr1 5279600 5280999 8 +chr1 5282800 5284599 7 +chr1 5285600 5287199 14 +chr1 5288200 5299399 47 +chr1 5301600 5302599 4 +chr1 5303400 5308999 36 +chr1 5310000 5311599 15 +chr1 5312400 5318599 29 +chr1 5323400 5333999 41 +chr1 5336200 5336799 3 +chr1 5338400 5338999 3 +chr1 5348600 5349199 6 +chr1 5353800 5356999 16 +chr1 5358400 5362799 15 +chr1 5363800 5365599 12 +chr1 5369400 5375799 29 +chr1 5376600 5378999 6 +chr1 5379800 5383199 11 +chr1 5384000 5384999 8 +chr1 5385800 5388799 15 +chr1 5391800 5398399 20 +chr1 5399600 5399799 2 +chr1 5400600 5404399 16 +chr1 5405200 5405799 2 +chr1 5407400 5413799 32 +chr1 5420800 5421199 3 +chr1 5428000 5433199 24 +chr1 5434000 5434599 4 +chr1 5439600 5440599 6 +chr1 5442000 5444999 15 +chr1 5446200 5446999 3 +chr1 5447800 5449199 11 +chr1 5451000 5458199 27 +chr1 5470600 5470999 3 +chr1 5475400 5475799 5 +chr1 5476600 5476799 2 +chr1 5478200 5478999 3 +chr1 5480800 5482199 3 +chr1 5483400 5483799 3 +chr1 5484800 5488999 13 +chr1 5492600 5493999 5 +chr1 5496000 5498999 15 +chr1 5501800 5512799 52 +chr1 5514400 5516599 11 +chr1 5522400 5524599 8 +chr1 5525800 5531199 18 +chr1 5532200 5535999 21 +chr1 5539400 5541799 11 +chr1 5548200 5551399 17 +chr1 5560800 5561599 3 +chr1 5563400 5565399 6 +chr1 5568400 5573599 33 +chr1 5576200 5590399 71 +chr1 5591200 5592399 5 +chr1 5593200 5613599 89 +chr1 5614400 5617799 22 +chr1 5619800 5620599 3 +chr1 5621400 5621999 6 +chr1 5624600 5625399 2 +chr1 5632000 5637799 20 +chr1 5643200 5643399 2 +chr1 5646400 5654999 60 +chr1 5655800 5656399 6 +chr1 5657200 5659399 8 +chr1 5660400 5661599 5 +chr1 5662400 5662799 3 +chr1 5663600 5666999 12 +chr1 5667800 5667999 2 +chr1 5676200 5677999 4 +chr1 5679000 5680999 15 +chr1 5688000 5690999 12 +chr1 5694600 5700599 24 +chr1 5704600 5710399 22 +chr1 5712400 5714799 10 +chr1 5715600 5719799 19 +chr1 5720600 5723399 9 +chr1 5724200 5724599 2 +chr1 5725400 5730199 24 +chr1 5741800 5747999 28 +chr1 5749400 5750599 3 +chr1 5751400 5753199 9 |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_2_test-W200-G600-islands-summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_test-W200-G600-islands-summary Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,417 @@\n+chr1\t3002000\t3005999\t13\t23\t1\t0.5651031829\t1\n+chr1\t3017800\t3022399\t26\t32\t1\t0.812335825419\t1\n+chr1\t3023200\t3023999\t4\t0\t9.015676528976497e-15\t988.396419034\t2.8056247108829846e-14\n+chr1\t3026800\t3029199\t9\t6\t0.08400751662009776\t1.49969690847\t0.17088358258819886\n+chr1\t3035400\t3039799\t20\t37\t1\t0.540431318366\t1\n+chr1\t3040800\t3041999\t6\t3\t0.03353910807935691\t1.99959587796\t0.07399898449254937\n+chr1\t3051600\t3053999\t8\t17\t1\t0.470493147754\t1\n+chr1\t3054800\t3055999\t7\t8\t1\t0.874823196605\t1\n+chr1\t3062200\t3063999\t10\t12\t1\t0.833164949148\t1\n+chr1\t3064800\t3067199\t8\t20\t1\t0.399919175591\t1\n+chr1\t3071000\t3072199\t5\t11\t1\t0.454453608626\t1\n+chr1\t3073400\t3074199\t4\t3\t0.18483864411731604\t1.33306391864\t0.36616491494974246\n+chr1\t3077400\t3077599\t2\t2\t1\t0.999797938978\t1\n+chr1\t3085600\t3087199\t16\t23\t1\t0.695511609724\t1\n+chr1\t3088400\t3088599\t3\t0\t4.3622705445725773e-14\t2965.1892571\t1.327785997873551e-13\n+chr1\t3089400\t3089999\t5\t4\t0.21499597452270133\t1.24974742372\t0.4