# HG changeset patch
# User iuc
# Date 1503393625 14400
# Node ID d3ebbf39b1c5367c8efb6ff4becbb989edd2a24d

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b

diff -r 000000000000 -r d3ebbf39b1c5 idr.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idr.xml	Tue Aug 22 05:20:25 2017 -0400
@@ -0,0 +1,135 @@
+<?xml version="1.0"?>
+<tool id="idr" name="IDR" version="@VERSION@">
+    <description>compare ranked list of identifications</description>
+    <macros>
+        <token name="@VERSION@">2.0.3</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">idr</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+        <![CDATA[
+        idr --samples '$primus' '$secundus'
+        #if $peak_list:
+            --peak-list '$peak_list'
+        #end if
+        #if $input_file_type:
+            #if $primus.dataset.ext == 'gff':
+                --input-file-type gff
+            #else:
+                --input-file-type $input_file_type
+            #end if
+        #end if
+        #if $idr_threshold:
+            --idr-threshold $idr_threshold
+        #end if
+        #if $rank != 'default':
+            --rank $rank
+        #end if
+        --output-file idrValues.bed
+        --soft-idr-threshold $soft_idr_threshold
+        $plot $use_nonoverlapping_peaks --peak-merge-method $peak_merge_method
+        --initial-mu $initial_mu --initial-sigma $initial_sigma --initial-rho $initial_rho
+        --initial-mix-param $initial_mix_param $fix_mu $fix_sigma
+        $dont_filter_peaks_below_noise_mean $use_best_multisummit_idr
+        $allow_negative_scores --random-seed $random_seed --max-iter $max_iter
+        --convergence-eps $convergence_eps $only_merge_peaks
+        ]]>
+    </command>
+    <inputs>
+        <param name="primus" argument="--samples" type="data" format="bed,gff" label="First set of peaks in GFF or BED format" />
+        <param name="secundus" argument="--samples" type="data" format="bed,gff" label="Second set of peaks in GFF or BED format" />
+        <param name="peak_list" argument="--peak-list" type="data" format="bed,gff" optional="True" label="List of peaks to filter by" />
+        <param name="input_file_type" argument="--input-file-type" type="select" label="Input BED format" help="This option is ignored if the input file is GFF">
+            <option value="" selected="true">Vanilla BED</option>
+            <option value="gff">GFF</option>
+            <option value="broadPeak">ENCODE broadPeak</option>
+            <option value="narrowPeak">ENCODE narrowPeak</option>
+        </param>
+        <param argument="--rank" type="select" label="Column to use for ranking peaks">
+            <option value="default">Use default</option>
+            <option value="signal.value">signal</option>
+            <option value="p.value">p value</option>
+            <option value="q.value">q value</option>
+        </param>
+        <param name="idr_threshold" argument="--idr-threshold" type="float" optional="true" value="" />
+        <param name="soft_idr_threshold" argument="--soft-idr-threshold" type="float" value="0.05" />
+        <param argument="--plot" type="boolean" truevalue="--plot" falsevalue="" label="Output PNG plot of peaks" />
+        <param name="use_nonoverlapping_peaks" argument="--use-nonoverlapping-peaks" type="boolean" truevalue="--use-nonoverlapping-peaks" falsevalue="" label="Use peaks without an overlapping match and set the value to 0" />
+        <param name="peak_merge_method" argument="--peak-merge-method" type="select" label="Method to use for merging peaks">
+            <option value="sum">Sum</option>
+            <option value="avg">Average</option>
+            <option value="min">Min</option>
+            <option value="max">Max</option>
+        </param>
+        <param name="initial_mu" argument="--initial-mu" type="float" value="0.1" label="Initial value of mu" />
+        <param name="initial_sigma" argument="--initial-sigma" type="float" value="1.0" label="Initial value of sigma" />
+        <param name="initial_rho" argument="--initial-rho" type="float" value="0.2" label="Initial value of rho" />
+        <param name="initial_mix_param" argument="--initial-mix-param" type="float" value="0.5" label="Initial value of the mixture parameters" />
+        <param name="fix_mu" argument="--fix-mu" type="boolean" truevalue="--fix-mu" falsevalue="" label="Fix mu to the starting point and do not let it vary" />
+        <param name="fix_sigma" argument="--fix-sigma" type="boolean" truevalue="--fix-sigma" falsevalue="" label="Fix sigma to the starting point and do not let it vary" />
+        <param name="dont_filter_peaks_below_noise_mean" argument="--dont-filter-peaks-below-noise-mean" type="boolean" truevalue="--dont-filter-peaks-below-noise-mean" falsevalue="" label="Allow signal points that are below the noise mean" />
+        <param name="use_best_multisummit_idr" argument="--use-best-multisummit-IDR" type="boolean" truevalue="--use-best-multisummit-IDR" falsevalue="" label="Set the IDR value for a group of multi summit peaks" help="A group of peaks with the same chr/start/stop but different summits" />
+        <param name="allow_negative_scores" argument="--allow-negative-scores" type="boolean" truevalue="--allow-negative-scores" falsevalue="" label="Allow negative values for scores" />
+        <param name="random_seed" argument="--random-seed" type="integer" value="0" label="The random seed value" />
+        <param name="max_iter" argument="--max-iter" type="integer" value="3000" label="The maximum number of optimization iterations" />
+        <param name="convergence_eps" argument="--convergence-eps" type="float" value="0.000001" label="The maximum change in parameter value changes for convergence" />
+        <param name="only_merge_peaks" argument="--only-merge-peaks" type="boolean" truevalue="--only-merge-peaks" falsevalue="" label="Only return the merged peak list" />
+    </inputs>
+    <outputs>
+        <data format="bed" name="idr_values" from_work_dir="idrValues.bed" label="${tool.name} on ${on_string}: IDR Values">
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="primus" param_attribute="ext" />
+                </action>
+            </actions>
+        </data>
+        <data format="png" name="idr_plot" from_work_dir="idrValues.bed.png" label="${tool.name} on ${on_string}: PNG Plot">
+            <filter>plot</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="primus" value="idr_input1.1.bed" ftype="bed" />
+            <param name="secundus" value="idr_input1.2.bed" ftype="bed" />
+            <param name="rank" value="default" />
+            <param name="plot" value="True" />
+            <output name="idr_values" file="idr_out1.bed" ftype="bed" />
+            <output name="idr_plot" file="idr_out1.png" ftype="png" />
+        </test>
+        <test>
+            <param name="primus" value="idr_input2.1.bed" ftype="bed" />
+            <param name="secundus" value="idr_input2.2.bed" ftype="bed" />
+            <param name="rank" value="default" />
+            <param name="plot" value="True" />
+            <output name="idr_values" file="idr_out2.bed" ftype="bed" />
+            <output name="idr_plot" file="idr_out2.png" ftype="png" />
+        </test>
+        <test>
+            <param name="primus" value="idr_input3.1.bed" ftype="bed" />
+            <param name="secundus" value="idr_input3.2.bed" ftype="bed" />
+            <param name="peak_list" value="idr_input3.3.bed" ftype="bed" />
+            <param name="rank" value="default" />
+            <param name="plot" value="True" />
+            <output name="idr_values" file="idr_out3.bed" ftype="bed" />
+            <output name="idr_plot" file="idr_out3.png" ftype="png" />
+        </test>
+        <test>
+            <param name="primus" value="idr_input4.1.gff" ftype="gff" />
+            <param name="secundus" value="idr_input4.2.gff" ftype="gff" />
+            <param name="input_file_type" value="gff" />
+            <param name="rank" value="default" />
+            <param name="plot" value="True" />
+            <output name="idr_values" file="idr_out4.gff" ftype="gff" />
+            <output name="idr_plot" file="idr_out4.png" ftype="png" />
+        </test>
+     </tests>
+    <help>
+<![CDATA[
+The `IDR <https://github.com/nboley/idr/blob/master/README.md>`__ (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. Unlike the usual scalar measures of reproducibility, the IDR approach creates a curve, which quantitatively assesses when the findings are no longer consistent across replicates.
