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Changeset 2:2abdd761461b (2018-04-27)

Previous changeset 1:ec59bf4c3d06 (2018-04-27) Next changeset 3:a48457358aa8 (2018-06-09)

Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dddc0b9035b8edadfd45d74b01aeca245c2725d7

modified:
hicAggregateContacts.xml

added:
static/images/hicCompareMatrices_QC_log2_m50_matrix_plot.png
static/images/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot.png
static/images/hicPlotDistVsCounts.png

diff -r ec59bf4c3d06 -r 2abdd761461b hicAggregateContacts.xml
--- a/hicAggregateContacts.xml Fri Apr 27 03:32:37 2018 -0400
+++ b/hicAggregateContacts.xml Fri Apr 27 08:40:40 2018 -0400

@@ -200,6 +200,7 @@
Below, you can find an example of an aggregate Hi-C matrix obtained from *Drosophila melanogaster* Hi-C data. The interactions are plotted at binding sites of a protein that were determined by ChIP-seq. We plot sub-matrices of 30 bins (1.5 kb bin size, 45 kb in total). The regions specified in the BED file will be centered between half number of bins and the other half number of bins.The considered range is 300-1000 kb. The range should be adjusted and only contain contacts larger than TAD size to reduce background interactions.

.. image:: $PATH_TO_IMAGES/hicAggregateContacts.png
+ :width: 80 %

This example was calculated using mean interactions of an observed vs. expected transformed Hi-C matrix. Additional options for the matrix transformation are total-counts or z-score. Aggregate contacts can be plotted in 2D or 3D.

diff -r ec59bf4c3d06 -r 2abdd761461b static/images/hicCompareMatrices_QC_log2_m50_matrix_plot (1).png

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diff -r ec59bf4c3d06 -r 2abdd761461b static/images/hicCompareMatrices_QC_log2_m50_matrix_plot.png

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diff -r ec59bf4c3d06 -r 2abdd761461b static/images/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot (1).png

Binary file static/images/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot (1).png has changed

diff -r ec59bf4c3d06 -r 2abdd761461b static/images/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot.png

Binary file static/images/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot.png has changed

diff -r ec59bf4c3d06 -r 2abdd761461b static/images/hicPlotDistVsCounts.png

Binary file static/images/hicPlotDistVsCounts.png has changed

diff -r ec59bf4c3d06 -r 2abdd761461b static/images/hicPlotDistvsCounts.png

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diff -r ec59bf4c3d06 -r 2abdd761461b test-data/find_TADs/multiBonferroni_boundaries.bed
--- a/test-data/find_TADs/multiBonferroni_boundaries.bed Fri Apr 27 03:32:37 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr2L 22922500 22927500 B09504 -0.06825625 .
-chrX 87500 92500 B09542 -0.0720205 .

diff -r ec59bf4c3d06 -r 2abdd761461b test-data/find_TADs/multiBonferroni_boundaries.gff
--- a/test-data/find_TADs/multiBonferroni_boundaries.gff Fri Apr 27 03:32:37 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr2L HiCExplorer boundary 22922500 22927500 -0.06825625 . . ID=B09504;delta=0.0219547105263;pvalue=0.0547512191318;tad_sep=-0.06825625
-chrX HiCExplorer boundary 87500 92500 -0.0720205 . . ID=B09542;delta=0.0197999736842;pvalue=0.0890201733631;tad_sep=-0.0720205