169921924463556\n+chr1\t3091600\t3091999\t2\t2\t1\t0.999797938978\t1\n+chr1\t3092800\t3093799\t4\t11\t1\t0.363562886901\t1\n+chr1\t3094800\t3095799\t9\t12\t1\t0.749848454233\t1\n+chr1\t3104200\t3105999\t8\t19\t1\t0.420967553254\t1\n+chr1\t3106800\t3113599\t45\t48\t1\t0.937310567791\t1\n+chr1\t3114400\t3115399\t4\t9\t1\t0.444354639546\t1\n+chr1\t3117800\t3124999\t29\t49\t1\t0.591717147558\t1\n+chr1\t3125800\t3127399\t5\t18\t1\t0.277721649716\t1\n+chr1\t3131000\t3132799\t4\t3\t0.18483864411731604\t1.33306391864\t0.36616491494974246\n+chr1\t3138800\t3139399\t5\t1\t0.0005948046440552834\t4.99898969489\t0.0013553745167817113\n+chr1\t3155600\t3159999\t22\t28\t1\t0.785555523482\t1\n+chr1\t3160800\t3163399\t13\t19\t1\t0.684072274037\t1\n+chr1\t3165800\t3165999\t2\t0\t1.7247482912266767e-10\t1976.79283807\t4.385488033180025e-10\n+chr1\t3168600\t3169399\t7\t10\t1\t0.699858557284\t1\n+chr1\t3172600\t3175599\t10\t11\t1\t0.908907217252\t1\n+chr1\t3179600\t3182599\t14\t21\t1\t0.666531959318\t1\n+chr1\t3185600\t3189799\t25\t52\t1\t0.480672086047\t1\n+chr1\t3191200\t3193399\t11\t16\t1\t0.687361083047\t1\n+chr1\t3194200\t3199599\t22\t48\t1\t0.458240722031\t1\n+chr1\t3201600\t3216199\t85\t123\t1\t0.690917274903\t1\n+chr1\t3217000\t3220599\t26\t24\t0.2965294975029217\t1.08311443389\t0.5672146810032952\n+chr1\t3226400\t3227399\t2\t1\t0.0803385753872012\t1.99959587796\t0.16834766802242662\n+chr1\t3236800\t3249399\t66\t116\t1\t0.568850551487\t1\n+chr1\t3251000\t3251599\t2\t2\t1\t0.999797938978\t1\n+chr1\t3254400\t3260799\t32\t49\t1\t0.652929266271\t1\n+chr1\t3273000\t3273399\t2\t0\t1.378752111611657e-09\t988.396419034\t3.323350465561046e-09\n+chr1\t3274600\t3275199\t5\t2\t0.01657820037651204\t2.49949484744\t0.03706761156571325\n+chr1\t3276600\t3277999\t5\t14\t1\t0.357070692492\t1\n+chr1\t3279800\t3281399\t12\t10\t0.20863511511727137\t1.19975752677\t0.4074980936950921\n+chr1\t3283600\t3292999\t39\t79\t1\t0.493571134432\t1\n+chr1\t3294800\t3295199\t2\t0\t1.378752111611657e-09\t988.396419034\t3.323350465561046e-09\n+chr1\t3301600\t3302799\t7\t11\t1\t0.636235052077\t1\n+chr1\t3309000\t3318399\t51\t100\t1\t0.509896948879\t1\n+chr1\t3320400\t3320999\t3\t4\t1\t0.749848454233\t1\n+chr1\t3322200\t3327199\t30\t36\t1\t0.833164949148\t1\n+chr1\t3334400\t3335399\t4\t6\t1\t0.666531959318\t1\n+chr1\t3342000\t3347799\t22\t36\t1\t0.610987629375\t1\n+chr1\t3348600\t3362399\t76\t114\t1\t0.666531959318\t1\n+chr1\t3363400\t3367599\t14\t32\t1\t0.437411598303\t1\n+chr1\t3368600\t3380399\t46\t83\t1\t0.554104881843\t1\n+chr1\t3381200\t3392799\t52\t90\t1\t0.577661031409\t1\n+chr1\t3395000\t3397799\t15\t26\t1\t0.576806503256\t1\n+chr1\t3398600\t3400599\t8\t16\t1\t0.499898969489\t1\n+chr1\t3401800\t3403799\t14\t24\t1\t0.583215464404\t1\n+chr1\t3404600\t3410999\t33\t66\t1\t0.499898969489\t1\n+chr1\t3411800\t3413999\t13\t15\t1\t0.866491547114\t1\n+chr1\t3415200\t3420799\t23\t45\t1\t0.511007835477\t1\n+chr1\t3421600\t3433999\t50\t106\t1\t0.471602801405\t1\n+chr1\t3435400\t3437199\t10\t15\t1\t0.666531959318\t1\n+chr1\t3438000\t3439999\t14\t16\t1\t0.874823196605\t1\n+chr1\t3440800\t3459399\t83\t149\t1\t0.556934422383\t1\n+chr1\t3460800\t3462999\t20\t14\t0.047989370254747664\t1.42828276997\t0.10422691352203008\n+chr1\t3465200\t3466599\t6\t14\t1\t0.42848483099\t1\n+chr