# HG changeset patch
# User iuc
# Date 1526580699 14400
# Node ID eb000bccef2832096b6bef0c6d355b6e9e5dbe59

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b

diff -r 000000000000 -r eb000bccef28 pureclip.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pureclip.xml	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,306 @@
+<tool id="pureclip" name="PureCLIP" version="1.0.4">
+    <description>- HMM based peak caller designed for eCLIP/iCLIP data</description>
+    <requirements>
+        <requirement type="package" version="1.0.4">pureclip</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+ln -s '${target_bam_file}' target.bam && 
+ln -f -s '${target_bam_file.metadata.bam_index}' target.bam.bai && 
+ln -s '${genome_fasta_file}' genome.fa &&
+#if $control_bam_file:
+    ln -s '${control_bam_file}' control.bam && 
+    ln -f -s '${control_bam_file.metadata.bam_index}' control.bam.bai && 
+#end if
+#if $motif_data.motif_data_selector == 'supply_CL_motifs':
+    ln -s '${motif_data.cl_motif_bed_file}' motif_hits.bed &&
+#end if
+
+pureclip
+    -o crosslink_sites.bed
+    -or binding_regions.bed
+    -i target.bam
+    -bai target.bam.bai
+    -g genome.fa
+    #if $learn_params_contigs
+        -iv '$learn_params_contigs'
+    #end if
+    #if $apply_hmm_contigs
+        -iv '$apply_hmm_contigs'
+    #end if
+    -dm $merge_dist
+    #if $control_bam_file:
+        -ibam control.bam
+        -ibai control.bam.bai
+    #end if
+    #if $motif_data.motif_data_selector == 'supply_CL_motifs':
+        -fis motif_hits.bed
+        -nim $motif_data.max_motif_id
+    #end if
+    #if $bc_data.bc_data_selector == 'bc_0':
+        -bc 0
+    #elif $bc_data.bc_data_selector == 'bc_1':
+        -bc 1
+    #elif $bc_data.bc_data_selector == 'manual_setting':
+        -bw $bc_data.bandwidth
+        -bwn $bc_data.bandwidthn
+        -b1p $bc_data.b1p
+        -b2p $bc_data.b2p
+        #if $bc_data.antp_option.antp_option_selector == 'antp_select':
+            -antp
+        #elif $bc_data.antp_option.antp_option_selector == 'manual_select':
+            -ntp $bc_data.antp_option.ntp
+            -ntp2 $bc_data.antp_option.ntp2
+        #end if
+    #end if
+    #if $advanced_params.advanced_params_selector == 'ap_specify':
+        $advanced_params.ld_precision
+        $advanced_params.use_viterbi
+        #if $advanced_params.max_iter_brent
+            -m $advanced_params.max_iter_brent
+        #end if
+        #if $advanced_params.max_iter_bw
+            -w $advanced_params.max_iter_bw
+        #end if
+        #if $advanced_params.g1kmin
+            -g1kmin $advanced_params.g1kmin
+        #end if
+        #if $advanced_params.g1kmax
+            -g1kmax $advanced_params.g1kmax
+        #end if
+        #if $advanced_params.g2kmin
+            -g2kmin $advanced_params.g2kmin
+        #end if
+        #if $advanced_params.g2kmax
+            -g2kmax $advanced_params.g2kmax
+        #end if
+        $advanced_params.fk
+        -mkn $advanced_params.mkn
+        -mtp $advanced_params.mtp
+        #if $advanced_params.mk
+            -mk $advanced_params.mk
+        #end if
+        #if $advanced_params.pa
+            -pa $advanced_params.pa
+        #end if
+        $advanced_params.ea1
+        $advanced_params.ea2
+        $advanced_params.et1
+        $advanced_params.et2
+        #if $advanced_params.mrtf
+            -mrtf $advanced_params.mrtf
+        #end if
+        -mtc $advanced_params.mtc
+        -pet $advanced_params.pet
+    #end if
+    ]]></command>
+    <inputs>
+        <param name="target_bam_file" type="data" format="bam" label="Target BAM file" argument="-i"/>
+        <param name="genome_fasta_file" type="data" format="fasta" label="Genome reference file" argument="-g"/>
+        <!-- Options -->
+        <param name="learn_params_contigs" type="text" optional="True"
+               label="Genomic chromosomes to learn HMM parameters" argument="-iv" 
+               help="Genomic chromosomes to learn HMM parameters, e.g. 'chr1;chr2;chr3'. Contigs have to be in the same order as in BAM file. Useful to reduce runtime and memory consumption. Default: all contigs from reference file are used (useful when applying to transcript-wise alignments or poor data).">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param name="apply_hmm_contigs" type="text" label="Contigs to apply HMM" argument="-chr" optional="True"
+               help="Contigs to apply HMM, e.g. 'chr1;chr2;chr3;'. Contigs have to be in the same order as in BAM file.">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param name="merge_dist" type="integer" value="8" min="1"
+               label="Distance used to merge individual crosslink sites to binding regions" argument="-dm"/>
+        <param name="control_bam_file" type="data" format="bam" optional="True"
+               label="BAM file containing mapped reads from control experiment" argument="-ibam"
+               help="Mapped reads in BAM format from a control experiment, e.g. eCLIP input"/>
+        <conditional name="motif_data">
+            <param name="motif_data_selector" type="select" label="Crosslink-associated (CL) motif options">
