| Previous changeset 3:b6c95ff7c3c3 (2018-06-09) Next changeset 5:55b4b8bc250d (2019-12-16) |
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Commit message:
"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty" |
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modified:
hicCompareMatrices.xml |
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removed:
test-data/Li_chrX30-35_cool.png test-data/Li_et_al_2015.cool test-data/Li_et_al_2015.h5 test-data/bedgraph_chrx_2e6_5e6.bg test-data/bigwig_chrx_2e6_5e6.bw test-data/compare_matrices_log2ratio.h5 test-data/compare_matrices_pearson_ratio.cool test-data/covariance_small_50kb.cool test-data/covariance_small_50kb.h5 test-data/diagnostic_plot.png test-data/distVsCounts.txt test-data/dm3_genes.bed.gz test-data/dm3_genes.bed6.gz test-data/domains.bed test-data/find_TADs/multiFDR_boundaries.bed test-data/find_TADs/multiFDR_boundaries.gff test-data/find_TADs/multiFDR_domains.bed test-data/find_TADs/multiFDR_score.bedgraph test-data/find_TADs/multiFDR_tad_score.bm test-data/hicAggregateContacts_results1.png test-data/hicCorrectMatrix_result1.npz.h5 test-data/hicCorrelate_heatmap_result1.png test-data/hicCorrelate_scatter_result1.png test-data/hicFindTADs_TAD_score.tabular test-data/hicFindTADs_find_score.bedgraph test-data/hicMergeMatrixBins_result1.npz.h5 test-data/hicPlotDistVsCounts_result1.png test-data/hicPlotDistVsCounts_result2.png test-data/hicPlotTADs_result1.svg test-data/hicSumMatrices_result1.npz.h5 test-data/li_32-33mb_interactions.bedgraph test-data/li_32mb_interactions.bedgraph test-data/li_viewpoint_32-33Mb.png test-data/li_viewpoint_32Mb.png test-data/master_TADs_plot.png test-data/master_matrix_plot.png test-data/obs_exp_small_50kb.cool test-data/obs_exp_small_50kb.h5 test-data/pca1.bedgraph test-data/pca1.bw test-data/pca2.bedgraph test-data/pca2.bw test-data/pearson_small_50kb.cool test-data/pearson_small_50kb.h5 test-data/pearson_small_50kb_transform.cool test-data/raw_qc_report test-data/small_matrix_50kb_pearson_pca1_plot.png test-data/small_matrix_50kb_pearson_pca1_plot.svg test-data/small_test_R1_unsorted.bam test-data/small_test_R1_unsorted.sam test-data/small_test_R2_unsorted.bam test-data/small_test_R2_unsorted.sam test-data/small_test_matrix.h5 test-data/small_test_matrix_2.h5 test-data/small_test_matrix_50kb_res.h5 test-data/small_test_matrix_result_sorted.bam test-data/tad_classification.bed test-data/tad_score.gz test-data/test_regions.bed |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b hicCompareMatrices.xml --- a/hicCompareMatrices.xml Sat Jun 09 15:32:48 2018 -0400 +++ b/hicCompareMatrices.xml Mon Dec 16 08:39:14 2019 -0500 |
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| @@ -44,7 +44,7 @@ <param name="matrix2" value="small_test_matrix.h5"/> <param name="operation" value='log2ratio' /> <param name="outputFormat" value="h5" /> - <output name="outFileName" file="compare_matrices_log2ratio.h5" ftype="h5" compare="sim_size" delta='2000'/> + <output name="outFileName" file="compare_matrices_log2ratio.h5" ftype="h5" compare="sim_size" delta='10000'/> </test> <test> <param name="matrix1" value="pearson_small_50kb.cool"/> |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/Li_chrX30-35_cool.png |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/Li_et_al_2015.cool |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/Li_et_al_2015.h5 |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/bedgraph_chrx_2e6_5e6.bg --- a/test-data/bedgraph_chrx_2e6_5e6.bg Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,11308 +0,0 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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/distVsCounts.txt --- a/test-data/distVsCounts.txt Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,62 +0,0 @@ - Chromosome Contacts Distance Matrix -0 all 2.673662429796039 0 small_test_matrix_50kb_res.h5 -1 all 1.6689429928741093 50000 small_test_matrix_50kb_res.h5 -2 all 0.7796660703637448 100000 small_test_matrix_50kb_res.h5 -3 all 0.4811377245508982 150000 small_test_matrix_50kb_res.h5 -4 all 0.3259170174383644 200000 small_test_matrix_50kb_res.h5 -5 all 0.2530193236714976 250000 small_test_matrix_50kb_res.h5 -6 all 0.19278569263413156 300000 small_test_matrix_50kb_res.h5 -7 all 0.1475958612294583 350000 small_test_matrix_50kb_res.h5 -8 all 0.12736713500305435 400000 small_test_matrix_50kb_res.h5 -9 all 0.11737664725712535 450000 small_test_matrix_50kb_res.h5 -10 all 0.09348093480934809 500000 small_test_matrix_50kb_res.h5 -11 all 0.08145634063560629 550000 small_test_matrix_50kb_res.h5 -12 all 0.07492260061919505 600000 small_test_matrix_50kb_res.h5 -13 all 0.06803355079217148 650000 small_test_matrix_50kb_res.h5 -14 all 0.06016209476309227 700000 small_test_matrix_50kb_res.h5 -15 all 0.05411323115420707 750000 small_test_matrix_50kb_res.h5 -16 all 0.0514752040175769 800000 small_test_matrix_50kb_res.h5 -17 all 0.043464566929133856 850000 small_test_matrix_50kb_res.h5 -18 all 0.04835651074589128 900000 small_test_matrix_50kb_res.h5 -19 all 0.04281636536631779 950000 small_test_matrix_50kb_res.h5 -20 all 0.04010184595798854 1000000 small_test_matrix_50kb_res.h5 -21 all 0.034493771957840945 1050000 small_test_matrix_50kb_res.h5 -22 all 0.035256410256410256 1100000 small_test_matrix_50kb_res.h5 -23 all 0.030556449018977163 1150000 small_test_matrix_50kb_res.h5 -24 all 0.027437056165267915 1200000 small_test_matrix_50kb_res.h5 -25 all 0.030774214447683836 1250000 small_test_matrix_50kb_res.h5 -26 all 0.03153446033810143 1300000 small_test_matrix_50kb_res.h5 -27 all 0.026753670473083198 1350000 small_test_matrix_50kb_res.h5 -28 all 0.025867714472822528 1400000 small_test_matrix_50kb_res.h5 -29 all 0.028252299605781867 1450000 small_test_matrix_50kb_res.h5 -30 all 0.025379037574159526 1500000 small_test_matrix_50kb_res.h5 -31 all 0.026124338624338623 1550000 small_test_matrix_50kb_res.h5 -32 all 0.025547445255474453 1600000 small_test_matrix_50kb_res.h5 -33 all 0.0262982689747004 1650000 small_test_matrix_50kb_res.h5 -34 all 0.018036072144288578 1700000 small_test_matrix_50kb_res.h5 -35 all 0.028820375335120642 1750000 small_test_matrix_50kb_res.h5 -36 all 0.024546065904505716 1800000 small_test_matrix_50kb_res.h5 -37 all 0.025303643724696356 1850000 small_test_matrix_50kb_res.h5 -38 all 0.01963439404197698 1900000 small_test_matrix_50kb_res.h5 -39 all 0.020380434782608696 1950000 small_test_matrix_50kb_res.h5 -40 all 0.026244035446489435 2000000 small_test_matrix_50kb_res.h5 -41 all 0.024623803009575923 2050000 small_test_matrix_50kb_res.h5 -42 all 0.024365133836650652 2100000 small_test_matrix_50kb_res.h5 -43 all 0.01928374655647383 2150000 small_test_matrix_50kb_res.h5 -44 all 0.017622667588113337 2200000 small_test_matrix_50kb_res.h5 -45 all 0.015256588072122053 2250000 small_test_matrix_50kb_res.h5 -46 all 0.021224773834377174 2300000 small_test_matrix_50kb_res.h5 -47 all 0.01920391061452514 2350000 small_test_matrix_50kb_res.h5 -48 all 0.014365802382620883 2400000 small_test_matrix_50kb_res.h5 -49 all 0.014416315049226441 2450000 small_test_matrix_50kb_res.h5 -50 all 0.016231474947071278 2500000 small_test_matrix_50kb_res.h5 -51 all 0.013456090651558074 2550000 small_test_matrix_50kb_res.h5 -52 all 0.01492007104795737 2600000 small_test_matrix_50kb_res.h5 -53 all 0.020306376914855716 2650000 small_test_matrix_50kb_res.h5 -54 all 0.013576277241872096 2700000 small_test_matrix_50kb_res.h5 -55 all 0.0146900752418488 2750000 small_test_matrix_50kb_res.h5 -56 all 0.017966223499820338 2800000 small_test_matrix_50kb_res.h5 -57 all 0.017297297297297298 2850000 small_test_matrix_50kb_res.h5 -58 all 0.018070112034694615 2900000 small_test_matrix_50kb_res.h5 -59 all 0.013773106197897789 2950000 small_test_matrix_50kb_res.h5 -60 all 0.01599418393311523 3000000 small_test_matrix_50kb_res.h5 |
| b |
| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/dm3_genes.bed.gz |
| b |
| Binary file test-data/dm3_genes.bed.gz has changed |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/dm3_genes.bed6.gz |
| b |
| Binary file test-data/dm3_genes.bed6.gz has changed |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/domains.bed --- a/test-data/domains.bed Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,498 +0,0 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|
| b |
| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/find_TADs/multiFDR_boundaries.bed --- a/test-data/find_TADs/multiFDR_boundaries.bed Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -chr2L 22922500 22927500 B09504 -0.0682563628914 . -chrX 87500 92500 B09542 -0.0720204010166 . |
| b |
| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/find_TADs/multiFDR_boundaries.gff --- a/test-data/find_TADs/multiFDR_boundaries.gff Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -chr2L HiCExplorer boundary 22922500 22927500 -0.0682563628914 . . ID=B09504;delta=0.0219548467205;pvalue=3.39647761363e-05;tad_sep=-0.0682563628914 -chrX HiCExplorer boundary 87500 92500 -0.0720204010166 . . ID=B09542;delta=0.0197999801036;pvalue=5.52234326074e-05;tad_sep=-0.0720204010166 |
| b |
| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/find_TADs/multiFDR_score.bedgraph --- a/test-data/find_TADs/multiFDR_score.bedgraph Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,23814 +0,0 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r3R\t27492500\t27497500\t0.0926243695908\n-chr3R\t27497500\t27502500\t0.0981449030292\n-chr3R\t27502500\t27507500\t0.0884518556514\n-chr3R\t27507500\t27512500\t0.0991195811149\n-chr3R\t27512500\t27517500\t0.0747706741268\n-chr3R\t27517500\t27522500\t0.0747706741268\n-chr3R\t27522500\t27527500\t0.0747706741268\n-chr3R\t27527500\t27532500\t0.0747706741268\n-chr3R\t27532500\t27537500\t0.0766743472887\n-chr3R\t27537500\t27542500\t0.0819888617495\n-chr3R\t27542500\t27547500\t0.0687920794808\n-chr3R\t27547500\t27552500\t0.00660554313528\n-chr3R\t27552500\t27557500\t-0.068663015437\n-chr3R\t27557500\t27562500\t-0.0630758560148\n-chr3R\t27562500\t27567500\t-0.0630758560148\n-chr3R\t27567500\t27572500\t-0.0809430698515\n-chr3R\t27572500\t27577500\t-0.0717723999989\n-chr3R\t27577500\t27582500\t0.000141647672875\n-chr3R\t27582500\t27587500\t-0.00442507235603\n-chr3R\t27587500\t27592500\t-0.00559045677864\n-chr3R\t27592500\t27597500\t0.0107725606946\n-chr3R\t27597500\t27602500\t0.0120760744751\n-chr3R\t27602500\t27607500\t0.00204356889653\n-chr3R\t27607500\t27612500\t0.0139153913065