diff -r ec59bf4c3d06 -r 2abdd761461b test-data/find_TADs/multiBonferroni_score.bedgraph
--- a/test-data/find_TADs/multiBonferroni_score.bedgraph Fri Apr 27 03:32:37 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,23814 +0,0 @@\n-chr2RHet\t2500\t3286880\t0.0\n-chr3RHet\t2500\t2516253\t0.0\n-chr2LHet\t2500\t366936\t0.0\n-chr4\t2500\t1350928\t0.0\n-chrYHet\t2500\t346019\t0.0\n-chr3L\t2500\t7500\t-0.15973725\n-chr3L\t7500\t12500\t-0.1550825\n-chr3L\t12500\t17500\t-0.1511685\n-chr3L\t17500\t22500\t-0.14787325\n-chr3L\t22500\t27500\t-0.14477275\n-chr3L\t27500\t32500\t-0.141869\n-chr3L\t32500\t37500\t-0.13920825\n-chr3L\t37500\t42500\t-0.13669525\n-chr3L\t42500\t47500\t-0.13435775\n-chr3L\t47500\t52500\t-0.13219825\n-chr3L\t52500\t57500\t-0.13013875\n-chr3L\t57500\t62500\t-0.09402375\n-chr3L\t62500\t67500\t-0.076427\n-chr3L\t67500\t72500\t-0.04183125\n-chr3L\t72500\t77500\t0.0197075\n-chr3L\t77500\t82500\t0.07052875\n-chr3L\t82500\t87500\t0.07283975\n-chr3L\t87500\t92500\t0.07045525\n-chr3L\t92500\t97500\t0.0683615\n-chr3L\t97500\t102500\t0.06999375\n-chr3L\t102500\t107500\t0.0683285\n-chr3L\t107500\t112500\t0.066853\n-chr3L\t112500\t117500\t0.06554\n-chr3L\t117500\t122500\t0.06436125\n-chr3L\t122500\t127500\t0.00960325\n-chr3L\t127500\t132500\t0.012285\n-chr3L\t132500\t137500\t-0.00142775\n-chr3L\t137500\t142500\t-0.060362\n-chr3L\t142500\t147500\t-0.05156225\n-chr3L\t147500\t152500\t-0.0552185\n-chr3L\t152500\t157500\t-0.06660375\n-chr3L\t157500\t162500\t-0.070088\n-chr3L\t162500\t167500\t-0.10316675\n-chr3L\t167500\t172500\t-0.10316675\n-chr3L\t172500\t177500\t-0.10316675\n-chr3L\t177500\t182500\t-0.089227\n-chr3L\t182500\t187500\t-0.0778915\n-chr3L\t187500\t192500\t-0.0547475\n-chr3L\t192500\t197500\t-0.06240725\n-chr3L\t197500\t202500\t-0.040267\n-chr3L\t202500\t207500\t-0.018089\n-chr3L\t207500\t212500\t-0.018089\n-chr3L\t212500\t217500\t-0.018089\n-chr3L\t217500\t222500\t0.0190635\n-chr3L\t222500\t227500\t0.01122225\n-chr3L\t227500\t232500\t-0.00338425\n-chr3L\t232500\t237500\t0.018671\n-chr3L\t237500\t242500\t0.015759\n-chr3L\t242500\t247500\t0.015759\n-chr3L\t247500\t252500\t-0.00807575\n-chr3L\t252500\t257500\t-0.01047525\n-chr3L\t257500\t262500\t-0.026655\n-chr3L\t262500\t267500\t-0.01461\n-chr3L\t267500\t272500\t-0.01739225\n-chr3L\t272500\t277500\t0.006616\n-chr3L\t277500\t282500\t0.02626725\n-chr3L\t282500\t287500\t0.02671675\n-chr3L\t287500\t292500\t0.04431375\n-chr3L\t292500\t297500\t0.075128\n-chr3L\t297500\t302500\t0.0517535\n-chr3L\t302500\t307500\t0.03498275\n-chr3L\t307500\t312500\t0.04280875\n-chr3L\t312500\t317500\t-0.00566075\n-chr3L\t317500\t322500\t-0.00566075\n-chr3L\t322500\t327500\t-0.01699625\n-chr3L\t327500\t332500\t0.0001575\n-chr3L\t332500\t337500\t-0.030848\n-chr3L\t337500\t342500\t-0.02264125\n-chr3L\t342500\t347500\t-0.01607175\n-chr3L\t347500\t352500\t-0.03003825\n-chr3L\t352500\t357500\t-0.0029145\n-chr3L\t357500\t362500\t-0.0580815\n-chr3L\t362500\t367500\t-0.042338\n-chr3L\t367500\t372500\t-0.0243195\n-chr3L\t372500\t377500\t-0.0233235\n-chr3L\t