# HG changeset patch
# User iuc
# Date 1485691163 18000
# Node ID 469c0d7489bdadb0ef4b7e071df8fbf004baa75e
# Parent  e8ca8941952afef8d07524e4d9abccae32d70a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232

diff -r e8ca8941952a -r 469c0d7489bd dexseq.xml
--- a/dexseq.xml	Tue Oct 13 17:21:57 2015 -0400
+++ b/dexseq.xml	Sun Jan 29 06:59:23 2017 -0500
@@ -1,17 +1,19 @@
-<tool id="dexseq" name="DEXSeq" version="1.0">
+<tool id="dexseq" name="DEXSeq" version="1.20.1">
     <description>Determines differential exon usage from count tables</description>
     <requirements>
-        <requirement type="package" version="1.14">dexseq</requirement>
+        <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="0.2.15">r-rjson</requirement>
     </requirements>
     <code file="dexseq_helper.py" />
     <stdio>
-        <regex match="Execution halted" 
-           source="both" 
-           level="fatal" 
+        <regex match="Execution halted"
+           source="both"
+           level="fatal"
            description="Execution halted." />
-        <regex match="Input-Error 01" 
-           source="both" 
-           level="fatal" 
+        <regex match="Input-Error 01"
+           source="both"
+           level="fatal"
            description="Error in your input parameters: Make sure you only apply factors to selected samples." />
         <regex match="Error in"
            source="both"
@@ -31,8 +33,8 @@
     <![CDATA[
         mkdir ./html_out &&
         #import json
-        Rscript $__tool_directory__/dexseq.R
-            -o "$dexseq_out"
+        Rscript '$__tool_directory__/dexseq.R'
+            -o '$dexseq_out'
             -p \${GALAXY_SLOTS:-4}
             #set $temp_factor_names = list()
             #for $factor in $rep_factorName:
@@ -57,11 +59,11 @@
             #if $report:
                 -r ./html_out
                 &&
-                mkdir $htmlreport.extra_files_path
+                mkdir '$htmlreport.extra_files_path'
                 &&
                 cp ./html_out/testForDEU.html $htmlreport
                 &&
-                cp -r ./html_out/* $htmlreport.extra_files_path
+                cp -r ./html_out/* '$htmlreport.extra_files_path'
             #end if
 
     ]]>
@@ -69,7 +71,7 @@
     <inputs>
         <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
         <repeat name="rep_factorName" title="Factor" min="1">
-            <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 
+            <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
                 help="Only letters, numbers and underscores will be retained in this field">
                 <sanitizer>
                     <valid initial="string.letters,string.digits"><add value="_" /></valid>
@@ -128,7 +130,7 @@
     <![CDATA[
 .. class:: infomark
 
-**What it does** 
+**What it does**
 
 Inference of differential exon usage in RNA-Seq.
 
@@ -144,7 +146,7 @@
 The following table gives some examples of factors and their levels:
 
 ========= ============== ===============
-Factor    Factor level 1 Factor level 2 
+Factor    Factor level 1 Factor level 2
 --------- -------------- ---------------
 condition Knockdown      Wildtype
 --------- -------------- ---------------
diff -r e8ca8941952a -r 469c0d7489bd dexseq_count.xml
--- a/dexseq_count.xml	Tue Oct 13 17:21:57 2015 -0400
+++ b/dexseq_count.xml	Sun Jan 29 06:59:23 2017 -0500
@@ -1,9 +1,8 @@
-<tool id="dexseq_count" name="DEXSeq-Count" version="1.0">
+<tool id="dexseq_count" name="DEXSeq-Count" version="1.20.1">
     <description>Prepare and count exon abundancies from RNA-seq data</description>
     <requirements>
-        <requirement type="package" version="1.14">dexseq</requirement>
-        <requirement type="package" version="0.6.1">htseq</requirement>
-        <requirement type="package" version="0.7.7">pysam</requirement>
+        <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement>
+        <requirement type="package" version="0.6.1.post1">htseq</requirement>
     </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -16,20 +15,20 @@
     <command>
     <![CDATA[
         #if $mode.mode_select == "prepare":
-            python \$DEXSEQ_ROOT/python_scripts/dexseq_prepare_annotation.py
+            dexseq_prepare_annotation.py
                 -r $mode.aggregate
-                $mode.gtffile
-                $flattened_gtf_out
+                '$mode.gtffile'
+                '$flattened_gtf_out'
         #elif $mode.mode_select == "count":
-            python \$DEXSEQ_ROOT/python_scripts/dexseq_count.py
+            dexseq_count.py
                 -f bam
                 -p $mode.paired
                 -s $mode.stranded
                 -a $mode.qual
                 -r $mode.order
                 $mode.flattened_gtf_in
-                $mode.bamfile
-                $counts_file
+                '$mode.bamfile'
+                '$counts_file'
         #end if
     ]]>
     </command>
@@ -42,7 +41,7 @@
             <when value="prepare">
                 <param name="gtffile" type="data" format="gff" label="GTF file"/>
                 <param name="aggregate" type="boolean" checked="True" truevalue="yes" falsevalue="no"
-                    label="Aggretare genes with exons?"
+                    label="Aggregate genes with exons?"
                     help="Indicates whether two or more genes sharing an exon should be merged into an 'aggregate gene'. If 'no', the exons that can not be assiged to a single gene are ignored."/>
             </when>
             <when value="count">
@@ -85,7 +84,7 @@
     <![CDATA[
 .. class:: infomark
 
-**What it does** 
+**What it does**
 
 The main goal of this tol is to count the number of reads/fragments per exon of each gene in RNA-seq sample. In addition it also prepares your annotation gtf file compatible for counting.
 
diff -r e8ca8941952a -r 469c0d7489bd dexseq_helper.py
--- a/dexseq_helper.py	Tue Oct 13 17:21:57 2015 -0400
+++ b/dexseq_helper.py	Sun Jan 29 06:59:23 2017 -0500
@@ -1,41 +1,36 @@
-
-from galaxy.tools.parameters import DataToolParameter
-
-def validate_input( trans, error_map, param_values, page_param_map ):
-    """
-        Validates the user input, before execution.
-    """
-    factors = param_values['rep_factorName']
-    factor_name_list = []
-    factor_duplication = False
-    level_duplication = False
-
-    for factor in factors:
-        # factor names should be unique
-        fn = factor['factorName']
-        if fn in factor_name_list:
-            factor_duplication = True
-            break
-        factor_name_list.append( fn )
-
-        level_name_list = list()
-        factor_index_list = list()
-
-        for level in ['factorLevel1', 'factorLevel2']:
-            # level names under one factor should be unique
-            fl = factor[level]
-            if fl in level_name_list:
-                level_duplication = True
-            level_name_list.append( fl )
-
-        if level_duplication:
-            error_map['rep_factorName'] = [ dict() for t in factors ]
-            for i in range( len( factors ) ):
-                error_map['rep_factorName'][i]['FactorLevel1'] = [ {'factorLevel': 'Factor levels for each factor need to be unique'} for t in [factor['factorLevel1'], factor['factorLevel2']] ]
-            break
-
-    if factor_duplication:
-        error_map['rep_factorName'] = [ dict() for t in factors ]
-        for i in range( len( factors ) ):
-            error_map['rep_factorName'][i]['factorName'] = 'Factor names need to be unique.'
-
+def validate_input( trans, error_map, param_values, page_param_map ):
+    """
+        Validates the user input, before execution.
+    """
+    factors = param_values['rep_factorName']
+    factor_name_list = []
+    factor_duplication = False
+    level_duplication = False
+
+    for factor in factors:
+        # factor names should be unique
+        fn = factor['factorName']
+        if fn in factor_name_list:
+            factor_duplication = True
+            break
+        factor_name_list.append( fn )
+
+        level_name_list = list()
+
+        for level in ['factorLevel1', 'factorLevel2']:
+            # level names under one factor should be unique
+            fl = factor[level]
+            if fl in level_name_list:
+                level_duplication = True
+            level_name_list.append( fl )
+
+        if level_duplication:
+            error_map['rep_factorName'] = [ dict() for t in factors ]
+            for i in range( len( factors ) ):
+                error_map['rep_factorName'][i]['FactorLevel1'] = [ {'factorLevel': 'Factor levels for each factor need to be unique'} for t in [factor['factorLevel1'], factor['factorLevel2']] ]
+            break
+
+    if factor_duplication:
+        error_map['rep_factorName'] = [ dict() for t in factors ]
+        for i in range( len( factors ) ):
+            error_map['rep_factorName'][i]['factorName'] = 'Factor names need to be unique.'