\n-chr3R\t27612500\t27617500\t0.0261687926169\n-chr3R\t27617500\t27622500\t0.0286298507012\n-chr3R\t27622500\t27627500\t0.0286298507012\n-chr3R\t27627500\t27632500\t0.0352164944657\n-chr3R\t27632500\t27637500\t0.000401173118025\n-chr3R\t27637500\t27642500\t0.0303094054812\n-chr3R\t27642500\t27647500\t0.0908420094422\n-chr3R\t27647500\t27652500\t0.104910058763\n-chr3R\t27652500\t27657500\t0.118801510524\n-chr3R\t27657500\t27662500\t0.0964990987183\n-chr3R\t27662500\t27667500\t0.0763621831154\n-chr3R\t27667500\t27672500\t0.0638054902132\n-chr3R\t27672500\t27677500\t0.0476018389011\n-chr3R\t27677500\t27682500\t0.0227499384692\n-chr3R\t27682500\t27687500\t0.0156368494306\n-chr3R\t27687500\t27692500\t0.0156368494306\n-chr3R\t27692500\t27697500\t0.0250628717201\n-chr3R\t27697500\t27702500\t-0.0153501339631\n-chr3R\t27702500\t27707500\t-0.0153501339631\n-chr3R\t27707500\t27712500\t0.00155093677552\n-chr3R\t27712500\t27717500\t0.00628832953637\n-chr3R\t27717500\t27722500\t0.00628832953637\n-chr3R\t27722500\t27727500\t-0.00858313357697\n-chr3R\t27727500\t27732500\t0.0262206216996\n-chr3R\t27732500\t27737500\t0.0973120916552\n-chr3R\t27737500\t27742500\t0.0679519287234\n-chr3R\t27742500\t27747500\t0.0387863613672\n-chr3R\t27747500\t27752500\t0.0135773284877\n-chr3R\t27752500\t27757500\t0.0253166135267\n-chr3R\t27757500\t27762500\t0.0333030070633\n-chr3R\t27762500\t27767500\t0.0503863505993\n-chr3R\t27767500\t27772500\t0.0229622694476\n-chr3R\t27772500\t27777500\t0.0405881951039\n-chr3R\t27777500\t27782500\t0.037479587368\n-chr3R\t27782500\t27787500\t0.029456572128\n-chr3R\t27787500\t27792500\t0.0745322715233\n-chr3R\t27792500\t27797500\t0.0836243348379\n-chr3R\t27797500\t27802500\t0.0688200327796\n-chr3R\t27802500\t27807500\t0.0759450550149\n-chr3R\t27807500\t27812500\t0.118065986623\n-chr3R\t27812500\t27817500\t0.152855110565\n-chr3R\t27817500\t27822500\t0.172142533307\n-chr3R\t27822500\t27827500\t0.170909037821\n-chr3R\t27827500\t27832500\t0.154663891259\n-chr3R\t27832500\t27837500\t0.176595521439\n-chr3R\t27837500\t27842500\t0.161702307533\n-chr3R\t27842500\t27847500\t0.164316603264\n-chr3R\t27847500\t27852500\t0.203539265274\n-chr3R\t27852500\t27857500\t0.192599593633\n-chr3R\t27857500\t27862500\t0.139037714041\n-chr3R\t27862500\t27867500\t0.165807374217\n-chr3R\t27867500\t27872500\t0.0335840423644\n-chr3R\t27872500\t27877500\t-0.0448126165606\n-chr3R\t27877500\t27882500\t-0.107944679472\n-chr3R\t27882500\t27887500\t-0.102460435442\n-chr3R\t27887500\t27892500\t-0.0917938917283\n-chr3R\t27892500\t27897500\t-0.153309285822\n-chr3R\t27897500\t27902500\t-0.158769428921\n-chr3R\t27902500\t27905026\t0.0\n-chrUextra\t2500\t29002328\t0.0\n-chrM\t2500\t17258\t0.0\n-chr3LHet\t2500\t2555245\t0.0\n' |
| b |
| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/find_TADs/multiFDR_tad_score.bm --- a/test-data/find_TADs/multiFDR_tad_score.bm Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,23830 +0,0 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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/hicFindTADs_TAD_score.tabular --- a/test-data/hicFindTADs_TAD_score.tabular Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,25261 +0,0 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|
| b |
| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/hicFindTADs_find_score.bedgraph --- a/test-data/hicFindTADs_find_score.bedgraph Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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|