1\t3467400\t3475599\t32\t65\t1\t0.492208216112\t1\n+chr1\t3477800\t3485399\t36\t56\t1\t0.642727246486\t1\n+chr1\t3486800\t3490799\t20\t51\t1\t0.392077623128\t1\n+chr1\t3493600\t3503799\t40\t77\t1\t0.519375552716\t1\n+chr1\t3504600\t350'..b'5475400\t5475799\t5\t0\t9.517157714109633e-20\t2470.99104759\t3.252995710478456e-19\n+chr1\t5476600\t5476799\t2\t0\t1.7247482912266767e-10\t1976.79283807\t4.385488033180025e-10\n+chr1\t5478200\t5478999\t3\t0\t1.1140331332442305e-11\t741.297314276\t3.036286382763687e-11\n+chr1\t5480800\t5482199\t3\t0\t1.0423077210918807e-10\t423.5984653\t2.768422418441492e-10\n+chr1\t5483400\t5483799\t3\t0\t6.973986184598647e-13\t1482.594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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_2_test-W200-G600-islands-summary-FDR0.01 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_test-W200-G600-islands-summary-FDR0.01 Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,184 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_2_test-W200-G600.scoreisland --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_test-W200-G600.scoreisland Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,417 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_3_test-W200-G600-FDR0.01-island.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_test-W200-G600-FDR0.01-island.bed Wed Oct 24 11:31:03 2018 -0400 |
| b |
| @@ -0,0 +1,184 @@ +chr1 3023200 3024000 4 +chr1 3088400 3088600 3 +chr1 3138800 3139400 5 +chr1 3165800 3166000 2 +chr1 3273000 3273400 2 +chr1 3294800 3295200 2 +chr1 3672800 3673000 4 +chr1 3810800 3811200 2 +chr1 3872600 3873600 2 +chr1 3976600 3976800 2 +chr1 4122200 4122400 2 +chr1 4232600 4232800 2 +chr1 4278600 4279200 6 +chr1 4323600 4327200 59 +chr1 4334200 4339400 83 +chr1 4392400 4392600 3 +chr1 4456400 4456800 2 +chr1 4625200 4625600 3 +chr1 4627200 4627400 2 +chr1 4668600 4670400 15 +chr1 4673800 4675200 7 +chr1 4676200 4701000 114 +chr1 4708400 4718200 71 +chr1 4719000 4722400 8 +chr1 4726200 4728000 12 +chr1 4729000 4746400 127 +chr1 4747200 4756000 66 +chr1 4756800 4762200 264 +chr1 4763200 4779400 145 +chr1 4780800 4781800 5 +chr1 4784200 4785600 6 +chr1 4786800 4787800 7 +chr1 4789400 4793400 31 +chr1 4794400 4798000 18 +chr1 4799000 4808200 50 +chr1 4809600 4818400 58 +chr1 4819600 4826000 35 +chr1 4827000 4827800 3 +chr1 4828600 4839600 64 +chr1 4840400 4853600 67 +chr1 4854400 4863600 49 +chr1 4864800 4866600 10 +chr1 4867600 4867800 2 +chr1 4868600 4869800 4 +chr1 4872000 4875200 25 +chr1 4876600 4887800 51 +chr1 4889400 4895800 50 +chr1 4896600 4907400 66 +chr1 4908200 4911000 22 +chr1 4912200 4912400 2 +chr1 4913400 4923800 64 +chr1 4924800 4931600 50 +chr1 4932400 4935000 22 +chr1 4935800 4938000 15 +chr1 4944800 4948800 22 +chr1 4952400 4964000 86 +chr1 4965800 4970600 31 +chr1 4975200 4976000 6 +chr1 4979800 4982000 16 +chr1 4982800 4983000 2 +chr1 4984400 4986200 6 +chr1 4991200 5000800 56 +chr1 5002000 5025800 121 +chr1 5032600 5035200 7 +chr1 5038800 5040200 6 +chr1 5044400 5048400 21 +chr1 5054200 5057800 24 +chr1 5058800 5063400 34 +chr1 5064200 5067600 19 +chr1 5074000 5079800 35 +chr1 5081600 5098200 89 +chr1 5099000 5100800 4 +chr1 5106000 5112800 37 +chr1 5113600 5117200 17 +chr1 5118800 5120800 10 +chr1 