377500\t382500\t0.01665375\n-chr3L\t382500\t387500\t0.01665375\n-chr3L\t387500\t392500\t0.030134\n-chr3L\t392500\t397500\t0.01966325\n-chr3L\t397500\t402500\t0.0270555\n-chr3L\t402500\t407500\t0.03715275\n-chr3L\t407500\t412500\t0.03215025\n-chr3L\t412500\t417500\t0.007102\n-chr3L\t417500\t422500\t0.01531925\n-chr3L\t422500\t427500\t0.04944275\n-chr3L\t427500\t432500\t0.017395\n-chr3L\t432500\t437500\t0.0233485\n-chr3L\t437500\t442500\t0.010935\n-chr3L\t442500\t447500\t0.015241\n-chr3L\t447500\t452500\t-0.00172725\n-chr3L\t452500\t457500\t-0.006215\n-chr3L\t457500\t462500\t-0.0121685\n-chr3L\t462500\t467500\t-0.0042425\n-chr3L\t467500\t472500\t0.00083775\n-chr3L\t472500\t477500\t-0.02013475\n-chr3L\t477500\t482500\t-0.058266\n-chr3L\t482500\t487500\t-0.07169775\n-chr3L\t487500\t492500\t-0.04601075\n-chr3L\t492500\t497500\t-0.02333825\n-chr3L\t497500\t502500\t-0.00838725\n-chr3L\t502500\t507500\t-0.0641845\n-chr3L\t507500\t512500\t-0.067458\n-chr3L\t512500\t517500\t-0.067458\n-chr3L\t517500\t522500\t-0.09926975\n-chr3L\t522500\t527500\t-0.1060405\n-chr3L\t527500\t532500\t-0.07751675\n-chr3L\t532500\t537500\t-0.07751675\n-chr3L\t537500\t542500\t-0.07751675\n-chr3L\t542500\t547500\t-0.06945475\n-chr3L\t547500\t552500\t-0.06322125\n-chr3L\t552500\t557500\t0.00947925\n-chr3L\t557500\t562500\t-0.02586475\n-chr3L\t562500\t567500\t0.030247\n-chr3L\t567500\t572500\t0.04485875\n-chr3L\t572500\t577500\t0.0579985\n-chr3L\t577500\t582500\t0.085449\n-chr3L\t582500\t587500\t0.10347075\n-chr3L\t587500\t592500\t0.1197795\n-chr3L\t592500\t597500\t0.115187\n-chr3L\t597500\t602500\t0.099483\n-chr3L\t602500\t607500\t0.100333\n-chr3L\t607500\t612500\t0.1935635\n-chr3L\t612500\t6'..b'52500\t27357500\t0.02843225\n-chr3R\t27357500\t27362500\t0.003006\n-chr3R\t27362500\t27367500\t0.02624575\n-chr3R\t27367500\t27372500\t0.01185675\n-chr3R\t27372500\t27377500\t0.0101145\n-chr3R\t27377500\t27382500\t-0.005061\n-chr3R\t27382500\t27387500\t-0.041305\n-chr3R\t27387500\t27392500\t-0.00143125\n-chr3R\t27392500\t27397500\t0.04561275\n-chr3R\t27397500\t27402500\t0.02985575\n-chr3R\t27402500\t27407500\t0.0173185\n-chr3R\t27407500\t27412500\t0.0272775\n-chr3R\t27412500\t27417500\t0.01093175\n-chr3R\t27417500\t27422500\t-0.0499295\n-chr3R\t27422500\t27427500\t-0.04139125\n-chr3R\t27427500\t27432500\t-0.0366555\n-chr3R\t27432500\t27437500\t-0.0366555\n-chr3R\t27437500\t27442500\t-0.04748775\n-chr3R\t27442500\t27447500\t-0.05511025\n-chr3R\t27447500\t27452500\t-0.05736225\n-chr3R\t27452500\t27457500\t-0.0233205\n-chr3R\t27457500\t27462500\t-0.0020265\n-chr3R\t27462500\t27467500\t0.02501975\n-chr3R\t27467500\t27472500\t0.036331\n-chr3R\t27472500\t27477500\t0.036331\n-chr3R\t27477500\t27482500\t0.036331\n-chr3R\t27482500\t27487500\t0.06726625\n-chr3R\t27487500\t27492500\t0.06726625\n-chr3R\t27492500\t27497500\t0.0926245\n-chr3R\t27497500\t27502500\t0.098145\n-chr3R\t27502500\t27507500\t0.088452\n-chr3R\t27507500\t27512500\t0.0991195\n-chr3R\t27512500\t27517500\t0.07477075\n-chr3R\t27517500\t27522500\t0.07477075\n-chr3R\t27522500