+                <option value="no_CL_motifs_available" selected="true">No CL motifs available</option>
+                <option value="supply_CL_motifs">Supply CL motifs</option>
+            </param>
+            <when value="no_CL_motifs_available" />
+            <when value="supply_CL_motifs">
+                <param name="cl_motif_bed_file" type="data" format="bed"
+                       label="FIMO input motif score covariates file" argument="-fis"
+                       help="FIMO input motif score covariates file"/>
+                <param name="max_motif_id" type="integer" value="1"
+                       label="Max. motif ID to use" argument="-nim"
+                       help="Max. motif ID to use (Default: only covariates with motif ID 1 are used)"/>
+            </when>
+        </conditional>
+
+        <conditional name="bc_data">
+            <param name="bc_data_selector" type="select" label="Define protein binding characteristics">
+                <option value="bc_0" selected="true">RBP with short defined binding regions (-bc 0)</option>
+                <option value="bc_1">RBP with larger crosslink clusters and lower read start counts (-bc 1)</option>
+                <option value="manual_setting">Manual setting</option>
+            </param>
+            <when value="bc_0" />
+            <when value="bc_1" />
+            <when value="manual_setting">
+                <param name="bandwidth" type="integer" value="50" min="1" max="500"
+                       label="Bandwidth for kernel density estimation used to access enrichment" argument="-bw"
+                       help="NOTE: Increasing the bandwidth increases runtime and memory consumption"/>
+                <param name="bandwidthn" type="integer" value="50" min="1" max="500"
+                       label="Bandwidth for kernel density estimation used to estimate n for binomial distributions" argument="-bwn"
+                       help="For proteins that rather slide along the RNA or show long crosslink clusters increase -bwn, e.g. to 100 (should be LE 4*bw)"/>
+                <param argument="-b1p" type="float" value="0.01"
+                       label="Initial value for binomial probability parameter of 'non-crosslink' state" />
+                <param argument="-b2p" type="float" value="0.15"
+                       label="Initial value for binomial probability parameter of 'crosslink' state" />
+                <conditional name="antp_option">
+                    <param name="antp_option_selector" type="select" label="Choose n threshold for estimating crosslink state parameters" help="Either automatically choose n threshold (-ntp, -ntp2) to estimate parameters linked to crosslink states based on expected read start count at crosslink sites, or manually set values">
+                        <option value="antp_select" selected="true">Automatically choose n threshold (-ntp, -ntp2)</option>
+                        <option value="manual_select">Manually set -ntp, -ntp2</option>
+                    </param>
+                    <when value="antp_select" />
+                    <when value="manual_select">
+                        <param argument="-ntp" type="integer" value="10" 
+                               label="Only sites with n >= ntp are used to learn binomial probability parameters"/>
+                        <param argument="-ntp2" type="integer" value="0" 
+                               label="Only sites with n >= ntp2 are used to learn probability of transition from state '2' to '2' or '3'"
+                               help="Useful for data with low truncation rates at crosslink sites or in general high fraction of non-coinciding read starts"/>
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+        <conditional name="advanced_params">
+            <param name="advanced_params_selector" type="select" label="Additional advanced parameters">
+                <option value="ap_not_specify" selected="true">Do not specify</option>
+                <option value="ap_specify">Manually specify</option>
+            </param>
+            <when value="ap_not_specify" />
+            <when value="ap_specify">
+                <param name="ld_precision" label="Use higher precision to compute emission probabilities (long double)" type="boolean"
+                       truevalue="-ld" falsevalue="" checked="False"
+                       help="Useful in cases of extreme outliers, e.g. extreme high read start counts whose emission probabilities are close to zero and which would be discarded in default setting (along with warning messages). Note: increases memory consumption. Use in combination with '-iv' (default: double)"/>
+                <param name="use_viterbi" label="Use Viterbi instead of posterior decoding" 
+                       type="boolean" truevalue="-vtb" falsevalue="" checked="False"/>
+                <param name="max_iter_brent" type="integer" optional="True" min="1" max="1000"
+                       label="Maximum number of iterations within BRENT algorithm" argument="-m"/>
+                <param name="max_iter_bw" type="integer" optional="True" min="0" max="500"
+                       label="Maximum number of iterations within Baum-Welch algorithm" argument="-w"/>