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1214/11-AOAS466</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_input1.1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/idr_input1.1.bed	Tue Aug 22 05:20:25 2017 -0400
@@ -0,0 +1,122 @@
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\ No newline at end of file
diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_input1.2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/idr_input1.2.bed	Tue Aug 22 05:20:25 2017 -0400
@@ -0,0 +1,173 @@
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+chr11	117014765	117015202	.	0	.	307.642558517359	-1	4.12368834166759	223
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+chr7	44240331	44240761	.	0	.	306.517938011207	-1	4.12368834166759	221
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\ No newline at end of file
diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_input2.1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/idr_input2.1.bed	Tue Aug 22 05:20:25 2017 -0400
@@ -0,0 +1,1500 @@
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diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_input2.2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/idr_input2.2.bed	Tue Aug 22 05:20:25 2017 -0400
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diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_input3.1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/idr_input3.1.bed	Tue Aug 22 05:20:25 2017 -0400
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diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_input3.2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/idr_input3.2.bed	Tue Aug 22 05:20:25 2017 -0400
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diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_input3.3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/idr_input3.3.bed	Tue Aug 22 05:20:25 2017 -0400
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+chrX	113829680	113830020	.	0	.	2.02552970808202	-1	3.16488496161468	170
+chrX	113847345	113847685	.	0	.	2.32088921035247	-1	3.34985093815599	170
+chrX	113981062	113981402	.	0	.	2.34554587982618	-1	3.34644094645187	170
+chrX	114133923	114134263	.	0	.	3.45318373814237	-1	3.76574304142104	170
+chrX	114155221	114155561	.	0	.	2.12243291426488	-1	3.2425069442368	170
+chrX	114177971	114178311	.	0	.	2.14269363259048	-1	3.26194839824365	170
+chrX	114274343	114274683	.	0	.	2.03261795973121	-1	3.18635868642911	170
+chrX	114299615	114299955	.	0	.	2.63967351584215	-1	3.49293522400488	170
+chrX	114303472	114303812	.	0	.	4.4711722017456	-1	3.93188144868211	170
+chrX	114333114	114333454	.	0	.	2.34570565510817	-1	3.34624220788448	170
+chrX	114342906	114343246	.	0	.	2.17093153519728	-1	3.27416241460931	170
+chrX	114382354	114382694	.	0	.	3.34835992136828	-1	3.73073909562981	170
+chrX	114424708	114425048	.	0	.	2.65818859600945	-1	3.49626296294314	170
+chrX	114425120	114425460	.	0	.	3.29373777074768	-1	3.68986494219782	170
+chrX	114431103	114431443	.	0	.	4.58136010211785	-1	3.91051412775319	170
+chrX	114450031	114450371	.	0	.	2.68613785969675	-1	3.50477885992889	170
+chrX	114525242	114525582	.	0	.	2.35868078517587	-1	3.34271190525306	170
+chrX	114556100	114556440	.	0	.	2.38535300150561	-1	3.34780119858785	170
+chrX	114562099	114562439	.	0	.	2.17775185293126	-1	3.27245528576762	170
+chrX	114795755	114796095	.	0	.	2.26195499148601	-1	3.32587055976547	170
+chrX	114925562	114925902	.	0	.	2.31888656137193	-1	3.35121431968375	170
+chrX	114934617	114934957	.	0	.	2.16245014037195	-1	3.27015842759546	170
+chrX	114937679	114938019	.	0	.	2.72994347183168	-1	3.51181852619409	170
+chrX	115004559	115004899	.	0	.	17.9843211257151	-1	3.54873327759815	170
+chrX	115009056	115009396	.	0	.	14.7317367058233	-1	3.6280004459889	170
+chrX	115011785	115012125	.	0	.	2.58529319738354	-1	3.48390412680742	170
+chrX	115022434	115022774	.	0	.	2.6232483441678	-1	3.48913804673801	170
+chrX	115066316	115066656	.	0	.	2.95133013728308	-1	3.62799333091247	170
+chrX	115069014	115069354	.	0	.	5.3491645403365	-1	3.83098818777379	170
+chrX	115074628	115074968	.	0	.	2.90415586246609	-1	3.60226984961588	170
+chrX	115109366	115109706	.	0	.	2.15233326516376	-1	3.26645248079035	170
+chrX	115764763	115765103	.	0	.	2.15044091000888	-1	3.26364146793269	170
+chrX	115841455	115841795	.	0	.	2.46546675871654	-1	3.40652551760166	170
+chrX	116323267	116323607	.	0	.	2.38813314049911	-1	3.34678784220359	170
+chrX	116923646	116923986	.	0	.	2.30450302983505	-1	3.34210491034799	170
+chrX	117005991	117006331	.	0	.	2.35727128512077	-1	3.34327101338322	170
+chrX	117135454	117135794	.	0	.	2.38535300150561	-1	3.34795033561715	170
+chrX	117202603	117202943	.	0	.	2.04362674814753	-1	3.19028541807879	170
+chrX	117250001	117250341	.	0	.	3.24247865536392	-1	3.68719135434468	170
+chrX	117415490	117415830	.	0	.	2.39557718275546	-1	3.35005838014479	170
+chrX	117428393	117428733	.	0	.	3.29993184690063	-1	3.70650896290149	170
+chrX	117438667	117439007	.	0	.	3.12612671090562	-1	3.64063292567133	170
+chrX	117471615	117471955	.	0	.	2.81919085209682	-1	3.54640262640291	170
+chrX	117479749	117480089	.	0	.	25.7629209213296	-1	3.6491725359736	170
+chrX	117480354	117480694	.	0	.	4.73582396656169	-1	3.88384684593682	170
+chrX	117491527	117491867	.	0	.	2.80548705904661	-1	3.54976762877467	170
+chrX	117506609	117506949	.	0	.	2.32408551896089	-1	3.34894777861707	170
+chrX	117512028	117512368	.	0	.	2.96579466330539	-1	3.6250543450693	170
+chrX	117517399	117517739	.	0	.	2.07653380042119	-1	3.21197937277184	170
+chrX	117563502	117563842	.	0	.	2.703392926444	-1	3.50984821651737	170
+chrX	117571750	117572090	.	0	.	2.76315248519572	-1	3.52219273483597	170
+chrX	117587381	117587721	.	0	.	2.46605141784222	-1	3.40585501031494	170
+chrX	117626743	117627083	.	0	.	2.32445382772256	-1	3.34864223220775	170
+chrX	117629637	117629977	.	0	.	4.80930721037978	-1	3.93339772533223	170
+chrX	117629860	117630200	.	0	.	2.17276578664116	-1	3.2735502302432	170
+chrX	117630278	117630618	.	0	.	2.35593594372536	-1	3.34342943552055	170
+chrX	117630477	117630817	.	0	.	2.0614380559813	-1	3.19912572976442	170