\t27527500\t0.07477075\n-chr3R\t27527500\t27532500\t0.07477075\n-chr3R\t27532500\t27537500\t0.07667425\n-chr3R\t27537500\t27542500\t0.08198875\n-chr3R\t27542500\t27547500\t0.068792\n-chr3R\t27547500\t27552500\t0.00660575\n-chr3R\t27552500\t27557500\t-0.06866275\n-chr3R\t27557500\t27562500\t-0.063076\n-chr3R\t27562500\t27567500\t-0.063076\n-chr3R\t27567500\t27572500\t-0.08094325\n-chr3R\t27572500\t27577500\t-0.07177225\n-chr3R\t27577500\t27582500\t0.00014175\n-chr3R\t27582500\t27587500\t-0.004425\n-chr3R\t27587500\t27592500\t-0.0055905\n-chr3R\t27592500\t27597500\t0.0107725\n-chr3R\t27597500\t27602500\t0.012076\n-chr3R\t27602500\t27607500\t0.00204375\n-chr3R\t27607500\t27612500\t0.01391525\n-chr3R\t27612500\t27617500\t0.02616875\n-chr3R\t27617500\t27622500\t0.02862975\n-chr3R\t27622500\t27627500\t0.02862975\n-chr3R\t27627500\t27632500\t0.03521625\n-chr3R\t27632500\t27637500\t0.00040125\n-chr3R\t27637500\t27642500\t0.0303095\n-chr3R\t27642500\t27647500\t0.090842\n-chr3R\t27647500\t27652500\t0.10491025\n-chr3R\t27652500\t27657500\t0.11880175\n-chr3R\t27657500\t27662500\t0.09649925\n-chr3R\t27662500\t27667500\t0.07636225\n-chr3R\t27667500\t27672500\t0.06380525\n-chr3R\t27672500\t27677500\t0.04760175\n-chr3R\t27677500\t27682500\t0.02274975\n-chr3R\t27682500\t27687500\t0.015637\n-chr3R\t27687500\t27692500\t0.015637\n-chr3R\t27692500\t27697500\t0.025063\n-chr3R\t27697500\t27702500\t-0.01535\n-chr3R\t27702500\t27707500\t-0.01535\n-chr3R\t27707500\t27712500\t0.00155075\n-chr3R\t27712500\t27717500\t0.006288\n-chr3R\t27717500\t27722500\t0.006288\n-chr3R\t27722500\t27727500\t-0.00858325\n-chr3R\t27727500\t27732500\t0.02622075\n-chr3R\t27732500\t27737500\t0.097312\n-chr3R\t27737500\t27742500\t0.067952\n-chr3R\t27742500\t27747500\t0.0387865\n-chr3R\t27747500\t27752500\t0.01357725\n-chr3R\t27752500\t27757500\t0.02531675\n-chr3R\t27757500\t27762500\t0.033303\n-chr3R\t27762500\t27767500\t0.050386\n-chr3R\t27767500\t27772500\t0.0229625\n-chr3R\t27772500\t27777500\t0.04058825\n-chr3R\t27777500\t27782500\t0.03747975\n-chr3R\t27782500\t27787500\t0.0294565\n-chr3R\t27787500\t27792500\t0.07453225\n-chr3R\t27792500\t27797500\t0.08362425\n-chr3R\t27797500\t27802500\t0.06882\n-chr3R\t27802500\t27807500\t0.075945\n-chr3R\t27807500\t27812500\t0.11806575\n-chr3R\t27812500\t27817500\t0.152855\n-chr3R\t27817500\t27822500\t0.1721425\n-chr3R\t27822500\t27827500\t0.17090925\n-chr3R\t27827500\t27832500\t0.15466375\n-chr3R\t27832500\t27837500\t0.1765955\n-chr3R\t27837500\t27842500\t0.16170225\n-chr3R\t27842500\t27847500\t0.16431675\n-chr3R\t27847500\t27852500\t0.20353925\n-chr3R\t27852500\t27857500\t0.19259975\n-chr3R\t27857500\t27862500\t0.13903775\n-chr3R\t27862500\t27867500\t0.1658075\n-chr3R\t27867500\t27872500\t0.033584\n-chr3R\t27872500\t27877500\t-0.044813\n-chr3R\t27877500\t27882500\t-0.1079445\n-chr3R\t27882500\t27887500\t-0.1024605\n-chr3R\t27887500\t27892500\t-0.09179375\n-chr3R\t27892500\t27897500\t-0.1533095\n-chr3R\t27897500\t27902500\t-0.15876925\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'