+                <param argument="-g1kmin" type="float" optional="True"
+                       label="Minimum shape k of 'non-enriched' gamma distribution" />
+                <param argument="-g1kmax" type="float" optional="True"
+                       label="Maximum shape k of 'non-enriched' gamma distribution" />
+                <param argument="-g2kmin" type="float" optional="True"
+                       label="Minimum shape k of 'enriched' gamma distribution" />
+                <param argument="-g2kmax" type="float" optional="True"
+                       label="Maximum shape k of 'enriched' gamma distribution" />
+                <param argument="-fk" label="Do not constrain 'non-enriched' shape parameter k" 
+                       type="boolean" truevalue="-fk" falsevalue="" checked="False"
+                       help="When incorporating input signal, do not constrain 'non-enriched' shape parameter k LE 'enriched' gamma parameter k"/>
+                <param argument="-mkn" type="float" value="1.0" min="0.5" max="1.5"
+                       label="Max. k/N ratio (read start sites/N) used to learn truncation probabilities for 'non-crosslink' and 'crosslink' emission probabilities" 
+                       help="NOTE: high ratios might originate from mapping artifacts that can disturb parameter learning"/>
+                <param argument="-mtp" type="float" value="0.0001"
+                       label="Min. transition probability from state '2' to '3'" 
+                       help="Helpful for poor data, where no clear distinction between 'enriched' and 'non-enriched' is possible"/>
+                <param argument="-mk" type="float" optional="True"
+                       label="Minimum KDE value used for fitting left-truncated gamma distributions" 
+                       help="Default: corresponding to singleton read start."/>
+                <param argument="-pa" type="integer" optional="True"
+                       label="Length threshold for internal poly-X stretches to get excluded" />
+                <param argument="-ea1" label="Exclude intervals containing poly-A stretches from learning" 
+                       type="boolean" truevalue="-ea1" falsevalue="" checked="False"/>
+                <param argument="-ea2" label="Exclude intervals containing poly-A stretches from analysis" 
+                       type="boolean" truevalue="-ea2" falsevalue="" checked="False"/>
+                <param argument="-et1" label="Exclude intervals containing poly-U stretches from learning" 
+                       type="boolean" truevalue="-et1" falsevalue="" checked="False"/>
+                <param argument="-et2" label="Exclude intervals containing poly-U stretches from analysis" 
+                       type="boolean" truevalue="-et2" falsevalue="" checked="False"/>
+                <param argument="-mrtf" type="float" optional="True"
+                       label="Fit gamma shape k only for positions with min. covariate value" />
+                <param argument="-mtc" type="integer" value="250" min="50" max="500"
+                       label="Maximum number of truncations at one position used for learning" 
+                       help="NOTE: for sites with counts above threshold the whole covered regions will be ignored for learning!"/>
+                <param argument="-pet" type="integer" value="7" min="2" max="50"
+                       label="Prior enrichment threshold" 
+                       help="A KDE threshold corresponding to -pet read start counts at one position will be used for initial classification of 'non-enriched' and 'enriched' site"/>
+            </when>
+        </conditional>
+        <section name="output_options" title="Additional output options">
+            <param name="crosslink_bed_stats" type="boolean" value="False" label="Output learned parameter statistics file?"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="bed" name="crosslink_bed_outfile" label="${tool.name} on ${on_string} crosslink sites (bed)" from_work_dir="crosslink_sites.bed"/>
+        <data format="bed" name="binding_region_bed_outfile" label="${tool.name} on ${on_string} binding regions (bed)" from_work_dir="binding_regions.bed"/>
+        <data format="txt" name="crosslink_bed_stats" label="${tool.name} on ${on_string} learned parameter statistcs (txt)" from_work_dir="crosslink_sites.bed.stats">
+            <filter>(output_options['crosslink_bed_stats'] is True)</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
+            <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
+            <param name="crosslink_bed_stats" value="True"/>
+            <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.bed"/>
+            <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.bed"/>
+            <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.bed.stats"/>
+        </test>
+        <test>
+            <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
+            <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
+            <param name="control_bam_file" value="input.aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
+            <param name="crosslink_bed_stats" value="True"/>