diff -r e8ca8941952a -r 469c0d7489bd test-data/dexseq_result.tabular
--- a/test-data/dexseq_result.tabular	Tue Oct 13 17:21:57 2015 -0400
+++ b/test-data/dexseq_result.tabular	Sun Jan 29 06:59:23 2017 -0500
@@ -1,134 +1,183 @@
-FBgn0000064:E005	FBgn0000064	E005	859.822533198768	0.00372195558605137	110.248504159842	1.14773467510188e-24	1.35432691662022e-22	27.4026942925537	27.8806448897375	-0.0249461825911985	3R	22082655	22082854	200	-	746	952	1227	542	790	802	722	FBtr0085000, FBtr0085001, FBtr0084995, FBtr0084994, FBtr0306657, FBtr0114544, FBtr0310661, FBtr0310660, FBtr0084999
-FBgn0000042:E001	FBgn0000042	E001	963.266257907235	0.0502044280160066	57.8426706201339	2.7518430820889e-13	1.62358741843245e-11	29.1456287540252	27.7014978680248	0.0733155376052489	X	5794894	5795046	153	+	3322	262	275	1633	3139	244	129	FBtr0100662, FBtr0100663, FBtr0070822
-FBgn0000064:E002	FBgn0000064	E002	7.3266084748515	0.01707286192962	53.7309384372156	2.15018072623491e-12	8.45737752319066e-11	4.55458396475058	4.34353926561023	0.0684481985350057	3R	22080926	22081153	228	-	0	7	12	0	0	10	12	FBtr0310660, FBtr0084995, FBtr0084994, FBtr0084999
-FBgn0000084:E003	FBgn0000084	E003	12.7120572355022	0.0887912514378509	50.3598123774543	1.16012740873979e-11	3.42237585578239e-10	5.99959570586144	6.06694051770199	-0.0161038815249051	X	20066074	20066255	182	-	0	16	13	0	0	29	11	FBtr0070025, FBtr0301931
-FBgn0000042:E005	FBgn0000042	E005	33.8277404051372	0.008826686875382	36.1644112317346	1.40280685802709e-08	3.31062418494392e-07	9.58147265579643	11.2091577033539	-0.226358555041545	X	5798498	5798821	324	+	119	20	29	45	52	14	8	FBtr0100662, FBtr0070823
-FBgn0000032:E005	FBgn0000032	E005	50.5080907808574	0.00493456081981282	35.1634122191381	2.31399307099611e-08	4.55085303962568e-07	11.1453896842345	11.6791120638017	-0.0674835341219757	3R	25818551	25818649	99	-	42	53	56	38	55	45	53	FBtr0085609, FBtr0085610
-FBgn0000117:E003	FBgn0000117	E003	651.648249450539	0.00617415865170719	33.5894584912735	5.08325344394025e-08	8.56891294835643e-07	25.5863609644879	26.3587665612206	-0.0429078882881053	X	1788541	1788813	273	-	676	728	799	493	606	574	569	FBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988
-FBgn0000117:E004	FBgn0000117	E004	566.705805129229	0.00367009391373741	30.8789228540862	1.97118369737245e-07	2.90749595362437e-06	25.2478976953119	24.8237303978564	0.0244433312224853	X	1788874	1789074	201	-	541	507	690	417	761	498	535	FBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988
-FBgn0000042:E003	FBgn0000042	E003	37923.6657937205	0.0385740484752454	28.7151085239498	5.81558503594718e-07	7.62487815824186e-06	51.6463704239338	51.5494314550159	0.0027104476793924	X	5796723	5798206	1484	+	53623	37301	41337	47230	50144	22833	26327	FBtr0100662, FBtr0100663, FBtr0070822, FBtr0070823
-FBgn0000084:E006	FBgn0000084	E006	59.8440945905321	0.0201537492391107	22.1992448368148	1.51180310325524e-05	0.000178392766184118	12.7814564102042	12.4783532683405	0.0346246780719152	X	20067507	20067552	46	-	132	23	34	71	150	35	46	FBtr0070025
-FBgn0000017:E004	FBgn0000017	E004	118.685044393895	0.00902890492864188	19.2111031647923	6.7353776603016e-05	0.000722522330832353	15.8860792124228	15.4507867306171	0.0400828022658053	3L	16619373	16619627	255	-	103	108	87	107	162	144	104	FBtr0330133, FBtr0330132, FBtr0330131, FBtr0330130
-FBgn0000042:E004	FBgn0000042	E004	2902.21264539337	0.041061850909975	18.8599314844935	8.02819501685372e-05	0.00076717563289585	36.0570377531486	34.5088537532999	0.0633143238060254	X	5798207	5798497	291	+	7007	1635	1666	3678	8835	1202	1091	FBtr0100662, FBtr0100663, FBtr0070823
-FBgn0000140:E002	FBgn0000140	E002	24.0938527740886	0.00618959397365643	18.7570601259765	8.4519349386831e-05	0.00076717563289585	8.79238345032345	7.87199695631269	0.159524643103097	3R	20579850	20580026	177	+	19	23	22	24	32	25	21	FBtr0084692
-FBgn0000117:E001	FBgn0000117	E001	1110.87821042994	0.00661398986859128	18.1779217088585	0.000112905332661573	0.00095163066100469	29.2452591928804	29.4965680787519	-0.0123443315343086	X	1785434	1786152	719	-	1892	943	1111	1063	2137	670	737	FBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988
-FBgn0000064:E011	FBgn0000064	E011	121.014747579775	0.0160408890614961	17.9500199436582	0.000126532676382513	0.000995390387542438	17.4235036221787	14.6480546556801	0.250325679518575	3R	22086876	22086879	4	-	154	77	97	210	219	76	86	FBtr0085001
-FBgn0000097:E005	FBgn0000097	E005	205.994534916873	0.00406403011457325	17.6138556630228	0.000149692430614958	0.00110398167578531	19.2579362303104	19.3771139908641	-0.00890060753148998	2L	2159312	2160582	1271	-	436	153	131	240	419	142	115	FBtr0330658, FBtr0330660, FBtr0077850, FBtr0077851, FBtr0330659
-FBgn0000054:E006	FBgn0000054	E006	186.13192889271	0.0027760593361146	16.6378264714751	0.000243860739407714	0.00169268042647707	18.5699853241204	18.5574185340857	0.00097663959615939	2R	2554225	2554518	294	+	295	134	161	246	299	133	134	FBtr0330252, FBtr0330251, FBtr0086111, FBtr0086113, FBtr0086112
-FBgn0000064:E007	FBgn0000064	E007	39.9808634639801	0.00545415831027776	14.8576151492616	0.000593895265633176	0.00368840217603762	11.1031214122589	10.7520319063227	0.0463559929912436	3R	22083764	22083999	236	-	74	33	39	53	76	18	22	FBtr0085000, FBtr0084999
-FBgn0000083:E006	FBgn0000083	E006	222.094875801226	0.0283102169571559	14.8933631528514	0.0005833742866895	0.00368840217603762	19.5673733568172	19.6994005992184	-0.00970162539332244	3R	16895035	16895476	442	+	474	152	158	241	525	133	120	FBtr0089519
-FBgn0000097:E003	FBgn0000097	E003	558.924889184516	0.00445818163251505	14.6033302866141	0.000674414842338019	0.00397904756979431	25.3221662151043	24.641840469488	0.0392908139065121	2L	2157427	2158405	979	-	725	462	477	524	1052	491	412	FBtr0330658, FBtr0330660, FBtr0077850, FBtr0077851, FBtr0330659
-FBgn0000097:E001	FBgn0000097	E001	461.645239176362	0.0074491975712251	13.7643497765581	0.00102591037661195	0.00576463925905764	23.6904105899612	24.3360570527128	-0.0387922375492536	2L	2156484	2156791	308	-	1032	322	349	473	887	310	283	FBtr0330658, FBtr0077850, FBtr0077851
-FBgn0000054:E005	FBgn0000054	E005	111.963009884098	0.00690698169868387	13.3935989423809	0.00123485778276322	0.00633535732026347	15.5738328330273	15.4442516787064	0.0120540761452392	2R	2550999	2551392	394	+	112	97	115	131	124	99	101	FBtr0330251
-FBgn0000140:E003	FBgn0000140	E003	26.5896581030249	0.0236543543364679	13.4606375822739	0.00119415221231374	0.00633535732026347	9.06090647303951	8.42913215137745	0.104271286411704	3R	20580079	20580291	213	+	27	25	22	29	20	32	23	FBtr0084692
-FBgn0000084:E005	FBgn0000084	E005	179.51917351967	0.0170655253005479	12.5449282119125	0.00188757167140586	0.00928056071774546	18.3720767709006	18.2192663318189	0.0120498525382459	X	20067402	20067506	105	-	307	96	143	186	408	128	138	FBtr0070025, FBtr0301931
-FBgn0000017:E003	FBgn0000017	E003	68.6033909674033	0.0102883711340824	11.5209162236597	0.00314966836754979	0.014592586489007	13.321895214652	12.2785840209972	0.117655142120258	3L	16616737	16618374	1638	-	60	55	46	48	132	83	62	FBtr0075357, FBtr0330136, FBtr0112790, FBtr0330135, FBtr0330134, FBtr0330133, FBtr0330132, FBtr0330131, FBtr0330130
-FBgn0000117:E008	FBgn0000117	E008	20.8971168975998	0.00774307215890262	11.4796594807976	0.00321531566706935	0.014592586489007	7.81221621365865	8.85151532667579	-0.18019257881713	X	1793414	1793431	18	-	53	16	19	22	31	11	13	FBtr0089990, FBtr0089989, FBtr0332583
-FBgn0000139:E007	FBgn0000139	E007	17.4740062043893	0.0168813732620275	11.1280422643081	0.00383333103382073	0.0167530763700313	8.02482011218845	5.55360407829421	0.531044722802228	3R	20478032	20478312	281	+	12	5	9	24	28	24	19	FBtr0084660, FBtr0084659, FBtr0306171
-FBgn0000053:E005	FBgn0000053	E005	62.2147652508149	0.0045081912155785	11.0096380005098	0.00406712466278988	0.0171400253646145	12.1265465290342	13.0097076914692	-0.101419797669048	2L	7018149	7018374	226	-	77	70	85	38	72	45	51	FBtr0079431, FBtr0100353