diff -r ec59bf4c3d06 -r 2abdd761461b test-data/find_TADs/multiBonferroni_tad_score.bm
--- a/test-data/find_TADs/multiBonferroni_tad_score.bm Fri Apr 27 03:32:37 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,23830 +0,0 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diff -r ec59bf4c3d06 -r 2abdd761461b test-data/find_TADs/multiBonferroni_zscore_matrix.h5

Binary file test-data/find_TADs/multiBonferroni_zscore_matrix.h5 has changed

diff -r ec59bf4c3d06 -r 2abdd761461b test-data/find_TADs/multiFDR_zscore_matrix.h5

Binary file test-data/find_TADs/multiFDR_zscore_matrix.h5 has changed

diff -r ec59bf4c3d06 -r 2abdd761461b test-data/find_TADs/multiNone_boundaries.bed
--- a/test-data/find_TADs/multiNone_boundaries.bed Fri Apr 27 03:32:37 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1408 +0,0 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diff -r ec59bf4c3d06 -r 2abdd761461b test-data/find_TADs/multiNone_boundaries.gff
--- a/test-data/find_TADs/multiNone_boundaries.gff Fri Apr 27 03:32:37 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1408 +0,0 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407500\t-0.00546225\t.\t.\tID=B23322;delta=0.0185628552632;pvalue=0.846835522646;tad_sep=-0.00546225\n-chr3R\tHiCExplorer\tboundary\t25567500\t25572500\t-0.04654075\t.\t.\tID=B23355;delta=0.0566089736842;pvalue=0.576192906383;tad_sep=-0.04654075\n-chr3R\tHiCExplorer\tboundary\t25577500\t25582500\t-0.01871575\t.\t.\tID=B23357;delta=0.0281310394737;pvalue=0.314699364851;tad_sep=-0.01871575\n-chr3R\tHiCExplorer\tboundary\t25727500\t25732500\t-0.00858875\t.\t.\tID=B23387;delta=0.0986943815789;pvalue=0.112031426493;tad_sep=-0.00858875\n-chr3R\tHiCExplorer\tboundary\t25877500\t25882500\t-0.10581625\t.\t.\tID=B23417;delta=0.0288810657895;pvalue=0.48806712443;tad_sep=-0.10581625\n-chr3R\tHiCExplorer\tboundary\t25987500\t25992500\t-0.090403\t.\t.\tID=B23439;delta=0.0182022894737;pvalue=0.952043612098;tad_sep=-0.090403\n-chr3R\tHiCExplorer\tboundary\t26047500\t26052500\t-0.0935315\t.\t.\tID=B23451;delta=0.0351577631579;pvalue=0.420309304718;tad_sep=-0.0935315\n-chr3R\tHiCExplorer\tboundary\t26177500\t26182500\t-0.11469275\t.\t.\tID=B23477;delta=0.0468813947368;pvalue=0.407773352255;tad_sep=-0.11469275\n-chr3R\tHiCExplorer\tboundary\t26272500\t26277500\t-0.1002735\t.\t.\tID=B23496;delta=0.0265311973684;pvalue=0.866273462912;tad_sep=-0.1002735\n-chr3R\tHiCExplorer\tboundary\t26327500\t26332500\t-0.092304\t.\t.\tID=B23507;delta=0.0340349736842;pvalue=0.801678295331;tad_sep=-0.092304\n-chr3R\tHiCExplorer\tboundary\t26487500\t26492500\t0.0627965\t.\t.\tID=B23539;delta=0.0261305394737;pvalue=0.917163037297;tad_sep=0.0627965\n-chr3R\tHiCExplorer\tboundary\t26562500\t26567500\t-0.01974475\t.\t.\tID=B23554;delta=0.0717252631579;pvalue=0.774996850942;tad_sep=-0.01974475\n-chr3R\tHiCExplorer\tboundary\t26637500\t26642500\t-0.07430725\t.\t.\tID=B23569;delta=0.0364784868421;pvalue=0.687771555077;tad_sep=-0.07430725\n-chr3R\tHiCExplorer\tboundary\t26712500\t26717500\t-0.049789\t.\t.\tID=B23584;delta=0.0413630789474;pvalue=0.926151939522;tad_sep=-0.049789\n-chr3R\tHiCExplorer\tboundary\t26867500\t26872500\t-0.0249905\t.\t.\tID=B23615;delta=0.0878640789474;pvalue=0.360644376149;tad_sep=-0.0249905\n-chr3R\tHiCExplorer\tboundary\t27042500\t27047500\t-0.074189\t.\t.\tID=B23650;delta=0.0714735131579;pvalue=0.596640534697;tad_sep=-0.074189\n-chr3R\tHiCExplorer\tboundary\t27152500\t27157500\t-0.00609925\t.\t.\tID=B23672;delta=0.0508306842105;pvalue=0.667062852012;tad_sep=-0.00609925\n-chr3R\tHiCExplorer\tboundary\t27182500\t27187500\t-0.01281025\t.\t.\tID=B23678;delta=0.0210053815789;pvalue=0.481433141582;tad_sep=-0.01281025\n-chr3R\tHiCExplorer\tboundary\t27247500\t27252500\t-0.04990275\t.\t.\tID=B23691;delta=0.0377629210526;pvalue=0.746434392485;tad_sep=-0.04990275\n-chr3R\tHiCExplorer\tboundary\t27382500\t27387500\t-0.041305\t.\t.\tID=B23718;delta=0.0604152368421;pvalue=0.443941047643;tad_sep=-0.041305\n-chr3R\tHiCExplorer\tboundary\t27417500\t27422500\t-0.0499295\t.\t.\tID=B23725;delta=0.040293;pvalue=0.772288553997;tad_sep=-0.0499295\n-chr3R\tHiCExplorer\tboundary\t27567500\t27572500\t-0.08094325\t.\t.\tID=B23755;delta=0.0899101052632;pvalue=0.377997904893;tad_sep=-0.08094325\n-chr3R\tHiCExplorer\tboundary\t27697500\t27702500\t-0.01535\t.\t.\tID=B23781;delta=0.0567128421053;pvalue=0.546627372724;tad_sep=-0.01535\n-chr3R\tHiCExplorer\tboundary\t27747500\t27752500\t0.01357725\t.\t.\tID=B23791;delta=0.0162098684211;pvalue=0.746434392485;tad_sep=0.01357725\n-chr3R\tHiCExplorer\tboundary\t27767500\t27772500\t0.0229625\t.\t.\tID=B23795;delta=0.0310075921053;pvalue=0.767420623706;tad_sep=0.0229625\n'