| b |
| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/li_32mb_interactions.bedgraph --- a/test-data/li_32mb_interactions.bedgraph Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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|
| b |
| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/pca1.bw |
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| Binary file test-data/pca1.bw has changed |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/pca2.bedgraph --- a/test-data/pca2.bedgraph Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/pearson_small_50kb.h5 |
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| Binary file test-data/pearson_small_50kb.h5 has changed |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/raw_qc_report --- a/test-data/raw_qc_report Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,29 +0,0 @@ - -File matrix.h5 -Pairs considered 983 -Min rest. site distance 300 -Max library insert size 1000 - -# count (percentage w.r.t. total sequenced reads) -Pairs mappable, unique and high quality 300 (30.52) -Pairs used 215 (21.87) -One mate unmapped 506 (51.48) -One mate not unique 13 (1.32) -One mate low quality 164 (16.68) - -# count (percentage w.r.t. mappable, unique and high quality pairs) -dangling end 0 (0.00) -self ligation (removed) 0 (0.00) -One mate not close to rest site 0 (0.00) -same fragment 85 (28.33) -self circle 0 (0.00) -duplicated pairs 0 (0.00) - -# count (percentage w.r.t. total valid pairs used) -inter chromosomal 24 (11.16) -short range < 20kb 61 (28.37) -long range 130 (60.47) -inward pairs 42 (19.53) -outward pairs 66 (30.70) -left pairs 48 (22.33) -right pairs 35 (16.28) |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_matrix_50kb_pearson_pca1_plot.png |
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| Binary file test-data/small_matrix_50kb_pearson_pca1_plot.png has changed |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_matrix_50kb_pearson_pca1_plot.svg --- a/test-data/small_matrix_50kb_pearson_pca1_plot.svg Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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:Z:22\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6008:2166\t0\tchr3R\t7743490\t41\t50M\t*\t0\t0\tGACGGTCAGTCCGAGAAGCATCTGGAGCCGATGGCCAGTTTCNNNNNGCG\t@@@FFDDDHAHFFFHIJIGIJEIGGGGGHGHIHIFGHJEHDI########\tAS:i:77\tXN:i:0\tXM:i:6\tXO:i:0\tXG:i:0\tNM:i:6\tMD:Z:16G25G0G0G0G0C3\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6164:2167\t0\tchrU\t1886379\t2\t14S36M\t*\t0\t0\tCGCATTTGAAAGCTAGCTTTCTAGTTTCACTTGTTTGTTTTTNNNNGTTT\tB@CFFFFFHHHHGJHIIIJJJJIJIIJJJJIJIIIJIGIJJJ########\tAS:i:60\tXS:i:56\tXN:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tNM:i:4\tMD:Z:28T0T0T0T4\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6028:2168\t16\tchr3L\t23880171\t0\t27S23M\t*\t0\t0\tAGGAANNNGGACACTATCGAAAAAGCTAGCTTGCAAAGTTCAAATGACCG\t?B800###IIHC<GGFCIHIJJJJJJIJJJJJIJJIIHHGHGFFFDB@@B\tAS:i:46\tXS:i:46\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:23\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6130:2172\t0\tchr3L\t20041224\t44\t50M\t*\t0\t0\tCGAGGAAGCTGCAAATGGTACGGAGCTGCTGGCTGAGGACGTGTTTGTTG\t@@@BDDDDDFDDF9ABGH<CFFHHHGIIIIGIDEG@F)?FG6B8BB;B@@\tAS:i:96\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:37T12\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6218:2174\t16\tchr2R\t19978961\t44\t50M\t*\t0\t0\tAGGAGCGTTCGTACAAGCGAAGCTCGCCGGAGGACGACAAGCTGAGGCGC\t3>9;AEEE?G@=@@@/A:=<BDDGIFC:AGIGFCGHBDDFHDDDDDD@@@