-FBgn0000117:E002	FBgn0000117	E002	252.254084844864	0.0502145573147171	10.6433414565869	0.00488458608800893	0.0196896740970805	19.7174344483318	20.9731942177044	-0.0890747542702277	X	1787436	1787532	97	-	259	283	348	72	287	232	237	FBtr0089989, FBtr0089988, FBtr0089991, FBtr0089992, FBtr0332583
-FBgn0000140:E004	FBgn0000140	E004	396.131203959444	0.00799205872320755	10.5942963619378	0.00500584934671538	0.0196896740970805	23.1297257079112	22.9569164001174	0.0108192868221518	3R	20580371	20585252	4882	+	717	355	274	503	729	250	241	FBtr0084692
-FBgn0000097:E002	FBgn0000097	E002	400.358490752986	0.00671605447778241	9.79126635587212	0.00747917207758907	0.0284691066179197	23.0708609303899	22.9329039800295	0.00865278766428061	2L	2156792	2157426	635	-	517	327	402	386	671	348	286	FBtr0330658, FBtr0330659, FBtr0077850, FBtr0077851
-FBgn0000064:E004	FBgn0000064	E004	27.138007646805	0.0451778594740317	9.71273488047558	0.00777868918474941	0.0286839163687634	7.38449487600853	10.5909286136521	-0.520257946175574	3R	22082196	22082345	150	-	74	30	39	9	25	20	9	FBtr0085000, FBtr0114544
-FBgn0000117:E010	FBgn0000117	E010	42.7651357723149	0.0142493435131404	9.50225205889245	0.00864195862242921	0.0309015490135348	11.3201737509023	10.8766620282552	0.0576602304907339	X	1793558	1793643	86	-	87	32	27	58	69	27	31	FBtr0089990, FBtr0089989
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-FBgn0000115:E001	FBgn0000115	E001	52.3822474504571	0.00490695687702017	9.24542856542574	0.00982608904875264	0.033127957364366	12.3047829604338	11.6972082045576	0.0730549707897167	3L	15976235	15976380	146	+	88	34	41	72	99	33	38	FBtr0075517
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-FBgn0000052:E003	FBgn0000052	E003	314.320768507933	0.00573690826666262	7.06844079407966	0.0291814981060301	0.0836965111961041	21.4613398552705	21.4838655938015	-0.00151345296461154	2L	6044428	6045526	1099	-	343	283	295	346	457	261	265	FBtr0079219, FBtr0079221, FBtr0079220
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-FBgn0000100:E001	FBgn0000100	E001	6.87698735532182	0.0148737067129652	6.86881836231453	0.0322444552370167	0.0884847841387899	4.4623003694264	5.55626821573721	-0.316328615169299	3L	22068967	22069026	60	+	16	5	9	9	9	3	3	FBtr0334113
-FBgn0000083:E005	FBgn0000083	E005	519.429405568491	0.00697813744931421	6.81376788682235	0.0331443192046352	0.0888870378669761	24.5309203269385	24.5621333804144	-0.00183451303709238	3R	16894560	16894741	182	+	567	413	615	536	584	399	524	FBtr0089518, FBtr0089519, FBtr0089520, FBtr0089517
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-FBgn0000018:E001	FBgn0000018	E001	75.3353185482626	0.00609033892122252	6.60849620516578	0.0367268162555215	0.0922077514500328	13.7510909166136	13.9810286095394	-0.0239244296577968	2L	10973443	10974210	768	-	152	41	62	106	141	37	57	FBtr0080168
-FBgn0000018:E002	FBgn0000018	E002	143.582443967402	0.00603386076726418	6.63254479167817	0.0362878466848943	0.0922077514500328	17.1509547224479	16.9774274097776	0.0146710236591656	2L	10974268	10975273	1006	-	217	109	114	182	242	98	117	FBtr0080168
-FBgn0000032:E009	FBgn0000032	E009	32.7707234445176	0.0442959838787389	6.45597106707049	0.039637266360712	0.0974416131367502	10.1401812864396	9.64944349348271	0.0715657988991993	3R	25818999	25819130	132	-	54	25	20	73	61	10	18	FBtr0085609
-FBgn0000017:E001	FBgn0000017	E001	1147.17152215341	0.00508079877593044	6.28685392561059	0.0431347232315574	0.0998019086534074	29.4202522379118	29.2795772357626	0.00691489288244868	3L	16615470	16616388	919	-	1564	806	875	1289	2492	911	820	FBtr0075357, FBtr0330136, FBtr0112790, FBtr0330135, FBtr0330134, FBtr0330133, FBtr0330132, FBtr0330131, FBtr0330130
-FBgn0000109:E002	FBgn0000109	E002	33.7700649662137	0.00629451419446441	6.32408004978461	0.0423392797342674	0.0998019086534074	9.84728439580287	10.0258106336745	-0.0259210602402124	3L	1884323	1884560	238	-	57	15	38	41	40	26	31	FBtr0089420
-FBgn0000115:E002	FBgn0000115	E002	121.3964552666	0.00320711854477144	6.31160611767764	0.04260417359301	0.0998019086534074	15.8537537123151	16.401042417194	-0.0489630430974867	3L	15976478	15976694	217	+	156	119	129	121	183	82	96	FBtr0075517
-FBgn0000117:E005	FBgn0000117	E005	3117.72913507179	0.0029811434777046	6.06426503352304	0.0482127140006367	0.109405774078368	35.8872788638547	35.6528451910391	0.00945532349296979	X	1789147	1790786	1640	-	4350	2733	3196	3198	4668	2293	2428	FBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988
-FBgn0000084:E004	FBgn0000084	E004	777.356281983227	0.0395084881851352	6.0131123725032	0.0494617227533213	0.110122326130036	26.9553974351869	27.0057434663796	-0.00269208505945231	X	20066338	20067049	712	-	767	653	748	799	1087	673	753	FBtr0070025, FBtr0301931
-FBgn0000083:E003	FBgn0000083	E003	84.235857406506	0.04526772383323	5.84590771670278	0.0537746098894381	0.117507480869513	14.8919474010355	13.40562858909	0.151693556866262	3R	16893168	16893221	54	+	119	60	55	93	238	36	74	FBtr0089518, FBtr0089519, FBtr0089520, FBtr0089517
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-FBgn0000139:E004	FBgn0000139	E004	6.44700256941908	0.0160799127779307	5.56297415526724	0.0619463198625985	0.12901283905004	4.00687137747981	5.64469469517543	-0.494419352705418	3R	20476902	20476973	72	+	14	7	6	3	10	4	5	FBtr0306171
-FBgn0000140:E005	FBgn0000140	E005	32.5533299591785	0.0108579043041109	5.48198106522651	0.0645064195250201	0.12901283905004	9.26492586828956	10.5148549867585	-0.182577615669745	3R	20585313	20585614	302	+	51	37	38	35	47	22	13	FBtr0084692
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-FBgn0000053:E002	FBgn0000053	E002	211.729712208868	0.00775603910557698	3.49406712169687	0.174290198621016	0.281132111713134	19.8001862162344	18.7126031000238	0.0815037335260781	2L	7016437	7017486	1050	-	295	164	223	247	282	155	176	FBtr0079431
-FBgn0000139:E005	FBgn0000139	E005	13.2470390620692	0.0198819588795418	3.47110020589945	0.176303188701457	0.281132111713134	5.95645806032007	7.18439735682315	-0.270412441758807	3R	20477139	20477352	214	+	18	13	14	10	17	5	18	FBtr0084659
-FBgn0000119:E005	FBgn0000119	E005	187.898456532462	0.00713450678420139	3.22410769823857	0.199477496379121	0.313844594303151	18.6121133497047	18.4577491955122	0.0120152421228986	2R	9344041	9347030	2990	-	264	142	176	218	266	139	168	FBtr0087702
-FBgn0000139:E009	FBgn0000139	E009	96.3385782859831	0.00642183657847803	3.19649338344098	0.202250815336729	0.314021002759659	14.7856179291691	14.5084682007018	0.0272993304935376	3R	20478820	20479098	279	+	92	64	93	95	166	87	94	FBtr0084660, FBtr0084659, FBtr0306171
-FBgn0000053:E001	FBgn0000053	E001	296.253588782233	0.00350535186835895	2.8249386048218	0.243541163269732	0.373218925530238	21.5818413538444	20.9004518153175	0.0462838301363275	2L	7014861	7016374	1514	-	414	275	301	312	429	184	257	FBtr0079431
-FBgn0000032:E002	FBgn0000032	E002	80.2953101927857	0.0659753146842281	2.57026672757397	0.2766136909226	0.418466865754702	13.1546794353507	15.0454105136998	-0.19374737902434	3R	25816863	25817415	553	-	213	67	51	112	71	52	51	FBtr0085609, FBtr0085610
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-FBgn0000119:E001	FBgn0000119	E001	71.3729832029852	0.0105906091109927	2.37688646735522	0.304695234319899	0.440122748418424	13.4236616462922	13.5402393753942	-0.0124749871664052	2R	9341159	9342741	1583	-	126	62	49	77	133	44	57	FBtr0087702
-FBgn0000139:E008	FBgn0000139	E008	112.43808666746	0.00349020082049688	2.26875223595222	0.321622713384353	0.457246749148839	15.7377439052995	15.2656264409735	0.0439419439033773	3R	20478504	20478761	258	+	130	73	89	133	199	85	116	FBtr0084660, FBtr0084659, FBtr0306171
