changeset 4:0170de5072d4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
author iuc
date Fri, 20 Mar 2020 05:11:17 -0400
parents c96f1a93beb7
children a1dc6db337ca
files chira_merge.xml macros.xml test-data/alignments.bed test-data/segments.bed
diffstat 4 files changed, 408 insertions(+), 362 deletions(-) [+]
line wrap: on
line diff
--- a/chira_merge.xml	Thu Mar 12 17:05:50 2020 -0400
+++ b/chira_merge.xml	Fri Mar 20 05:11:17 2020 -0400
@@ -9,9 +9,17 @@
         -b '$alignments'
         #if str($annotation.choice) == "yes":
             -g '$annotation.gtf'
-        #end if            
-        -ao '$alignment_overlap'
+        #end if
         -so '$segment_overlap'
+        #if str($merge.mode) == "blockbuster":
+            -bb
+            -d '$merge.distance'
+            -mc '$merge.min_cluster_height'
+            -mb '$merge.min_block_height'
+            -sc '$merge.scale'
+        #else:
+            -ao '$merge.alignment_overlap'
+        #end if
         -o ./
     ]]></command>
 
@@ -27,12 +35,30 @@
             </when>
             <when value="no">
                 <!-- Do nothing -->
-            </when>        
+            </when>
         </conditional>
-        <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1"
-            help="Minimum fraction of BED entries that must overlap inorder to merge"/>
         <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1"
             help="Matching read positions with greater than this fraction overlap are merged into a segment"/>
+        <conditional name="merge">
+            <param name="mode" type="select" label="Select the mode of merging">
+                <option value="overlap">Overlap based</option>
+                <option value="blockbuster">Gaussian based (blockbuster)</option>
+            </param>
+            <when value="overlap">
+                <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1"
+                    help="Minimum fraction of BED entries that must overlap inorder to merge"/>
+            </when>
+            <when value="blockbuster">
+                <param name="distance" type="integer" value="30" label="Blockbuster parameter distance"
+                    help="Minimum distance between two clusters"/>
+                <param name="min_cluster_height" type="float" value="10" label="Blockbuster parameter minClusterHeight"
+                    help="minimum height (readno) of a cluster"/>
+                <param name="min_block_height" type="float" value="1" label="Blockbuster parameter minBlockHeight"
+                    help="minimum height (readno) of a block"/>
+                <param name="scale" type="float" value="0.4" label="Blockbuster parameter scale" min="0" max="1"
+                    help="scale stddev for a single read"/>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data format="bed" name="segments_bed" from_work_dir="segments.bed" label="ChiRA aligned read segments on ${on_string}"/>
@@ -40,34 +66,54 @@
     </outputs>
 
     <tests>
-        <!-- Test: Map without annotation -->
+        <!-- Test: Merge without annotation -->