+chrX	117637820	117638160	.	0	.	2.95266133800027	-1	3.62771159880172	170
+chrX	117638867	117639207	.	0	.	5.1730449503265	-1	3.8657097138981	170
+chrX	117643324	117643664	.	0	.	2.34555883493521	-1	3.34631260486197	170
+chrX	117646596	117646936	.	0	.	3.27319383977194	-1	3.69577999064465	170
+chrX	117674936	117675276	.	0	.	2.93458107275745	-1	3.60744767841246	170
+chrX	117676109	117676449	.	0	.	2.03805237870537	-1	3.18964950641551	170
+chrX	117710231	117710571	.	0	.	2.73581711387261	-1	3.51936786367749	170
+chrX	117760130	117760470	.	0	.	2.39892463154654	-1	3.35340684368273	170
+chrX	117768752	117769092	.	0	.	3.03314327150086	-1	3.64918181319322	170
+chrX	117771290	117771630	.	0	.	2.12626829909285	-1	3.24433565607574	170
+chrX	117849402	117849742	.	0	.	2.33377262715848	-1	3.34583337856802	170
+chrX	117858682	117859022	.	0	.	3.29809180034223	-1	3.68861774485547	170
+chrX	117861182	117861522	.	0	.	13.279541431332	-1	3.67085788818931	170
+chrX	117861855	117862195	.	0	.	4.14166212866946	-1	3.86488102868395	170
+chrX	117904411	117904751	.	0	.	3.53201791259249	-1	3.8212197155537	170
+chrX	117909083	117909423	.	0	.	4.37251862681087	-1	3.89876066171548	170
+chrX	117934154	117934494	.	0	.	2.84567931155857	-1	3.57102512775395	170
+chrX	117958217	117958557	.	0	.	3.33063809381994	-1	3.73534818714781	170
+chrX	117958443	117958783	.	0	.	4.40187036604046	-1	3.94665855501865	170
+chrX	117959167	117959507	.	0	.	2.16560333740812	-1	3.2720792490871	170
+chrX	117973218	117973558	.	0	.	4.8491413569342	-1	3.92673413244569	170
+chrX	117977199	117977539	.	0	.	2.57972741103203	-1	3.47053319208035	170
+chrX	118012639	118012979	.	0	.	4.55963516947965	-1	3.9144101563779	170
+chrX	118030875	118031215	.	0	.	2.52440273757008	-1	3.42531953944548	170
+chrX	118034782	118035122	.	0	.	4.2905972820445	-1	3.91903192112505	170
+chrX	118037387	118037727	.	0	.	2.23962409123051	-1	3.30895278462828	170
diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_input4.1.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/idr_input4.1.gff	Tue Aug 22 05:20:25 2017 -0400
@@ -0,0 +1,499 @@
+##gff-version 2
+##bed_to_gff_converter.py
+chr19	bed2gff	.	50083710	50084074	0	.	.	.;
+chr1	bed2gff	.	44678951	44679261	0	.	.	.;
+chr6	bed2gff	.	28048576	28048870	0	.	.	.;
+chr22	bed2gff	.	22337038	22337397	0	.	.	.;
+chr11	bed2gff	.	59578147	59578443	0	.	.	.;
+chr15	bed2gff	.	35261840	35262132	0	.	.	.;
+chr12	bed2gff	.	109490191	109490472	0	.	.	.;
+chr5	bed2gff	.	148724797	148725118	0	.	.	.;
+chr8	bed2gff	.	56987001	56987305	0	.	.	.;
+chr6	bed2gff	.	31515127	31515462	0	.	.	.;
+chr12	bed2gff	.	69080591	69080876	0	.	.	.;
+chr16	bed2gff	.	740288	740602	0	.	.	.;
+chr19	bed2gff	.	11039250	11039594	0	.	.	.;
+chr17	bed2gff	.	30771317	30771592	0	.	.	.;
+chr1	bed2gff	.	10003302	10003624	0	.	.	.;
+chr13	bed2gff	.	41345218	41345502	0	.	.	.;
+chr16	bed2gff	.	31085463	31085852	0	.	.	.;
+chr9	bed2gff	.	131084619	131084946	0	.	.	.;
+chr1	bed2gff	.	28655398	28655693	0	.	.	.;
+chr21	bed2gff	.	30365080	30365419	0	.	.	.;
+chr2	bed2gff	.	55496260	55496554	0	.	.	.;
+chr5	bed2gff	.	102455722	102456060	0	.	.	.;
+chr7	bed2gff	.	127983843	127984113	0	.	.	.;
+chr1	bed2gff	.	155112892	155113167	0	.	.	.;
+chr19	bed2gff	.	50879460	50879818	0	.	.	.;
+chr16	bed2gff	.	2653190	2653529	0	.	.	.;
+chr16	bed2gff	.	84220528	84220849	0	.	.	.;
+chr1	bed2gff	.	173683884	173684188	0	.	.	.;
+chr11	bed2gff	.	47600410	47600710	0	.	.	.;
+chr15	bed2gff	.	49447769	49448060	0	.	.	.;
+chr22	bed2gff	.	20861684	20862012	0	.	.	.;
+chr6	bed2gff	.	131949256	131949559	0	.	.	.;
+chr8	bed2gff	.	37707279	37707606	0	.	.	.;
+chr15	bed2gff	.	23810631	23810906	0	.	.	.;
+chr7	bed2gff	.	141437944	141438285	0	.	.	.;
+chr21	bed2gff	.	46359726	46360023	0	.	.	.;
+chr6	bed2gff	.	28219918	28220206	0	.	.	.;
+chr7	bed2gff	.	102987942	102988206	0	.	.	.;
+chr7	bed2gff	.	96746760	96747035	0	.	.	.;
+chr6	bed2gff	.	159420748	159421012	0	.	.	.;
+chr17	bed2gff	.	40925310	40925566	0	.	.	.;
+chr1	bed2gff	.	38455582	38455905	0	.	.	.;
+chr20	bed2gff	.	57226117	57226411	0	.	.	.;
+chrX	bed2gff	.	64754698	64754986	0	.	.	.;
+chr17	bed2gff	.	49230696	49231019	0	.	.	.;
+chr20	bed2gff	.	31989221	31989517	0	.	.	.;
+chr22	bed2gff	.	31555974	31556248	0	.	.	.;
+chr11	bed2gff	.	68671189	68671471	0	.	.	.;
+chr1	bed2gff	.	145096233	145096542	0	.	.	.;
+chr6	bed2gff	.	17707127	17707437	0	.	.	.;
+chr19	bed2gff	.	13885106	13885378	0	.	.	.;
+chr16	bed2gff	.	67260861	67261153	0	.	.	.;
+chr8	bed2gff	.	143751279	143751554	0	.	.	.;
+chr6	bed2gff	.	28104505	28104786	0	.	.	.;
+chr16	bed2gff	.	29801823	29802106	0	.	.	.;
+chr6	bed2gff	.	36842447	36842765	0	.	.	.;
+chr3	bed2gff	.	127842654	127842984	0	.	.	.;
+chr16	bed2gff	.	67906807	67907079	0	.	.	.;
+chr2	bed2gff	.	233415231	233415501	0	.	.	.;
+chr7	bed2gff	.	75677177	75677464	0	.	.	.;
+chr7	bed2gff	.	44240379	44240704	0	.	.	.;
+chr1	bed2gff	.	224301663	224301925	0	.	.	.;
+chr3	bed2gff	.	52029807	52030102	0	.	.	.;
+chr20	bed2gff	.	34824215	34824488	0	.	.	.;
+chr22	bed2gff	.	19419872	19420176	0	.	.	.;
+chr2	bed2gff	.	74681965	74682322	0	.	.	.;
+chr5	bed2gff	.	43515151	43515431	0	.	.	.;
+chr9	bed2gff	.	37800622	37800902	0	.	.	.;
+chr7	bed2gff	.	129691099	129691376	0	.	.	.;
+chr12	bed2gff	.	123459110	123459398	0	.	.	.;
+chr19	bed2gff	.	56146184	56146483	0	.	.	.;
+chr1	bed2gff	.	38478186	38478507	0	.	.	.;
+chr16	bed2gff	.	1823030	1823306	0	.	.	.;
+chr7	bed2gff	.	5553329	5553581	0	.	.	.;
+chr8	bed2gff	.	145133270	145133670	0	.	.	.;
+chr12	bed2gff	.	124086465	124086754	0	.	.	.;
+chr11	bed2gff	.	31391240	31391510	0	.	.	.;
+chr1	bed2gff	.	218458480	218458748	0	.	.	.;
+chr19	bed2gff	.	59031045	59031449	0	.	.	.;
+chr2	bed2gff	.	70120939	70121198	0	.	.	.;
+chr12	bed2gff	.	124118112	124118446	0	.	.	.;
+chr12	bed2gff	.	50794457	50794722	0	.	.	.;
+chr20	bed2gff	.	62612264	62612568	0	.	.	.;
+chr2	bed2gff	.	242041624	242041899	0	.	.	.;
+chr20	bed2gff	.	34638795	34639068	0	.	.	.;
+chr7	bed2gff	.	44530151	44530427	0	.	.	.;
+chr10	bed2gff	.	1102536	1102869	0	.	.	.;
+chr13	bed2gff	.	52768476	52768744	0	.	.	.;
+chr16	bed2gff	.	2732287	2732616	0	.	.	.;
+chr16	bed2gff	.	1470652	1471004	0	.	.	.;