-FBgn0000064:E006	FBgn0000064	E006	2814.5524025292	0.0146416171254255	2.14699333032632	0.341811225968739	0.474514407815426	35.3966749106453	34.9180886181076	0.0196392535104732	3R	22082947	22083763	817	-	3729	2672	3078	2786	4155	2022	2100	FBtr0085000, FBtr0085001, FBtr0084995, FBtr0084994, FBtr0306657, FBtr0114544, FBtr0310661, FBtr0310660, FBtr0084999
-FBgn0000109:E003	FBgn0000109	E003	18.3940473673953	0.0293509640721157	2.16353302889742	0.338996154796667	0.474514407815426	7.99615489244294	7.4883418236827	0.0946601268360629	3L	1884691	1884885	195	-	32	6	19	38	29	9	11	FBtr0089420
-FBgn0000017:E002	FBgn0000017	E002	40.9148553776179	0.00607089485497556	2.01463848616271	0.365196672013288	0.501083805785675	10.8565006482446	10.277193636993	0.0791127915579019	3L	16616389	16616736	348	-	47	29	29	36	83	48	28	FBtr0330136, FBtr0075357, FBtr0330133, FBtr0112790, FBtr0330130
-FBgn0000071:E002	FBgn0000071	E002	14.9999389961672	0.0159369633948631	1.74720290438725	0.417445429009518	0.566190351989921	6.42544031833974	6.30834977761789	0.0265326666231467	3R	2589128	2589222	95	+	57	24	18	3	10	5	3	FBtr0081619, FBtr0081620
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-FBgn0000054:E001	FBgn0000054	E001	30.2913156353099	0.015955334815816	1.55597922225876	0.459328512631074	0.615909660198052	9.23538457228044	9.87735660216497	-0.09695295856857	2R	2549775	2549941	167	+	56	22	27	43	33	21	23	FBtr0330252, FBtr0086111, FBtr0086113, FBtr0086112
-FBgn0000084:E001	FBgn0000084	E001	53.2358303205052	0.175612575447698	1.49597039880035	0.473319236566507	0.620574110164975	10.9120641584659	13.2533407921191	-0.280432036151527	X	20065478	20065681	204	-	144	41	40	12	73	50	45	FBtr0070025, FBtr0301931
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+FBgn0000053:E003	FBgn0000053	E003	84.096019529742	0.00934649633010802	0.196920407055273	0.906231756723715	0.94399141325387	14.3998034225915	14.0605017229117	-0.0344010417774943	2L	7017545	7017966	422	-	117	77	91	96	93	65	64	FBtr0079431
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+FBgn0000052:E001	FBgn0000052	E001	202.231888834538	0.0147308170628665	0.0578180259028329	0.971504854804779	0.977088216039289	18.9733872307433	19.0907918643205	0.00889968594069081	2L	6041178	6042011	834	-	266	187	161	277	264	124	191	FBtr0079219, FBtr0079221, FBtr0079220
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 FBgn0000003:E001	FBgn0000003	E001	0.15316821713762	NA	NA	NA	NA	NA	NA	NA	3R	2648220	2648518	299	+	0	0	1	0	0	0	0	FBtr0081624
-FBgn0000008:E001	FBgn0000008	E001	0	NA	NA	NA	NA	0.0948360378901043	0.0743865272170741	0.350394044304503	2R	18024494	18024495	2	+	0	0	0	0	0	0	0	FBtr0100521
-FBgn0000008:E002	FBgn0000008	E002	0.205235479273134	0.281215674321156	2.21242626317474	0.330809323479709	NA	0.939195295474676	0.0476355829140882	4.30131363355654	2R	18024496	18024531	36	+	0	0	0	0	0	1	0	FBtr0071763, FBtr0100521
-FBgn0000008:E003	FBgn0000008	E003	0.594344937209466	0.0968538125516843	0.645303449176424	0.724226040572747	NA	1.60132701407228	1.05950556890012	0.595876786352192	2R	18024532	18024713	182	+	0	1	0	1	1	1	0	FBtr0071763
-FBgn0000008:E004	FBgn0000008	E004	0.522626439341238	0.103462369452504	0.101770743974669	0.950387605331279	NA	1.30656104503449	1.48745805800773	-0.187074457480603	2R	18024938	18025504	567	+	1	0	1	0	1	0	1	FBtr0071764
-FBgn0000008:E005	FBgn0000008	E005	1.32353144265853	0.0459878450164219	1.88720765333161	0.389222613957095	NA	2.05783835401508	2.5556984924881	-0.312587983914312	2R	18025505	18025756	252	+	4	1	1	2	2	0	1	FBtr0071764, FBtr0071763, FBtr0100521
-FBgn0000008:E006	FBgn0000008	E006	0.0933261680585749	0.299122084909831	1.8785125604006	0.390918461072644	NA	0.0578623652924577	1.03994127882261	-4.16773295859812	2R	18039159	18039200	42	+	1	0	0	0	0	0	0	FBtr0071764, FBtr0071763, FBtr0100521
-FBgn0000008:E008	FBgn0000008	E008	1.63933440281406	0.109484103343906	0.37069435505957	0.830815793201498	NA	2.30438268043009	2.314649547651	-0.00641345722945448	2R	18052282	18052494	213	+	4	1	0	0	1	4	1	FBtr0071764, FBtr0071763, FBtr0100521
-FBgn0000008:E011	FBgn0000008	E011	1.99928611112699	0.0364601891575936	2.65301612830849	0.265402413274536	NA	3.16019906636034	2.0995791205971	0.589915283343486	2R	18059587	18059757	171	+	2	0	2	3	6	1	2	FBtr0071764, FBtr0071763, FBtr0100521
-FBgn0000008:E012	FBgn0000008	E012	0.661887298226701	0.0886117417223106	1.92286917613052	0.382343986227271	NA	1.59298610396471	1.79969924808889	-0.176022152675381	2R	18059821	18059938	118	+	3	0	0	0	2	1	0	FBtr0071764, FBtr0071763, FBtr0100521
-FBgn0000008:E013	FBgn0000008	E013	3.91734100140517	0.0293996888447881	6.83620051593773	0.0327746391939249	NA	4.05034478889257	3.70647357969554	0.127997496136844	2R	18060002	18060339	338	+	11	1	1	5	10	5	0	FBtr0071764, FBtr0071763, FBtr0100521
-FBgn0000008:E014	FBgn0000008	E014	0.55498474117927	0.0866602205345716	1.17569168541739	0.555522679969109	NA	1.58703045222552	1.4877597658848	0.0931882232243094	2R	18060340	18060346	7	+	1	0	1	1	2	0	0	FBtr0071763, FBtr0071764
-FBgn0000014:E001	FBgn0000014	E001	0.298561647331709	0.595682542318035	0.477481494733636	0.787619048218473	NA	NA	NA	NA	3R	12632936	12633348	413	-	1	0	0	0	0	1	0	FBtr0306337
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+FBgn0000014:E001	FBgn0000014	E001	0.298561647331709	14	0.0441608888174834	0.978161544259054	NA	1.27264365403058	0.805558937331108	-0.659766464456778	3R	12632936	12633348	413	-	1	0	0	0	0	1	0	FBtr0306337
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@@ -136,62 +185,55 @@
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-FBgn0000014:E009	FBgn0000014	E009	0.0933261680585749	14	0.0866990806721333	0.95757661990907	NA	NA	NA	NA	3R	12653620	12653845	226	-	1	0	0	0	0	0	0	FBtr0083388
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-FBgn0000015:E002	FBgn0000015	E002	0.0933261680585749	0.654287411414569	3.2288542265987	0.199004644904909	NA	NA	NA	NA	3R	12753395	12755302	1908	-	1	0	0	0	0	0	0	FBtr0330709, FBtr0083385, FBtr0083384, FBtr0083383, FBtr0083382, FBtr0083381
+FBgn0000015:E002	FBgn0000015	E002	0.0933261680585749	14	0.381778750542054	0.826223983900076	NA	0.0362778896152491	1.03426437561497	4.83337066726416	3R	12753395	12755302	1908	-	1	0	0	0	0	0	0	FBtr0330709, FBtr0083385, FBtr0083384, FBtr0083383, FBtr0083382, FBtr0083381
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-FBgn0000015:E006	FBgn0000015	E006	0.82233114731192	0.1744728483509	3.83308058413458	0.147115057824768	NA	NA	NA	NA	3R	12758093	12760298	2206	-	0	0	1	0	1	1	2	FBtr0083384
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 FBgn0000015:E008	FBgn0000015	E008	0	NA	NA	NA	NA	NA	NA	NA	3R	12768975	12769021	47	-	0	0	0	0	0	0	0	FBtr0083385, FBtr0083383, FBtr0083382, FBtr0083381
 FBgn0000015:E009	FBgn0000015	E009	0	NA	NA	NA	NA	NA	NA	NA	3R	12769504	12769991	488	-	0	0	0	0	0	0	0	FBtr0083383
 FBgn0000015:E010	FBgn0000015	E010	0	NA	NA	NA	NA	NA	NA	NA	3R	12785694	12786228	535	-	0	0	0	0	0	0	0	FBtr0083382
 FBgn0000015:E011	FBgn0000015	E011	0	NA	NA	NA	NA	NA	NA	NA	3R	12788881	12789667	787	-	0	0	0	0	0	0	0	FBtr0083381
 FBgn0000015:E012	FBgn0000015	E012	0	NA	NA	NA	NA	NA	NA	NA	3R	12797481	12797958	478	-	0	0	0	0	0	0	0	FBtr0083385
-FBgn0000017:E008	FBgn0000017	E008	4.44081189153106	0.167403595435021	1.10011563974882	0.576916452179302	NA	3.43069518953709	4.43225136363948	-0.369538751417677	3L	16620602	16621188	587	-	5	1	10	5	3	2	5	FBtr0075357, FBtr0330136, FBtr0112790, FBtr0330135, FBtr0330134, FBtr0330133, FBtr0330132, FBtr0330131, FBtr0330130
 FBgn0000022:E001	FBgn0000022	E001	0.0883366573889214	NA	NA	NA	NA	NA	NA	NA	X	264064	264980	917	+	0	0	0	0	1	0	0	FBtr0070072
-FBgn0000024:E001	FBgn0000024	E001	0.318469377322382	0.247774833325402	3.33065898820414	0.189128331044754	NA	NA	NA	NA	3R	9053964	9055492	1529	-	2	0	0	1	0	0	0	FBtr0082780, FBtr0300486
-FBgn0000024:E002	FBgn0000024	E002	0.374191238615313	0.246336803853357	6.08610121889127	0.0476891862832677	NA	NA	NA	NA	3R	9058401	9058564	164	-	0	1	0	0	0	1	0	FBtr0082780, FBtr0300486