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6240:2175\t16\tchr2L\t8736543\t42\t50M\t*\t0\t0\tTTAAGTGGACTTCGTTAATGTTTTAAATTTGAAGAATATTTTACGAGTTA\tHIGIHEHFBGIIFJJJIGGJJIJJIJJJJJIIIJIJJHHHHHDFFFFB@@\tAS:i:85\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:4A25C19\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6080:2181\t0\tchr2L\t22737721\t44\t1S49M\t*\t0\t0\tACTCAGTATATATTAAAAGTTTGTTTATACAATATCCTTTTAATAGGTAT\t<@@FFFDDHAHHHJJIEGICHHGFHHEIJJJIIJJJJJIJJGIJIII?FI\tAS:i:98\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:49\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6184:2183\t16\tchr2L\t1627623\t44\t50M\t*\t0\t0\tTTTAGTTATTGGGCTTTAAAAAAATCTAAATTCTGTCATGATTGATTCTG\tJJJJJJIGIIIIIIJIJJJJJJJJJJJJJJIIJIJIJHHHHHFFFFFBCC\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6206:2186\t16\tchr3R\t5530104\t44\t50M\t*\t0\t0\tCACGACGGGACGCCCTAACGGTATCGTGTGTAATTGCAGTTGCACAAGCA\t<@GHCBJIHBJIJJJJJHIJJJIJJJJIGJIIIIGIGHHHGGFDFFFC@@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6022:2190\t0\tchr3R\t17305312\t36\t40M10S\t*\t0\t0\tACTATAGAAATCTATTAAAAGTATTCCATGTAAGCTAGCTTCTCCACTGT\t?@@BDDDFG?HHHEHIIIIIIHHIIIIFIGIIIIIIIIIGDDHGFFHDGD\tAS:i:72\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:36T3\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6130:2190\t0\tchr2R\t13131924\t36\t36M14S\t*\t0\t0\tATATTGAATTCGAGTCAGAAAAAATAAAACGAAGCTAGCTTATCTGTCAT\tCCCFFDFFGGGHDHHGEIHIIJEIJJJJIJJGIJJJJJJJJJJJJIIIJJ\tAS:i:72\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:36\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6163:2192\t16\tchr2L\t7371337\t2\t26M24S\t*\t0\t0\tGGGTTCTCCACCAGCCGGCAAAAGCTAGCTTAAATTAACTTTTAGTTTTA\tFB)B;B=HD9JJJJIJJJJJJJJJJJJJJJJJJJJJHFHHGHFFFFFCCC\tAS:i:52\tXS:i:48\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:26\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6060:2193\t16\tchr3R\t9331177\t44\t50M\t*\t0\t0\tGCTTACTCCTTTGCAGCACTAGTACTAATTTTTTATTTTTTCGAATTTTC\tGGHFCHFGGIJJIGIIHGIIEFGDIJJJIJJJJJIJIHHHHHFFFFFCC@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n-HWI-ST1180:36:C0TU1ACXX:1:1101:6038:2194\t0\tchrYHet\t283249\t2\t17S33M\t*\t0\t0\tAGGCAGTAAGGCAGTAAGCTAGCTTGCTATGGTATTTTTCCTTAAGTTCC\t@@@DDDDDHHHHHIIGIDC<<EEHICG@?<C>11?ECG<CCDHAAAFFGE\tAS:i:66\tXS:i:60\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:33\tYT:Z:UU\n' |
| b |
| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_test_R2_unsorted.bam |
| b |
| Binary file test-data/small_test_R2_unsorted.bam has changed |
| b |
| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_test_R2_unsorted.sam --- a/test-data/small_test_R2_unsorted.sam Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1000 +0,0 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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_test_matrix_2.h5 |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_test_matrix_50kb_res.h5 |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/small_test_matrix_result_sorted.bam |
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| Binary file test-data/small_test_matrix_result_sorted.bam has changed |