+            <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_input_signal.bed"/>
+            <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_input_signal.bed"/>
+            <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_input_signal.bed.stats"/>
+        </test>
+        <test>
+            <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
+            <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
+            <param name="motif_data_selector" value="supply_CL_motifs"/>
+            <param name="cl_motif_bed_file" value="fimo_clmotif_occurences.chrM:4000-8300.bed" ftype="bed"/>
+            <param name="max_motif_id" value="4"/>
+            <param name="crosslink_bed_stats" value="True"/>
+            <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed"/>
+            <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_CLmotifs.bed"/>
+            <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats"/>
+        </test>
+        <test>
+            <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
+            <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
+            <param name="control_bam_file" value="input.aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
+            <param name="bc_data_selector" value="manual_setting"/>
+            <param name="bandwidthn" value="50"/>
+            <param name="b1p" value="0.01"/>
+            <param name="b2p" value="0.15"/>
+            <param name="antp_option_selector" value="manual_select"/>
+            <param name="ntp" value="10"/>
+            <param name="ntp2" value="0"/>
+            <param name="advanced_params_selector" value="ap_specify"/>
+            <param name="fk" value="True"/>
+            <param name="mkn" value="0.9"/>
+            <param name="mtc" value="200"/>
+            <param name="crosslink_bed_stats" value="True"/>
+            <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.test4.bed"/>
+            <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.test4.bed"/>
+            <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.test4.bed.stats"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+    PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP. It accepts mapped eCLIP/iCLIP reads in BAM format as input and also supports control library and crosslink-associated (CL) motifs input for bias correction.
+
+    PureCLIP outputs two BED files, containing the found crosslink sites (first file) and binding regions (second file) that merge nearby crosslink sites to contiguous regions (region width controlled by -dm parameter).
+
+    By default, the tool parameters are set to values optimized for proteins binding to short defined binding regions, e.g. proteins binding to short specific motifs such as PUM2 and RBFOX2. This behaviour can be changed with the -bc option. The default setting -bc 0 is equivalent to manually setting -bdwn 50 -ntp 10 -ntp2 0 -b1p 0.01 -b2p 0.15. The second setting -bc 1 is designed for RBPs that produce larger clusters (proteins causing larger crosslink clusters with relatively lower read start counts, e.g. proteins binding to low complexity motifs). -bc 1 corresponds to the manual setting -bdwn 100 -antp -b2p 0.01 -b2p 0.1.
+
+    In case of different binding characteristics, you can manually adjust parameters -bdw, -bdwn, -b1p, -b2p, -antp or have a look at the online documentation for more details:
+
+    http://pureclip.readthedocs.io/en/latest/index.html
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1186/s13059-017-1364-2</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r eb000bccef28 test-data/aligned.prepro.R2.chrM:4000-8300.bam
Binary file test-data/aligned.prepro.R2.chrM:4000-8300.bam has changed
diff -r 000000000000 -r eb000bccef28 test-data/chrM:4000-8300.binding_regions.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM:4000-8300.binding_regions.bed	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,48 @@
+chrM	4291	4314	2.94929;4.64074;1.94087;52.6504;30.3923;4.80211;6.66437;60.3029;24.7976;22.3709;14.6446;	226.156	+
+chrM	4401	4404	58.8257;6.06023;	64.8859	+
+chrM	4417	4419	52.5488;78.3902;3.67021;	134.609	+
+chrM	4433	4434	7.25741;65.6233;	72.8807	+
+chrM	4445	4446	9.12652;	9.12652	+
+chrM	4823	4824	2.39621;	2.39621	+
+chrM	4840	4841	3.53076;	3.53076	+
+chrM	4896	4897	7.22391;	7.22391	+
+chrM	4909	4910	1.87438;2.20671;	4.08108	+
+chrM	4921	4922	1.69262;	1.69262	+
+chrM	4945	4955	8.75681;1.91605;4.3546;2.13593;	17.1634	+
+chrM	5314	5316	8.38192;0.241933;0.0023646;	8.62622	+
+chrM	5331	5332	2.6509;2.66322;	5.31412	+
+chrM	5343	5344	5.44813;5.47323;	10.9214	+
+chrM	5361	5364	2.30985;0.0245996;	2.33445	+
+chrM	5374	5375	0.238708;	0.238708	+
+chrM	5455	5465	10.1669;3.92435;2.26717;4.40821;4.41924;	25.1858	+
+chrM	6010	6018	4.02549;19.905;9.19498;19.905;19.905;9.19141;8.55025;1.02799;	91.7052	+
+chrM	6202	6203	10.8234;	10.8234	+
+chrM	6214	6225	2.83587;0.500624;1.30892;13.5581;	18.2036	+
+chrM	6241	6253	27.2127;11.6542;12.296;12.3448;11.7528;49.4979;0.836268;5.37351;	130.968	+
+chrM	6345	6352	14.5165;3.37477;1.02112;8.63183;	27.5443	+
+chrM	6372	6376	8.64158;1.22687;2.22685;3.027;4.99741;	20.1197	+
+chrM	6412	6413	1.96883;	1.96883	+