+chr19	bed2gff	.	59010761	59011062	0	.	.	.;
+chr5	bed2gff	.	167913289	167913559	0	.	.	.;
+chr16	bed2gff	.	28857523	28857833	0	.	.	.;
+chr20	bed2gff	.	44485922	44486239	0	.	.	.;
+chr18	bed2gff	.	33552457	33552728	0	.	.	.;
+chr1	bed2gff	.	46153686	46153989	0	.	.	.;
+chr1	bed2gff	.	20834539	20834840	0	.	.	.;
+chr15	bed2gff	.	34517028	34517331	0	.	.	.;
+chr5	bed2gff	.	93954202	93954466	0	.	.	.;
+chr8	bed2gff	.	11141764	11142084	0	.	.	.;
+chr6	bed2gff	.	170893599	170893890	0	.	.	.;
+chr1	bed2gff	.	163291428	163291749	0	.	.	.;
+chr19	bed2gff	.	9938401	9938695	0	.	.	.;
+chr7	bed2gff	.	73668667	73668954	0	.	.	.;
+chr19	bed2gff	.	4182458	4182705	0	.	.	.;
+chr16	bed2gff	.	89787228	89787505	0	.	.	.;
+chr11	bed2gff	.	8710370	8710722	0	.	.	.;
+chr3	bed2gff	.	149470175	149470450	0	.	.	.;
+chr9	bed2gff	.	127177598	127177871	0	.	.	.;
+chr12	bed2gff	.	54582617	54582998	0	.	.	.;
+chr14	bed2gff	.	24657997	24658289	0	.	.	.;
+chr7	bed2gff	.	139024854	139025179	0	.	.	.;
+chr2	bed2gff	.	3622619	3622940	0	.	.	.;
+chr5	bed2gff	.	133702770	133703057	0	.	.	.;
+chr7	bed2gff	.	99097811	99098072	0	.	.	.;
+chr2	bed2gff	.	74699681	74699975	0	.	.	.;
+chr9	bed2gff	.	137029867	137030208	0	.	.	.;
+chr9	bed2gff	.	139294531	139294815	0	.	.	.;
+chr11	bed2gff	.	62358925	62359223	0	.	.	.;
+chr8	bed2gff	.	145158562	145158845	0	.	.	.;
+chr13	bed2gff	.	31191867	31192130	0	.	.	.;
+chr1	bed2gff	.	156710856	156711174	0	.	.	.;
+chr1	bed2gff	.	11322685	11323021	0	.	.	.;
+chr16	bed2gff	.	2771003	2771296	0	.	.	.;
+chr17	bed2gff	.	42264182	42264463	0	.	.	.;
+chr11	bed2gff	.	64037355	64037701	0	.	.	.;
+chr19	bed2gff	.	9879283	9879554	0	.	.	.;
+chr10	bed2gff	.	53459240	53459533	0	.	.	.;
+chr13	bed2gff	.	53191470	53191730	0	.	.	.;
+chr4	bed2gff	.	106629756	106630035	0	.	.	.;
+chr20	bed2gff	.	2451326	2451638	0	.	.	.;
+chr12	bed2gff	.	49110412	49110744	0	.	.	.;
+chr1	bed2gff	.	150039674	150039924	0	.	.	.;
+chr3	bed2gff	.	131221703	131221982	0	.	.	.;
+chr15	bed2gff	.	66161636	66161900	0	.	.	.;
+chr7	bed2gff	.	32529878	32530186	0	.	.	.;
+chr20	bed2gff	.	34542302	34542600	0	.	.	.;
+chr1	bed2gff	.	1342564	1342834	0	.	.	.;
+chr17	bed2gff	.	56429458	56429747	0	.	.	.;
+chr5	bed2gff	.	40835213	40835571	0	.	.	.;
+chrX	bed2gff	.	21857529	21857813	0	.	.	.;
+chr12	bed2gff	.	49961786	49962057	0	.	.	.;
+chr19	bed2gff	.	45582360	45582627	0	.	.	.;
+chr3	bed2gff	.	15468897	15469195	0	.	.	.;
+chr8	bed2gff	.	23351716	23351994	0	.	.	.;
+chr7	bed2gff	.	2281728	2281978	0	.	.	.;
+chr2	bed2gff	.	45838296	45838560	0	.	.	.;
+chr6	bed2gff	.	28367415	28367688	0	.	.	.;
+chr17	bed2gff	.	42092241	42092535	0	.	.	.;
+chr20	bed2gff	.	35917909	35918177	0	.	.	.;
+chr19	bed2gff	.	19302859	19303130	0	.	.	.;
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+chr19	bed2gff	.	49497016	49497239	0	.	.	.;
+chr9	bed2gff	.	127703264	127703518	0	.	.	.;
+chr1	bed2gff	.	1259956	1260183	0	.	.	.;
+chr2	bed2gff	.	224822010	224822233	0	.	.	.;
+chr1	bed2gff	.	110091048	110091317	0	.	.	.;
+chr10	bed2gff	.	15902412	15902693	0	.	.	.;
+chr21	bed2gff	.	37692339	37692598	0	.	.	.;
+chr8	bed2gff	.	9413265	9413491	0	.	.	.;
+chr1	bed2gff	.	204485371	204485648	0	.	.	.;
+chr19	bed2gff	.	19626893	19627156	0	.	.	.;
+chr1	bed2gff	.	224622437	224622668	0	.	.	.;
+chr19	bed2gff	.	6279907	6280204	0	.	.	.;
+chr6	bed2gff	.	30539107	30539364	0	.	.	.;
+chr13	bed2gff	.	115000193	115000439	0	.	.	.;
+chr4	bed2gff	.	119606391	119606637	0	.	.	.;
+chr3	bed2gff	.	50606771	50607014	0	.	.	.;
+chr15	bed2gff	.	83419150	83419393	0	.	.	.;
+chr12	bed2gff	.	49412479	49412764	0	.	.	.;
+chr5	bed2gff	.	140044247	140044517	0	.	.	.;
+chr9	bed2gff	.	140100012	140100242	0	.	.	.;
+chr1	bed2gff	.	160001665	160001925	0	.	.	.;
+chr6	bed2gff	.	43655443	43655668	0	.	.	.;
+chr11	bed2gff	.	62599072	62599326	0	.	.	.;
+chr11	bed2gff	.	94706657	94706895	0	.	.	.;
+chr9	bed2gff	.	129567159	129567399	0	.	.	.;
+chr11	bed2gff	.	64885065	64885321	0	.	.	.;
+chr10	bed2gff	.	102747144	102747420	0	.	.	.;
+chr8	bed2gff	.	21867670	21867893	0	.	.	.;
+chr8	bed2gff	.	27630030	27630288	0	.	.	.;
+chr5	bed2gff	.	75012842	75013077	0	.	.	.;
+chr10	bed2gff	.	12238026	12238278	0	.	.	.;
+chr12	bed2gff	.	6772190	6772599	0	.	.	.;
+chr11	bed2gff	.	117014829	117015123	0	.	.	.;
+chr20	bed2gff	.	55043566	55043810	0	.	.	.;
+chr9	bed2gff	.	140149616	140149862	0	.	.	.;
+chr3	bed2gff	.	178865770	178866013	0	.	.	.;
+chr10	bed2gff	.	52310124	52310439	0	.	.	.;
+chr9	bed2gff	.	135282127	135282353	0	.	.	.;
+chr1	bed2gff	.	150293864	150294122	0	.	.	.;
+chr11	bed2gff	.	65729031	65729293	0	.	.	.;
+chr1	bed2gff	.	40723527	40724002	0	.	.	.;
+chr10	bed2gff	.	135207528	135207810	0	.	.	.;
+chr16	bed2gff	.	30366532	30366782	0	.	.	.;
+chr9	bed2gff	.	127631291	127631515	0	.	.	.;
+chr1	bed2gff	.	44501663	44501935	0	.	.	.;
+chr16	bed2gff	.	20817684	20817919	0	.	.	.;
+chr16	bed2gff	.	31128853	31129096	0	.	.	.;
+chr16	bed2gff	.	30933694	30933969	0	.	.	.;
+chr7	bed2gff	.	91509917	91510189	0	.	.	.;
+chr4	bed2gff	.	4249856	4250137	0	.	.	.;
+chr22	bed2gff	.	20104674	20104975	0	.	.	.;
+chr12	bed2gff	.	120105559	120105893	0	.	.	.;
+chr8	bed2gff	.	33342570	33342802	0	.	.	.;
+chr16	bed2gff	.	57496431	57496665	0	.	.	.;
+chr17	bed2gff	.	48450420	48450700	0	.	.	.;
+chr8	bed2gff	.	125551204	125551448	0	.	.	.;
+chr14	bed2gff	.	105957214	105957456	0	.	.	.;
+chr6	bed2gff	.	30923363	30923615	0	.	.	.;
+chr3	bed2gff	.	121468701	121468944	0	.	.	.;
+chr11	bed2gff	.	33966342	33966618	0	.	.	.;
+chr2	bed2gff	.	99797501	99797719	0	.	.	.;
+chr19	bed2gff	.	8070519	8070780	0	.	.	.;
+chr3	bed2gff	.	47554851	47555125	0	.	.	.;
+chr9	bed2gff	.	138853135	138853462	0	.	.	.;
+chr2	bed2gff	.	9563634	9563872	0	.	.	.;
+chr11	bed2gff	.	46958108	46958369	0	.	.	.;
+chr17	bed2gff	.	44271409	44271640	0	.	.	.;
diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_input4.2.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/idr_input4.2.gff	Tue Aug 22 05:20:25 2017 -0400
@@ -0,0 +1,499 @@
+##gff-version 2
+##bed_to_gff_converter.py
+chr16	bed2gff	.	31085417	31086009	0	.	.	.;
+chr12	bed2gff	.	109490130	109490582	0	.	.	.;
+chr13	bed2gff	.	41345147	41345561	0	.	.	.;
+chr6	bed2gff	.	159420670	159421082	0	.	.	.;