5122400 5123200 9 +chr1 5124200 5127600 14 +chr1 5128400 5136200 56 +chr1 5137200 5139600 11 +chr1 5140400 5144600 14 +chr1 5145400 5145600 3 +chr1 5146800 5147400 2 +chr1 5148400 5156200 45 +chr1 5160000 5162600 9 +chr1 5164200 5164800 6 +chr1 5166000 5169400 22 +chr1 5170200 5171600 4 +chr1 5172600 5175200 24 +chr1 5176200 5180600 41 +chr1 5187000 5187600 3 +chr1 5193800 5206000 83 +chr1 5206800 5219200 78 +chr1 5220000 5227800 55 +chr1 5229400 5231600 13 +chr1 5232400 5233200 5 +chr1 5234200 5238400 17 +chr1 5239800 5241200 10 +chr1 5247800 5252000 28 +chr1 5253200 5258200 25 +chr1 5264400 5265400 8 +chr1 5266200 5266400 2 +chr1 5267200 5268200 10 +chr1 5269800 5278800 43 +chr1 5279600 5281000 8 +chr1 5282800 5284600 7 +chr1 5285600 5287200 14 +chr1 5288200 5299400 47 +chr1 5301600 5302600 4 +chr1 5303400 5309000 36 +chr1 5310000 5311600 15 +chr1 5312400 5318600 29 +chr1 5323400 5334000 41 +chr1 5336200 5336800 3 +chr1 5338400 5339000 3 +chr1 5348600 5349200 6 +chr1 5353800 5357000 16 +chr1 5358400 5362800 15 +chr1 5363800 5365600 12 +chr1 5369400 5375800 29 +chr1 5376600 5379000 6 +chr1 5379800 5383200 11 +chr1 5384000 5385000 8 +chr1 5385800 5388800 15 +chr1 5391800 5398400 20 +chr1 5399600 5399800 2 +chr1 5400600 5404400 16 +chr1 5405200 5405800 2 +chr1 5407400 5413800 32 +chr1 5420800 5421200 3 +chr1 5428000 5433200 24 +chr1 5434000 5434600 4 +chr1 5439600 5440600 6 +chr1 5442000 5445000 15 +chr1 5446200 5447000 3 +chr1 5447800 5449200 11 +chr1 5451000 5458200 27 +chr1 5470600 5471000 3 +chr1 5475400 5475800 5 +chr1 5476600 5476800 2 +chr1 5478200 5479000 3 +chr1 5480800 5482200 3 +chr1 5483400 5483800 3 +chr1 5484800 5489000 13 +chr1 5492600 5494000 5 +chr1 5496000 5499000 15 +chr1 5501800 5512800 52 +chr1 5514400 5516600 11 +chr1 5522400 5524600 8 +chr1 5525800 5531200 18 +chr1 5532200 5536000 21 +chr1 5539400 5541800 11 +chr1 5548200 5551400 17 +chr1 5560800 5561600 3 +chr1 5563400 5565400 6 +chr1 5568400 5573600 33 +chr1 5576200 5590400 71 +chr1 5591200 5592400 5 +chr1 5593200 5613600 89 +chr1 5614400 5617800 22 +chr1 5619800 5620600 3 +chr1 5621400 5622000 6 +chr1 5624600 5625400 2 +chr1 5632000 5637800 20 +chr1 5643200 5643400 2 +chr1 5646400 5655000 60 +chr1 5655800 5656400 6 +chr1 5657200 5659400 8 +chr1 5660400 5661600 5 +chr1 5662400 5662800 3 +chr1 5663600 5667000 12 +chr1 5667800 5668000 2 +chr1 5676200 5678000 4 +chr1 5679000 5681000 15 +chr1 5688000 5691000 12 +chr1 5694600 5700600 24 +chr1 5704600 5710400 22 +chr1 5712400 5714800 10 +chr1 5715600 5719800 19 +chr1 5720600 5723400 9 +chr1 5724200 5724600 2 +chr1 5725400 5730200 24 +chr1 5741800 5748000 28 +chr1 5749400 5750600 3 +chr1 5751400 5753200 9 |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_3_test-W200-G600-islands-summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_test-W200-G600-islands-summary Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,417 