-FBgn0000024:E003	FBgn0000024	E003	0.0883366573889214	0.348368896825561	1.07521530658517	0.584144057195624	NA	NA	NA	NA	3R	9058683	9058846	164	-	0	0	0	0	1	0	0	FBtr0082780, FBtr0300486
-FBgn0000024:E004	FBgn0000024	E004	0.131817041205232	0.446820818235668	1.14430095201552	0.564310596524486	NA	NA	NA	NA	3R	9062851	9063000	150	-	0	0	0	1	0	0	0	FBtr0082780, FBtr0300486
-FBgn0000024:E005	FBgn0000024	E005	0.0933261680585749	0.430855141730833	1.25696146609535	0.5334015650974	NA	NA	NA	NA	3R	9063779	9063921	143	-	1	0	0	0	0	0	0	FBtr0082780, FBtr0300486
-FBgn0000024:E006	FBgn0000024	E006	0.0883366573889214	0.348368896825561	1.07521530658517	0.584144057195624	NA	NA	NA	NA	3R	9068941	9069148	208	-	0	0	0	0	1	0	0	FBtr0082780, FBtr0300486
-FBgn0000024:E007	FBgn0000024	E007	0.609263156530486	0.114044368320611	2.11163878762147	0.347907237443678	NA	NA	NA	NA	3R	9069308	9069853	546	-	0	1	0	2	2	0	0	FBtr0082780, FBtr0300486
-FBgn0000024:E008	FBgn0000024	E008	0.0883366573889214	0.348368896825561	1.07521530658517	0.584144057195624	NA	NA	NA	NA	3R	9069983	9070121	139	-	0	0	0	0	1	0	0	FBtr0082780, FBtr0300486
-FBgn0000024:E009	FBgn0000024	E009	0.979078995544713	0.151379497421444	5.44653681488543	0.0656598003588393	NA	NA	NA	NA	3R	9071532	9072376	845	-	1	2	3	0	1	0	0	FBtr0082780, FBtr0300486
+FBgn0000024:E001	FBgn0000024	E001	0.318469377322382	1.07533551564632	0.436423720925561	0.803955097323608	NA	1.06154208443538	1.23815728445098	0.222033025817963	3R	9053964	9055492	1529	-	2	0	0	1	0	0	0	FBtr0082780, FBtr0300486
+FBgn0000024:E002	FBgn0000024	E002	0.374191238615313	0.571000572346018	4.05097830595211	0.131929293795164	NA	1.0868228474317	0.955213191472962	-0.186222134208037	3R	9058401	9058564	164	-	0	1	0	0	0	1	0	FBtr0082780, FBtr0300486
+FBgn0000024:E003	FBgn0000024	E003	0.0883366573889214	2.36516011407251	0.482893890395601	0.785490476725373	NA	0.981612957470203	0.0220685827974236	-5.47508840240173	3R	9058683	9058846	164	-	0	0	0	0	1	0	0	FBtr0082780, FBtr0300486
+FBgn0000024:E004	FBgn0000024	E004	0.131817041205232	2.38298239616915	0.498748047093954	0.779288446640235	NA	1.06187018359142	0.0221942734115519	-5.58027611446832	3R	9062851	9063000	150	-	0	0	0	1	0	0	0	FBtr0082780, FBtr0300486
+FBgn0000024:E005	FBgn0000024	E005	0.0933261680585749	2.66019831166054	-0.0666222009918442	1	NA	0.0285074207662781	0.869475496492234	4.93073594895451	3R	9063779	9063921	143	-	1	0	0	0	0	0	0	FBtr0082780, FBtr0300486
+FBgn0000024:E006	FBgn0000024	E006	0.0883366573889214	2.36516011407251	0.482893890395601	0.785490476725373	NA	0.981612957470203	0.0220685827974236	-5.47508840240173	3R	9068941	9069148	208	-	0	0	0	0	1	0	0	FBtr0082780, FBtr0300486
+FBgn0000024:E008	FBgn0000024	E008	0.0883366573889214	2.36516011407251	0.482893890395601	0.785490476725373	NA	0.981612957470203	0.0220685827974236	-5.47508840240173	3R	9069983	9070121	139	-	0	0	0	0	1	0	0	FBtr0082780, FBtr0300486
 FBgn0000024:E010	FBgn0000024	E010	0	NA	NA	NA	NA	NA	NA	NA	3R	9084025	9084147	123	-	0	0	0	0	0	0	0	FBtr0082780, FBtr0300486
-FBgn0000024:E011	FBgn0000024	E011	0.2572924167311	0.209743976276536	0.263365479175025	0.876619067493304	NA	NA	NA	NA	3R	9084148	9084590	443	-	0	1	0	0	1	0	0	FBtr0082780
+FBgn0000024:E011	FBgn0000024	E011	0.2572924167311	0.375188972952962	0.5808743295506	0.747936524595224	NA	1.03704268244909	0.947941602938094	-0.129605182516137	3R	9084148	9084590	443	-	0	1	0	0	1	0	0	FBtr0082780
 FBgn0000024:E012	FBgn0000024	E012	0	NA	NA	NA	NA	NA	NA	NA	3R	9085175	9085240	66	-	0	0	0	0	0	0	0	FBtr0300486
-FBgn0000028:E001	FBgn0000028	E001	0.2572924167311	14	0.0873130985219426	0.957282680463803	NA	NA	NA	NA	X	15245315	15245991	677	-	0	1	0	0	1	0	0	FBtr0100328, FBtr0305191
+FBgn0000028:E001	FBgn0000028	E001	0.2572924167311	14	0.04484624025201	0.977826409474831	NA	1.23601853743904	0.763775367343898	-0.6944800833091	X	15245315	15245991	677	-	0	1	0	0	1	0	0	FBtr0100328, FBtr0305191
 FBgn0000028:E002	FBgn0000028	E002	0	NA	NA	NA	NA	NA	NA	NA	X	15246367	15246389	23	-	0	0	0	0	0	0	0	FBtr0100328, FBtr0305191
 FBgn0000028:E003	FBgn0000028	E003	0	NA	NA	NA	NA	NA	NA	NA	X	15246390	15247200	811	-	0	0	0	0	0	0	0	FBtr0305195, FBtr0305189, FBtr0305196, FBtr0074015, FBtr0305194, FBtr0100328, FBtr0290063, FBtr0305191, FBtr0305190, FBtr0305193, FBtr0305192, FBtr0290064, FBtr0100326
 FBgn0000028:E004	FBgn0000028	E004	0	NA	NA	NA	NA	NA	NA	NA	X	15247258	15247415	158	-	0	0	0	0	0	0	0	FBtr0305195, FBtr0305189, FBtr0305196, FBtr0074015, FBtr0305194, FBtr0100328, FBtr0290063, FBtr0305191, FBtr0305190, FBtr0305193, FBtr0305192, FBtr0290064, FBtr0100326
 FBgn0000028:E005	FBgn0000028	E005	0	NA	NA	NA	NA	NA	NA	NA	X	15247416	15247421	6	-	0	0	0	0	0	0	0	FBtr0074015, FBtr0305196, FBtr0305191, FBtr0305193, FBtr0305192
-FBgn0000028:E006	FBgn0000028	E006	0.15316821713762	14	0.0873522882162447	0.957263922839776	NA	NA	NA	NA	X	15248260	15248491	232	-	0	0	1	0	0	0	0	FBtr0305195, FBtr0305189, FBtr0305196, FBtr0074015, FBtr0305194, FBtr0100328, FBtr0290063, FBtr0305191, FBtr0305190, FBtr0305193, FBtr0305192, FBtr0290064, FBtr0100326
+FBgn0000028:E006	FBgn0000028	E006	0.15316821713762	14	0.0448649614922942	0.977817256456086	NA	0.0665935882332338	0.733003872592276	3.46036563692957	X	15248260	15248491	232	-	0	0	1	0	0	0	0	FBtr0305195, FBtr0305189, FBtr0305196, FBtr0074015, FBtr0305194, FBtr0100328, FBtr0290063, FBtr0305191, FBtr0305190, FBtr0305193, FBtr0305192, FBtr0290064, FBtr0100326
 FBgn0000028:E007	FBgn0000028	E007	0	NA	NA	NA	NA	NA	NA	NA	X	15248569	15248709	141	-	0	0	0	0	0	0	0	FBtr0305195, FBtr0305189, FBtr0305196, FBtr0074015, FBtr0305194, FBtr0100328, FBtr0290063, FBtr0305191, FBtr0305190, FBtr0305193, FBtr0305192, FBtr0290064, FBtr0100326
 FBgn0000028:E008	FBgn0000028	E008	0	NA	NA	NA	NA	NA	NA	NA	X	15248788	15248965	178	-	0	0	0	0	0	0	0	FBtr0305195, FBtr0305189, FBtr0305196, FBtr0074015, FBtr0305194, FBtr0100328, FBtr0290063, FBtr0305191, FBtr0305190, FBtr0305193, FBtr0305192, FBtr0290064, FBtr0100326
 FBgn0000028:E009	FBgn0000028	E009	0	NA	NA	NA	NA	NA	NA	NA	X	15248966	15248986	21	-	0	0	0	0	0	0	0	FBtr0305195, FBtr0074015, FBtr0100328, FBtr0290064, FBtr0290063, FBtr0305191
 FBgn0000028:E010	FBgn0000028	E010	0	NA	NA	NA	NA	NA	NA	NA	X	15265545	15265721	177	-	0	0	0	0	0	0	0	FBtr0305195, FBtr0305189, FBtr0305196, FBtr0074015, FBtr0305194, FBtr0100328, FBtr0290063, FBtr0305191, FBtr0305190, FBtr0305193, FBtr0305192, FBtr0290064, FBtr0100326
 FBgn0000028:E011	FBgn0000028	E011	0	NA	NA	NA	NA	NA	NA	NA	X	15266185	15266241	57	-	0	0	0	0	0	0	0	FBtr0305195, FBtr0305189, FBtr0074015, FBtr0305194, FBtr0305196, FBtr0100328
-FBgn0000032:E001	FBgn0000032	E001	0	NA	NA	NA	NA	0.103470925044295	0.110057721741713	-0.0890349368877479	3R	25816861	25816862	2	-	0	0	0	0	0	0	0	FBtr0085610
-FBgn0000032:E007	FBgn0000032	E007	2.52959384340906	0.0412474955137068	2.49864605526861	0.28669881835649	NA	3.20399452004655	3.01340131485321	0.0884788611376788	3R	25818904	25818983	80	-	5	3	0	4	7	2	0	FBtr0085610
-FBgn0000036:E001	FBgn0000036	E001	0.225143209263807	14	0.146671571061994	0.929288735918743	NA	NA	NA	NA	3R	20226948	20227667	720	-	1	0	0	1	0	0	0	FBtr0084619, FBtr0330310
+FBgn0000032:E001	FBgn0000032	E001	0	NA	NA	NA	NA	NA	NA	NA	3R	25816861	25816862	2	-	0	0	0	0	0	0	0	FBtr0085610
+FBgn0000036:E001	FBgn0000036	E001	0.225143209263807	14	0.0753841619066407	0.963009424186269	NA	0.744388050549727	1.15690288516914	0.636140962694898	3R	20226948	20227667	720	-	1	0	0	1	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E002	FBgn0000036	E002	0	NA	NA	NA	NA	NA	NA	NA	3R	20228937	20229232	296	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E003	FBgn0000036	E003	0	NA	NA	NA	NA	NA	NA	NA	3R	20230404	20230615	212	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E004	FBgn0000036	E004	0	NA	NA	NA	NA	NA	NA	NA	3R	20230691	20231151	461	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E005	FBgn0000036	E005	0	NA	NA	NA	NA	NA	NA	NA	3R	20233040	20233220	181	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E006	FBgn0000036	E006	0	NA	NA	NA	NA	NA	NA	NA	3R	20238230	20238339	110	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E007	FBgn0000036	E007	0	NA	NA	NA	NA	NA	NA	NA	3R	20240569	20240613	45	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