         <test expect_num_outputs="2">
             <param name="alignments" value="alignments.bed"/>
             <param name="choice" value="no" />
             <output name="segments_bed" >
                 <assert_contents>
-                    <has_text_matching expression="ENSMUST00000160533\t69\t82\t6|1|4,ENSMUST00000160533,69,82,+,42S13M\t0\t+" />
+                    <has_text_matching expression="ENSMUST00000160533\t69\t82\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t\+" />
                 </assert_contents>
             </output>
             <output name="merged_bed" >
                 <assert_contents>
-                    <has_text_matching expression="ENSMUST00000182010\t19\t74\t+\t6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M" />
+                    <has_text_matching expression="ENSMUST00000182010\t408\t477\t\+" />
+                    <has_text_matching expression="mmu-miR-106a-3p\t4\t15\t\+" />
                 </assert_contents>
             </output>
         </test>
-        <!-- Test: Map with annotation -->
+        <!-- Test: Merge with annotation -->
         <test expect_num_outputs="2">
             <param name="alignments" value="alignments.bed" />
             <param name="choice" value="yes" />
             <param name="gtf" value="annotation.gtf" />
             <output name="segments_bed" >
                 <assert_contents>
-                    <has_text_matching expression="5\t137142331\t137142344\t6|1|4,ENSMUST00000160533,69,82,+,42S13M\t0\t-" />
+                    <has_text_matching expression="5\t137142331\t137142344\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t-" />
                 </assert_contents>
             </output>
             <output name="merged_bed" >
                 <assert_contents>
-                    <has_text_matching expression="17\t39846976\t39847031\t+\t6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M" />
+                    <has_text_matching expression="17\t39846957\t39847016\t\+" />
+                    <has_text_matching expression="5\t137142331\t137142344\t-" />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test: Merge using blockbuster -->
+        <test expect_num_outputs="2">
+            <param name="alignments" value="alignments.bed" />
+            <param name="choice" value="yes" />
+            <param name="gtf" value="annotation.gtf" />
+            <param name="mode" value="blockbuster" />
+            <param name="min_cluster_height" value="5" />
+            <output name="segments_bed" >
+                <assert_contents>
+                    <has_text_matching expression="5\t137142331\t137142344\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t-" />
+                </assert_contents>
+            </output>
+            <output name="merged_bed" >
+                <assert_contents>
+                    <has_text_matching expression="17\t39846957\t39847016\t\+" />
                 </assert_contents>
             </output>
         </test>
--- a/macros.xml	Thu Mar 12 17:05:50 2020 -0400