+chrM	6430	6438	3.92122;1.51198;1.87923;3.18803;	10.5005	+
+chrM	6451	6453	10.3462;3.31758;	13.6638	+
+chrM	6469	6473	5.44285;0.701889;	6.14474	+
+chrM	6488	6497	0.728631;0.695958;21.6573;1.07347;1.07377;	25.2291	+
+chrM	6546	6562	9.5425;5.19601;13.8026;3.58048;0.676667;4.90231;	37.7006	+
+chrM	6637	6640	10.2661;10.734;15.4334;12.4627;	48.8961	+
+chrM	6678	6682	0.847222;1.10454;7.71147;8.23266;1.81499;	19.7109	+
+chrM	7192	7193	1.43403;	1.43403	+
+chrM	7210	7211	0.769414;	0.769414	+
+chrM	7221	7222	17.213;	17.213	+
+chrM	7230	7231	5.24055;	5.24055	+
+chrM	7242	7243	0.472322;	0.472322	+
+chrM	7282	7283	1.14827;4.21847;	5.36674	+
+chrM	7309	7315	1.42725;3.12262;5.3952;2.25968;12.5975;12.5975;8.70982;	46.1096	+
+chrM	7679	7701	15.927;13.5543;4.88487;7.09817;14.1506;9.51016;11.4765;4.21065;11.5544;16.1749;0.223123;11.2651;3.53734;	123.567	+
+chrM	7802	7809	4.67003;14.2629;5.1441;6.77224;4.33274;27.3548;	62.5368	+
+chrM	7836	7842	2.23801;1.37029;4.33807;7.945;4.16801;31.2228;	51.2822	+
+chrM	7876	7877	3.83204;	3.83204	+
+chrM	7901	7902	25.4903;	25.4903	+
+chrM	7964	7968	0.511204;5.45474;6.86356;	12.8295	+
+chrM	7992	7998	2.17243;0.314156;3.37377;4.417;2.55146;	12.8288	+
+chrM	8044	8050	2.45822;11.5147;14.7416;9.44352;0.128457;7.20489;	45.4914	+
+chrM	8133	8143	4.07616;13.8083;14.0775;21.0458;2.48387;8.5671;7.23971;0.221711;24.765;	96.2852	+
+chrM	5843	5861	0.792428;52.2404;52.2404;10.0907;37.5647;5.30998;37.7931;1.06251;13.3019;	210.396	-
diff -r 000000000000 -r eb000bccef28 test-data/chrM:4000-8300.binding_regions.cov_CLmotifs.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM:4000-8300.binding_regions.cov_CLmotifs.bed	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,48 @@
+chrM	4291	4314	2.87655;4.57544;1.9093;52.3973;30.5686;4.69146;6.57447;60.2542;24.9111;22.4555;14.6916;	225.905	+
+chrM	4401	4404	58.7899;5.94153;	64.7314	+
+chrM	4417	4419	52.9006;78.1395;3.46575;	134.506	+
+chrM	4433	4434	7.10406;65.4345;	72.5386	+
+chrM	4445	4446	9.0675;	9.0675	+
+chrM	4823	4824	2.37396;	2.37396	+
+chrM	4840	4841	3.59728;	3.59728	+
+chrM	4896	4897	7.26981;	7.26981	+
+chrM	4909	4910	1.84891;2.16833;	4.01724	+
+chrM	4921	4922	1.7173;	1.7173	+
+chrM	4945	4955	8.86501;1.93776;4.40328;2.15768;	17.3637	+
+chrM	5314	5315	8.45847;0.181168;	8.63964	+
+chrM	5331	5332	2.65729;2.6687;	5.32599	+
+chrM	5343	5344	5.46374;5.48628;	10.95	+
+chrM	5361	5364	2.34726;0.0359933;	2.38326	+
+chrM	5374	5375	0.241802;	0.241802	+
+chrM	5455	5465	10.0936;3.90451;2.2512;4.38388;4.38348;	25.0167	+
+chrM	6010	6018	4.02774;19.8597;9.21876;19.8597;19.8597;9.21549;8.61924;1.05759;	91.718	+
+chrM	6202	6203	10.9092;	10.9092	+
+chrM	6214	6225	2.78068;0.343238;1.17331;13.6565;	17.9538	+
+chrM	6241	6253	27.4703;11.6802;12.277;12.3268;11.7805;49.9134;0.686498;5.27793;	131.413	+
+chrM	6345	6352	14.6293;3.35198;0.973817;8.67785;	27.633	+
+chrM	6372	6376	8.64682;1.1145;2.1039;2.91354;4.96066;	19.7394	+
+chrM	6412	6413	1.97814;	1.97814	+
+chrM	6430	6438	3.93886;1.49557;1.81725;3.14121;	10.3929	+
+chrM	6451	6453	10.4438;3.33301;	13.7768	+
+chrM	6469	6473	5.47678;0.685062;	6.16184	+
+chrM	6488	6497	0.700916;0.671846;21.8827;1.01619;1.01644;	25.2881	+
+chrM	6546	6562	9.57336;5.16057;13.9491;3.55403;0.6238;4.95052;	37.8114	+
+chrM	6637	6640	10.3353;10.7671;15.5213;12.5687;	49.1924	+
+chrM	6678	6682	0.818671;1.05925;7.72861;8.18387;1.80946;	19.5999	+
+chrM	7192	7193	1.45455;	1.45455	+
+chrM	7210	7211	0.79438;	0.79438	+
+chrM	7221	7222	17.4136;	17.4136	+
+chrM	7230	7231	5.31736;	5.31736	+
+chrM	7242	7243	0.495479;	0.495479	+
+chrM	7282	7283	1.13057;4.25317;	5.38374	+
+chrM	7309	7315	0.120627;1.31503;2.70833;1.53398;12.2368;12.2368;8.78236;	38.9339	+
+chrM	7679	7701	16.0725;13.6444;4.83849;7.07543;14.2109;9.51666;11.5284;4.20094;11.5889;16.2681;0.117034;11.3302;3.57763;	123.97	+
+chrM	7802	7809	4.65424;14.3051;5.08178;6.76985;4.3113;27.6012;	62.7235	+
+chrM	7836	7842	2.14601;1.25468;4.26851;7.94601;4.08522;31.4939;	51.1943	+
+chrM	7876	7877	3.85842;	3.85842	+
+chrM	7901	7902	25.4582;	25.4582	+
+chrM	7964	7968	0.476707;5.49676;6.95434;	12.9278	+
+chrM	7992	7998	2.19539;0.269487;3.33675;4.3845;2.53573;	12.7219	+
+chrM	8044	8050	2.4415;11.5628;14.8144;9.50755;0.084919;7.25686;	45.668	+
+chrM	8133	8143	4.07108;13.87;14.136;21.183;2.40429;8.54041;7.21096;0.115654;24.6698;	96.2012	+
+chrM	5843	5861	0.699158;52.1487;52.1487;10.0984;37.9219;5.25451;38.1317;0.969962;13.3358;	210.709	-
diff -r 000000000000 -r eb000bccef28 test-data/chrM:4000-8300.binding_regions.cov_input_signal.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM:4000-8300.binding_regions.cov_input_signal.bed	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,8 @@
+chrM	4300	4301	103.952;6.50886;	110.461	+
+chrM	4311	4312	97.4565;	97.4565	+
+chrM	4401	4402	152.834;	152.834	+
+chrM	4417	4418	2.50947;159.42;	161.93	+
+chrM	4434	4435	160.189;	160.189	+
+chrM	6241	6242	7.33835;	7.33835	+
+chrM	6251	6252	23.9886;	23.9886	+
+chrM	5849	5860	233.272;110.411;21.5287;21.8534;	387.065	-
diff -r 000000000000 -r eb000bccef28 test-data/chrM:4000-8300.binding_regions.test4.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM:4000-8300.binding_regions.test4.bed	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,8 @@
+chrM	4300	4301	104.705;6.84184;	111.547	+