-FBgn0000036:E008	FBgn0000036	E008	0.0883366573889214	14	0.146666385814946	0.929291145217703	NA	NA	NA	NA	3R	20247417	20247626	210	-	0	0	0	0	1	0	0	FBtr0084619, FBtr0330310
+FBgn0000036:E008	FBgn0000036	E008	0.0883366573889214	14	0.0753821435284827	0.963010396045353	NA	0.640643943923777	0.0784399443423851	-3.02986234384538	3R	20247417	20247626	210	-	0	0	0	0	1	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E009	FBgn0000036	E009	0	NA	NA	NA	NA	NA	NA	NA	3R	20277617	20278355	739	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E010	FBgn0000036	E010	0	NA	NA	NA	NA	NA	NA	NA	3R	20282157	20282651	495	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
-FBgn0000037:E001	FBgn0000037	E001	4.93059492840277	0.0433513062913661	3.33472901301585	0.188743843895526	NA	NA	NA	NA	2R	20266159	20269379	3221	-	9	5	4	5	9	3	3	FBtr0072367, FBtr0072368
 FBgn0000037:E002	FBgn0000037	E002	0	NA	NA	NA	NA	NA	NA	NA	2R	20270713	20270763	51	-	0	0	0	0	0	0	0	FBtr0072368
 FBgn0000037:E003	FBgn0000037	E003	0	NA	NA	NA	NA	NA	NA	NA	2R	20270764	20270900	137	-	0	0	0	0	0	0	0	FBtr0072367, FBtr0072368
-FBgn0000037:E004	FBgn0000037	E004	0.131817041205232	0.352429843890349	1.56192126479755	0.457965863083139	NA	NA	NA	NA	2R	20270959	20271142	184	-	0	0	0	1	0	0	0	FBtr0072367, FBtr0072368
-FBgn0000037:E005	FBgn0000037	E005	2.87103694900597	0.0585147463404514	4.40741117623399	0.110393327296906	NA	NA	NA	NA	2R	20271447	20272571	1125	-	1	5	7	1	4	0	2	FBtr0072367, FBtr0072368
+FBgn0000037:E004	FBgn0000037	E004	0.131817041205232	0.638713869754204	0.621336919360012	0.732956840336235	NA	1.0361289221476	0.0551771658418421	-4.2309883588067	2R	20270959	20271142	184	-	0	0	0	1	0	0	0	FBtr0072367, FBtr0072368
 FBgn0000037:E006	FBgn0000037	E006	0	NA	NA	NA	NA	NA	NA	NA	2R	20277121	20277235	115	-	0	0	0	0	0	0	0	FBtr0072367, FBtr0072368
 FBgn0000038:E001	FBgn0000038	E001	0	NA	NA	NA	NA	NA	NA	NA	3L	4429349	4429502	154	+	0	0	0	0	0	0	0	FBtr0073299, FBtr0073300
 FBgn0000038:E002	FBgn0000038	E002	0	NA	NA	NA	NA	NA	NA	NA	3L	4429566	4429715	150	+	0	0	0	0	0	0	0	FBtr0073299, FBtr0073300
@@ -212,96 +254,54 @@
 FBgn0000039:E009	FBgn0000039	E009	0.0883366573889214	NA	NA	NA	NA	NA	NA	NA	3R	20315321	20315522	202	+	0	0	0	0	1	0	0	FBtr0084639, FBtr0084640
 FBgn0000039:E010	FBgn0000039	E010	0	NA	NA	NA	NA	NA	NA	NA	3R	20316540	20316875	336	+	0	0	0	0	0	0	0	FBtr0084639, FBtr0084640
 FBgn0000045:E001	FBgn0000045	E001	0	NA	NA	NA	NA	NA	NA	NA	3L	21978310	21978348	39	+	0	0	0	0	0	0	0	FBtr0334090, FBtr0078478
-FBgn0000045:E002	FBgn0000045	E002	2.68093910810214	0.0655762059991564	2.62587438933238	0.269028705099552	NA	NA	NA	NA	3L	21978349	21978424	76	+	2	3	6	4	4	0	1	FBtr0334090
-FBgn0000045:E003	FBgn0000045	E003	1.90232166678076	0.0718217621875294	2.56225549903376	0.277723920762044	NA	NA	NA	NA	3L	21978425	21979375	951	+	6	1	2	1	6	1	0	FBtr0334090, FBtr0078478
-FBgn0000046:E001	FBgn0000046	E001	0.467517406673888	0.139029449769923	0.72171941003414	0.697076787983094	NA	1.02069052776044	1.36063515246501	-0.414734758239586	3R	9251707	9251764	58	+	1	1	0	0	0	1	0	FBtr0082785
-FBgn0000046:E002	FBgn0000046	E002	0.205235479273134	0.299191853446159	2.38000361605968	0.304220714026078	NA	1.02924569375674	0.137159658829884	2.90765928665271	3R	9252169	9252304	136	+	0	0	0	0	0	1	0	FBtr0082786
+FBgn0000046:E002	FBgn0000046	E002	0.205235479273134	0.460793423141561	1.25123939241761	0.534929831796245	NA	1.04321764776999	0.051486438340568	-4.34070389748626	3R	9252169	9252304	136	+	0	0	0	0	0	1	0	FBtr0082786
 FBgn0000047:E001	FBgn0000047	E001	0	NA	NA	NA	NA	NA	NA	NA	3R	11265710	11265768	59	+	0	0	0	0	0	0	0	FBtr0083143
-FBgn0000047:E002	FBgn0000047	E002	4.10256379465508	0.0663269846820962	1.37736015699205	0.502238547218893	NA	NA	NA	NA	3R	11266322	11267262	941	+	7	5	6	2	7	3	1	FBtr0083143
-FBgn0000047:E003	FBgn0000047	E003	1.47614278023545	0.1155196175669	1.2389015625323	0.538239967905535	NA	NA	NA	NA	3R	11267324	11267895	572	+	1	2	1	4	2	0	1	FBtr0083143
-FBgn0000052:E004	FBgn0000052	E004	2.50560510092783	0.103515739743035	1.02584039728106	0.598744570329988	NA	3.24310628241199	2.39289084765952	0.438621714807052	2L	6045527	6045593	67	-	3	0	2	2	5	5	1	FBtr0079221
-FBgn0000052:E005	FBgn0000052	E005	5.95928508029525	0.0206833776605933	6.22483224330095	0.0444933240839088	NA	4.70958106769016	4.82158333537383	-0.0339082503862604	2L	6045894	6045920	27	-	12	2	7	10	15	2	2	FBtr0079219
-FBgn0000053:E004	FBgn0000053	E004	6.32535175423168	0.0465064521008484	12.0922502181496	0.00236701618885719	NA	3.07822322246814	5.77547075087308	-0.907840688572734	2L	7018085	7018148	64	-	13	7	15	0	3	3	4	FBtr0100353
-FBgn0000054:E002	FBgn0000054	E002	5.12918186544468	0.0221901722234639	1.13596449532206	0.566667680969691	NA	4.46650278057517	3.68992306119231	0.275554925197352	2R	2549942	2549953	12	+	3	5	4	10	8	3	4	FBtr0086113, FBtr0086112
 FBgn0000061:E001	FBgn0000061	E001	0	NA	NA	NA	NA	NA	NA	NA	2L	378112	378481	370	+	0	0	0	0	0	0	0	FBtr0078053
-FBgn0000061:E002	FBgn0000061	E002	0.481367533418178	0.479884323993537	1.66474457123859	0.435016078886412	NA	NA	NA	NA	2L	384511	384894	384	+	0	0	0	0	1	1	1	FBtr0078053
 FBgn0000061:E003	FBgn0000061	E003	0	NA	NA	NA	NA	NA	NA	NA	2L	385701	385746	46	+	0	0	0	0	0	0	0	FBtr0078053
-FBgn0000061:E004	FBgn0000061	E004	0.375590793512245	0.334190062018809	1.37029705876098	0.504015362925403	NA	NA	NA	NA	2L	386308	386576	269	+	0	0	0	0	0	0	2	FBtr0078053
-FBgn0000061:E005	FBgn0000061	E005	0.374447732873272	0.238422610206756	3.73444611208443	0.154552249392985	NA	NA	NA	NA	2L	386703	387439	737	+	2	0	0	0	0	0	1	FBtr0078053
-FBgn0000064:E009	FBgn0000064	E009	1.15788898853292	0.353993859000304	3.35410308459947	0.186924302732997	NA	1.840453971985	2.56332183272022	-0.477952954944166	3R	22084992	22084996	5	-	5	2	0	0	4	0	0	FBtr0114544
-FBgn0000064:E010	FBgn0000064	E010	4.52637441420982	0.0429382059742037	5.95875766513493	0.0508243945203125	NA	4.29187089687112	4.161301891273	0.0445717234237537	3R	22085524	22085552	29	-	10	5	3	5	14	1	1	FBtr0084995
-FBgn0000071:E001	FBgn0000071	E001	0	NA	NA	NA	NA	0.134691007539629	0.0547473837794001	1.29879160524834	3R	2588315	2588718	404	+	0	0	0	0	0	0	0	FBtr0081618
-FBgn0000071:E003	FBgn0000071	E003	4.48674647444507	0.0217254584388527	0.863108331818822	0.64949888088783	NA	2.90376270702015	3.65506998776432	-0.331975468999781	3R	2589223	2589238	16	+	16	8	7	0	2	1	1	FBtr0081619
+FBgn0000061:E005	FBgn0000061	E005	0.374447732873272	14	0.368028250211317	0.831924052728534	NA	0.634996936298325	2.16261613381655	1.76795607206982	2L	386703	387439	737	+	2	0	0	0	0	0	1	FBtr0078053
+FBgn0000071:E001	FBgn0000071	E001	0	NA	NA	NA	NA	NA	NA	NA	3R	2588315	2588718	404	+	0	0	0	0	0	0	0	FBtr0081618
 FBgn0000075:E001	FBgn0000075	E001	0	NA	NA	NA	NA	NA	NA	NA	2L	19110159	19110350	192	+	0	0	0	0	0	0	0	FBtr0081153
 FBgn0000075:E002	FBgn0000075	E002	0	NA	NA	NA	NA	NA	NA	NA	2L	19110412	19110646	235	+	0	0	0	0	0	0	0	FBtr0081153
-FBgn0000075:E003	FBgn0000075	E003	0.486357044087831	0.31038722745716	0.430835068396579	0.806204751838054	NA	NA	NA	NA	2L	19111844	19112315	472	+	1	0	0	0	0	1	1	FBtr0081154
-FBgn0000075:E004	FBgn0000075	E004	0.628403179247171	0.19810890053709	0.459113637812973	0.794885802812619	NA	NA	NA	NA	2L	19112794	19114110	1317	+	1	0	1	0	2	1	0	FBtr0081153, FBtr0081154
 FBgn0000077:E001	FBgn0000077	E001	115.669685732003	NA	NA	NA	NA	NA	NA	NA	X	9139948	9140185	238	-	179	85	89	167	196	70	92	FBtr0071331
 FBgn0000078:E001	FBgn0000078	E001	16.3910327521687	NA	NA	NA	NA	NA	NA	NA	2R	13012267	13013887	1621	+	10	11	11	24	30	16	15	FBtr0086983
 FBgn0000079:E001	FBgn0000079	E001	84.9770030139345	NA	NA	NA	NA	NA	NA	NA	2R	13006211	13007808	1598	-	44	51	53	78	132	115	99	FBtr0087004
-FBgn0000084:E002	FBgn0000084	E002	0	NA	NA	NA	NA	0.098623007983802	0.109220943510334	-0.147253364209614	X	20065962	20065964	3	-	0	0	0	0	0	0	0	FBtr0301931