diff -r ec59bf4c3d06 -r 2abdd761461b test-data/find_TADs/multiNone_domains.bed
--- a/test-data/find_TADs/multiNone_domains.bed Fri Apr 27 03:32:37 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1403 +0,0 @@\n-chr3L\t165000\t260000\tID_0.01_1\t-0.10316675\t.\t165000\t260000\t31,120,180\n-chr3L\t260000\t335000\tID_0.01_2\t-0.026655\t.\t260000\t335000\t51,160,44\n-chr3L\t335000\t360000\tID_0.01_3\t-0.030848\t.\t335000\t360000\t31,120,180\n-chr3L\t360000\t485000\tID_0.01_4\t-0.0580815\t.\t360000\t485000\t51,160,44\n-chr3L\t485000\t525000\tID_0.01_5\t-0.07169775\t.\t485000\t525000\t31,120,180\n-chr3L\t525000\t680000\tID_0.01_6\t-0.1060405\t.\t525000\t680000\t51,160,44\n-chr3L\t680000\t705000\tID_0.01_7\t-0.0148855\t.\t680000\t705000\t31,120,180\n-chr3L\t705000\t740000\tID_0.01_8\t0.002784\t.\t705000\t740000\t51,160,44\n-chr3L\t740000\t870000\tID_0.01_9\t0.00949975\t.\t740000\t870000\t31,120,180\n-chr3L\t870000\t1010000\tID_0.01_10\t-0.09546975\t.\t870000\t1010000\t51,160,44\n-chr3L\t1010000\t1040000\tID_0.01_11\t-0.05182175\t.\t1010000\t1040000\t31,120,180\n-chr3L\t1040000\t1110000\tID_0.01_12\t-0.05874875\t.\t1040000\t1110000\t51,160,44\n-chr3L\t1110000\t1210000\tID_0.01_13\t-0.048349\t.\t1110000\t1210000\t31,120,180\n-chr3L\t1210000\t1245000\tID_0.01_14\t-0.0567565\t.\t1210000\t1245000\t51,160,44\n-chr3L\t1245000\t1300000\tID_0.01_15\t-0.0641435\t.\t1245000\t1300000\t31,120,180\n-chr3L\t1300000\t1465000\tID_0.01_16\t-0.091379\t.\t1300000\t1465000\t51,160,44\n-chr3L\t1465000\t1535000\tID_0.01_17\t-0.01307225\t.\t1465000\t1535000\t31,120,180\n-chr3L\t1535000\t1580000\tID_0.01_18\t-0.08711525\t.\t1535000\t1580000\t51,160,44\n-chr3L\t1580000\t1640000\tID_0.01_19\t-0.08235875\t.\t1580000\t1640000\t31,120,180\n-chr3L\t1640000\t1670000\tID_0.01_20\t-0.0628755\t.\t1640000\t1670000\t51,160,44\n-chr3L\t1670000\t1735000\tID_0.01_21\t-0.037945\t.\t1670000\t1735000\t31,120,180\n-chr3L\t1735000\t1815000\tID_0.01_22\t-0.050313\t.\t1735000\t1815000\t51,160,44\n-chr3L\t1815000\t1850000\tID_0.01_23\t-0.01723525\t.\t1815000\t1850000\t31,120,180\n-chr3L\t1850000\t1925000\tID_0.01_24\t-0.0259975\t.\t1850000\t1925000\t51,160,44\n-chr3L\t1925000\t2155000\tID_0.01_25\t8.325e-05\t.\t1925000\t2155000\t31,120,180\n-chr3L\t2155000\t2260000\tID_0.01_26\t-0.0401965\t.\t2155000\t2260000\t51,160,44\n-chr3L\t2260000\t2390000\tID_0.01_27\t-0.07518575\t.\t2260000\t2390000\t31,120,180\n-chr3L\t2390000\t2460000\tID_0.01_28\t-0.072071\t.\t2390000\t2460000\t51,160,44\n-chr3L\t2460000\t2560000\tID_0.01_29\t-0.09132325\t.\t2460000\t2560000\t31,120,180\n-chr3L\t2560000\t2600000\tID_0.01_30\t-0.09179675\t.\t2560000\t2600000\t51,160,44\n-chr3L\t2600000\t2740000\tID_0.01_31\t-0.0934855\t.\t2600000\t2740000\t31,120,180\n-chr3L\t2740000\t2885000\tID_0.01_32\t-0.08927875\t.\t2740000\t2885000\t51,160,44\n-chr3L\t2885000\t2945000\tID_0.01_33\t-0.08972575\t.