+chrM	4311	4312	98.1746;	98.1746	+
+chrM	4401	4402	154.574;	154.574	+
+chrM	4417	4418	3.19537;162.132;	165.328	+
+chrM	4434	4435	161.885;	161.885	+
+chrM	6241	6242	7.62247;	7.62247	+
+chrM	6251	6252	24.013;	24.013	+
+chrM	5849	5860	234.547;111.161;21.8547;22.1785;	389.741	-
diff -r 000000000000 -r eb000bccef28 test-data/chrM:4000-8300.crosslink_sites.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM:4000-8300.crosslink_sites.bed	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,176 @@
+chrM	4291	4292	3	2.94929	+
+chrM	4292	4293	3	4.64074	+
+chrM	4295	4296	3	1.94087	+
+chrM	4300	4301	3	52.6504	+
+chrM	4301	4302	3	30.3923	+
+chrM	4302	4303	3	4.80211	+
+chrM	4303	4304	3	6.66437	+
+chrM	4311	4312	3	60.3029	+
+chrM	4312	4313	3	24.7976	+
+chrM	4313	4314	3	22.3709	+
+chrM	4314	4315	3	14.6446	+
+chrM	4401	4402	3	58.8257	+
+chrM	4404	4405	3	6.06023	+
+chrM	4417	4418	3	52.5488	+
+chrM	4418	4419	3	78.3902	+
+chrM	4419	4420	3	3.67021	+
+chrM	4433	4434	3	7.25741	+
+chrM	4434	4435	3	65.6233	+
+chrM	4445	4446	3	9.12652	+
+chrM	4823	4824	3	2.39621	+
+chrM	4840	4841	3	3.53076	+
+chrM	4896	4897	3	7.22391	+
+chrM	4909	4910	3	1.87438	+
+chrM	4910	4911	3	2.20671	+
+chrM	4921	4922	3	1.69262	+
+chrM	4945	4946	3	8.75681	+
+chrM	4947	4948	3	1.91605	+
+chrM	4952	4953	3	4.3546	+
+chrM	4955	4956	3	2.13593	+
+chrM	5314	5315	3	8.38192	+
+chrM	5315	5316	3	0.241933	+
+chrM	5316	5317	3	0.0023646	+
+chrM	5331	5332	3	2.6509	+
+chrM	5332	5333	3	2.66322	+
+chrM	5343	5344	3	5.44813	+
+chrM	5344	5345	3	5.47323	+
+chrM	5361	5362	3	2.30985	+
+chrM	5364	5365	3	0.0245996	+
+chrM	5374	5375	3	0.238708	+
+chrM	5455	5456	3	10.1669	+
+chrM	5456	5457	3	3.92435	+
+chrM	5457	5458	3	2.26717	+
+chrM	5464	5465	3	4.40821	+
+chrM	5465	5466	3	4.41924	+
+chrM	6010	6011	3	4.02549	+
+chrM	6011	6012	3	19.905	+
+chrM	6012	6013	3	9.19498	+
+chrM	6013	6014	3	19.905	+
+chrM	6014	6015	3	19.905	+
+chrM	6015	6016	3	9.19141	+
+chrM	6016	6017	3	8.55025	+
+chrM	6018	6019	3	1.02799	+
+chrM	6202	6203	3	10.8234	+
+chrM	6214	6215	3	2.83587	+
+chrM	6216	6217	3	0.500624	+
+chrM	6217	6218	3	1.30892	+
+chrM	6225	6226	3	13.5581	+
+chrM	6241	6242	3	27.2127	+
+chrM	6246	6247	3	11.6542	+
+chrM	6247	6248	3	12.296	+
+chrM	6248	6249	3	12.3448	+
+chrM	6249	6250	3	11.7528	+
+chrM	6251	6252	3	49.4979	+
+chrM	6252	6253	3	0.836268	+
+chrM	6253	6254	3	5.37351	+
+chrM	6345	6346	3	14.5165	+
+chrM	6346	6347	3	3.37477	+
+chrM	6351	6352	3	1.02112	+
+chrM	6352	6353	3	8.63183	+
+chrM	6372	6373	3	8.64158	+
+chrM	6373	6374	3	1.22687	+
+chrM	6374	6375	3	2.22685	+
+chrM	6375	6376	3	3.027	+
+chrM	6376	6377	3	4.99741	+
+chrM	6412	6413	3	1.96883	+
+chrM	6430	6431	3	3.92122	+
+chrM	6435	6436	3	1.51198	+
+chrM	6437	6438	3	1.87923	+
+chrM	6438	6439	3	3.18803	+
+chrM	6451	6452	3	10.3462	+
+chrM	6453	6454	3	3.31758	+
+chrM	6469	6470	3	5.44285	+
+chrM	6473	6474	3	0.701889	+
+chrM	6488	6489	3	0.728631	+
+chrM	6490	6491	3	0.695958	+
+chrM	6493	6494	3	21.6573	+
+chrM	6495	6496	3	1.07347	+
+chrM	6497	6498	3	1.07377	+
+chrM	6546	6547	3	9.5425	+
+chrM	6547	6548	3	5.19601	+
+chrM	6551	6552	3	13.8026	+
+chrM	6557	6558	3	3.58048	+
+chrM	6558	6559	3	0.676667	+
+chrM	6562	6563	3	4.90231	+
+chrM	6637	6638	3	10.2661	+
+chrM	6638	6639	3	10.734	+
+chrM	6639	6640	3	15.4334	+
+chrM	6640	6641	3	12.4627	+
+chrM	6678	6679	3	0.847222	+
+chrM	6679	6680	3	1.10454	+
+chrM	6680	6681	3	7.71147	+
+chrM	6681	6682	3	8.23266	+
+chrM	6682	6683	3	1.81499	+
+chrM	7192	7193	3	1.43403	+
+chrM	7210	7211	3	0.769414	+
+chrM	7221	7222	3	17.213	+
+chrM	7230	7231	3	5.24055	+
+chrM	7242	7243	3	0.472322	+
+chrM	7282	7283	3	1.14827	+
+chrM	7283	7284	3	4.21847	+
+chrM	7309	7310	3	1.42725	+
+chrM	7310	7311	3	3.12262	+
+chrM	7311	7312	3	5.3952	+
+chrM	7312	7313	3	2.25968	+
+chrM	7313	7314	3	12.5975	+
+chrM	7314	7315	3	12.5975	+
+chrM	7315	7316	3	8.70982	+
+chrM	7679	7680	3	15.927	+
+chrM	7681	7682	3	13.5543	+
+chrM	7682	7683	3	4.88487	+
+chrM	7683	7684	3	7.09817	+
+chrM	7684	7685	3	14.1506	+
+chrM	7685	7686	3	9.51016	+
+chrM	7686	7687	3	11.4765	+
+chrM	7690	7691	3	4.21065	+
+chrM	7691	7692	3	11.5544	+
+chrM	7692	7693	3	16.1749	+
+chrM	7694	7695	3	0.223123	+
+chrM	7695	7696	3	11.2651	+
+chrM	7701	7702	3	3.53734	+
+chrM	7802	7803	3	4.67003	+
+chrM	7803	7804	3	14.2629	+
+chrM	7804	7805	3	5.1441	+
+chrM	7805	7806	3	6.77224	+
+chrM	7808	7809	3	4.33274	+
+chrM	7809	7810	3	27.3548	+
+chrM	7836	7837	3	2.23801	+
+chrM	7837	7838	3	1.37029	+
+chrM	7838	7839	3	4.33807	+
+chrM	7840	7841	3	7.945	+
+chrM	7841	7842	3	4.16801	+
+chrM	7842	7843	3	31.2228	+
+chrM	7876	7877	3	3.83204	+
+chrM	7901	7902	3	25.4903	+
+chrM	7964	7965	3	0.511204	+
+chrM	7965	7966	3	5.45474	+
+chrM	7968	7969	3	6.86356	+
+chrM	7992	7993	3	2.17243	+
+chrM	7995	7996	3	0.314156	+
+chrM	7996	7997	3	3.37377	+
+chrM	7997	7998	3	4.417	+
+chrM	7998	7999	3	2.55146	+
+chrM	8044	8045	3	2.45822	+
+chrM	8045	8046	3	11.5147	+
+chrM	8046	8047	3	14.7416	+
+chrM	8047	8048	3	9.44352	+
+chrM	8049	8050	3	0.128457	+
+chrM	8050	8051	3	7.20489	+
+chrM	8133	8134	3	4.07616	+
+chrM	8134	8135	3	13.8083	+
+chrM	8135	8136	3	14.0775	+
+chrM	8136	8137	3	21.0458	+
+chrM	8138	8139	3	2.48387	+
+chrM	8139	8140	3	8.5671	+
+chrM	8140	8141	3	7.23971	+
+chrM	8141	8142	3	0.221711	+
+chrM	8143	8144	3	24.765	+
+chrM	5860	5861	3	0.792428	-
+chrM	5859	5860	3	52.2404	-
+chrM	5858	5859	3	52.2404	-