+chr2	bed2gff	.	55496202	55496615	0	.	.	.;
+chr1	bed2gff	.	44678905	44679348	0	.	.	.;
+chr11	bed2gff	.	59578081	59578477	0	.	.	.;
+chr17	bed2gff	.	49230636	49231074	0	.	.	.;
+chr11	bed2gff	.	71823368	71824025	0	.	.	.;
+chr3	bed2gff	.	150264251	150264681	0	.	.	.;
+chr7	bed2gff	.	5553250	5553652	0	.	.	.;
+chr14	bed2gff	.	24657924	24658351	0	.	.	.;
+chr6	bed2gff	.	36842324	36842832	0	.	.	.;
+chr15	bed2gff	.	85259190	85259628	0	.	.	.;
+chr1	bed2gff	.	155112833	155113238	0	.	.	.;
+chr6	bed2gff	.	7389798	7390349	0	.	.	.;
+chr1	bed2gff	.	10003218	10003670	0	.	.	.;
+chr1	bed2gff	.	227922820	227923232	0	.	.	.;
+chrX	bed2gff	.	21857474	21857872	0	.	.	.;
+chr5	bed2gff	.	43515095	43515472	0	.	.	.;
+chr18	bed2gff	.	33552398	33552791	0	.	.	.;
+chr8	bed2gff	.	37707215	37707643	0	.	.	.;
+chr19	bed2gff	.	50083643	50084077	0	.	.	.;
+chr20	bed2gff	.	34824170	34824561	0	.	.	.;
+chr6	bed2gff	.	28048536	28048949	0	.	.	.;
+chr7	bed2gff	.	32529782	32530217	0	.	.	.;
+chr7	bed2gff	.	96746717	96747107	0	.	.	.;
+chr20	bed2gff	.	31989139	31989561	0	.	.	.;
+chr15	bed2gff	.	23810570	23810980	0	.	.	.;
+chr19	bed2gff	.	4723594	4724088	0	.	.	.;
+chr6	bed2gff	.	30923305	30923674	0	.	.	.;
+chr3	bed2gff	.	127842593	127843003	0	.	.	.;
+chr9	bed2gff	.	35102966	35103346	0	.	.	.;
+chr2	bed2gff	.	242041551	242041987	0	.	.	.;
+chr15	bed2gff	.	64679784	64680194	0	.	.	.;
+chr9	bed2gff	.	131084567	131085042	0	.	.	.;
+chr17	bed2gff	.	40925279	40925637	0	.	.	.;
+chr19	bed2gff	.	50879406	50879889	0	.	.	.;
+chr11	bed2gff	.	10772537	10772959	0	.	.	.;
+chr13	bed2gff	.	52768380	52768795	0	.	.	.;
+chr21	bed2gff	.	46221518	46221946	0	.	.	.;
+chr6	bed2gff	.	28367332	28367730	0	.	.	.;
+chr3	bed2gff	.	52029720	52030144	0	.	.	.;
+chr5	bed2gff	.	112196781	112197218	0	.	.	.;
+chr1	bed2gff	.	28655351	28655735	0	.	.	.;
+chr19	bed2gff	.	59010715	59011133	0	.	.	.;
+chr21	bed2gff	.	45148507	45148912	0	.	.	.;
+chr2	bed2gff	.	3622559	3622998	0	.	.	.;
+chr14	bed2gff	.	105282251	105282630	0	.	.	.;
+chr15	bed2gff	.	64648205	64648630	0	.	.	.;
+chr20	bed2gff	.	2451205	2451677	0	.	.	.;
+chr7	bed2gff	.	44530077	44530536	0	.	.	.;
+chr9	bed2gff	.	35812131	35812468	0	.	.	.;
+chr1	bed2gff	.	20834456	20834934	0	.	.	.;
+chr2	bed2gff	.	74681919	74682387	0	.	.	.;
+chr6	bed2gff	.	31515117	31515505	0	.	.	.;
+chr19	bed2gff	.	59066162	59066668	0	.	.	.;
+chr19	bed2gff	.	9879234	9879636	0	.	.	.;
+chr6	bed2gff	.	170863169	170863611	0	.	.	.;
+chr2	bed2gff	.	113299813	113300203	0	.	.	.;
+chr3	bed2gff	.	10362634	10363017	0	.	.	.;
+chr3	bed2gff	.	15468789	15469289	0	.	.	.;
+chr5	bed2gff	.	443032	443785	0	.	.	.;
+chr7	bed2gff	.	92076558	92076974	0	.	.	.;
+chr19	bed2gff	.	45542119	45542499	0	.	.	.;
+chr16	bed2gff	.	740211	740646	0	.	.	.;
+chr11	bed2gff	.	8710285	8710774	0	.	.	.;
+chr20	bed2gff	.	62612200	62612613	0	.	.	.;
+chr17	bed2gff	.	61627482	61628045	0	.	.	.;
+chr22	bed2gff	.	46731380	46731880	0	.	.	.;
+chr2	bed2gff	.	85839021	85839378	0	.	.	.;
+chr11	bed2gff	.	62358846	62359289	0	.	.	.;
+chr7	bed2gff	.	99679065	99679600	0	.	.	.;
+chr20	bed2gff	.	35917858	35918251	0	.	.	.;
+chr22	bed2gff	.	19419728	19420264	0	.	.	.;
+chr7	bed2gff	.	127983718	127984163	0	.	.	.;
+chr1	bed2gff	.	145096204	145096647	0	.	.	.;
+chr1	bed2gff	.	11322433	11323065	0	.	.	.;
+chr7	bed2gff	.	75677117	75677538	0	.	.	.;
+chr20	bed2gff	.	34542154	34542667	0	.	.	.;
+chr1	bed2gff	.	28969411	28969802	0	.	.	.;
+chr2	bed2gff	.	71357543	71357920	0	.	.	.;
+chr4	bed2gff	.	159644369	159644762	0	.	.	.;
+chr9	bed2gff	.	114393299	114393693	0	.	.	.;
+chr19	bed2gff	.	45582279	45582694	0	.	.	.;
+chr1	bed2gff	.	28414928	28415336	0	.	.	.;
+chr1	bed2gff	.	224301625	224301992	0	.	.	.;
+chr17	bed2gff	.	61678038	61678422	0	.	.	.;
+chr16	bed2gff	.	77224830	77225214	0	.	.	.;
+chr8	bed2gff	.	125551161	125551510	0	.	.	.;
+chr18	bed2gff	.	22006382	22006786	0	.	.	.;
+chr22	bed2gff	.	22336865	22337449	0	.	.	.;
+chr15	bed2gff	.	35261788	35262189	0	.	.	.;
+chr2	bed2gff	.	233415170	233415593	0	.	.	.;
+chr8	bed2gff	.	56986816	56987359	0	.	.	.;
+chr16	bed2gff	.	1470585	1471075	0	.	.	.;
+chr20	bed2gff	.	62289431	62290034	0	.	.	.;
+chr11	bed2gff	.	68671114	68671535	0	.	.	.;
+chr16	bed2gff	.	89723919	89724272	0	.	.	.;
+chr6	bed2gff	.	31633376	31633849	0	.	.	.;
+chrX	bed2gff	.	64754637	64755010	0	.	.	.;
+chr3	bed2gff	.	155572080	155572552	0	.	.	.;
+chr1	bed2gff	.	163291404	163291800	0	.	.	.;
+chr21	bed2gff	.	47705961	47706679	0	.	.	.;
+chr12	bed2gff	.	75905240	75905604	0	.	.	.;
+chr1	bed2gff	.	149982513	149982894	0	.	.	.;
+chr13	bed2gff	.	113862847	113863215	0	.	.	.;
+chr1	bed2gff	.	36554264	36554715	0	.	.	.;
+chr7	bed2gff	.	99214372	99214769	0	.	.	.;
+chr20	bed2gff	.	2644691	2645038	0	.	.	.;
+chr2	bed2gff	.	70120920	70121259	0	.	.	.;
+chr20	bed2gff	.	44485857	44486285	0	.	.	.;
+chr11	bed2gff	.	31391194	31391568	0	.	.	.;
+chr7	bed2gff	.	44084024	44084427	0	.	.	.;
+chr9	bed2gff	.	140473118	140473601	0	.	.	.;
+chr7	bed2gff	.	141437930	141438371	0	.	.	.;
+chr6	bed2gff	.	170893516	170893965	0	.	.	.;
+chr3	bed2gff	.	9404556	9404917	0	.	.	.;
+chr3	bed2gff	.	53381463	53381851	0	.	.	.;
+chr21	bed2gff	.	27107078	27107574	0	.	.	.;
+chr8	bed2gff	.	27629970	27630330	0	.	.	.;
+chr1	bed2gff	.	27648415	27649024	0	.	.	.;
+chr10	bed2gff	.	53459188	53459772	0	.	.	.;
+chr5	bed2gff	.	102455691	102456105	0	.	.	.;
+chr6	bed2gff	.	28192864	28193253	0	.	.	.;
+chr5	bed2gff	.	171433567	171434137	0	.	.	.;
+chr15	bed2gff	.	91473214	91473571	0	.	.	.;
+chr11	bed2gff	.	117014766	117015202	0	.	.	.;
+chr16	bed2gff	.	2653135	2653607	0	.	.	.;
+chr11	bed2gff	.	32605162	32605589	0	.	.	.;
+chr5	bed2gff	.	74062759	74063310	0	.	.	.;
+chr1	bed2gff	.	38478080	38478578	0	.	.	.;
+chr7	bed2gff	.	44240332	44240761	0	.	.	.;
+chr9	bed2gff	.	140117949	140118355	0	.	.	.;
+chr20	bed2gff	.	1373664	1374043	0	.	.	.;
+chr17	bed2gff	.	30771269	30771646	0	.	.	.;
+chr17	bed2gff	.	42092183	42092553	0	.	.	.;
+chr15	bed2gff	.	76195998	76196428	0	.	.	.;
+chr5	bed2gff	.	130506253	130506593	0	.	.	.;
+chr9	bed2gff	.	95432316	95432809	0	.	.	.;
+chr1	bed2gff	.	179846805	179847169	0	.	.	.;
+chr13	bed2gff	.	53191417	53191786	0	.	.	.;
+chr12	bed2gff	.	54867242	54867587	0	.	.	.;