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| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/tad_classification.bed --- a/test-data/tad_classification.bed Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2685 +0,0 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19389270\t19399952\tactive\t2\t.\t19389270\t19399952\t255,255,153\n-chrX\t19399952\t19416481\tactive\t4\t.\t19399952\t19416481\t255,255,153\n-chrX\t19416481\t19456185\tinactive\t1\t.\t19416481\t19456185\t0,0,0\n-chrX\t19456185\t19473065\tactive\t4\t.\t19456185\t19473065\t255,255,153\n-chrX\t19473065\t19491987\tinactive\t1\t.\t19473065\t19491987\t0,0,0\n-chrX\t19491987\t19507538\tactive\t2\t.\t19491987\t19507538\t255,255,153\n-chrX\t19507538\t19531934\tactive\t4\t.\t19507538\t19531934\t255,255,153\n-chrX\t19531934\t19557899\tactive\t4\t.\t19531934\t19557899\t255,255,153\n-chrX\t19557899\t19577569\tactive\t4\t.\t19557899\t19577569\t255,255,153\n-chrX\t19577569\t19607671\tactive\t4\t.\t19577569\t19607671\t255,255,153\n-chrX\t19607671\t19625150\tinactive\t1\t.\t19607671\t19625150\t0,0,0\n-chrX\t19625150\t19639107\tactive\t2\t.\t19625150\t19639107\t255,255,153\n-chrX\t19639107\t19644907\tactive\t4\t.\t19639107\t19644907\t255,255,153\n-chrX\t19644907\t19657054\tactive\t2\t.\t19644907\t19657054\t255,255,153\n-chrX\t19657054\t19686912\tinactive\t1\t.\t19657054\t19686912\t0,0,0\n-chrX\t19686912\t19745861\tinactive\t1\t.\t19686912\t19745861\t0,0,0\n-chrX\t19745861\t19760530\tactive\t4\t.\t19745861\t19760530\t255,255,153\n-chrX\t19760530\t19815382\tactive\t2\t.\t19760530\t19815382\t255,255,153\n-chrX\t19815382\t19987457\tinactive\t1\t.\t19815382\t19987457\t0,0,0\n-chrX\t19987457\t20054086\tinactive\t1\t.\t19987457\t20054086\t0,0,0\n-chrX\t20054086\t20068910\tactive\t2\t.\t20054086\t20068910\t255,255,153\n-chrX\t20068910\t20125761\tinactive\t1\t.\t20068910\t20125761\t0,0,0\n-chrX\t20125761\t20262048\tinactive\t1\t.\t20125761\t20262048\t0,0,0\n-chrX\t20262048\t20294608\tactive\t4\t.\t20262048\t20294608\t255,255,153\n-chrX\t20294608\t20305771\tactive\t4\t.\t20294608\t20305771\t255,255,153\n-chrX\t20305771\t20339275\tinactive\t1\t.\t20305771\t20339275\t0,0,0\n-chrX\t20339275\t20382809\tactive\t2\t.\t20339275\t20382809\t255,255,153\n-chrX\t20382809\t20395830\tactive\t4\t.\t20382809\t20395830\t255,255,153\n-chrX\t20395830\t20508892\tinactive\t1\t.\t20395830\t20508892\t0,0,0\n-chrX\t20508892\t20526971\tinactive\t1\t.\t20508892\t20526971\t0,0,0\n-chrX\t20526971\t20631727\tinactive\t1\t.\t20526971\t20631727\t0,0,0\n-chrX\t20631727\t20894364\tinactive\t1\t.\t20631727\t20894364\t0,0,0\n-chrX\t20894364\t20907117\tactive\t4\t.\t20894364\t20907117\t255,255,153\n-chrX\t20907117\t20916940\tactive\t4\t.\t20907117\t20916940\t255,255,153\n-chrX\t20916940\t20931445\tactive\t2\t.\t20916940\t20931445\t255,255,153\n-chrX\t20931445\t20944384\tactive\t2\t.\t20931445\t20944384\t255,255,153\n-chrX\t20944384\t20996348\tinactive\t1\t.\t20944384\t20996348\t0,0,0\n-chrX\t20996348\t21012072\tinactive\t1\t.\t20996348\t21012072\t0,0,0\n-chrX\t21012072\t21178100\tinactive\t1\t.\t21012072\t21178100\t0,0,0\n-chrX\t21178100\t21186628\tinactive\t1\t.\t21178100\t21186628\t0,0,0\n-chrX\t21186628\t21194946\tactive\t4\t.\t21186628\t21194946\t255,255,153\n-chrX\t21194946\t21220857\tactive\t4\t.\t21194946\t21220857\t255,255,153\n-chrX\t21220857\t21240098\tactive\t4\t.\t21220857\t21240098\t255,255,153\n-chrX\t21240098\t21271964\tinactive\t1\t.\t21240098\t21271964\t0,0,0\n-chrX\t21271964\t21343699\tinactive\t1\t.\t21271964\t21343699\t0,0,0\n-chrX\t21343699\t21656357\tinactive\t1\t.\t21343699\t21656357\t0,0,0\n-chrX\t21656357\t21857607\tHP1\t3\t.\t21656357\t21857607\t51,160,44\n-chrX\t21857607\t21873688\tactive\t4\t.\t21857607\t21873688\t255,255,153\n-chrX\t21873688\t21889804\tactive\t2\t.\t21873688\t21889804\t255,255,153\n-chrX\t21889804\t21907001\tactive\t4\t.\t21889804\t21907001\t255,255,153\n-chrX\t21907001\t21931844\tinactive\t1\t.