\t2885000\t2945000\t31,120,180\n-chr3L\t2945000\t2960000\tID_0.01_34\t0.029899\t.\t2945000\t2960000\t51,160,44\n-chr3L\t2960000\t3045000\tID_0.01_35\t0.0356865\t.\t2960000\t3045000\t31,120,180\n-chr3L\t3045000\t3135000\tID_0.01_36\t-0.00466875\t.\t3045000\t3135000\t51,160,44\n-chr3L\t3135000\t3220000\tID_0.01_37\t0.055702\t.\t3135000\t3220000\t31,120,180\n-chr3L\t3220000\t3255000\tID_0.01_38\t-0.059463\t.\t3220000\t3255000\t51,160,44\n-chr3L\t3255000\t3315000\tID_0.01_39\t-0.045796\t.\t3255000\t3315000\t31,120,180\n-chr3L\t3315000\t3345000\tID_0.01_40\t-0.05499875\t.\t3315000\t3345000\t51,160,44\n-chr3L\t3345000\t3475000\tID_0.01_41\t-0.04234075\t.\t3345000\t3475000\t31,120,180\n-chr3L\t3475000\t3515000\tID_0.01_42\t-0.05097675\t.\t3475000\t3515000\t51,160,44\n-chr3L\t3515000\t3545000\tID_0.01_43\t-0.012488\t.\t3515000\t3545000\t31,120,180\n-chr3L\t3545000\t3615000\tID_0.01_44\t0.02457925\t.\t3545000\t3615000\t51,160,44\n-chr3L\t3615000\t3670000\tID_0.01_45\t0.019683\t.\t3615000\t3670000\t31,120,180\n-chr3L\t3670000\t3765000\tID_0.01_46\t0.09945325\t.\t3670000\t3765000\t51,160,44\n-chr3L\t3765000\t3785000\tID_0.01_47\t-0.047454\t.\t3765000\t3785000\t31,120,180\n-chr3L\t3785000\t3825000\tID_0.01_48\t-0.041084\t.\t3785000\t3825000\t51,160,44\n-chr3L\t3825000\t3900000\tID_0.01_49\t-0.06101175\t.\t3825000\t3900000\t31,120,180\n-chr3L\t3900000\t4000000\tID_0.01_50\t-0.0684535\t.\t3900000\t4000000\t51,160,44\n-chr3L\t4000000\t4120000\tID_0.01_51\t-0.03007875\t.\t4000000\t4120000\t31,120,180\n-chr3L\t4120000\t4165000\tID_0.01_52\t-0.0807515\t.\t4120000\t4165000\t51,160,44\n-chr3L\t4165000\t4200000\tID_0.01_53\t-0.088488\t.\t4165000\t4200000\t31,120,180\n-chr3L\t4200000\t4220000\tID_0.01_54\t-0.098724\t.\t4200000\t4220000\t51,160,44\n-chr3L\t4220000\t4270000\tID_0.01_55\t-0.088911\t.\t4220000\t4270000\t'..b'0\t31,120,180\n-chr3R\t22605000\t22695000\tID_0.01_1354\t-0.011252\t.\t22605000\t22695000\t51,160,44\n-chr3R\t22695000\t22780000\tID_0.01_1355\t-0.089033\t.\t22695000\t22780000\t31,120,180\n-chr3R\t22780000\t22885000\tID_0.01_1356\t-0.04050025\t.\t22780000\t22885000\t51,160,44\n-chr3R\t22885000\t22985000\tID_0.01_1357\t-0.05683475\t.\t22885000\t22985000\t31,120,180\n-chr3R\t22985000\t23110000\tID_0.01_1358\t-0.0237815\t.\t22985000\t23110000\t51,160,44\n-chr3R\t23110000\t23185000\tID_0.01_1359\t-0.100625\t.\t2311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diff -r ec59bf4c3d06 -r 2abdd761461b test-data/find_TADs/multiNone_score.bedgraph
--- a/test-data/find_TADs/multiNone_score.bedgraph Fri Apr 27 03:32:37 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r ec59bf4c3d06 -r 2abdd761461b test-data/find_TADs/multiNone_tad_score.bm
--- a/test-data/find_TADs/multiNone_tad_score.bm Fri Apr 27 03:32:37 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r ec59bf4c3d06 -r 2abdd761461b test-data/find_TADs/multiNone_zscore_matrix.h5