-FBgn0000092:E001	FBgn0000092	E001	2.91279031750449	0.052120091583627	1.09842826184428	0.577403395601899	NA	NA	NA	NA	X	2586765	2587130	366	-	6	5	3	1	4	0	3	FBtr0070504
-FBgn0000092:E002	FBgn0000092	E002	3.3888188217205	0.0431406736897965	0.819718552621026	0.663743648019541	NA	NA	NA	NA	X	2587189	2587681	493	-	7	2	4	2	6	3	2	FBtr0070504
-FBgn0000092:E003	FBgn0000092	E003	0.860804776961103	0.189698807060238	0.224623904778547	0.893765401755233	NA	NA	NA	NA	X	2587766	2587919	154	-	3	0	0	0	0	1	2	FBtr0070504
-FBgn0000094:E002	FBgn0000094	E002	2.87825776924099	0.0387011778886164	3.81550949885979	0.148413237695119	NA	3.6447537342531	3.18368328804674	0.195124514896835	3R	26035865	26036011	147	+	9	2	0	3	8	2	1	FBtr0085611
+FBgn0000084:E002	FBgn0000084	E002	0	NA	NA	NA	NA	NA	NA	NA	X	20065962	20065964	3	-	0	0	0	0	0	0	0	FBtr0301931
 FBgn0000099:E001	FBgn0000099	E001	0	NA	NA	NA	NA	NA	NA	NA	2R	1593707	1594728	1022	-	0	0	0	0	0	0	0	FBtr0300505, FBtr0086058, FBtr0086059
-FBgn0000099:E002	FBgn0000099	E002	0.574693701476753	0.199792033938147	1.251557266549	0.534844818374497	NA	NA	NA	NA	2R	1594729	1595611	883	-	1	0	0	0	1	1	1	FBtr0300505, FBtr0086058, FBtr0086059, FBtr0300504
-FBgn0000099:E003	FBgn0000099	E003	0.0933261680585749	0.522096827637421	1.5863692048489	0.452401778983129	NA	NA	NA	NA	2R	1595688	1595884	197	-	1	0	0	0	0	0	0	FBtr0300505, FBtr0086058, FBtr0086059, FBtr0300504
-FBgn0000099:E004	FBgn0000099	E004	0.0883366573889214	0.534447528998108	1.24973620114661	0.535332033850842	NA	NA	NA	NA	2R	1596116	1596372	257	-	0	0	0	0	1	0	0	FBtr0300505, FBtr0086058, FBtr0086059, FBtr0300504
+FBgn0000099:E003	FBgn0000099	E003	0.0933261680585749	8.24727293760506	0.167758711123923	0.919542187053798	NA	0.0181896949718858	1.14255481527734	5.97299822130791	2R	1595688	1595884	197	-	1	0	0	0	0	0	0	FBtr0300505, FBtr0086058, FBtr0086059, FBtr0300504
+FBgn0000099:E004	FBgn0000099	E004	0.0883366573889214	8.32831107111954	0.0753073656847008	0.963046402638951	NA	0.674689760173148	0.026887613203348	-4.64921066722288	2R	1596116	1596372	257	-	0	0	0	0	1	0	0	FBtr0300505, FBtr0086058, FBtr0086059, FBtr0300504
 FBgn0000099:E005	FBgn0000099	E005	0	NA	NA	NA	NA	NA	NA	NA	2R	1596431	1596604	174	-	0	0	0	0	0	0	0	FBtr0300505, FBtr0086058, FBtr0086059, FBtr0300504
 FBgn0000099:E006	FBgn0000099	E006	0	NA	NA	NA	NA	NA	NA	NA	2R	1596664	1596797	134	-	0	0	0	0	0	0	0	FBtr0086059
-FBgn0000099:E007	FBgn0000099	E007	0.168955759342179	0.826995773300627	2.42798757074101	0.297008718506218	NA	NA	NA	NA	2R	1604154	1604293	140	-	0	1	0	0	0	0	0	FBtr0300505, FBtr0086058, FBtr0300504
+FBgn0000099:E007	FBgn0000099	E007	0.168955759342179	14	0.193694774340941	0.907694521392659	NA	0.0181899442426268	1.4315097812054	6.29825259705369	2R	1604154	1604293	140	-	0	1	0	0	0	0	0	FBtr0300505, FBtr0086058, FBtr0300504
 FBgn0000099:E008	FBgn0000099	E008	0	NA	NA	NA	NA	NA	NA	NA	2R	1604294	1604554	261	-	0	0	0	0	0	0	0	FBtr0300505
 FBgn0000099:E009	FBgn0000099	E009	0	NA	NA	NA	NA	NA	NA	NA	2R	1604787	1605003	217	-	0	0	0	0	0	0	0	FBtr0086058, FBtr0300504
 FBgn0000099:E010	FBgn0000099	E010	0	NA	NA	NA	NA	NA	NA	NA	2R	1605060	1605268	209	-	0	0	0	0	0	0	0	FBtr0086058, FBtr0300504
 FBgn0000099:E011	FBgn0000099	E011	0	NA	NA	NA	NA	NA	NA	NA	2R	1605269	1605271	3	-	0	0	0	0	0	0	0	FBtr0086058
 FBgn0000099:E012	FBgn0000099	E012	0	NA	NA	NA	NA	NA	NA	NA	2R	1613326	1614335	1010	-	0	0	0	0	0	0	0	FBtr0086058, FBtr0300504
-FBgn0000108:E001	FBgn0000108	E001	2.75903382413077	0.0352765277912979	1.953095127342	0.376609075825931	NA	3.44470057258627	2.547669341227	0.43520053926197	X	424503	424567	65	+	4	1	1	1	6	5	2	FBtr0307294, FBtr0307295, FBtr0070109, FBtr0307292, FBtr0307293
-FBgn0000108:E002	FBgn0000108	E002	0.947741879453093	0.088484938766678	0.40398925973323	0.81709931586277	NA	1.61434647620667	2.07607687546002	-0.362909618849774	X	425203	425222	20	+	3	1	0	0	1	2	0	FBtr0307291
-FBgn0000108:E003	FBgn0000108	E003	0.764700251448577	0.217576234242283	1.40380154022992	0.495642305781567	NA	1.87026362382992	1.06103038784681	0.817775664614957	X	425660	425909	250	+	0	1	0	1	1	0	2	FBtr0307294, FBtr0307295, FBtr0307291, FBtr0070109, FBtr0307293, FBtr0307292
-FBgn0000108:E004	FBgn0000108	E004	1.90433405030327	0.0352977858996905	0.485610053203025	0.784424440761796	NA	2.60276909051657	2.75340397862893	-0.0811689712039896	X	454639	454809	171	+	4	2	1	0	5	2	1	FBtr0307294, FBtr0307295, FBtr0307291, FBtr0070109, FBtr0307293
-FBgn0000108:E005	FBgn0000108	E005	5.90311493930572	0.0480749982872309	0.986383764039061	0.610674080447218	NA	4.08487977360948	4.95231669137882	-0.277809957626917	X	464895	465033	139	+	8	5	10	3	9	5	3	FBtr0307294, FBtr0307295, FBtr0307291, FBtr0070109, FBtr0307293, FBtr0307292
-FBgn0000108:E006	FBgn0000108	E006	0.864384408056277	0.0761658199463111	9.90027072716275	0.00708245015834393	NA	0.155803221383085	2.74792529653671	-4.14054581649625	X	465164	465166	3	+	4	2	1	0	0	0	0	FBtr0307295, FBtr0307293
-FBgn0000108:E007	FBgn0000108	E007	2.0755759309234	0.0671021365769184	2.87776097640352	0.237193150630287	NA	2.91431535300551	2.11765759801284	0.46068765713975	X	465167	465385	219	+	0	3	1	0	5	2	3	FBtr0307294, FBtr0307295, FBtr0307291, FBtr0070109, FBtr0307293, FBtr0307292
-FBgn0000108:E009	FBgn0000108	E009	1.57262265911296	0.059833286111432	1.70395040771075	0.426571533543393	NA	2.29247264923385	2.08960060513039	0.133677301795608	X	466092	466103	12	+	2	0	2	0	1	3	2	FBtr0307291, FBtr0070109, FBtr0307292, FBtr0307293
-FBgn0000108:E010	FBgn0000108	E010	0.974055918507825	0.39602602893438	0.996956773051679	0.607454267445727	NA	2.09982303262026	1.4767177036514	0.507873686551565	X	466170	466181	12	+	1	0	1	2	1	0	2	FBtr0307295, FBtr0307293
-FBgn0000108:E011	FBgn0000108	E011	4.33255157059706	0.0237942040876617	8.7926134060727	0.0123227676026087	NA	3.94402236548656	4.45333881466794	-0.175219644828544	X	466182	466322	141	+	13	4	2	1	14	1	3	FBtr0307294, FBtr0307295, FBtr0307291, FBtr0070109, FBtr0307293, FBtr0307292
 FBgn0000114:E001	FBgn0000114	E001	0	NA	NA	NA	NA	NA	NA	NA	2L	12175004	12175420	417	+	0	0	0	0	0	0	0	FBtr0331998
-FBgn0000114:E002	FBgn0000114	E002	0.293572136662055	0.396426897644781	3.75923650146655	0.15264836803795	NA	NA	NA	NA	2L	12201326	12201771	446	+	0	0	0	0	1	1	0	FBtr0331648
+FBgn0000114:E002	FBgn0000114	E002	0.293572136662055	14	0.380904021358191	0.826585424050438	NA	1.52727541848932	0.0127771491956068	-6.90125045939522	2L	12201326	12201771	446	+	0	0	0	0	1	1	0	FBtr0331648
 FBgn0000114:E003	FBgn0000114	E003	0	NA	NA	NA	NA	NA	NA	NA	2L	12205843	12206130	288	+	0	0	0	0	0	0	0	FBtr0331646, FBtr0080344
 FBgn0000114:E004	FBgn0000114	E004	0	NA	NA	NA	NA	NA	NA	NA	2L	12222197	12222337	141	+	0	0	0	0	0	0	0	FBtr0331647, FBtr0331645
-FBgn0000114:E005	FBgn0000114	E005	0.441683286944607	0.160342497440679	3.30197692402441	0.191860168372598	NA	NA	NA	NA	2L	12240868	12241780	913	+	0	0	0	0	5	0	0	FBtr0080344, FBtr0331645
-FBgn0000114:E006	FBgn0000114	E006	0.15316821713762	0.601938199042331	2.03382078736412	0.361710759411937	NA	NA	NA	NA	2L	12270932	12271347	416	+	0	0	1	0	0	0	0	FBtr0331644, FBtr0080345, FBtr0300567
+FBgn0000114:E006	FBgn0000114	E006	0.15316821713762	14	0.172605989659559	0.917316247028269	NA	0.0161637136951942	1.00562209278475	5.95918573727722	2L	12270932	12271347	416	+	0	0	1	0	0	0	0	FBtr0331644, FBtr0080345, FBtr0300567
 FBgn0000114:E007	FBgn0000114	E007	0	NA	NA	NA	NA	NA	NA	NA	2L	12271591	12272084	494	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080344, FBtr0080345, FBtr0331998
 FBgn0000114:E008	FBgn0000114	E008	0	NA	NA	NA	NA	NA	NA	NA	2L	12278837	12278919	83	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080344, FBtr0080345, FBtr0331998
 FBgn0000114:E009	FBgn0000114	E009	0	NA	NA	NA	NA	NA	NA	NA	2L	12282514	12282562	49	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080344, FBtr0080345, FBtr0331998