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62855\t2.00562223377768e-12\n+chr1\t5484800\t5489000\t13\t0\t4.295500428190877e-35\t611.864449878\t1.9902485317284396e-34\n+chr1\t5492600\t5494000\t5\t0\t1.7419375160618114e-16\t705.997442167\t5.502938971195268e-16\n+chr1\t5496000\t5499000\t15\t0\t3.730258228178575e-43\t988.396419034\t1.9203921989511924e-42\n+chr1\t5501800\t5512800\t52\t0\t7.132269809998869e-137\t934.483887087\t1.1896626043078114e-135\n+chr1\t5514400\t5516600\t11\t0\t7.460018523373669e-33\t988.396419034\t3.3093911960072556e-32\n+chr1\t5522400\t5524600\t8\t0\t7.14563606488997e-24\t718.833759298\t2.721214830190975e-23\n+chr1\t5525800\t5531200\t18\t0\t1.5698376164295928e-47\t658.930946023\t9.220032197903385e-47\n+chr1\t5532200\t5536000\t21\t0\t1.532292532223248e-59\t1092.43814735\t1.0649433098951573e-58\n+chr1\t5539400\t5541800\t11\t0\t2.1173715280854036e-32\t906.030050781\t9.245486148812704e-32\n+chr1\t5548200\t5551400\t17\t0\t8.961848488727932e-49\t1050.17119522\t5.495721793822864e-48\n+chr1\t5560800\t5561600\t3\t0\t1.1140331332442305e-11\t741.297314276\t3.036286382763687e-11\n+chr1\t5563400\t5565400\t6\t0\t2.134061357888946e-18\t593.03785142\t7.062726874918179e-18\n+chr1\t5568400\t5573600\t33\t0\t6.312072510115897e-93\t1254.50314724\t6.749062145431613e-92\n+chr1\t5576200\t5590400\t71\t0\t6.883227538070833e-187\t988.396419034\t2.3919215694796144e-185\n+chr1\t5591200\t5592400\t5\t0\t6.913984684758452e-17\t823.663682528\t2.2092962555894825e-16\n+chr1\t5593200\t5613600\t89\t0\t1.0326417164555111e-227\t862.424326412\t4.784573286243868e-226\n+chr1\t5614400\t5617800\t22\t0\t9.937008604835146e-64\t1279.10124816\t7.206491457767402e-63\n+chr1\t5619800\t5620600\t3\t0\t1.1140331332442305e-11\t741.297314276\t3.036286382763687e-11\n+chr1\t5621400\t5622000\t6\t0\t4.696201482198409e-22\t1976.79283807\t1.6955117039625425e-21\n+chr1\t5624600\t5625400\t2\t0\t1.1013292864775921e-08\t494.198209517\t2.5800804070851458e-08\n+chr1\t5632000\t5637800\t20\t0\t1.2482361924057113e-52\t681.652702782\t8.133038941143462e-52\n+chr1\t5643200\t5643400\t2\t0\t1.7247482912266767e-10\t1976.79283807\t4.385488033180025e-10\n+chr1\t5646400\t5655000\t60\t0\t1.6853150149323002e-167\t1379.157794\t3.9043131179264954e-166\n+chr1\t5655800\t5656400\t6\t0\t4.696201482198409e-22\t1976.79283807\t1.6955117039625425e-21\n+chr1\t5657200\t5659400\t8\t0\t7.14563606488997e-24\t718.833759298\t2.721214830190975e-23\n+chr1\t5660400\t5661600\t5\t0\t6.913984684758452e-17\t823.663682528\t2.2092962555894825e-16\n+chr1\t5662400\t5662800\t3\t0\t6.973986184598647e-13\t1482.59462855\t2.00562223377768e-12\n+chr1\t5663600\t5667000\t12\t0\t1.8218586984886047e-33\t697.691589906\t8.168979325481164e-33\n+chr1\t5667800\t5668000\t2\t0\t1.7247482912266767e-10\t1976.79283807\t4.385488033180025e-10\n+chr1\t5676200\t5678000\t4\t0\t5.177026577521231e-13\t439.287297349\t1.5256679030574933e-12\n+chr1\t5679000\t5681000\t15\t0\t5.706192234932869e-46\t1482.59462855\t3.172642882622675e-45\n+chr1\t5688000\t5691000\t12\t0\t3.5865842165111983e-34\t790.717135227\t1.6435226574562304e-33\n+chr1\t5694600\t5700600\t24\t0\t7.102840834795353e-64\t790.717135227\t5.289079693052968e-63\n+chr1\t5704600\t5710400\t22\t0\t2.1233989699202116e-58\t749.81797306\t1.428157049123755e-57\n+chr1\t5712400\t5714800\t10\t0\t2.092965441327545e-29\t823.663682528\t8.556535186603787e-29\n+chr1\t5715600\t5719800\t19\t0\t1.4153060203967038e-52\t894.263426745\t9.079732469314238e-52\n+chr1\t5720600\t5723400\t9\t0\t8.843286933772389e-26\t635.397697951\t3.446402477928118e-25\n+chr1\t5724200\t5724600\t2\t0\t1.378752111611657e-09\t988.396419034\t3.323350465561046e-09\n+chr1\t5725400\t5730200\t24\t0\t2.699085353898604e-66\t988.396419034\t2.1236199859919203e-65\n+chr1\t5741800\t5748000\t28\t0\t2.733881234553177e-75\t892.745152676\t2.4783227713232063e-74\n+chr1\t5749400\t5750600\t3\t0\t5.630672055656213e-11\t494.198209517\t1.5051219533388723e-10\n+chr1\t5751400\t5753200\t9\t0\t1.0709162757052508e-27\t988.396419034\t4.335651329796986e-27\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_3_test-W200-G600-islands-summary-FDR0.01 