+chr10	bed2gff	.	96122556	96122945	0	.	.	.;
+chr1	bed2gff	.	109618452	109618807	0	.	.	.;
+chr1	bed2gff	.	85725174	85725559	0	.	.	.;
+chr16	bed2gff	.	89787144	89787565	0	.	.	.;
+chr6	bed2gff	.	43655351	43655712	0	.	.	.;
+chr16	bed2gff	.	84220434	84220881	0	.	.	.;
+chr6	bed2gff	.	111303048	111303403	0	.	.	.;
+chr14	bed2gff	.	74353347	74353732	0	.	.	.;
+chr12	bed2gff	.	69080535	69080964	0	.	.	.;
+chr7	bed2gff	.	1609501	1609974	0	.	.	.;
+chr6	bed2gff	.	131949193	131949648	0	.	.	.;
+chr20	bed2gff	.	34287061	34287496	0	.	.	.;
+chr5	bed2gff	.	167913236	167913644	0	.	.	.;
+chr3	bed2gff	.	180319743	180320146	0	.	.	.;
+chr14	bed2gff	.	100842494	100842986	0	.	.	.;
+chr22	bed2gff	.	29949584	29949946	0	.	.	.;
+chr5	bed2gff	.	148724750	148725160	0	.	.	.;
+chr12	bed2gff	.	123459062	123459482	0	.	.	.;
+chr11	bed2gff	.	45939242	45939685	0	.	.	.;
+chr12	bed2gff	.	124118043	124118495	0	.	.	.;
+chr2	bed2gff	.	45838232	45838613	0	.	.	.;
+chr5	bed2gff	.	40835141	40835649	0	.	.	.;
+chr16	bed2gff	.	717882	718299	0	.	.	.;
+chr5	bed2gff	.	158690027	158690489	0	.	.	.;
+chr9	bed2gff	.	130699949	130700332	0	.	.	.;
+chr19	bed2gff	.	55791267	55791701	0	.	.	.;
+chr1	bed2gff	.	7887268	7887687	0	.	.	.;
+chr8	bed2gff	.	146052737	146053129	0	.	.	.;
+chr17	bed2gff	.	56429392	56429820	0	.	.	.;
+chr19	bed2gff	.	17530481	17530964	0	.	.	.;
+chr1	bed2gff	.	150266102	150266431	0	.	.	.;
+chr1	bed2gff	.	209957845	209958254	0	.	.	.;
+chr16	bed2gff	.	23652600	23652963	0	.	.	.;
+chr15	bed2gff	.	90437069	90437469	0	.	.	.;
+chr3	bed2gff	.	13493222	13493574	0	.	.	.;
+chr9	bed2gff	.	137029853	137030264	0	.	.	.;
+chr2	bed2gff	.	73964274	73964849	0	.	.	.;
+chr9	bed2gff	.	37800544	37800969	0	.	.	.;
+chr1	bed2gff	.	46153665	46154077	0	.	.	.;
+chr7	bed2gff	.	39662946	39663488	0	.	.	.;
+chr19	bed2gff	.	13260990	13261358	0	.	.	.;
+chr11	bed2gff	.	118230040	118230460	0	.	.	.;
+chr12	bed2gff	.	117348559	117348928	0	.	.	.;
+chr16	bed2gff	.	2732215	2732706	0	.	.	.;
+chr1	bed2gff	.	55181321	55181677	0	.	.	.;
+chr2	bed2gff	.	96971078	96971497	0	.	.	.;
+chr17	bed2gff	.	34891141	34891511	0	.	.	.;
+chr12	bed2gff	.	120105495	120106100	0	.	.	.;
+chr10	bed2gff	.	44101681	44102069	0	.	.	.;
+chr17	bed2gff	.	73042906	73043391	0	.	.	.;
+chr5	bed2gff	.	149379944	149380413	0	.	.	.;
+chr16	bed2gff	.	2097766	2098164	0	.	.	.;
+chr16	bed2gff	.	28857454	28857889	0	.	.	.;
+chr15	bed2gff	.	66161575	66161967	0	.	.	.;
+chr3	bed2gff	.	101280505	101280870	0	.	.	.;
+chr20	bed2gff	.	60961834	60962295	0	.	.	.;
+chr7	bed2gff	.	99612990	99613364	0	.	.	.;
+chr20	bed2gff	.	1099002	1099387	0	.	.	.;
+chr7	bed2gff	.	104624192	104624575	0	.	.	.;
+chr1	bed2gff	.	20987711	20988306	0	.	.	.;
+chr22	bed2gff	.	40742326	40742709	0	.	.	.;
+chr20	bed2gff	.	44992841	44993250	0	.	.	.;
+chr19	bed2gff	.	34919085	34919497	0	.	.	.;
+chr11	bed2gff	.	64037293	64037765	0	.	.	.;
+chr1	bed2gff	.	165737897	165738353	0	.	.	.;
+chr7	bed2gff	.	91509884	91510258	0	.	.	.;
+chr19	bed2gff	.	4182379	4182751	0	.	.	.;
+chr6	bed2gff	.	36853494	36853953	0	.	.	.;
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+chr19	bed2gff	.	58125396	58125759	0	.	.	.;
+chr11	bed2gff	.	118122706	118123175	0	.	.	.;
+chr17	bed2gff	.	33905477	33905837	0	.	.	.;
+chr11	bed2gff	.	64884987	64885382	0	.	.	.;
+chr2	bed2gff	.	128848548	128848935	0	.	.	.;
+chr19	bed2gff	.	13885097	13885432	0	.	.	.;
+chr9	bed2gff	.	128469302	128469682	0	.	.	.;
+chr19	bed2gff	.	10514061	10514440	0	.	.	.;
diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_out1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/idr_out1.bed	Tue Aug 22 05:20:25 2017 -0400
@@ -0,0 +1,71 @@
+chr1	44678904	44679348	.	1000	.	616.97545	-1	-1	208	2.44	3.04	44678950	44679261	264.09119	158	44678904	44679348	352.88426	212
+chr12	109490129	109490582	.	1000	.	612.34747	-1	-1	210	2.48	3.07	109490190	109490472	252.01797	145	109490129	109490582	360.32950	215
+chr16	31085416	31086009	.	1000	.	608.40709	-1	-1	254	2.33	2.98	31085462	31085852	245.86041	213	31085416	31086009	362.54668	250
+chr13	41345146	41345561	.	1000	.	604.83885	-1	-1	204	2.75	3.12	41345217	41345502	246.21463	131	41345146	41345561	358.62422	207
+chr11	59578080	59578477	.	1000	.	599.79940	-1	-1	212	2.76	3.15	59578146	59578443	252.90901	153	59578080	59578477	346.89039	206
+chr19	50083642	50084077	.	1000	.	597.22316	-1	-1	235	2.34	3.01	50083709	50084074	266.60394	186	50083642	50084077	330.61921	217
+chr2	55496201	55496615	.	1000	.	594.96066	-1	-1	207	2.94	3.23	55496259	55496554	241.61053	151	55496201	55496615	353.35014	205
+chr6	28048535	28048949	.	1000	.	592.34385	-1	-1	188	2.77	3.16	28048575	28048870	262.46293	143	28048535	28048949	329.88092	194
+chr6	159420669	159421082	.	1000	.	586.21200	-1	-1	208	2.87	3.20	159420747	159421012	228.49880	123	159420669	159421082	357.71320	216
+chr1	10003217	10003670	.	1000	.	578.85225	-1	-1	235	3.15	3.29	10003301	10003624	246.24793	155	10003217	10003670	332.60432	232
+chr1	155112832	155113238	.	1000	.	577.03543	-1	-1	196	3.20	3.33	155112891	155113167	241.18825	145	155112832	155113238	335.84718	188
+chr17	49230635	49231074	.	1000	.	572.40640	-1	-1	244	3.09	3.27	49230695	49231019	227.20968	174	49230635	49231074	345.19672	254
+chr22	22336864	22337449	.	1000	.	569.73619	-1	-1	347	2.75	3.13	22337037	22337397	256.48297	187	22336864	22337449	313.25322	334
+chr6	31515116	31515505	.	1000	.	567.62068	-1	-1	175	3.15	3.28	31515126	31515462	248.82820	154	31515116	31515505	318.79248	187
+chr9	131084566	131085042	.	1000	.	566.89305	-1	-1	219	3.30	3.35	131084618	131084946	243.95134	163	131084566	131085042	322.94171	224
+chr15	35261787	35262189	.	1000	.	565.12551	-1	-1	198	2.89	3.22	35261839	35262132	252.45870	155	35261787	35262189	312.66682	189
+chr16	740210	740646	.	1000	.	564.27450	-1	-1	231	3.20	3.32	740287	740602	247.84900	156	740210	740646	316.42549	230
+chr1	28655350	28655735	.	1000	.	563.85958	-1	-1	197	3.32	3.36	28655397	28655693	242.70733	149	28655350	28655735	321.15225	199
+chr8	37707214	37707643	.	1000	.	563.31118	-1	-1	239	3.29	3.35	37707278	37707606	232.25045	174	37707214	37707643	331.06072	240
+chr8	56986815	56987359	.	1000	.	562.24124	-1	-1	331	3.01	3.25	56987000	56987305	249.89139	146	56986815	56987359	312.34984	331
+chr6	36842323	36842832	.	1000	.	562.21263	-1	-1	289	3.17	3.30	36842446	36842765	223.41944	173	36842323	36842832	338.79319	282
+chr19	50879405	50879889	.	1000	.	561.80328	-1	-1	214	3.36	3.38	50879459	50879818	239.62116	152	50879405	50879889	322.18212	223
+chr15	23810569	23810980	.	1000	.	560.21193	-1	-1	198	3.35	3.37	23810630	23810906	231.56449	140	23810569	23810980	328.64744	195
+chr7	96746716	96747107	.	1000	.	558.18377	-1	-1	181	3.34	3.37	96746759	96747035	229.05438	138	96746716	96747107	329.12939	182
+chr7	127983717	127984163	.	1000	.	556.66743	-1	-1	265	3.32	3.36	127983842	127984113	241.49514	142	127983717	127984163	315.17229	263
+chr7	5553249	5553652	.	1000	.	556.55763	-1	-1	203	2.98	3.24	5553328	5553581	217.58750	126	5553249	5553652	338.97013	202
+chr20	31989138	31989561	.	1000	.	556.06385	-1	-1	224	3.35	3.37	31989220	31989517	227.08105	148	31989138	31989561	328.98280	218
+chr5	148724749	148725160	.	1000	.	554.76110	-1	-1	207	2.14	2.90	148724796	148725118	251.67540	170	148724749	148725160	303.08569	197
+chr17	30771268	30771646	.	1000	.	553.30497	-1	-1	186	2.80	3.18	30771316	30771592	247.39526	141	30771268	30771646	305.90971	183
+chr12	69080534	69080964	.	1000	.	551.73517	-1	-1	204	2.58	3.10	69080590	69080876	248.05995	145	69080534	69080964	303.67521	208
+chr17	40925278	40925637	.	1000	.	551.06498	-1	-1	164	3.39	3.39	40925309	40925566	228.42787	127	40925278	40925637	322.63711	170
+chr14	24657923	24658351	.	1000	.	550.60172	-1	-1	233	2.24	2.94	24657996	24658289	211.63339	161	24657923	24658351	338.96833	233
+chr20	34824169	34824561	.	1000	.	550.26004	-1	-1	186	3.26	3.34	34824214	34824488	219.73831	137	34824169	34824561	330.52173	191
+chr5	102455690	102456105	.	1000	.	550.13571	-1	-1	192	3.08	3.26	102455721	102456060	241.52908	168	102455690	102456105	308.60664	186
+chr5	43515094	43515472	.	1000	.	549.74669	-1	-1	192	3.16	3.29	43515150	43515431	218.23208	137	43515094	43515472	331.51462	192
+chr3	127842592	127843003	.	1000	.	548.95200	-1	-1	208	3.35	3.37	127842653	127842984	223.13715	149	127842592	127843003	325.81485	207
+chr16	2653134	2653607	.	1000	.	546.24335	-1	-1	208	3.11	3.28	2653189	2653529	238.67113	151	2653134	2653607	307.57222	211
+chr18	33552397	33552791	.	1000	.	545.68792	-1	-1	200	2.86	3.19	33552456	33552728	214.28071	138	33552397	33552791	331.40721	203
+chr16	84220433	84220881	.	246	.	542.02215	-1	-1	254	-0.00	0.59	84220527	84220849	238.01207	160	84220433	84220881	304.01007	254
+chr3	52029719	52030144	.	1000	.	541.69255	-1	-1	240	3.37	3.38	52029806	52030102	220.34762	154	52029719	52030144	321.34493	240
+chr7	141437929	141438371	.	1000	.	541.01664	-1	-1	197	3.22	3.33	141437943	141438285	231.51615	162	141437929	141438371	309.50050	219
+chr1	145096203	145096647	.	1000	.	540.31938	-1	-1	187	3.39	3.39	145096232	145096542	225.36233	134	145096203	145096647	314.95705	212
+chr2	242041550	242041987	.	1000	.	539.45393	-1	-1	216	3.20	3.31	242041623	242041899	215.92088	145	242041550	242041987	323.53305	214
+chrX	64754636	64755010	.	1000	.	538.88716	-1	-1	202	3.32	3.36	64754697	64754986	227.45225	151	64754636	64755010	311.43491	193
+chr11	68671113	68671535	.	1000	.	538.58984	-1	-1	224	3.34	3.36	68671188	68671471	226.52627	152	68671113	68671535	312.06357	221
+chr2	74681918	74682387	.	1000	.	537.49482	-1	-1	227	3.37	3.38	74681964	74682322	218.54974	183	74681918	74682387	318.94509	226
+chr13	52768379	52768795	.	1000	.	537.48132	-1	-1	224	3.19	3.31	52768475	52768744	215.79771	128	52768379	52768795	321.68361	224
+chr7	75677116	75677538	.	1000	.	536.21529	-1	-1	205	3.39	3.39	75677176	75677464	221.78080	143	75677116	75677538	314.43450	208
+chr6	131949192	131949648	.	246	.	536.05596	-1	-1	213	-0.00	0.59	131949255	131949559	232.46498	143	131949192	131949648	303.59098	221
+chr19	59010714	59011133	.	1000	.	535.61270	-1	-1	193	3.17	3.30	59010760	59011062	215.06314	137	59010714	59011133	320.54956	204
+chr7	44530076	44530536	.	1000	.	535.48237	-1	-1	219	3.24	3.34	44530150	44530427	215.88170	147	44530076	44530536	319.60067	218
+chr1	224301624	224301992	.	1000	.	534.63434	-1	-1	172	3.38	3.39	224301662	224301925	220.97149	127	224301624	224301992	313.66285	180
+chr2	233415169	233415593	.	1000	.	534.42878	-1	-1	188	3.36	3.38	233415230	233415501	222.07088	124	233415169	233415593	312.35790	192
+chr22	19419727	19420264	.	1000	.	533.88939	-1	-1	301	3.38	3.38	19419871	19420176	218.68614	155	19419727	19420264	315.20325	304
+chr1	20834455	20834934	.	246	.	533.27346	-1	-1	224	-0.00	0.59	20834538	20834840	214.08403	133	20834455	20834934	319.18943	232
+chr20	62612199	62612613	.	1000	.	532.56584	-1	-1	202	3.29	3.35	62612263	62612568	216.22069	138	62612199	62612613	316.34514	202
+chr2	3622558	3622998	.	246	.	532.03457	-1	-1	220	-0.00	0.59	3622618	3622940	211.58300	162	3622558	3622998	320.45157	218
+chr11	8710284	8710774	.	246	.	528.70021	-1	-1	264	-0.00	0.59	8710369	8710722	212.30821	191	8710284	8710774	316.39200	253
+chr11	31391193	31391568	.	246	.	527.89563	-1	-1	184	-0.00	0.59	31391239	31391510	217.35615	139	31391193	31391568	310.53948	183
+chr7	44240331	44240761	.	246	.	527.88990	-1	-1	218	-0.00	0.59	44240378	44240704	221.37196	169	44240331	44240761	306.51794	221
+chr16	1470584	1471075	.	246	.	527.63980	-1	-1	249	-0.00	0.59	1470651	1471004	215.46013	190	1470584	1471075	312.17967	242
+chr2	70120919	70121259	.	246	.	527.33276	-1	-1	151	-0.00	0.59	70120938	70121198	216.63171	122	70120919	70121259	310.70106	161
+chr11	62358845	62359289	.	246	.	525.46944	-1	-1	231	-0.00	0.59	62358924	62359223	210.14237	153	62358845	62359289	315.32707	231
+chr20	44485856	44486285	.	246	.	525.33383	-1	-1	210	-0.00	0.59	44485921	44486239	214.67116	150	44485856	44486285	310.66267	206
+chr1	38478079	38478578	.	246	.	524.83780	-1	-1	270	-0.00	0.59	38478185	38478507	217.62089	143	38478079	38478578	307.21691	292
+chr1	163291403	163291800	.	246	.	524.75644	-1	-1	193	-0.00	0.59	163291427	163291749	213.54352	173	163291403	163291800	311.21292	189
+chr6	170893515	170893965	.	246	.	523.17889	-1	-1	225	-0.00	0.59	170893598	170893890	213.68570	146	170893515	170893965	309.49319	222
+chr12	123459061	123459482	.	246	.	520.77669	-1	-1	192	-0.00	0.59	123459109	123459398	217.72734	144	123459061	123459482	303.04935	193
+chr12	124118042	124118495	.	246	.	519.55524	-1	-1	229	-0.00	0.59	124118111	124118446	216.61597	153	124118042	124118495	302.93927	237
+chr5	167913235	167913644	.	246	.	518.53402	-1	-1	195	-0.00	0.59	167913288	167913559	215.06279	138	167913235	167913644	303.47123	200
+chr16	89787143	89787565	.	246	.	517.09331	-1	-1	226	-0.00	0.59	89787227	89787505	212.65171	137	89787143	89787565	304.44160	231
diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_out1.png
Binary file test-data/idr_out1.png has changed
diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_out2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/idr_out2.bed	Tue Aug 22 05:20:25 2017 -0400
@@ -0,0 +1,279 @@
+chrX	119077570	119077896	.	1000	.	447.12953	-1	-1	193	3.86	3.86	119077642	119077884	181.51100	132	119077570	119077896	265.61853	183
+chrX	150565472	150565829	.	1000	.	404.52906	-1	-1	188	3.63	3.71	150565549	150565775	123.48069	112	150565472	150565829	281.04838	188
+chrX	153236525	153236876	.	1000	.	381.13237	-1	-1	182	3.74	3.80	153236590	153236814	146.19310	115	153236525	153236876	234.93927	185
+chrX	153775643	153776125	.	1000	.	355.34789	-1	-1	178	3.65	3.74	153775704	153775951	126.78607	121	153775643	153776125	228.56182	175
+chrX	131352114	131352386	.	1000	.	302.32517	-1	-1	129	3.48	3.62	131352128	131352330	114.27644	110	131352114	131352386	188.04873	134
+chrX	152989744	152990042	.	1000	.	295.97751	-1	-1	144	3.44	3.59	152989805	152989990	89.28166	93	152989744	152990042	206.69586	135
+chrX	153200355	153200667	.	1000	.	287.33948	-1	-1	166	3.49	3.66	153200427	153200604	92.98512	98	153200355	153200667	194.35435	163
+chrX	149862247	149862563	.	1000	.	246.94022	-1	-1	152	3.25	3.46	149862298	149862457	61.34470	94	149862247	149862563	185.59553	159
+chrX	153031057	153031329	.	1000	.	238.20076	-1	-1	145	3.32	3.51	153031119	153031304	81.26575	91	153031057	153031329	156.93501	138
+chrX	129039951	129040219	.	1000	.	225.69836	-1	-1	135	3.32	3.55	129040010	129040180	92.78955	76	129039951	129040219	132.90881	136
+chrX	151903079	151903347	.	1000	.	220.50968	-1	-1	140	3.28	3.48	151903127	151903293	77.94676	98	151903079	151903347	142.56292	134
+chrX	119378986	119379242	.	1000	.	194.97151	-1	-1	120	3.22	3.43	119379033	119379191	67.54318	76	119378986	119379242	127.42833	118
+chrX	129473746	129473988	.	1000	.	163.35468	-1	-1	120	3.13	3.40	129473795	129473925	47.61756	72	129473746	129473988	115.73712	120
+chrX	119694848	119695076	.	1000	.	143.32059	-1	-1	110	2.99	3.33	119694901	119694967	36.69754	30	119694848	119695076	106.62305	138
+chrX	153193673	153193967	.	1000	.	141.04147	-1	-1	132	3.06	3.36	153193746	153193851	47.20471	51	153193673	153193967	93.83676	141
+chrX	153991108	153991375	.	1000	.	132.55117	-1	-1	131	2.74	3.07	153991110	153991370	28.78908	130	153991108	153991375	103.76209	131
+chrX	153192249	153192513	.	1000	.	130.11011	-1	-1	129	2.96	3.27	153192249	153192509	36.17965	130	153192277	153192513	93.93046	101
+chrX	119737785	119738045	.	1000	.	126.49681	-1	-1	128	2.99	3.29	119737785	119738045	51.17957	130	119737831	119738023	75.31724	81
+chrX	118602931	118603193	.	1000	.	117.83040	-1	-1	130	2.96	3.24	118602931	118603191	37.86942	130	118602965	118603193	79.96098	96
+chrX	153744699	153744976	.	1000	.	112.78510	-1	-1	137	2.85	3.21	153744716	153744976	31.26523	130	153744699	153744933	81.51987	127
+chrX	154255102	154255599	.	1000	.	111.45970	-1	-1	127	2.50	2.83	154255102	154255569	22.11573	130	154255132	154255599	89.34397	132
+chrX	119695105	119695390	.	1000	.	105.54349	-1	-1	117	2.54	2.89	119695130	119695390	22.37145	130	119695105	119695320	83.17205	80
+chrX	155110753	155111013	.	1000	.	103.38682	-1	-1	140	2.75	3.09	155110753	155111013	47.11138	130	155110833	155110982	56.27544	70
+chrX	130964707	130964981	.	1000	.	100.38451	-1	-1	123	2.78	3.17	130964721	130964981	31.14163	130	130964707	130964917	69.24288	102
+chrX	131351274	131351995	.	1000	.	97.50042	-1	-1	137	2.77	3.12	131351274	131351995	34.06969	130	131351313	131351790	63.43073	138
+chrX	119005588	119005848	.	1000	.	97.21086	-1	-1	143	2.77	3.14	119005588	119005848	34.73936	130	119005617	119005847	62.47151	128
+chrX	134049072	134049334	.	1000	.	94.84423	-1	-1	115	2.65	2.99	134049074	134049334	25.58390	130	134049072	134049298	69.26033	98
+chrX	134996596	134996936	.	546	.	94.72860	-1	-1	168	0.45	1.32	134996693	134996860	82.71086	69	134996596	134996936	12.01773	170
+chrX	122898897	122899157	.	1000	.	93.79580	-1	-1	122	2.74	3.05	122898897	122899157	29.91352	130	122898911	122899140	63.88228	100
+chrX	122993843	122994327	.	1000	.	93.70732	-1	-1	122	2.50	2.82	122993843	122994307	21.49137	130	122993884	122994327	72.21594	121
+chrX	129226111	129226371	.	1000	.	93.47036	-1	-1	127	2.58	2.92	129226111	129226371	24.11072	130	129226135	129226336	69.35964	100
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+chrX	151142949	151143304	.	98	.	4.43030	-1	-1	197	-0.00	0.24	151143044	151143304	2.14638	130	151142949	151143289	2.28392	170
+chrX	151335778	151336180	.	98	.	4.28203	-1	-1	181	-0.00	0.24	151335778	151336038	2.19300	130	151335840	151336180	2.08902	170
+chrX	151629023	151629400	.	98	.	4.21558	-1	-1	208	-0.00	0.24	151629140	151629400	2.07288	130	151629023	151629363	2.14269	170
diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_out2.png
Binary file test-data/idr_out2.png has changed
diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_out3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/idr_out3.bed	Tue Aug 22 05:20:25 2017 -0400
@@ -0,0 +1,107 @@
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diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_out3.png
Binary file test-data/idr_out3.png has changed
diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_out4.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/idr_out4.gff	Tue Aug 22 05:20:25 2017 -0400
@@ -0,0 +1,353 @@
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diff -r 000000000000 -r d3ebbf39b1c5 test-data/idr_out4.png
Binary file test-data/idr_out4.png has changed