+++ b/macros.xml	Fri Mar 20 05:11:17 2020 -0400
@@ -1,6 +1,6 @@
 <macros>
     <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token>
-    <token name="@TOOL_VERSION@">1.0.4</token>
+    <token name="@TOOL_VERSION@">1.1.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">chira</requirement>
--- a/test-data/alignments.bed	Thu Mar 12 17:05:50 2020 -0400
+++ b/test-data/alignments.bed	Fri Mar 20 05:11:17 2020 -0400
@@ -1,337 +1,337 @@
-mmu-miR-124-3p	0	20	3|2,mmu-miR-124-3p,0,20,+,5S20M30S	0	+
-ENSMUST00000182884	6023	6051	28|3,ENSMUST00000182884,6023,6051,+,27S28M	0	+
-ENSMUST00000182010	428	477	36|10,ENSMUST00000182010,428,477,+,5S49M1S	0	+
-ENSMUST00000113560	1969	1992	38|2,ENSMUST00000113560,1969,1992,+,32S23M	0	+
-mmu-miR-9-5p	0	23	11|1,mmu-miR-9-5p,0,23,+,5S23M27S	0	+
-mmu-miR-9-5p	0	23	38|2,mmu-miR-9-5p,0,23,+,5S23M27S	0	+
-ENSMUST00000138581	1621	1644	38|2,ENSMUST00000138581,1621,1644,+,32S23M	0	+
-ENSMUST00000182010	419	468	34|1,ENSMUST00000182010,419,468,+,5S49M1S	0	+
-ENSMUST00000047061	2204	2232	28|3,ENSMUST00000047061,2204,2232,+,27S28M	0	+
-ENSMUST00000100207	1580	1603	38|2,ENSMUST00000100207,1580,1603,+,32S23M	0	+
-ENSMUST00000172109	1499	1514	11|1,ENSMUST00000172109,1499,1514,+,35S15M5S	0	+
-ENSMUST00000182795	2429	2457	28|3,ENSMUST00000182795,2429,2457,+,27S28M	0	+
-ENSMUST00000075326	1661	1684	38|2,ENSMUST00000075326,1661,1684,+,32S23M	0	+
-ENSMUST00000106215	953	1003	21|3,ENSMUST00000106215,953,1003,+,5S50M	0	+
-ENSMUST00000182439	2218	2246	28|3,ENSMUST00000182439,2218,2246,+,27S28M	0	+
-ENSMUST00000185502	4240	4290	7|1,ENSMUST00000185502,4240,4290,+,5S50M	0	+
-ENSMUST00000166060	435	467	19|2,ENSMUST00000166060,435,467,+,26S12M3D17M	0	+
-ENSMUST00000107857	399	431	19|2,ENSMUST00000107857,399,431,+,26S12M3D17M	0	+
-ENSMUST00000155835	2617	2667	4|2,ENSMUST00000155835,2617,2667,+,5S50M	0	+
-ENSMUST00000071555	1077	1127	21|3,ENSMUST00000071555,1077,1127,+,5S50M	0	+
-ENSMUST00000181221	1499	1514	11|1,ENSMUST00000181221,1499,1514,+,35S15M5S	0	+
-ENSMUST00000182010	424	474	35|9,ENSMUST00000182010,424,474,+,5S50M	0	+
-ENSMUST00000100208	1748	1771	38|2,ENSMUST00000100208,1748,1771,+,32S23M	0	+
-ENSMUST00000113562	1759	1782	38|2,ENSMUST00000113562,1759,1782,+,32S23M	0	+
-ENSMUST00000128302	226	257	6|4,ENSMUST00000128302,226,257,+,24S31M	0	+
-ENSMUST00000148758	777	805	27|1,ENSMUST00000148758,777,805,+,27S28M	0	+
-ENSMUST00000111596	608	626	19|2,ENSMUST00000111596,608,626,+,30S18M7S	0	+
-ENSMUST00000106992	3071	3121	16|3,ENSMUST00000106992,3071,3121,+,5S50M	0	+
-mmu-miR-9-5p	0	23	32|1,mmu-miR-9-5p,0,23,+,5S23M27S	0	+
-ENSMUST00000182972	3233	3261	28|3,ENSMUST00000182972,3233,3261,+,27S28M	0	+
-ENSMUST00000064989	2466	2516	29|1,ENSMUST00000064989,2466,2516,+,5S50M	0	+
-ENSMUST00000182029	3343	3371	28|3,ENSMUST00000182029,3343,3371,+,27S28M	0	+
-ENSMUST00000182010	426	476	15|2,ENSMUST00000182010,426,476,+,5S50M	0	+
-ENSMUST00000187980	1254	1305	24|1,ENSMUST00000187980,1254,1305,+,4S51M	0	+
-ENSMUST00000182692	3374	3402	28|3,ENSMUST00000182692,3374,3402,+,27S28M	0	+
-ENSMUST00000167541	285	336	1|3,ENSMUST00000167541,285,336,+,4S51M	0	+