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_test-W200-G600-islands-summary-FDR0.01 Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,184 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1195268e-16\n+chr1\t5496000\t5499000\t15\t0\t3.730258228178575e-43\t988.396419034\t1.9203921989511924e-42\n+chr1\t5501800\t5512800\t52\t0\t7.132269809998869e-137\t934.483887087\t1.1896626043078114e-135\n+chr1\t5514400\t5516600\t11\t0\t7.460018523373669e-33\t988.396419034\t3.3093911960072556e-32\n+chr1\t5522400\t5524600\t8\t0\t7.14563606488997e-24\t718.833759298\t2.721214830190975e-23\n+chr1\t5525800\t5531200\t18\t0\t1.5698376164295928e-47\t658.930946023\t9.220032197903385e-47\n+chr1\t5532200\t5536000\t21\t0\t1.532292532223248e-59\t1092.43814735\t1.0649433098951573e-58\n+chr1\t5539400\t5541800\t11\t0\t2.1173715280854036e-32\t906.030050781\t9.245486148812704e-32\n+chr1\t5548200\t5551400\t17\t0\t8.961848488727932e-49\t1050.17119522\t5.495721793822864e-48\n+chr1\t5560800\t5561600\t3\t0\t1.1140331332442305e-11\t741.297314276\t3.036286382763687e-11\n+chr1\t5563400\t5565400\t6\t0\t2.134061357888946e-18\t593.03785142\t7.062726874918179e-18\n+chr1\t5568400\t5573600\t33\t0\t6.312072510115897e-93\t1254.50314724\t6.749062145431613e-92\n+chr1\t5576200\t5590400\t71\t0\t6.883227538070833e-187\t988.396419034\t2.3919215694796144e-185\n+chr1\t5591200\t5592400\t5\t0\t6.913984684758452e-17\t823.663682528\t2.2092962555894825e-16\n+chr1\t5593200\t5613600\t89\t0\t1.0326417164555111e-227\t862.424326412\t4.784573286243868e-226\n+chr1\t5614400\t5617800\t22\t0\t9.937008604835146e-64\t1279.10124816\t7.206491457767402e-63\n+chr1\t5619800\t5620600\t3\t0\t1.1140331332442305e-11\t741.297314276\t3.036286382763687e-11\n+chr1\t5621400\t5622000\t6\t0\t4.696201482198409e-22\t1976.79283807\t1.6955117039625425e-21\n+chr1\t5624600\t5625400\t2\t0\t1.1013292864775921e-08\t494.198209517\t2.5800804070851458e-08\n+chr1\t5632000\t5637800\t20\t0\t1.2482361924057113e-52\t681.652702782\t8.133038941143462e-52\n+chr1\t5643200\t5643400\t2\t0\t1.7247482912266767e-10\t1976.79283807\t4.385488033180025e-10\n+chr1\t5646400\t5655000\t60\t0\t1.6853150149323002e-167\t1379.157794\t3.9043131179264954e-166\n+chr1\t5655800\t5656400\t6\t0\t4.696201482198409e-22\t1976.79283807\t1.6955117039625425e-21\n+chr1\t5657200\t5659400\t8\t0\t7.14563606488997e-24\t718.833759298\t2.721214830190975e-23\n+chr1\t5660400\t5661600\t5\t0\t6.913984684758452e-17\t823.663682528\t2.2092962555894825e-16\n+chr1\t5662400\t5662800\t3\t0\t6.973986184598647e-13\t1482.59462855\t2.00562223377768e-12\n+chr1\t5663600\t5667000\t12\t0\t1.8218586984886047e-33\t697.691589906\t8.168979325481164e-33\n+chr1\t5667800\t5668000\t2\t0\t1.7247482912266767e-10\t1976.79283807\t4.385488033180025e-10\n+chr1\t5676200\t5678000\t4\t0\t5.177026577521231e-13\t439.287297349\t1.5256679030574933