Galaxy |

Changeset 4:c4f273c3c73f (2018-04-27)

Previous changeset 3:745e77f4e81e (2018-04-27) Next changeset 5:67bd57e960a3 (2018-06-09)

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

modified:
hicPlotViewpoint.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 745e77f4e81e -r c4f273c3c73f hicPlotViewpoint.xml
--- a/hicPlotViewpoint.xml Fri Apr 27 03:35:16 2018 -0400
+++ b/hicPlotViewpoint.xml Fri Apr 27 08:43:05 2018 -0400

@@ -85,7 +85,7 @@
**hicPlotViewpoint** outputs an image with the plotted interactions around the reference point in png or svg format, an example plot can be found bellow. An option allows to also output the interactions as a bedgraph file.

.. image:: $PATH_TO_IMAGES/pulication_plots_viewpoint.png
- :width: 80 %
+ :width: 50 %

_________________

diff -r 745e77f4e81e -r c4f273c3c73f static/images/hicCompareMatrices_QC_log2_m50_matrix_plot (1).png

Binary file static/images/hicCompareMatrices_QC_log2_m50_matrix_plot (1).png has changed

diff -r 745e77f4e81e -r c4f273c3c73f static/images/hicCompareMatrices_QC_log2_m50_matrix_plot.png

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diff -r 745e77f4e81e -r c4f273c3c73f 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 745e77f4e81e -r c4f273c3c73f 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 745e77f4e81e -r c4f273c3c73f static/images/hicPlotDistVsCounts.png

Binary file static/images/hicPlotDistVsCounts.png has changed

diff -r 745e77f4e81e -r c4f273c3c73f static/images/hicPlotDistvsCounts.png

Binary file static/images/hicPlotDistvsCounts.png has changed

diff -r 745e77f4e81e -r c4f273c3c73f test-data/find_TADs/multiBonferroni_boundaries.bed
--- a/test-data/find_TADs/multiBonferroni_boundaries.bed Fri Apr 27 03:35:16 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 745e77f4e81e -r c4f273c3c73f test-data/find_TADs/multiBonferroni_boundaries.gff
--- a/test-data/find_TADs/multiBonferroni_boundaries.gff Fri Apr 27 03:35:16 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 745e77f4e81e -r c4f273c3c73f test-data/find_TADs/multiBonferroni_score.bedgraph
--- a/test-data/find_TADs/multiBonferroni_score.bedgraph Fri Apr 27 03:35:16 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 745e77f4e81e -r c4f273c3c73f test-data/find_TADs/multiBonferroni_tad_score.bm
--- a/test-data/find_TADs/multiBonferroni_tad_score.bm Fri Apr 27 03:35:16 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,23830 +0,0 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diff -r 745e77f4e81e -r c4f273c3c73f test-data/find_TADs/multiBonferroni_zscore_matrix.h5

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

diff -r 745e77f4e81e -r c4f273c3c73f test-data/find_TADs/multiFDR_zscore_matrix.h5

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

diff -r 745e77f4e81e -r c4f273c3c73f test-data/find_TADs/multiNone_boundaries.bed
--- a/test-data/find_TADs/multiNone_boundaries.bed Fri Apr 27 03:35:16 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1408 +0,0 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diff -r 745e77f4e81e -r c4f273c3c73f test-data/find_TADs/multiNone_boundaries.gff
--- a/test-data/find_TADs/multiNone_boundaries.gff Fri Apr 27 03:35:16 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 745e77f4e81e -r c4f273c3c73f test-data/find_TADs/multiNone_domains.bed
--- a/test-data/find_TADs/multiNone_domains.bed Fri Apr 27 03:35:16 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 745e77f4e81e -r c4f273c3c73f test-data/find_TADs/multiNone_score.bedgraph
--- a/test-data/find_TADs/multiNone_score.bedgraph Fri Apr 27 03:35:16 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 745e77f4e81e -r c4f273c3c73f test-data/find_TADs/multiNone_tad_score.bm
--- a/test-data/find_TADs/multiNone_tad_score.bm Fri Apr 27 03:35:16 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 745e77f4e81e -r c4f273c3c73f test-data/find_TADs/multiNone_zscore_matrix.h5

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

diff -r 745e77f4e81e -r c4f273c3c73f test-data/hicBuildMatrix_result1.bam

Binary file test-data/hicBuildMatrix_result1.bam has changed

diff -r 745e77f4e81e -r c4f273c3c73f test-data/merged_matrix.npz.h5

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

diff -r 745e77f4e81e -r c4f273c3c73f test-data/multiFDR_boundaries.bed
--- a/test-data/multiFDR_boundaries.bed Fri Apr 27 03:35:16 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 745e77f4e81e -r c4f273c3c73f test-data/multiFDR_boundaries.gff
--- a/test-data/multiFDR_boundaries.gff Fri Apr 27 03:35:16 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 745e77f4e81e -r c4f273c3c73f test-data/multiFDR_score.bedgraph
--- a/test-data/multiFDR_score.bedgraph Fri Apr 27 03:35:16 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,23814 +0,0 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diff -r 745e77f4e81e -r c4f273c3c73f test-data/multiFDR_tad_score.bm
--- a/test-data/multiFDR_tad_score.bm Fri Apr 27 03:35:16 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,23830 +0,0 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diff -r 745e77f4e81e -r c4f273c3c73f test-data/small_test_matrix_result.bam

Binary file test-data/small_test_matrix_result.bam has changed