-ENSMUST00000113564	1723	1746	38|2,ENSMUST00000113564,1723,1746,+,32S23M	0	+
-ENSMUST00000128500	1065	1088	38|2,ENSMUST00000128500,1065,1088,+,32S23M	0	+
-ENSMUST00000045218	5944	5972	3|2,ENSMUST00000045218,5944,5972,+,27S28M	0	+
-ENSMUST00000111134	233	264	6|4,ENSMUST00000111134,233,264,+,24S31M	0	+
-ENSMUST00000182010	9	59	8|4,ENSMUST00000182010,9,59,+,5S50M	0	+
-ENSMUST00000167930	463	495	19|2,ENSMUST00000167930,463,495,+,26S12M3D17M	0	+
-ENSMUST00000075012	856	906	14|1,ENSMUST00000075012,856,906,+,5S50M	0	+
-ENSMUST00000041591	326	377	1|3,ENSMUST00000041591,326,377,+,4S51M	0	+
-ENSMUST00000106746	905	955	14|1,ENSMUST00000106746,905,955,+,5S50M	0	+
-ENSMUST00000182437	2388	2416	28|3,ENSMUST00000182437,2388,2416,+,27S28M	0	+
-ENSMUST00000171545	470	521	1|3,ENSMUST00000171545,470,521,+,4S51M	0	+
-ENSMUST00000181455	1765	1780	11|1,ENSMUST00000181455,1765,1780,+,35S15M5S	0	+
-ENSMUST00000032571	4128	4178	20|1,ENSMUST00000032571,4128,4178,+,5S15M1D34M	0	+
-ENSMUST00000092432	5519	5547	28|3,ENSMUST00000092432,5519,5547,+,27S28M	0	+
-ENSMUST00000182010	0	47	31|10,ENSMUST00000182010,0,47,+,8S47M	0	+
-mmu-miR-124-3p	0	20	19|2,mmu-miR-124-3p,0,20,+,6S20M29S	0	+
-ENSMUST00000182010	0	44	5|12,ENSMUST00000182010,0,44,+,9S44M2S	0	+
-ENSMUST00000062147	344	394	21|3,ENSMUST00000062147,344,394,+,5S50M	0	+
-ENSMUST00000166972	469	501	19|2,ENSMUST00000166972,469,501,+,26S12M3D17M	0	+
-ENSMUST00000085399	463	495	19|2,ENSMUST00000085399,463,495,+,26S12M3D17M	0	+
-ENSMUST00000027103	804	832	27|1,ENSMUST00000027103,804,832,+,27S28M	0	+
-mmu-miR-124-3p	0	20	27|1,mmu-miR-124-3p,0,20,+,6S20M29S	0	+
-ENSMUST00000183169	5204	5232	28|3,ENSMUST00000183169,5204,5232,+,27S28M	0	+
-ENSMUST00000182010	0	46	13|8,ENSMUST00000182010,0,46,+,9S46M	0	+
-mmu-miR-9-5p	0	22	28|3,mmu-miR-9-5p,0,22,+,5S22M28S	0	+
-ENSMUST00000130489	1065	1115	18|2,ENSMUST00000130489,1065,1115,+,5S50M	0	+
-ENSMUST00000182010	0	46	17|4,ENSMUST00000182010,0,46,+,9S46M	0	+
-ENSMUST00000118936	1387	1402	11|1,ENSMUST00000118936,1387,1402,+,33S15M7S	0	+
-ENSMUST00000183148	5792	5820	28|3,ENSMUST00000183148,5792,5820,+,27S28M	0	+
-ENSMUST00000092434	5573	5601	28|3,ENSMUST00000092434,5573,5601,+,27S28M	0	+
-ENSMUST00000182010	9	34	37|2,ENSMUST00000182010,9,34,+,30S25M	0	+
-ENSMUST00000183023	1361	1389	28|3,ENSMUST00000183023,1361,1389,+,27S28M	0	+
-ENSMUST00000100301	1765	1780	11|1,ENSMUST00000100301,1765,1780,+,35S15M5S	0	+
-ENSMUST00000113559	1621	1644	38|2,ENSMUST00000113559,1621,1644,+,32S23M	0	+
-ENSMUST00000173516	342	393	1|3,ENSMUST00000173516,342,393,+,4S51M	0	+
-ENSMUST00000113555	1676	1699	38|2,ENSMUST00000113555,1676,1699,+,32S23M	0	+
-ENSMUST00000182010	408	458	22|1,ENSMUST00000182010,408,458,+,5S50M	0	+
-ENSMUST00000128621	775	803	27|1,ENSMUST00000128621,775,803,+,27S28M	0	+
-ENSMUST00000182207	1067	1095	28|3,ENSMUST00000182207,1067,1095,+,27S28M	0	+
-ENSMUST00000182010	9	59	33|2,ENSMUST00000182010,9,59,+,5S50M	0	+
-ENSMUST00000100305	917	967	14|1,ENSMUST00000100305,917,967,+,5S50M	0	+
-ENSMUST00000107586	2666	2716	4|2,ENSMUST00000107586,2666,2716,+,5S50M	0	+
-mmu-miR-124-3p	0	20	25|1,mmu-miR-124-3p,0,20,+,5S20M30S	0	+