e-12\n+chr1\t5679000\t5681000\t15\t0\t5.706192234932869e-46\t1482.59462855\t3.172642882622675e-45\n+chr1\t5688000\t5691000\t12\t0\t3.5865842165111983e-34\t790.717135227\t1.6435226574562304e-33\n+chr1\t5694600\t5700600\t24\t0\t7.102840834795353e-64\t790.717135227\t5.289079693052968e-63\n+chr1\t5704600\t5710400\t22\t0\t2.1233989699202116e-58\t749.81797306\t1.428157049123755e-57\n+chr1\t5712400\t5714800\t10\t0\t2.092965441327545e-29\t823.663682528\t8.556535186603787e-29\n+chr1\t5715600\t5719800\t19\t0\t1.4153060203967038e-52\t894.263426745\t9.079732469314238e-52\n+chr1\t5720600\t5723400\t9\t0\t8.843286933772389e-26\t635.397697951\t3.446402477928118e-25\n+chr1\t5724200\t5724600\t2\t0\t1.378752111611657e-09\t988.396419034\t3.323350465561046e-09\n+chr1\t5725400\t5730200\t24\t0\t2.699085353898604e-66\t988.396419034\t2.1236199859919203e-65\n+chr1\t5741800\t5748000\t28\t0\t2.733881234553177e-75\t892.745152676\t2.4783227713232063e-74\n+chr1\t5749400\t5750600\t3\t0\t5.630672055656213e-11\t494.198209517\t1.5051219533388723e-10\n+chr1\t5751400\t5753200\t9\t0\t1.0709162757052508e-27\t988.396419034\t4.335651329796986e-27\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_3_test-W200-G600.scoreisland --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_test-W200-G600.scoreisland Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,417 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_3_test-W200.graph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3_test-W200.graph Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,5667 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\t2\n+chr1\t5652800\t5653000\t3\n+chr1\t5653400\t5653600\t6\n+chr1\t5653600\t5653800\t2\n+chr1\t5653800\t5654000\t1\n+chr1\t5654200\t5654400\t1\n+chr1\t5654600\t5654800\t1\n+chr1\t5654800\t5655000\t1\n+chr1\t5655800\t5656000\t4\n+chr1\t5656000\t5656200\t1\n+chr1\t5656200\t5656400\t1\n+chr1\t5657200\t5657400\t1\n+chr1\t5657600\t5657800\t3\n+chr1\t5657800\t5658000\t1\n+chr1\t5658400\t5658600\t1\n+chr1\t5659200\t5659400\t2\n+chr1\t5660400\t5660600\t3\n+chr1\t5660800\t5661000\t1\n+chr1\t5661400\t5661600\t1\n+chr1\t5662400\t5662600\t2\n+chr1\t5662600\t5662800\t1\n+chr1\t5663600\t5663800\t2\n+chr1\t5663800\t5664000\t1\n+chr1\t5664600\t5664800\t2\n+chr1\t5665000\t5665200\t1\n+chr1\t5665800\t5666000\t1\n+chr1\t5666400\t5666600\t1\n+chr1\t5666600\t5666800\t3\n+chr1\t5666800\t5667000\t1\n+chr1\t5667800\t5668000\t2\n+chr1\t5674000\t5674200\t1\n+chr1\t5675000\t5675200\t1\n+chr1\t5676200\t5676400\t1\n+chr1\t5676600\t5676800\t1\n+chr1\t5677200\t5677400\t1\n+chr1\t5677800\t5678000\t1\n+chr1\t5679000\t5679200\t1\n+chr1\t5679200\t5679400\t4\n+chr1\t5679400\t5679600\t2\n+chr1\t5679600\t5679800\t1\n+chr1\t5680000\t5680200\t1\n+chr1\t5680200\t5680400\t2\n+chr1\t5680400\t5680600\t2\n+chr1\t5680800\t5681000\t2\n+chr1\t5682800\t5683000\t1\n+chr1\t5688000\t5688200\t1\n+chr1\t5688200\t5688400\t1\n+chr1\t5688400\t5688600\t1\n+chr1\t5688600\t5688800\t1\n+chr1\t5688800\t5689000\t1\n+chr1\t5689000\t5689200\t1\n+chr1\t5689200\t5689400\t1\n+chr1\t5689400\t5689600\t1\n+chr1\t5689800\t5690000\t1\n+chr1\t5690200\t5690400\t1\n+chr1\t5690800\t5691000\t2\n+chr1\t5694600\t5694800\t1\n+chr1\t5694800\t5695000\t2\n+chr1\t5695000\t5695200\t1\n+chr1\t5695400\t5695600\t3\n+chr1\t5696000