Binary file test-data/find_TADs/multiNone_zscore_matrix.h5 has changed

diff -r ec59bf4c3d06 -r 2abdd761461b test-data/hicBuildMatrix_result1.bam

Binary file test-data/hicBuildMatrix_result1.bam has changed

diff -r ec59bf4c3d06 -r 2abdd761461b test-data/merged_matrix.npz.h5

Binary file test-data/merged_matrix.npz.h5 has changed

diff -r ec59bf4c3d06 -r 2abdd761461b test-data/multiFDR_boundaries.bed
--- a/test-data/multiFDR_boundaries.bed Fri Apr 27 03:32:37 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr2L 22922500 22927500 B04585 -0.068256362891 .
-chrX 87500 92500 B19358 -0.072020401017 .

diff -r ec59bf4c3d06 -r 2abdd761461b test-data/multiFDR_boundaries.gff
--- a/test-data/multiFDR_boundaries.gff Fri Apr 27 03:32:37 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr2L HiCExplorer boundary 22922500 22927500 -0.068256362891 . . ID=B04585;delta=0.021954846720;pvalue=0.000033964776;tad_sep=-0.068256362891
-chrX HiCExplorer boundary 87500 92500 -0.072020401017 . . ID=B19358;delta=0.019799980104;pvalue=0.000055223433;tad_sep=-0.072020401017

diff -r ec59bf4c3d06 -r 2abdd761461b test-data/multiFDR_score.bedgraph
--- a/test-data/multiFDR_score.bedgraph Fri Apr 27 03:32:37 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,23814 +0,0 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diff -r ec59bf4c3d06 -r 2abdd761461b test-data/multiFDR_tad_score.bm
--- a/test-data/multiFDR_tad_score.bm Fri Apr 27 03:32:37 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,23830 +0,0 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diff -r ec59bf4c3d06 -r 2abdd761461b test-data/small_test_matrix_result.bam

Binary file test-data/small_test_matrix_result.bam has changed