-ENSMUST00000181974	2606	2634	28|3,ENSMUST00000181974,2606,2634,+,27S28M	0	+
-ENSMUST00000039796	1502	1517	11|1,ENSMUST00000039796,1502,1517,+,33S15M7S	0	+
-ENSMUST00000068237	606	624	19|2,ENSMUST00000068237,606,624,+,30S18M7S	0	+
-ENSMUST00000149559	180	198	37|2,ENSMUST00000149559,180,198,+,20S18M17S	0	+
-ENSMUST00000092433	3616	3644	28|3,ENSMUST00000092433,3616,3644,+,27S28M	0	+
-ENSMUST00000182010	430	477	30|4,ENSMUST00000182010,430,477,+,5S47M3S	0	+
-ENSMUST00000044730	2734	2784	4|2,ENSMUST00000044730,2734,2784,+,5S50M	0	+
-ENSMUST00000092431	5510	5538	28|3,ENSMUST00000092431,5510,5538,+,27S28M	0	+
-ENSMUST00000139950	1170	1220	18|2,ENSMUST00000139950,1170,1220,+,5S50M	0	+
-ENSMUST00000182010	409	459	12|3,ENSMUST00000182010,409,459,+,5S50M	0	+
-ENSMUST00000172835	4128	4178	20|1,ENSMUST00000172835,4128,4178,+,5S15M1D34M	0	+
-ENSMUST00000182155	5247	5275	28|3,ENSMUST00000182155,5247,5275,+,27S28M	0	+
-ENSMUST00000028829	496	511	11|1,ENSMUST00000028829,496,511,+,29S15M11S	0	+
-ENSMUST00000182269	2748	2776	28|3,ENSMUST00000182269,2748,2776,+,27S28M	0	+
-ENSMUST00000094844	1360	1410	18|2,ENSMUST00000094844,1360,1410,+,5S50M	0	+
-ENSMUST00000183074	3336	3364	28|3,ENSMUST00000183074,3336,3364,+,27S28M	0	+
-ENSMUST00000182992	7998	8026	28|3,ENSMUST00000182992,7998,8026,+,27S28M	0	+
-ENSMUST00000054167	5456	5484	28|3,ENSMUST00000054167,5456,5484,+,27S28M	0	+
-ENSMUST00000073879	1565	1588	38|2,ENSMUST00000073879,1565,1588,+,32S23M	0	+
-ENSMUST00000183261	3336	3364	28|3,ENSMUST00000183261,3336,3364,+,27S28M	0	+
-ENSMUST00000110901	232	247	11|1,ENSMUST00000110901,232,247,+,29S15M11S	0	+
-mmu-miR-124-3p	0	20	6|4,mmu-miR-124-3p,0,20,+,5S20M30S	0	+
-mmu-miR-124-3p	8	19	14|1,mmu-miR-124-3p,8,19,+,2S11M42S	0	+
-mmu-miR-127-3p	12	22	29|1,mmu-miR-127-3p,12,22,+,17S10M28S	0	+
-mmu-miR-188-3p	1	11	10|2,mmu-miR-188-3p,1,11,+,22S10M23S	0	+
-mmu-miR-344d-1-5p	8	17	9|1,mmu-miR-344d-1-5p,8,17,+,3S9M43S	0	+
-mmu-miR-344c-5p	8	17	9|1,mmu-miR-344c-5p,8,17,+,3S9M43S	0	+
-mmu-miR-344d-2-5p	8	17	9|1,mmu-miR-344d-2-5p,8,17,+,3S9M43S	0	+
-mmu-miR-196a-2-3p	6	16	25|1,mmu-miR-196a-2-3p,6,16,+,29S10M16S	0	+
-mmu-miR-208a-5p	0	10	26|1,mmu-miR-208a-5p,0,10,+,10M45S	0	+
-mmu-miR-22-3p	8	18	12|3,mmu-miR-22-3p,8,18,+,10M45S	0	+
-mmu-miR-33-3p	1	11	29|1,mmu-miR-33-3p,1,11,+,1S10M44S	0	+
-mmu-miR-181c-5p	8	18	14|1,mmu-miR-181c-5p,8,18,+,44S10M1S	0	+
-mmu-miR-3109-3p	3	13	2|1,mmu-miR-3109-3p,3,13,+,41S10M3S	0	+
-mmu-miR-6407	7	17	2|1,mmu-miR-6407,7,17,+,33S10M11S	0	+
-mmu-miR-3076-5p	13	22	18|2,mmu-miR-3076-5p,13,22,+,9M46S	0	+
-mmu-miR-106a-3p	4	13	18|2,mmu-miR-106a-3p,4,13,+,9M46S	0	+
-mmu-miR-871-5p	10	19	18|2,mmu-miR-871-5p,10,19,+,1S9M45S	0	+
-mmu-miR-25-3p	0	10	32|1,mmu-miR-25-3p,0,10,+,44S10M1S	0	+
-mmu-miR-497a-3p	3	13	7|1,mmu-miR-497a-3p,3,13,+,42S10M3S	0	+
-mmu-miR-190b-5p	6	17	18|2,mmu-miR-190b-5p,6,17,+,32S11M12S	0	+
-mmu-miR-3098-3p	3	14	16|3,mmu-miR-3098-3p,3,14,+,39S11M5S	0	+
-mmu-miR-6900-5p	0	10	18|2,mmu-miR-6900-5p,0,10,+,45S10M	0	+
-mmu-miR-3104-3p	10	20	21|3,mmu-miR-3104-3p,10,20,+,40S10M5S	0	+
-mmu-miR-7651-3p	6	16	24|1,mmu-miR-7651-3p,6,16,+,6S10M39S	0	+