+chrM	5857	5858	3	10.0907	-
+chrM	5855	5856	3	37.5647	-
+chrM	5851	5852	3	5.30998	-
+chrM	5849	5850	3	37.7931	-
+chrM	5844	5845	3	1.06251	-
+chrM	5843	5844	3	13.3019	-
diff -r 000000000000 -r eb000bccef28 test-data/chrM:4000-8300.crosslink_sites.bed.stats
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM:4000-8300.crosslink_sites.bed.stats	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,7 @@
+gamma1.theta	0.241477
+gamma1.k	1
+gamma1.tp	0.00807885
+gamma2.theta	0.458321
+gamma2.k	3.27989
+gamma2.tp	0.00807885
+options.useKdeThreshold	0.00807885
diff -r 000000000000 -r eb000bccef28 test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,175 @@
+chrM	4291	4292	3	2.87655	+
+chrM	4292	4293	3	4.57544	+
+chrM	4295	4296	3	1.9093	+
+chrM	4300	4301	3	52.3973	+
+chrM	4301	4302	3	30.5686	+
+chrM	4302	4303	3	4.69146	+
+chrM	4303	4304	3	6.57447	+
+chrM	4311	4312	3	60.2542	+
+chrM	4312	4313	3	24.9111	+
+chrM	4313	4314	3	22.4555	+
+chrM	4314	4315	3	14.6916	+
+chrM	4401	4402	3	58.7899	+
+chrM	4404	4405	3	5.94153	+
+chrM	4417	4418	3	52.9006	+
+chrM	4418	4419	3	78.1395	+
+chrM	4419	4420	3	3.46575	+
+chrM	4433	4434	3	7.10406	+
+chrM	4434	4435	3	65.4345	+
+chrM	4445	4446	3	9.0675	+
+chrM	4823	4824	3	2.37396	+
+chrM	4840	4841	3	3.59728	+
+chrM	4896	4897	3	7.26981	+
+chrM	4909	4910	3	1.84891	+
+chrM	4910	4911	3	2.16833	+
+chrM	4921	4922	3	1.7173	+
+chrM	4945	4946	3	8.86501	+
+chrM	4947	4948	3	1.93776	+
+chrM	4952	4953	3	4.40328	+
+chrM	4955	4956	3	2.15768	+
+chrM	5314	5315	3	8.45847	+
+chrM	5315	5316	3	0.181168	+
+chrM	5331	5332	3	2.65729	+
+chrM	5332	5333	3	2.6687	+
+chrM	5343	5344	3	5.46374	+
+chrM	5344	5345	3	5.48628	+
+chrM	5361	5362	3	2.34726	+
+chrM	5364	5365	3	0.0359933	+
+chrM	5374	5375	3	0.241802	+
+chrM	5455	5456	3	10.0936	+
+chrM	5456	5457	3	3.90451	+
+chrM	5457	5458	3	2.2512	+
+chrM	5464	5465	3	4.38388	+
+chrM	5465	5466	3	4.38348	+
+chrM	6010	6011	3	4.02774	+
+chrM	6011	6012	3	19.8597	+
+chrM	6012	6013	3	9.21876	+
+chrM	6013	6014	3	19.8597	+
+chrM	6014	6015	3	19.8597	+
+chrM	6015	6016	3	9.21549	+
+chrM	6016	6017	3	8.61924	+
+chrM	6018	6019	3	1.05759	+
+chrM	6202	6203	3	10.9092	+
+chrM	6214	6215	3	2.78068	+
+chrM	6216	6217	3	0.343238	+
+chrM	6217	6218	3	1.17331	+
+chrM	6225	6226	3	13.6565	+
+chrM	6241	6242	3	27.4703	+
+chrM	6246	6247	3	11.6802	+
+chrM	6247	6248	3	12.277	+
+chrM	6248	6249	3	12.3268	+
+chrM	6249	6250	3	11.7805	+
+chrM	6251	6252	3	49.9134	+
+chrM	6252	6253	3	0.686498	+
+chrM	6253	6254	3	5.27793	+
+chrM	6345	6346	3	14.6293	+
+chrM	6346	6347	3	3.35198	+
+chrM	6351	6352	3	0.973817	+
+chrM	6352	6353	3	8.67785	+
+chrM	6372	6373	3	8.64682	+
+chrM	6373	6374	3	1.1145	+
+chrM	6374	6375	3	2.1039	+
+chrM	6375	6376	3	2.91354	+
+chrM	6376	6377	3	4.96066	+
+chrM	6412	6413	3	1.97814	+
+chrM	6430	6431	3	3.93886	+
+chrM	6435	6436	3	1.49557	+
+chrM	6437	6438	3	1.81725	+
+chrM	6438	6439	3	3.14121	+
+chrM	6451	6452	3	10.4438	+
+chrM	6453	6454	3	3.33301	+
+chrM	6469	6470	3	5.47678	+
+chrM	6473	6474	3	0.685062	+
+chrM	6488	6489	3	0.700916	+
+chrM	6490	6491	3	0.671846	+
+chrM	6493	6494	3	21.8827	+
+chrM	6495	6496	3	1.01619	+
+chrM	6497	6498	3	1.01644	+
+chrM	6546	6547	3	9.57336	+
+chrM	6547	6548	3	5.16057	+
+chrM	6551	6552	3	13.9491	+
+chrM	6557	6558	3	3.55403	+
+chrM	6558	6559	3	0.6238	+
+chrM	6562	6563	3	4.95052	+
+chrM	6637	6638	3	10.3353	+
+chrM	6638	6639	3	10.7671	+
+chrM	6639	6640	3	15.5213	+
+chrM	6640	6641	3	12.5687	+
+chrM	6678	6679	3	0.818671	+
+chrM	6679	6680	3	1.05925	+
+chrM	6680	6681	3	7.72861	+
+chrM	6681	6682	3	8.18387	+
+chrM	6682	6683	3	1.80946	+
+chrM	7192	7193	3	1.45455	+
+chrM	7210	7211	3	0.79438	+
+chrM	7221	7222	3	17.4136	+
+chrM	7230	7231	3	5.31736	+
+chrM	7242	7243	3	0.495479	+
+chrM	7282	7283	3	1.13057	+
+chrM	7283	7284	3	4.25317	+
+chrM	7309	7310	3	0.120627	+
+chrM	7310	7311	3	1.31503	+
+chrM	7311	7312	3	2.70833	+
+chrM	7312	7313	3	1.53398	+
+chrM	7313	7314	3	12.2368	+
+chrM	7314	7315	3	12.2368	+
+chrM	7315	7316	3	8.78236	+
+chrM	7679	7680	3	16.0725	+
+chrM	7681	7682	3	13.6444	+
+chrM	7682	7683	3	4.83849	+
+chrM	7683	7684	3	7.07543	+
+chrM	7684	7685	3	14.2109	+
+chrM	7685	7686	3	9.51666	+
+chrM	7686	7687	3	11.5284	+
+chrM	7690	7691	3	4.20094	+
+chrM	7691	7692	3	11.5889	+
+chrM	7692	7693	3	16.2681	+
+chrM	7694	7695	3	0.117034	+
+chrM	7695	7696	3	11.3302	+
+chrM	7701	7702	3	3.57763	+
+chrM	7802	7803	3	4.65424	+
+chrM	7803	7804	3	14.3051	+
+chrM	7804	7805	3	5.08178	+
+chrM	7805	7806	3	6.76985	+
+chrM	7808	7809	3	4.3113	+
+chrM	7809	7810	3	27.6012	+
+chrM	7836	7837	3	2.14601	+
+chrM	7837	7838	3	1.25468	+
+chrM	7838	7839	3	4.26851	+
+chrM	7840	7841	3	7.94601	+
+chrM	7841	7842	3	4.08522	+
+chrM	7842	7843	3	31.4939	+
+chrM	7876	7877	3	3.85842	+
+chrM	7901	7902	3	25.4582	+
+chrM	7964	7965	3	0.476707	+
+chrM	7965	7966	3	5.49676	+
+chrM	7968	7969	3	6.95434	+
+chrM	7992	7993	3	2.19539	+
+chrM	7995	7996	3	0.269487	+
+chrM	7996	7997	3	3.33675	+
+chrM	7997	7998	3	4.3845	+
+chrM	7998	7999	3	2.53573	+
+chrM	8044	8045	3	2.4415	+
+chrM	8045	8046	3	11.5628	+
+chrM	8046	8047	3	14.8144	+
+chrM	8047	8048	3	9.50755	+
+chrM	8049	8050	3	0.084919	+
+chrM	8050	8051	3	7.25686	+
+chrM	8133	8134	3	4.07108	+
+chrM	8134	8135	3	13.87	+
+chrM	8135	8136	3	14.136	+
+chrM	8136	8137	3	21.183	+
+chrM	8138	8139	3	2.40429	+
+chrM	8139	8140	3	8.54041	+