\t5696200\t1\n+chr1\t5696600\t5696800\t1\n+chr1\t5696800\t5697000\t3\n+chr1\t5697000\t5697200\t1\n+chr1\t5697200\t5697400\t2\n+chr1\t5698000\t5698200\t1\n+chr1\t5698200\t5698400\t2\n+chr1\t5698800\t5699000\t2\n+chr1\t5699400\t5699600\t1\n+chr1\t5700000\t5700200\t1\n+chr1\t5700400\t5700600\t2\n+chr1\t5703600\t5703800\t1\n+chr1\t5704600\t5704800\t1\n+chr1\t5705000\t5705200\t3\n+chr1\t5705600\t5705800\t1\n+chr1\t5706200\t5706400\t5\n+chr1\t5706400\t5706600\t1\n+chr1\t5706800\t5707000\t1\n+chr1\t5707200\t5707400\t2\n+chr1\t5707800\t5708000\t2\n+chr1\t5708400\t5708600\t1\n+chr1\t5708600\t5708800\t1\n+chr1\t5709000\t5709200\t2\n+chr1\t5709600\t5709800\t1\n+chr1\t5710200\t5710400\t1\n+chr1\t5711400\t5711600\t1\n+chr1\t5712400\t5712600\t1\n+chr1\t5712600\t5712800\t2\n+chr1\t5712800\t5713000\t1\n+chr1\t5713600\t5713800\t1\n+chr1\t5714200\t5714400\t1\n+chr1\t5714400\t5714600\t1\n+chr1\t5714600\t5714800\t3\n+chr1\t5715600\t5715800\t2\n+chr1\t5715800\t5716000\t1\n+chr1\t5716200\t5716400\t4\n+chr1\t5717000\t5717200\t1\n+chr1\t5717400\t5717600\t2\n+chr1\t5717600\t5717800\t1\n+chr1\t5718200\t5718400\t1\n+chr1\t5718400\t5718600\t2\n+chr1\t5718600\t5718800\t1\n+chr1\t5718800\t5719000\t3\n+chr1\t5719600\t5719800\t1\n+chr1\t5720600\t5720800\t1\n+chr1\t5721400\t5721600\t1\n+chr1\t5721600\t5721800\t1\n+chr1\t5722200\t5722400\t2\n+chr1\t5722600\t5722800\t1\n+chr1\t5723200\t5723400\t3\n+chr1\t5724200\t5724400\t1\n+chr1\t5724400\t5724600\t1\n+chr1\t5725400\t5725600\t2\n+chr1\t5725800\t5726000\t1\n+chr1\t5726000\t5726200\t1\n+chr1\t5726200\t5726400\t3\n+chr1\t5726400\t5726600\t5\n+chr1\t5726800\t5727000\t1\n+chr1\t5727200\t5727400\t1\n+chr1\t5727400\t5727600\t1\n+chr1\t5727600\t5727800\t3\n+chr1\t5728000\t5728200\t1\n+chr1\t5728600\t5728800\t1\n+chr1\t5728800\t5729000\t1\n+chr1\t5729600\t5729800\t1\n+chr1\t5730000\t5730200\t2\n+chr1\t5735000\t5735200\t1\n+chr1\t5738200\t5738400\t1\n+chr1\t5741800\t5742000\t2\n+chr1\t5742200\t5742400\t2\n+chr1\t5742400\t5742600\t1\n+chr1\t5742600\t5742800\t1\n+chr1\t5742800\t5743000\t1\n+chr1\t5743400\t5743600\t1\n+chr1\t5743800\t5744000\t2\n+chr1\t5744200\t5744400\t1\n+chr1\t5744600\t5744800\t2\n+chr1\t5744800\t5745000\t2\n+chr1\t5745600\t5745800\t2\n+chr1\t5745800\t5746000\t2\n+chr1\t5746000\t5746200\t2\n+chr1\t5746400\t5746600\t2\n+chr1\t5746600\t5746800\t2\n+chr1\t5746800\t5747000\t1\n+chr1\t5747000\t5747200\t1\n+chr1\t5747800\t5748000\t1\n+chr1\t5749400\t5749600\t1\n+chr1\t5750000\t5750200\t1\n+chr1\t5750400\t5750600\t1\n+chr1\t5751400\t5751600\t2\n+chr1\t5751600\t5751800\t2\n+chr1\t5751800\t5752000\t2\n+chr1\t5752400\t5752600\t2\n+chr1\t5753000\t5753200\t1\n+chr1\t5754400\t5754600\t1\n' |
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 test-data/test_4_test-W200-G600-E0.01.scoreisland --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_4_test-W200-G600-E0.01.scoreisland Wed Oct 24 11:31:03 2018 -0400 |
| b |
| b'@@ -0,0 +1,352 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|
| b |
| diff -r 4a14714649b4 -r 74c9214cc8e6 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jul 21 15:59:56 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="SICER" version="1.1"> - <repository changeset_revision="48c84c1cab2b" name="package_sicer_1_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |