Mercurial > repos > iuc > idr
changeset 0:d3ebbf39b1c5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
| author | iuc |
|---|---|
| date | Tue, 22 Aug 2017 05:20:25 -0400 |
| parents | |
| children | de7795890bc5 |
| files | idr.xml test-data/idr_input1.1.bed test-data/idr_input1.2.bed test-data/idr_input2.1.bed test-data/idr_input2.2.bed test-data/idr_input3.1.bed test-data/idr_input3.2.bed test-data/idr_input3.3.bed test-data/idr_input4.1.gff test-data/idr_input4.2.gff test-data/idr_out1.bed test-data/idr_out1.png test-data/idr_out2.bed test-data/idr_out2.png test-data/idr_out3.bed test-data/idr_out3.png test-data/idr_out4.gff test-data/idr_out4.png |
| diffstat | 18 files changed, 9238 insertions(+), 0 deletions(-) [+] |
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--- /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>
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--- /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 @@ -0,0 +1,1500 @@ +chrX 118072033 118072373 . 0 . 2.96924878881134 -1 3.62416098062197 170 +chrX 118074545 118074885 . 0 . 2.47242172846173 -1 3.40416852878204 170 +chrX 118078586 118078926 . 0 . 2.10753833547811 -1 3.23155453800687 170 +chrX 118101037 118101377 . 0 . 2.74127079540973 -1 3.51814023537091 170 +chrX 118108988 118109328 . 0 . 22.5280631414826 -1 3.69463444336857 170 +chrX 118109193 118109533 . 0 . 2.92466012281489 -1 3.59756794971349 170 +chrX 118109999 118110241 . 0 . 73.1079911129054 -1 4.12368834166759 124 +chrX 118110780 118111120 . 0 . 2.59393377595773 -1 3.48174511188689 170 +chrX 118111936 118112276 . 0 . 4.22096283305949 -1 3.84484684472316 170 +chrX 118188726 118189066 . 0 . 2.28513993065215 -1 3.34321059998609 170 +chrX 118200975 118201315 . 0 . 2.22138576432 -1 3.29466581893791 170 +chrX 118204814 118205154 . 0 . 2.27753579623159 -1 3.34193822442175 170 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--- /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 @@ -0,0 +1,1500 @@ +chrX 49041160 49041420 . 0 . 2.09520241991715 -1 2.73718920926179 130 +chrX 49044937 49045197 . 0 . 2.32930031865457 -1 2.83361306486221 130 +chrX 49047517 49047777 . 0 . 45.9310038485514 -1 4.5777559727315 130 +chrX 49047716 49047976 . 0 . 3.68687471354172 -1 3.53782315577876 130 +chrX 49050764 49051024 . 0 . 2.39163220649692 -1 2.88100298728708 130 +chrX 49054368 49054628 . 0 . 4.76197008096259 -1 3.97126922026137 130 +chrX 49056374 49056634 . 0 . 3.05596124131372 -1 3.22495662682877 130 +chrX 49061298 49061558 . 0 . 2.07084518519691 -1 2.71545996848813 130 +chrX 49061661 49061921 . 0 . 2.46324402282957 -1 2.90345118857794 130 +chrX 49074390 49074650 . 0 . 3.16100502288848 -1 3.31182447230409 130 +chrX 49082201 49082461 . 0 . 3.61361523007231 -1 3.52788366307667 130 +chrX 49090029 49090289 . 0 . 2.22060187703187 -1 2.78592076453693 130 +chrX 49091851 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--- /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 @@ -0,0 +1,1500 @@ +chrX 48849648 48849988 . 0 . 2.2432990622895 -1 3.311229189147 170 +chrX 48854832 48855172 . 0 . 5.33510444469038 -1 3.83367169623395 170 +chrX 48857264 48857604 . 0 . 2.29617338265326 -1 3.34011414055965 170 +chrX 48858431 48858771 . 0 . 5.48184711840229 -1 3.80774832427714 170 +chrX 48885362 48885702 . 0 . 3.00403291602511 -1 3.655755671447 170 +chrX 48887353 48887693 . 0 . 2.03640107162808 -1 3.19024052230551 170 +chrX 48891564 48891904 . 0 . 4.18230120527543 -1 3.85464432130558 170 +chrX 48896082 48896422 . 0 . 2.04149897286068 -1 3.1907110090086 170 +chrX 48897528 48897868 . 0 . 5.32674895632621 -1 3.83557838661578 170 +chrX 48897733 48898073 . 0 . 3.4468055754205 -1 3.7676070811689 170 +chrX 48899949 48900289 . 0 . 2.27602377683503 -1 3.34225274041928 170 +chrX 48900982 48901139 . 0 . 42.2033950424999 -1 4.12368834166759 73 +chrX 48901353 48901693 . 0 . 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3.3397460230155 170 +chrX 109694827 109695167 . 0 . 2.75126370945657 -1 3.51606238224008 170 +chrX 109869457 109869797 . 0 . 2.36979385674846 -1 3.33880103506012 170 +chrX 109965260 109965600 . 0 . 2.3048694330812 -1 3.34161526932761 170 +chrX 109966200 109966540 . 0 . 2.92656801822483 -1 3.59715234427268 170 +chrX 110038649 110038989 . 0 . 4.09926981313704 -1 3.87503093065435 170 +chrX 110087564 110087904 . 0 . 2.09996061400181 -1 3.22804608944442 170 +chrX 110118464 110118804 . 0 . 2.54484317841203 -1 3.44615164259589 170 +chrX 110245715 110246055 . 0 . 3.40289860361721 -1 3.75698505739262 170 +chrX 110246257 110246597 . 0 . 2.89168491587947 -1 3.59383103905213 170 +chrX 110339222 110339562 . 0 . 4.95351238955314 -1 3.90791135495268 170 +chrX 110351625 110351965 . 0 . 2.20772649795773 -1 3.29144847486166 170 +chrX 110368669 110369009 . 0 . 2.7302036487792 -1 3.52038294860998 170 +chrX 110512620 110512960 . 0 . 2.11636127983953 -1 3.24104374591487 170 +chrX 110578891 110579231 . 0 . 2.43907467423479 -1 3.37679918995277 170 +chrX 110674233 110674573 . 0 . 3.32687051868478 -1 3.73712789511134 170 +chrX 110749942 110750282 . 0 . 5.07440538680703 -1 3.88476487384679 170 +chrX 110867458 110867798 . 0 . 4.46168545095329 -1 3.93336241445244 170 +chrX 110899929 110900269 . 0 . 2.60432228583049 -1 3.49380091442854 170 +chrX 110924234 110924560 . 0 . 178.319461180183 -1 4.12368834166759 162 +chrX 110924427 110924767 . 0 . 19.6491995965575 -1 3.51685255081836 170 +chrX 111051157 111051497 . 0 . 2.47103359888472 -1 3.40472386655815 170 +chrX 111099330 111099670 . 0 . 2.13906713884979 -1 3.25093894368342 170 +chrX 111311795 111312135 . 0 . 2.79482955150217 -1 3.54238350970928 170 +chrX 111326731 111327071 . 0 . 2.43907467423478 -1 3.37689202971991 170 +chrX 111465713 111466053 . 0 . 3.1545619459155 -1 3.67814575397916 170 +chrX 111798601 111798941 . 0 . 3.53426569064422 -1 3.81980070044688 170 +chrX 111871491 111871831 . 0 . 4.37153578682597 -1 3.89929573744333 170 +chrX 111915664 111916004 . 0 . 3.40596884459489 -1 3.7788295500722 170 +chrX 111923202 111923542 . 0 . 5.34694462252384 -1 3.83132330296511 170 +chrX 112058654 112058994 . 0 . 2.82499572898645 -1 3.54525011322516 170 +chrX 112084081 112084421 . 0 . 4.14801961933984 -1 3.86318969005975 170 +chrX 112084518 112084858 . 0 . 9.47686596512632 -1 3.83435711271841 170 +chrX 112401270 112401610 . 0 . 3.55492740946652 -1 3.81577263799102 170 +chrX 112517382 112517722 . 0 . 4.49077571599468 -1 3.92774323758412 170 +chrX 112589757 112590097 . 0 . 2.77401263042329 -1 3.54705621339731 170 +chrX 112596385 112596725 . 0 . 2.43907467423479 -1 3.37680803269047 170 +chrX 112608932 112609272 . 0 . 3.67446055665673 -1 3.85066665287339 170 +chrX 112635624 112635964 . 0 . 4.66300027229138 -1 3.89568400174313 170 +chrX 112671174 112671514 . 0 . 2.98680987441302 -1 3.63329204886361 170 +chrX 112791955 112792295 . 0 . 2.34554587982618 -1 3.34651338060437 170 +chrX 112943463 112943803 . 0 . 2.63091642158659 -1 3.4946396313459 170 +chrX 113004653 113004993 . 0 . 3.68637293558179 -1 3.84806817760299 170 +chrX 113114968 113115308 . 0 . 2.38236596915994 -1 3.34416170765551 170 +chrX 113339862 113340202 . 0 . 2.02272273152393 -1 3.16571471060825 170 +chrX 113370479 113370819 . 0 . 2.28123640148624 -1 3.34080802027333 170 +chrX 113623123 113623463 . 0 . 2.64180594750302 -1 3.49205908433595 170 +chrX 113624967 113625307 . 0 . 2.77696455211262 -1 3.54635687716666 170 +chrX 113745055 113745395 . 0 . 2.36319923517461 -1 3.34131726059662 170 +chrX 113752841 113753181 . 0 . 4.36773850883069 -1 3.90012605483296 170 +chrX 113774934 113775274 . 0 . 2.31491064071278 -1 3.35232296528398 170 +chrX 113818982 113819322 . 0 . 2.36977715165782 -1 3.33880524794272 170 +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
--- /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 . . .; +chr9 bed2gff . 35103030 35103302 0 . . .; +chr3 bed2gff . 139062706 139062962 0 . . .; +chr1 bed2gff . 155990642 155990891 0 . . .; +chr15 bed2gff . 40674995 40675277 0 . . .; +chr9 bed2gff . 98638135 98638441 0 . . .; +chr11 bed2gff . 47429850 47430141 0 . . .; +chr1 bed2gff . 149982575 149982829 0 . . .; +chr9 bed2gff . 133454818 133455093 0 . . .; +chr1 bed2gff . 179851718 179851996 0 . . .; +chr3 bed2gff . 155572158 155572487 0 . . .; +chr9 bed2gff . 140473232 140473536 0 . . .; +chr12 bed2gff . 53574326 53574567 0 . . .; +chr5 bed2gff . 74062846 74063148 0 . . .; +chr17 bed2gff . 61678076 61678361 0 . . .; +chr5 bed2gff . 154033485 154033803 0 . . .; +chr6 bed2gff . 7389868 7390154 0 . . .; +chr20 bed2gff . 44992935 44993209 0 . . .; +chr9 bed2gff . 123555554 123555870 0 . . .; +chr7 bed2gff . 134855228 134855753 0 . . .; +chr15 bed2gff . 90437138 90437401 0 . . .; +chr11 bed2gff . 43902161 43902435 0 . . .; +chr7 bed2gff . 44084080 44084355 0 . . .; +chr1 bed2gff . 85725249 85725499 0 . . .; +chr17 bed2gff . 57287227 57287480 0 . . .; +chr15 bed2gff . 64679824 64680146 0 . . .; +chr19 bed2gff . 4246829 4247170 0 . . .; +chr1 bed2gff . 227922908 227923177 0 . . .; +chr7 bed2gff . 1609578 1609872 0 . . .; +chr3 bed2gff . 53381513 53381800 0 . . .; +chr22 bed2gff . 19419157 19419437 0 . . .; +chr9 bed2gff . 130700024 130700283 0 . . .; +chr4 bed2gff . 84377027 84377316 0 . . .; +chr9 bed2gff . 35812179 35812422 0 . . .; +chr7 bed2gff . 6616904 6617170 0 . . .; +chr12 bed2gff . 56223272 56223554 0 . . .; +chr19 bed2gff . 16770836 16771104 0 . . .; +chr5 bed2gff . 443139 443420 0 . . .; +chr16 bed2gff . 31044610 31044900 0 . . .; +chr17 bed2gff . 79633577 79633869 0 . . .; +chr11 bed2gff . 47270293 47270542 0 . . .; +chr1 bed2gff . 209957899 209958170 0 . . .; +chr3 bed2gff . 13493276 13493523 0 . . .; +chr15 bed2gff . 85259265 85259540 0 . . .; +chr15 bed2gff . 74753402 74753694 0 . . .; +chr16 bed2gff . 420428 420683 0 . . .; +chr5 bed2gff . 112196823 112197098 0 . . .; +chr8 bed2gff . 22461962 22462392 0 . . .; +chr2 bed2gff . 73964341 73964771 0 . . .; +chr1 bed2gff . 24117465 24117770 0 . . .; +chr20 bed2gff . 34287162 34287418 0 . . .; +chr21 bed2gff . 27107147 27107503 0 . . .; +chr3 bed2gff . 10362687 10362964 0 . . .; +chr16 bed2gff . 717947 718229 0 . . .; +chr1 bed2gff . 165737996 165738300 0 . . .; +chr1 bed2gff . 150459621 150459883 0 . . .; +chr1 bed2gff . 55181367 55181623 0 . . .; +chr10 bed2gff . 75490127 75490413 0 . . .; +chr1 bed2gff . 28969473 28969752 0 . . .; +chr3 bed2gff . 9404591 9404852 0 . . .; +chr11 bed2gff . 118888952 118889288 0 . . .; +chr10 bed2gff . 43278068 43278338 0 . . .; +chr1 bed2gff . 183441020 183441320 0 . . .; +chr19 bed2gff . 2950496 2950815 0 . . .; +chr6 bed2gff . 111303090 111303341 0 . . .; +chr12 bed2gff . 117348630 117348860 0 . . .; +chr12 bed2gff . 105629904 105630185 0 . . .; +chr20 bed2gff . 2644751 2645000 0 . . .; +chr12 bed2gff . 75905284 75905547 0 . . .; +chr21 bed2gff . 46221615 46221878 0 . . .; +chr5 bed2gff . 153418354 153418649 0 . . .; +chr1 bed2gff . 3541251 3541500 0 . . .; +chr14 bed2gff . 75179681 75179940 0 . . .; +chr1 bed2gff . 44435385 44435719 0 . . .; +chr2 bed2gff . 71357596 71357848 0 . . .; +chr19 bed2gff . 17530521 17530795 0 . . .; +chr12 bed2gff . 7079748 7080121 0 . . .; +chr2 bed2gff . 96971152 96971429 0 . . .; +chr6 bed2gff . 17600382 17600633 0 . . .; +chr11 bed2gff . 10772608 10772880 0 . . .; +chr1 bed2gff . 36554313 36554613 0 . . .; +chr11 bed2gff . 65479568 65479834 0 . . .; +chr6 bed2gff . 42185492 42185753 0 . . .; +chr19 bed2gff . 10216905 10217140 0 . . .; +chr2 bed2gff . 113299870 113300125 0 . . .; +chr17 bed2gff . 42343979 42344264 0 . . .; +chr10 bed2gff . 75503954 75504263 0 . . .; +chr12 bed2gff . 132195327 132195740 0 . . .; +chr4 bed2gff . 492858 493103 0 . . .; +chr8 bed2gff . 144363746 144364026 0 . . .; +chr11 bed2gff . 61559975 61560244 0 . . .; +chr1 bed2gff . 155904112 155904431 0 . . .; +chr19 bed2gff . 51963773 51964019 0 . . .; +chr16 bed2gff . 2097831 2098091 0 . . .; +chr15 bed2gff . 74988260 74988498 0 . . .; +chr20 bed2gff . 1373730 1373994 0 . . .; +chr11 bed2gff . 111957410 111957697 0 . . .; +chr1 bed2gff . 20987812 20988156 0 . . .; +chr7 bed2gff . 156742255 156742541 0 . . .; +chr19 bed2gff . 2740074 2740337 0 . . .; +chr17 bed2gff . 26662413 26662686 0 . . .; +chr21 bed2gff . 45432007 45432300 0 . . .; +chr1 bed2gff . 43637870 43638117 0 . . .; +chr5 bed2gff . 892814 893089 0 . . .; +chr3 bed2gff . 101280549 101280796 0 . . .; +chr7 bed2gff . 99214429 99214697 0 . . .; +chr2 bed2gff . 15731831 15732087 0 . . .; +chr19 bed2gff . 58892000 58892281 0 . . .; +chr8 bed2gff . 144373406 144373660 0 . . .; +chr16 bed2gff . 89160107 89160406 0 . . .; +chr2 bed2gff . 24299130 24299470 0 . . .; +chr1 bed2gff . 247267567 247267830 0 . . .; +chr19 bed2gff . 40476927 40477164 0 . . .; +chr7 bed2gff . 99679225 99679528 0 . . .; +chr6 bed2gff . 170863215 170863530 0 . . .; +chr10 bed2gff . 27443231 27443479 0 . . .; +chr5 bed2gff . 158690151 158690410 0 . . .; +chr16 bed2gff . 21610673 21610958 0 . . .; +chr19 bed2gff . 12721452 12721704 0 . . .; +chr1 bed2gff . 156163736 156163977 0 . . .; +chr17 bed2gff . 61627556 61627934 0 . . .; +chr22 bed2gff . 20012938 20013251 0 . . .; +chr2 bed2gff . 99224833 99225114 0 . . .; +chr6 bed2gff . 43484533 43484798 0 . . .; +chr1 bed2gff . 38273744 38274012 0 . . .; +chr9 bed2gff . 95432415 95432762 0 . . .; +chr10 bed2gff . 13628800 13629072 0 . . .; +chr19 bed2gff . 2273689 2273951 0 . . .; +chr16 bed2gff . 3156422 3156666 0 . . .; +chr5 bed2gff . 110427856 110428134 0 . . .; +chr8 bed2gff . 145582086 145582342 0 . . .; +chr4 bed2gff . 76911981 76912228 0 . . .; +chr19 bed2gff . 47759636 47759901 0 . . .; +chr12 bed2gff . 51566553 51566845 0 . . .; +chr9 bed2gff . 140317535 140317810 0 . . .; +chr19 bed2gff . 45542162 45542420 0 . . .; +chr19 bed2gff . 44711450 44711731 0 . . .; +chr16 bed2gff . 11945351 11945591 0 . . .; +chr20 bed2gff . 1099052 1099329 0 . . .; +chr11 bed2gff . 86013059 86013396 0 . . .; +chr8 bed2gff . 146017699 146017958 0 . . .; +chr20 bed2gff . 62289515 62289802 0 . . .; +chr1 bed2gff . 179846856 179847113 0 . . .; +chr21 bed2gff . 47706044 47706387 0 . . .; +chr6 bed2gff . 3069065 3069362 0 . . .; +chr9 bed2gff . 132565296 132565564 0 . . .; +chr19 bed2gff . 8617695 8617967 0 . . .; 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+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 . . .;
--- /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 . . .; +chr13 bed2gff . 100150696 100151061 0 . . .; +chr4 bed2gff . 492802 493179 0 . . .; +chr1 bed2gff . 2322955 2323491 0 . . .; +chr22 bed2gff . 20861629 20862139 0 . . .; +chr21 bed2gff . 30364997 30365474 0 . . .; +chr16 bed2gff . 29801758 29802163 0 . . .; +chr11 bed2gff . 47600338 47600783 0 . . .; +chr11 bed2gff . 62389429 62389842 0 . . .; +chr17 bed2gff . 26662348 26662843 0 . . .; +chr2 bed2gff . 15731766 15732140 0 . . .; +chr7 bed2gff . 129691042 129691415 0 . . .; +chr12 bed2gff . 97300830 97301219 0 . . .; +chr7 bed2gff . 1543856 1544274 0 . . .; +chr4 bed2gff . 4249784 4250193 0 . . .; +chr3 bed2gff . 45883488 45883923 0 . . .; +chr16 bed2gff . 1755854 1756335 0 . . .; +chr3 bed2gff . 48956095 48956485 0 . . .; +chr10 bed2gff . 71930093 71930471 0 . . .; +chr19 bed2gff . 2783228 2783648 0 . . .; +chr15 bed2gff . 74988191 74988551 0 . . .; +chr4 bed2gff . 106629698 106630095 0 . . .; +chr1 bed2gff . 155904053 155904434 0 . . .; +chr7 bed2gff . 99149577 99149948 0 . . .; +chr8 bed2gff . 144363650 144364065 0 . . .; +chr8 bed2gff . 67837612 67837992 0 . . .; +chr8 bed2gff . 22461905 22462464 0 . . .; +chr1 bed2gff . 44435336 44435778 0 . . .; +chr1 bed2gff . 231664234 231664574 0 . . .; +chr11 bed2gff . 2421358 2421999 0 . . .; +chr6 bed2gff . 142468206 142468573 0 . . .; +chr19 bed2gff . 16295894 16296384 0 . . .; +chr5 bed2gff . 140070803 140071274 0 . . .; +chr16 bed2gff . 24740740 24741133 0 . . .; +chr20 bed2gff . 19997775 19998150 0 . . .; +chr3 bed2gff . 12598324 12598684 0 . . .; +chr17 bed2gff . 79633499 79633939 0 . . .; +chr1 bed2gff . 1550617 1550959 0 . . .; +chr19 bed2gff . 56146159 56146540 0 . . .; +chr1 bed2gff . 150039613 150039965 0 . . .; +chr11 bed2gff . 3078493 3078907 0 . . .; +chr3 bed2gff . 44666320 44666727 0 . . .; +chr4 bed2gff . 84376822 84377375 0 . . .; +chr8 bed2gff . 11141735 11142163 0 . . .; +chr7 bed2gff . 6616877 6617238 0 . . .; +chr12 bed2gff . 56223233 56223604 0 . . .; +chr6 bed2gff . 43484445 43484855 0 . . .; +chr11 bed2gff . 61197333 61197798 0 . . .; +chr1 bed2gff . 218458427 218458794 0 . . .; +chr8 bed2gff . 21867600 21867953 0 . . .; +chr6 bed2gff . 31926625 31927080 0 . . .; +chr8 bed2gff . 95565550 95565978 0 . . .; +chr1 bed2gff . 156163675 156164050 0 . . .; +chr16 bed2gff . 2918074 2918416 0 . . .; +chr16 bed2gff . 89160022 89160464 0 . . .; +chr10 bed2gff . 75545145 75545494 0 . . .; +chr4 bed2gff . 120221616 120221961 0 . . .; +chr11 bed2gff . 65819578 65819992 0 . . .; +chr14 bed2gff . 69658053 69658410 0 . . .; +chr16 bed2gff . 56485100 56485514 0 . . .; +chr19 bed2gff . 58891924 58892399 0 . . .; +chr19 bed2gff . 14682691 14683100 0 . . .; +chr9 bed2gff . 127631210 127631600 0 . . .; +chr1 bed2gff . 63988789 63989310 0 . . .; +chr12 bed2gff . 69863952 69864372 0 . . .; +chr16 bed2gff . 1832498 1833065 0 . . .; +chrX bed2gff . 19002758 19003304 0 . . .; +chr9 bed2gff . 98638054 98638487 0 . . .; +chr8 bed2gff . 33342500 33342882 0 . . .; +chr1 bed2gff . 22351831 22352192 0 . . .; +chr6 bed2gff . 42185441 42185810 0 . . .; +chr9 bed2gff . 127703222 127703613 0 . . .; +chr14 bed2gff . 21457942 21458300 0 . . .; +chr19 bed2gff . 4246792 4247200 0 . . .; +chr9 bed2gff . 139294464 139294872 0 . . .; +chr2 bed2gff . 224821962 224822303 0 . . .; +chr2 bed2gff . 74699611 74700027 0 . . .; +chr16 bed2gff . 2892531 2892943 0 . . .; +chr9 bed2gff . 125693625 125694007 0 . . .; +chr1 bed2gff . 150459587 150459913 0 . . .; +chr12 bed2gff . 6602345 6602690 0 . . .; +chr6 bed2gff . 30539036 30539432 0 . . .; +chr17 bed2gff . 1945121 1945530 0 . . .; +chr13 bed2gff . 46038854 46039250 0 . . .; +chr11 bed2gff . 64084816 64085300 0 . . .; +chr1 bed2gff . 173683851 173684250 0 . . .; +chr11 bed2gff . 43902099 43902526 0 . . .; +chr12 bed2gff . 122326388 122326735 0 . . .; +chr8 bed2gff . 145581959 145582416 0 . . .; +chr22 bed2gff . 29784379 29784735 0 . . .; +chr19 bed2gff . 14800654 14801032 0 . . .; +chr4 bed2gff . 76911860 76912270 0 . . .; +chr8 bed2gff . 144766417 144766831 0 . . .; +chr11 bed2gff . 3400145 3400589 0 . . .; +chr16 bed2gff . 67260803 67261229 0 . . .; +chr5 bed2gff . 93954153 93954538 0 . . .; +chr19 bed2gff . 12807292 12807630 0 . . .; +chr6 bed2gff . 17600331 17600675 0 . . .; +chr22 bed2gff . 31555917 31556300 0 . . .; +chr10 bed2gff . 135207484 135207874 0 . . .; +chr3 bed2gff . 131221630 131222013 0 . . .; +chrX bed2gff . 1710258 1710652 0 . . .; +chr19 bed2gff . 44439259 44439666 0 . . .; +chr19 bed2gff . 56186305 56186794 0 . . .; +chr1 bed2gff . 40506175 40506651 0 . . .; +chr10 bed2gff . 1102322 1102959 0 . . .; +chr5 bed2gff . 133968375 133968728 0 . . .; +chrX bed2gff . 100075168 100075543 0 . . .; +chr19 bed2gff . 32896310 32896689 0 . . .; +chr1 bed2gff . 224622385 224622748 0 . . .; +chr7 bed2gff . 97601500 97601865 0 . . .; +chr7 bed2gff . 135661823 135662305 0 . . .; +chr5 bed2gff . 139936883 139937240 0 . . .; +chr12 bed2gff . 57118952 57119320 0 . . .; +chr22 bed2gff . 19466541 19466905 0 . . .; +chr12 bed2gff . 133562771 133563160 0 . . .; +chr2 bed2gff . 162164740 162165143 0 . . .; +chr8 bed2gff . 144349418 144349768 0 . . .; +chr10 bed2gff . 95462183 95462572 0 . . .; +chr12 bed2gff . 7079688 7080184 0 . . .; +chr7 bed2gff . 102987915 102988274 0 . . .; +chr17 bed2gff . 40306826 40307281 0 . . .; +chr15 bed2gff . 55488745 55489352 0 . . .; +chr12 bed2gff . 49412415 49412816 0 . . .; +chr17 bed2gff . 38975027 38975518 0 . . .; +chr16 bed2gff . 734257 734653 0 . . .; +chr9 bed2gff . 104295846 104296265 0 . . .; +chr2 bed2gff . 27632297 27632659 0 . . .; +chr9 bed2gff . 133454723 133455163 0 . . .; +chr1 bed2gff . 155990589 155990932 0 . . .; +chr1 bed2gff . 3566507 3566854 0 . . .; +chr16 bed2gff . 11945302 11945633 0 . . .; +chr10 bed2gff . 122610601 122611016 0 . . .; +chr15 bed2gff . 74753321 74753744 0 . . .; +chr19 bed2gff . 10216845 10217256 0 . . .; +chr5 bed2gff . 110427799 110428206 0 . . .; +chr15 bed2gff . 40674947 40675322 0 . . .; +chr12 bed2gff . 129308454 129308784 0 . . .; +chr17 bed2gff . 55927250 55927600 0 . . .; +chr2 bed2gff . 177133992 177134405 0 . . .; +chr22 bed2gff . 38082181 38082718 0 . . .; +chr19 bed2gff . 36139049 36139411 0 . . .; +chr8 bed2gff . 144373308 144373710 0 . . .; +chr6 bed2gff . 3068965 3069419 0 . . .; +chr5 bed2gff . 36876595 36876960 0 . . .; +chr2 bed2gff . 174829962 174830379 0 . . .; +chrX bed2gff . 14047857 14048268 0 . . .; +chr6 bed2gff . 41755155 41755542 0 . . .; +chr11 bed2gff . 102962751 102963107 0 . . .; +chrX bed2gff . 150565473 150565829 0 . . .; +chr16 bed2gff . 67225876 67226237 0 . . .; +chr3 bed2gff . 183602505 183602885 0 . . .; +chr4 bed2gff . 77069456 77069864 0 . . .; +chr19 bed2gff . 12721383 12721783 0 . . .; +chr21 bed2gff . 37692288 37692652 0 . . .; +chr11 bed2gff . 65337620 65338083 0 . . .; +chr9 bed2gff . 123555359 123555926 0 . . .; +chr16 bed2gff . 67906743 67907183 0 . . .; +chr18 bed2gff . 812261 812646 0 . . .; +chr22 bed2gff . 22020032 22020761 0 . . .; +chr11 bed2gff . 47270228 47270619 0 . . .; +chr7 bed2gff . 6676722 6677105 0 . . .; +chr12 bed2gff . 49961699 49962083 0 . . .; +chr10 bed2gff . 124713599 124713941 0 . . .; +chr10 bed2gff . 102747046 102747488 0 . . .; +chr9 bed2gff . 127177464 127177914 0 . . .; +chr5 bed2gff . 133984099 133984631 0 . . .; +chr14 bed2gff . 75348414 75348949 0 . . .; +chr15 bed2gff . 65903319 65903682 0 . . .; +chr11 bed2gff . 65655802 65656238 0 . . .; +chr6 bed2gff . 32143734 32144086 0 . . .; +chr1 bed2gff . 100435343 100435733 0 . . .; +chr16 bed2gff . 20817590 20817987 0 . . .; +chr19 bed2gff . 35263963 35264319 0 . . .; +chr12 bed2gff . 124086377 124086836 0 . . .; +chr17 bed2gff . 42264135 42264529 0 . . .; +chr8 bed2gff . 146017602 146018011 0 . . .; +chr8 bed2gff . 124780505 124780886 0 . . .; +chr10 bed2gff . 44069787 44070250 0 . . .; +chr11 bed2gff . 65625495 65625912 0 . . .; +chr2 bed2gff . 118845767 118846148 0 . . .; +chr5 bed2gff . 80597224 80597582 0 . . .; +chr11 bed2gff . 576274 576655 0 . . .; +chr5 bed2gff . 180288083 180288473 0 . . .; +chr9 bed2gff . 140099930 140100342 0 . . .; +chr8 bed2gff . 56685769 56686177 0 . . .; +chr2 bed2gff . 197664272 197664624 0 . . .; +chr20 bed2gff . 18547853 18548353 0 . . .; +chr11 bed2gff . 63741881 63742259 0 . . .; +chr20 bed2gff . 34129653 34130107 0 . . .; +chr1 bed2gff . 213224384 213224790 0 . . .; +chr9 bed2gff . 19380126 19380479 0 . . .; +chr15 bed2gff . 49447724 49448112 0 . . .; +chr11 bed2gff . 43380307 43380633 0 . . .; +chr16 bed2gff . 21610624 21611024 0 . . .; +chr5 bed2gff . 10353561 10353944 0 . . .; +chr17 bed2gff . 47022022 47022394 0 . . .; +chr20 bed2gff . 55043511 55043860 0 . . .; +chr10 bed2gff . 103347832 103348189 0 . . .; +chr5 bed2gff . 16465598 16466133 0 . . .; +chr1 bed2gff . 36396484 36397041 0 . . .; +chr16 bed2gff . 57496383 57496733 0 . . .; +chr19 bed2gff . 9546091 9546416 0 . . .; +chr9 bed2gff . 140317456 140317871 0 . . .; +chr15 bed2gff . 89787011 89787384 0 . . .; +chr15 bed2gff . 40331180 40331604 0 . . .; +chr19 bed2gff . 15947509 15947899 0 . . .; +chr10 bed2gff . 27530926 27531286 0 . . .; +chr3 bed2gff . 149470118 149470494 0 . . .; +chr11 bed2gff . 77348674 77349033 0 . . .; +chr19 bed2gff . 58962770 58963161 0 . . .; +chr7 bed2gff . 2281631 2282041 0 . . .; +chr6 bed2gff . 100016398 100016745 0 . . .; +chr1 bed2gff . 246729406 246729882 0 . . .; +chr16 bed2gff . 1822945 1823411 0 . . .; +chr19 bed2gff . 11039199 11039634 0 . . .; +chr20 bed2gff . 34638723 34639117 0 . . .; +chr1 bed2gff . 40723315 40724054 0 . . .; +chr9 bed2gff . 132404268 132404669 0 . . .; +chr20 bed2gff . 57226043 57226463 0 . . .; +chr5 bed2gff . 133702725 133703080 0 . . .; +chr19 bed2gff . 47759574 47759972 0 . . .; +chr3 bed2gff . 37217699 37218123 0 . . .; +chr22 bed2gff . 39077771 39078131 0 . . .; +chr5 bed2gff . 125936425 125936783 0 . . .; +chr19 bed2gff . 58071082 58071392 0 . . .; +chr12 bed2gff . 120632340 120632744 0 . . .; +chr1 bed2gff . 212964871 212965373 0 . . .; +chr20 bed2gff . 61903953 61904327 0 . . .; +chr19 bed2gff . 50379333 50379727 0 . . .; +chr12 bed2gff . 66524369 66524730 0 . . .; +chr7 bed2gff . 140714580 140714991 0 . . .; +chr17 bed2gff . 26684420 26684852 0 . . .; +chr19 bed2gff . 19626815 19627239 0 . . .; +chr14 bed2gff . 35761429 35761781 0 . . .; +chr21 bed2gff . 46707607 46708009 0 . . .; +chr1 bed2gff . 1342451 1342952 0 . . .; +chr9 bed2gff . 135282087 135282403 0 . . .; +chr12 bed2gff . 50794436 50794786 0 . . .; +chr2 bed2gff . 27994400 27994927 0 . . .; +chr19 bed2gff . 9938321 9938769 0 . . .; +chrX bed2gff . 73163925 73164264 0 . . .; +chr17 bed2gff . 80009598 80009978 0 . . .; +chr8 bed2gff . 145133190 145133759 0 . . .; +chr10 bed2gff . 121652049 121652380 0 . . .; +chr7 bed2gff . 73668617 73669010 0 . . .; +chr9 bed2gff . 131534068 131534448 0 . . .; +chr22 bed2gff . 50639239 50639593 0 . . .; +chr12 bed2gff . 133405330 133405896 0 . . .; +chr22 bed2gff . 26908303 26908683 0 . . .; +chr1 bed2gff . 32687777 32688181 0 . . .; +chr10 bed2gff . 27443173 27443509 0 . . .; +chr7 bed2gff . 135346959 135347414 0 . . .; +chr13 bed2gff . 29233052 29233417 0 . . .; +chr3 bed2gff . 49203621 49203989 0 . . .; +chr14 bed2gff . 75179631 75179963 0 . . .; +chr2 bed2gff . 201753880 201754248 0 . . .; +chr11 bed2gff . 18655780 18656169 0 . . .; +chr1 bed2gff . 38455516 38455994 0 . . .; +chr10 bed2gff . 75503912 75504319 0 . . .; +chr6 bed2gff . 28104435 28104841 0 . . .; +chr12 bed2gff . 54582542 54583006 0 . . .; +chr6 bed2gff . 28109444 28109816 0 . . .; +chr4 bed2gff . 164415509 164415981 0 . . .; +chr16 bed2gff . 81779797 81780155 0 . . .; +chr21 bed2gff . 46359654 46360072 0 . . .; +chr2 bed2gff . 128051501 128051925 0 . . .; +chr19 bed2gff . 2950350 2950884 0 . . .; +chr10 bed2gff . 105156095 105156537 0 . . .; +chr2 bed2gff . 219536540 219536894 0 . . .; +chr12 bed2gff . 112037144 112037585 0 . . .; +chr19 bed2gff . 49954965 49955398 0 . . .; +chr9 bed2gff . 132565248 132565710 0 . . .; +chr3 bed2gff . 179065293 179065649 0 . . .; +chr19 bed2gff . 10230421 10230792 0 . . .; +chr8 bed2gff . 145158475 145158949 0 . . .; +chr20 bed2gff . 62496407 62496811 0 . . .; +chr11 bed2gff . 64901854 64902211 0 . . .; +chr16 bed2gff . 31044510 31044939 0 . . .; +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 . . .;
--- /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 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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
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