-FBgn0000114:E010	FBgn0000114	E010	0.576335917111657	0.136065985608524	2.37237112502385	0.305383913077311	NA	NA	NA	NA	2L	12287223	12287808	586	+	1	0	2	0	2	0	0	FBtr0080347
-FBgn0000114:E011	FBgn0000114	E011	0.0883366573889214	0.56160886675747	0.284210800995659	0.867529813592701	NA	NA	NA	NA	2L	12288905	12289344	440	+	0	0	0	0	1	0	0	FBtr0080347
-FBgn0000114:E012	FBgn0000114	E012	0.0933261680585749	1.61859398755609	0.815866425637815	0.665023292370316	NA	NA	NA	NA	2L	12298568	12298749	182	+	1	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
+FBgn0000114:E011	FBgn0000114	E011	0.0883366573889214	14	0.0422451536000494	0.979098942398376	NA	0.901165948893395	0.0127751610731135	-6.14037941516088	2L	12288905	12289344	440	+	0	0	0	0	1	0	0	FBtr0080347
+FBgn0000114:E012	FBgn0000114	E012	0.0933261680585749	14	0.0165742552848158	0.991747115940935	NA	0.0161636584595612	0.822669226222095	5.66948679957666	2L	12298568	12298749	182	+	1	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
 FBgn0000114:E013	FBgn0000114	E013	0	NA	NA	NA	NA	NA	NA	NA	2L	12298814	12299111	298	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
-FBgn0000114:E014	FBgn0000114	E014	0.0883366573889214	0.56160886675747	0.284210800995659	0.867529813592701	NA	NA	NA	NA	2L	12299188	12299394	207	+	0	0	0	0	1	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
-FBgn0000114:E015	FBgn0000114	E015	0.0883366573889214	0.56160886675747	0.284210800995659	0.867529813592701	NA	NA	NA	NA	2L	12300361	12300396	36	+	0	0	0	0	1	0	0	FBtr0331644
+FBgn0000114:E014	FBgn0000114	E014	0.0883366573889214	14	0.0422451536000494	0.979098942398376	NA	0.901165948893395	0.0127751610731135	-6.14037941516088	2L	12299188	12299394	207	+	0	0	0	0	1	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
+FBgn0000114:E015	FBgn0000114	E015	0.0883366573889214	14	0.0422451536000494	0.979098942398376	NA	0.901165948893395	0.0127751610731135	-6.14037941516088	2L	12300361	12300396	36	+	0	0	0	0	1	0	0	FBtr0331644
 FBgn0000114:E016	FBgn0000114	E016	0	NA	NA	NA	NA	NA	NA	NA	2L	12300610	12300621	12	+	0	0	0	0	0	0	0	FBtr0331644
 FBgn0000114:E017	FBgn0000114	E017	0	NA	NA	NA	NA	NA	NA	NA	2L	12304446	12304595	150	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
 FBgn0000114:E018	FBgn0000114	E018	0	NA	NA	NA	NA	NA	NA	NA	2L	12310682	12311093	412	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
 FBgn0000114:E019	FBgn0000114	E019	0	NA	NA	NA	NA	NA	NA	NA	2L	12311094	12311104	11	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331645, FBtr0080347, FBtr0331998
-FBgn0000116:E002	FBgn0000116	E002	0.0883366573889214	0.282766465728211	2.01127325191983	0.365811675448866	NA	1.07827840605447	0.0146951570997782	6.19724513023531	3L	9044230	9044817	588	-	0	0	0	0	1	0	0	FBtr0331550, FBtr0076546
-FBgn0000116:E003	FBgn0000116	E003	0.40181652404165	0.0974629307398967	6.02870700146762	0.0490775538355085	NA	1.87262787701226	0.887825140243837	1.07671677337537	3L	9044818	9045001	184	-	1	0	0	1	2	0	0	FBtr0076546
-FBgn0000116:E004	FBgn0000116	E004	0.15316821713762	0.296390832816979	1.1371386880015	0.566335090089352	NA	0.0201916309542209	0.901324736307787	-5.48021763271138	3L	9046620	9046661	42	-	0	0	1	0	0	0	0	FBtr0331550
-FBgn0000116:E005	FBgn0000116	E005	1.25599426711867	0.510503716927147	0.324279389152636	0.850322410814094	NA	2.0761033293771	2.24393157600357	-0.112150435045726	3L	9050643	9050681	39	-	1	0	5	1	3	0	0	FBtr0076545
-FBgn0000116:E006	FBgn0000116	E006	0.15316821713762	0.296390832816979	1.1371386880015	0.566335090089352	NA	0.0201916309542209	0.901324736307787	-5.48021763271138	3L	9055007	9055567	561	-	0	0	1	0	0	0	0	FBtr0076543, FBtr0076544
-FBgn0000116:E007	FBgn0000116	E007	0	NA	NA	NA	NA	0.0201921726660679	0.014692887224756	0.458678231732963	3L	9055912	9056048	137	-	0	0	0	0	0	0	0	FBtr0076544
-FBgn0000116:E008	FBgn0000116	E008	0.205235479273134	0.288940762923654	3.11971830829101	0.210165670079664	NA	1.11038521915022	0.0146952088058185	6.2395706000068	3L	9057564	9057617	54	-	0	0	0	0	0	1	0	FBtr0112791, FBtr0076543
-FBgn0000117:E007	FBgn0000117	E007	4.5734995655629	0.069980253920095	3.3362555894048	0.188599832915634	NA	4.25024580229025	4.13730637770574	0.0388544816644843	X	1793337	1793413	77	-	10	5	2	3	15	1	3	FBtr0332583
-FBgn0000119:E007	FBgn0000119	E007	2.5085164052321	0.026869378720391	6.44202453635987	0.0399146334903555	NA	3.59815529575842	2.3653275825246	0.605217453095769	2R	9370660	9370723	64	-	3	2	0	6	8	1	1	FBtr0087702
+FBgn0000116:E002	FBgn0000116	E002	0.0883366573889214	0.649506832951611	0.955102166349974	0.620300597862845	NA	1.06977392668418	0.0168077984590731	-5.99203136858692	3L	9044230	9044817	588	-	0	0	0	0	1	0	0	FBtr0331550, FBtr0076546
+FBgn0000116:E004	FBgn0000116	E004	0.15316821713762	0.43977187338658	0.328021702700227	0.848732811933342	NA	0.0232213523500242	0.90648447279086	5.2867584097007	3L	9046620	9046661	42	-	0	0	1	0	0	0	0	FBtr0331550
+FBgn0000116:E006	FBgn0000116	E006	0.15316821713762	0.43977187338658	0.328021702700227	0.848732811933342	NA	0.0232213523500242	0.90648447279086	5.2867584097007	3L	9055007	9055567	561	-	0	0	1	0	0	0	0	FBtr0076543, FBtr0076544
+FBgn0000116:E007	FBgn0000116	E007	0	NA	NA	NA	NA	NA	NA	NA	3L	9055912	9056048	137	-	0	0	0	0	0	0	0	FBtr0076544
+FBgn0000116:E008	FBgn0000116	E008	0.205235479273134	0.353436872439287	1.98242161309956	0.371127055796381	NA	1.12162424681281	0.0168071427941747	-6.06037114417562	3L	9057564	9057617	54	-	0	0	0	0	0	1	0	FBtr0112791, FBtr0076543
 FBgn0000120:E001	FBgn0000120	E001	0	NA	NA	NA	NA	NA	NA	NA	2L	18078269	18078496	228	+	0	0	0	0	0	0	0	FBtr0307350, FBtr0081030
 FBgn0000120:E002	FBgn0000120	E002	0	NA	NA	NA	NA	NA	NA	NA	2L	18078916	18079723	808	+	0	0	0	0	0	0	0	FBtr0307350, FBtr0081030
 FBgn0000120:E003	FBgn0000120	E003	0	NA	NA	NA	NA	NA	NA	NA	2L	18079957	18080086	130	+	0	0	0	0	0	0	0	FBtr0307350, FBtr0081030
 FBgn0000120:E004	FBgn0000120	E004	0	NA	NA	NA	NA	NA	NA	NA	2L	18080147	18080415	269	+	0	0	0	0	0	0	0	FBtr0307350, FBtr0081030
-FBgn0000121:E001	FBgn0000121	E001	1.0078404227901	0.0813154020717312	4.34385793851407	0.11395758408448	NA	NA	NA	NA	3L	8640361	8640745	385	-	4	0	1	0	1	1	1	FBtr0076599
-FBgn0000121:E002	FBgn0000121	E002	1.2324267524932	0.164974109301381	0.172760800185486	0.91724524467096	NA	NA	NA	NA	3L	8640808	8641002	195	-	2	1	0	3	1	1	1	FBtr0076599
-FBgn0000121:E003	FBgn0000121	E003	2.30524126345099	0.0717993341520124	4.19882575909892	0.122528346036444	NA	NA	NA	NA	3L	8641070	8642036	967	-	2	0	1	3	11	2	1	FBtr0076599
 FBgn0000137:E001	FBgn0000137	E001	0	NA	NA	NA	NA	NA	NA	NA	X	354533	357209	2677	+	0	0	0	0	0	0	0	FBtr0070075
-FBgn0000139:E001	FBgn0000139	E001	0.187795396756122	0.28662869942016	1.95879645587128	0.375537018555398	NA	0.879924294236769	0.212535063477741	2.04967853146798	3R	20475810	20476066	257	+	0	0	0	0	0	0	1	FBtr0084660
-FBgn0000139:E002	FBgn0000139	E002	1.96739811366688	0.133921979075896	2.6487965202692	0.265962951457817	NA	2.65120798807141	2.93475897219182	-0.146592167088059	3R	20476127	20476311	185	+	4	3	0	2	7	1	0	FBtr0084660
-FBgn0000139:E003	FBgn0000139	E003	3.61191788404307	0.0548308983756597	4.22287462031892	0.121063835042901	NA	3.56858441566967	3.96107908395784	-0.150541605141237	3R	20476372	20476716	345	+	8	4	1	3	12	1	2	FBtr0084660
+FBgn0000139:E001	FBgn0000139	E001	0.187795396756122	0.374758883334333	0.855539171390518	0.651961618776603	NA	0.887149388069345	0.0477444815800361	-4.21577116420462	3R	20475810	20476066	257	+	0	0	0	0	0	0	1	FBtr0084660
diff -r e8ca8941952a -r 469c0d7489bd tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Oct 13 17:21:57 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="pysam" version="0.7.7">
-        <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="htseq" version="0.6.1">
-        <repository changeset_revision="0d05080e2809" name="package_htseq_0_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="dexseq" version="1.14">
-       <repository changeset_revision="6346a4883a01" name="package_dexseq_1_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>