-mmu-miR-742-3p	7	16	16|3,mmu-miR-742-3p,7,16,+,35S9M11S	0	+
-mmu-miR-6936-3p	2	11	20|1,mmu-miR-6936-3p,2,11,+,31S9M14S	0	+
-mmu-miR-6936-3p	2	11	20|1,mmu-miR-6936-3p,2,11,+,33S9M12S	0	+
-mmu-miR-6992-5p	0	10	6|4,mmu-miR-6992-5p,0,10,+,21S10M24S	0	+
-mmu-miR-7016-3p	10	20	23|1,mmu-miR-7016-3p,10,20,+,34S10M11S	0	+
-mmu-miR-7019-5p	6	16	4|2,mmu-miR-7019-5p,6,16,+,30S10M15S	0	+
-mmu-miR-7046-5p	13	22	2|1,mmu-miR-7046-5p,13,22,+,24S9M21S	0	+
-mmu-miR-7046-5p	8	19	1|3,mmu-miR-7046-5p,8,19,+,11S11M33S	0	+
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+ENSMUST00000182010	408	445	22|1,ENSMUST00000182010,408,445,+,5S37M13S	1	+
+ENSMUST00000182010	409	445	12|3,ENSMUST00000182010,409,445,+,5S36M14S	1	+
+ENSMUST00000182010	419	445	34|1,ENSMUST00000182010,419,445,+,5S26M24S	1	+
+ENSMUST00000182010	424	445	35|9,ENSMUST00000182010,424,445,+,5S21M29S	1	+
+ENSMUST00000182010	426	445	15|2,ENSMUST00000182010,426,445,+,5S19M31S	1	+
+ENSMUST00000182010	428	445	36|10,ENSMUST00000182010,428,445,+,5S17M33S	1	+
+ENSMUST00000182010	430	445	30|4,ENSMUST00000182010,430,445,+,5S15M35S	1	+
+ENSMUST00000182010	446	458	22|1,ENSMUST00000182010,446,458,+,43S12M	1	+
+ENSMUST00000182010	446	459	12|3,ENSMUST00000182010,446,459,+,42S13M	1	+
+ENSMUST00000182010	446	458	34|1,ENSMUST00000182010,446,458,+,32S12M11S	1	+
+ENSMUST00000182010	446	468	35|9,ENSMUST00000182010,446,468,+,27S22M6S	1	+
+ENSMUST00000182010	446	468	15|2,ENSMUST00000182010,446,468,+,25S22M8S	1	+
+ENSMUST00000182010	446	468	36|10,ENSMUST00000182010,446,468,+,23S22M10S	1	+
+ENSMUST00000182010	446	468	30|4,ENSMUST00000182010,446,468,+,21S22M12S	1	+
+ENSMUST00000064314	967	982	23|1,ENSMUST00000064314,967,982,+,18S15M22S	1	+
--- a/test-data/segments.bed	Thu Mar 12 17:05:50 2020 -0400
+++ b/test-data/segments.bed	Fri Mar 20 05:11:17 2020 -0400
@@ -1,13 +1,13 @@
-ENSMUST00000182010	19	68	6|1|1,ENSMUST00000182010,19,68,+,5S49M1S	0	+
-ENSMUST00000182010	24	74	7|9|1,ENSMUST00000182010,24,74,+,5S50M	0	+
-mmu-miR-20a-5p	0	23	3|2|1,mmu-miR-20a-5p,0,23,+,5S23M27S	0	+
-mmu-miR-6898-5p	11	21	2|2|1,mmu-miR-6898-5p,11,21,+,10M39S	0	+
-mmu-miR-6979-3p	2	12	4|1|1,mmu-miR-6979-3p,2,12,+,29S10M15S	0	+
-ENSMUST00000137264	12	27	2|2|2,ENSMUST00000137264,12,27,+,4S15M30S	0	+
-ENSMUST00000136025	32	46	4|1|2,ENSMUST00000136025,32,46,+,1S14M39S	0	+
-ENSMUST00000136025	132	142	3|2|2,ENSMUST00000136025,132,142,+,34S10M11S	0	+
-ENSMUST00000182010	19	45	6|1|2,ENSMUST00000182010,19,45,+,5S26M24S	0	+
-ENSMUST00000182010	24	45	7|9|2,ENSMUST00000182010,24,45,+,5S21M29S	0	+
-ENSMUST00000182010	46	58	6|1|3,ENSMUST00000182010,46,58,+,32S12M11S	0	+
-ENSMUST00000182010	46	68	7|9|3,ENSMUST00000182010,46,68,+,27S22M6S	0	+
-ENSMUST00000160533	69	82	6|1|4,ENSMUST00000160533,69,82,+,42S13M	0	+
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+ENSMUST00000182010	24	74	7|9|1,ENSMUST00000182010,24,74,+,5S50M	1	+
+mmu-miR-20a-5p	0	23	3|2|1,mmu-miR-20a-5p,0,23,+,5S23M27S	1	+
+mmu-miR-6898-5p	11	21	2|2|1,mmu-miR-6898-5p,11,21,+,10M39S	1	+
+mmu-miR-6979-3p	2	12	4|1|1,mmu-miR-6979-3p,2,12,+,29S10M15S	1	+
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