\t21907001\t21931844\t0,0,0\n-chrX\t21931844\t21954371\tactive\t2\t.\t21931844\t21954371\t255,255,153\n-chrX\t21954371\t22120033\tinactive\t1\t.\t21954371\t22120033\t0,0,0\n-chrX\t22120033\t22274227\tinactive\t1\t.\t22120033\t22274227\t0,0,0\n-chrX\t22274227\t22287785\tinactive\t1\t.\t22274227\t22287785\t0,0,0\n-chrX\t22287785\t22349277\tinactive\t1\t.\t22287785\t22349277\t0,0,0\n-chrX\t22349277\t22380885\tinactive\t1\t.\t22349277\t22380885\t0,0,0\n-chrX\t22380885\t22421267\tinactive\t1\t.\t22380885\t22421267\t0,0,0\n' |
| b |
| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/tad_score.gz |
| b |
| Binary file test-data/tad_score.gz has changed |
| b |
| diff -r b6c95ff7c3c3 -r 6d2c4187805b test-data/test_regions.bed --- a/test-data/test_regions.bed Sat Jun 09 15:32:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,60 +0,0 @@ -2L 7998826 7998827 msl2_peak_350 17.17982 -2L 9895070 9895071 msl2_peak_415 6.67520 -2L 14024214 14024215 msl2_peak_602 4.46806 -2L 19791941 19791942 msl2_peak_823 3.40020 -2L 21573354 21573355 msl2_peak_1023 10.76434 -2R 5441451 5441452 msl2_peak_1532 9.54697 -2R 8291271 8291272 msl2_peak_1644 7.36770 -2R 14575573 14575574 msl2_peak_1947 4.41313 -3L 628463 628464 msl2_peak_2780 11.60203 -3L 3903421 3903422 msl2_peak_2958 4.32242 -3L 8759529 8759530 msl2_peak_3195 4.10429 -3R 2901523 2901524 msl2_peak_4559 2.22040 -3R 3932152 3932153 msl2_peak_4603 9.59945 -3R 11851634 11851635 msl2_peak_4969 8.43238 -3R 20545331 20545332 msl2_peak_5267 4.72876 -X 147841 147842 msl2_peak_22671 16.59036 -X 366894 366895 msl2_peak_22686 25.37647 -X 517100 517101 msl2_peak_22694 8.54298 -X 548547 548548 msl2_peak_22696 27.53758 -X 656427 656428 msl2_peak_22697 14.11897 -X 692287 692288 msl2_peak_22698 15.96065 -X 818016 818017 msl2_peak_22713 10.66184 -X 937135 937136 msl2_peak_22717 67.84654 -X 1112721 1112722 msl2_peak_22727 26.81313 -X 1268823 1268824 msl2_peak_22735 29.73846 -X 1356647 1356648 msl2_peak_22736 9.58288 -X 1375009 1375010 msl2_peak_22738 4.49598 -X 1375616 1375617 msl2_peak_22739 128.36397 -X 1409093 1409094 msl2_peak_22742 14.72497 -X 1588015 1588016 msl2_peak_22757 102.61334 -X 1679121 1679122 msl2_peak_22767 16.12354 -X 1754043 1754044 msl2_peak_22769 20.51431 -X 1775025 1775026 msl2_peak_22773 43.05813 -X 1787755 1787756 msl2_peak_22774 142.73460 -X 1798236 1798237 msl2_peak_22775 80.66115 -X 1819545 1819546 msl2_peak_22777 11.21560 -X 1918989 1918990 msl2_peak_22793 74.48118 -X 1956476 1956477 msl2_peak_22794 32.73601 -X 1972291 1972292 msl2_peak_22795 37.39349 -X 2007235 2007236 msl2_peak_22798 11.21560 -X 2015927 2015928 msl2_peak_22799 68.80555 -X 2044335 2044336 msl2_peak_22804 36.60362 -X 2050114 2050115 msl2_peak_22805 47.23102 -X 2072937 2072938 msl2_peak_22807 52.37415 -X 2126007 2126008 msl2_peak_22808 42.23372 -X 2162302 2162303 msl2_peak_22810 78.64520 -X 2237610 2237611 msl2_peak_22817 43.05813 -X 2340287 2340288 msl2_peak_22825 14.72497 -X 2493295 2493296 msl2_peak_22827 23.47760 -X 2503119 2503120 msl2_peak_22828 80.83590 -X 2520611 2520612 msl2_peak_22839 17.87077 -X 2521079 2521080 msl2_peak_22840 60.08352 -X 2613112 2613113 msl2_peak_22844 43.87985 -X 2628624 2628625 msl2_peak_22847 115.37079 -X 3382405 3382406 msl2_peak_22879 6.13203 -X 3593688 3593689 msl2_peak_22908 10.66184 -X 3596515 3596516 msl2_peak_22909 6.59200 -X 3755342 3755343 msl2_peak_22919 164.76546 -X 3848197 3848198 msl2_peak_22920 74.65739 -X 4021813 4021814 msl2_peak_22929 32.73601 |