+chrM	8140	8141	3	7.21096	+
+chrM	8141	8142	3	0.115654	+
+chrM	8143	8144	3	24.6698	+
+chrM	5860	5861	3	0.699158	-
+chrM	5859	5860	3	52.1487	-
+chrM	5858	5859	3	52.1487	-
+chrM	5857	5858	3	10.0984	-
+chrM	5855	5856	3	37.9219	-
+chrM	5851	5852	3	5.25451	-
+chrM	5849	5850	3	38.1317	-
+chrM	5844	5845	3	0.969962	-
+chrM	5843	5844	3	13.3358	-
diff -r 000000000000 -r eb000bccef28 test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,7 @@
+gamma1.theta	0.24151
+gamma1.k	1
+gamma1.tp	0.00807885
+gamma2.theta	0.458315
+gamma2.k	3.28001
+gamma2.tp	0.00807885
+options.useKdeThreshold	0.00807885
diff -r 000000000000 -r eb000bccef28 test-data/chrM:4000-8300.crosslink_sites.cov_input_signal.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM:4000-8300.crosslink_sites.cov_input_signal.bed	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,13 @@
+chrM	4300	4301	3	103.952	+
+chrM	4301	4302	3	6.50886	+
+chrM	4311	4312	3	97.4565	+
+chrM	4401	4402	3	152.834	+
+chrM	4417	4418	3	2.50947	+
+chrM	4418	4419	3	159.42	+
+chrM	4434	4435	3	160.189	+
+chrM	6241	6242	3	7.33835	+
+chrM	6251	6252	3	23.9886	+
+chrM	5859	5860	3	233.272	-
+chrM	5858	5859	3	110.411	-
+chrM	5855	5856	3	21.5287	-
+chrM	5849	5850	3	21.8534	-
diff -r 000000000000 -r eb000bccef28 test-data/chrM:4000-8300.crosslink_sites.cov_input_signal.bed.stats
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM:4000-8300.crosslink_sites.cov_input_signal.bed.stats	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,11 @@
+gamma1.b0	-1.3954
+gamma1.b1	0.777914
+gamma1.theta	0.0247733
+gamma1.k	10
+gamma1.tp	0.00797885
+gamma2.b0	1.05185
+gamma2.b1	0.0663266
+gamma2.theta	0.286295
+gamma2.k	10
+gamma2.tp	0.00797885
+options.useKdeThreshold	0.00797885
diff -r 000000000000 -r eb000bccef28 test-data/chrM:4000-8300.crosslink_sites.test4.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM:4000-8300.crosslink_sites.test4.bed	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,13 @@
+chrM	4300	4301	3	104.705	+
+chrM	4301	4302	3	6.84184	+
+chrM	4311	4312	3	98.1746	+
+chrM	4401	4402	3	154.574	+
+chrM	4417	4418	3	3.19537	+
+chrM	4418	4419	3	162.132	+
+chrM	4434	4435	3	161.885	+
+chrM	6241	6242	3	7.62247	+
+chrM	6251	6252	3	24.013	+
+chrM	5859	5860	3	234.547	-
+chrM	5858	5859	3	111.161	-
+chrM	5855	5856	3	21.8547	-
+chrM	5849	5850	3	22.1785	-
diff -r 000000000000 -r eb000bccef28 test-data/chrM:4000-8300.crosslink_sites.test4.bed.stats
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM:4000-8300.crosslink_sites.test4.bed.stats	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,11 @@
+gamma1.b0	-1.39741
+gamma1.b1	0.776752
+gamma1.theta	0.0247235
+gamma1.k	10
+gamma1.tp	0.00797885
+gamma2.b0	1.05131
+gamma2.b1	0.0543217
+gamma2.theta	0.497519
+gamma2.k	5.75133
+gamma2.tp	0.00797885
+options.useKdeThreshold	0.00797885
diff -r 000000000000 -r eb000bccef28 test-data/fimo_clmotif_occurences.chrM:4000-8300.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_clmotif_occurences.chrM:4000-8300.bed	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,310 @@
+chrM	4548	4549	1	9.36364	+
+chrM	4549	4550	1	9.36364	+
+chrM	4550	4551	1	9.36364	+
+chrM	4551	4552	1	9.36364	+
+chrM	4552	4553	1	9.36364	+
+chrM	4553	4554	1	9.36364	+
+chrM	4554	4555	1	5.03636	+
+chrM	4602	4603	1	6.87273	-
+chrM	4603	4604	1	10.3636	-
+chrM	4604	4605	1	10.3636	-
+chrM	4605	4606	1	10.3636	-
+chrM	4606	4607	1	10.3636	-
+chrM	4607	4608	1	10.3636	-
+chrM	4608	4609	1	10.3636	-
+chrM	4644	4645	2	9	+
+chrM	4645	4646	2	9	+
+chrM	4646	4647	2	9	+
+chrM	4647	4648	2	9	+
+chrM	4648	4649	2	9	+
+chrM	4649	4650	2	9	+
+chrM	4868	4869	1	10.3636	-
+chrM	4869	4870	1	10.3636	-
+chrM	4870	4871	1	10.3636	-
+chrM	4871	4872	1	10.3636	-
+chrM	4872	4873	1	10.3636	-
+chrM	4873	4874	1	10.3636	-
+chrM	4995	4996	1	5.61818	-
+chrM	4996	4997	1	5.61818	-
+chrM	4997	4998	1	5.61818	-
+chrM	4998	4999	1	5.61818	-
+chrM	4999	5000	1	5.61818	-
+chrM	5000	5001	1	5.61818	-
+chrM	5031	5032	3	9.37143	-
+chrM	5032	5033	3	9.37143	-
+chrM	5033	5034	3	9.37143	-
+chrM	5034	5035	3	9.37143	-
+chrM	5035	5036	3	9.37143	-
+chrM	5036	5037	3	9.37143	-
+chrM	5088	5089	4	8.05634	+
+chrM	5089	5090	4	8.05634	+
+chrM	5090	5091	4	8.05634	+
+chrM	5091	5092	4	8.05634	+
+chrM	5092	5093	4	8.05634	+
+chrM	5093	5094	3	8.82857	+
+chrM	5094	5095	3	8.82857	+
+chrM	5095	5096	3	8.82857	+
+chrM	5096	5097	3	8.82857	+
+chrM	5097	5098	3	8.82857	+
+chrM	5098	5099	3	8.82857	+
+chrM	5246	5247	1	10.3636	+
+chrM	5247	5248	1	10.3636	+
+chrM	5248	5249	1	10.3636	+
+chrM	5249	5250	1	10.3636	+
+chrM	5250	5251	1	10.3636	+
+chrM	5251	5252	1	10.3636	+
+chrM	5252	5253	1	5.61818	+
+chrM	5264	5265	3	8.82857	+
+chrM	5265	5266	3	8.82857	+
+chrM	5266	5267	3	8.82857	+
+chrM	5267	5268	3	8.82857	+
+chrM	5268	5269	3	8.82857	+
+chrM	5269	5270	3	8.82857	+
+chrM	5278	5279	4	9.39437	-
+chrM	5279	5280	4	9.39437	-
+chrM	5280	5281	1	10.3636	-
+chrM	5281	5282	1	10.3636	-
+chrM	5282	5283	1	10.3636	-
+chrM	5283	5284	1	10.3636	-
+chrM	5284	5285	1	10.3636	-
+chrM	5285	5286	1	10.3636	-
+chrM	5297	5298	3	8.77143	+
+chrM	5298	5299	3	8.77143	+
+chrM	5299	5300	3	8.77143	+
+chrM	5300	5301	3	8.77143	+
+chrM	5301	5302	3	8.77143	+
+chrM	5302	5303	3	8.77143	+
+chrM	5399	5400	1	5.03636	-
+chrM	5400	5401	1	9.36364	-
+chrM	5401	5402	1	9.36364	-
+chrM	5402	5403	1	9.36364	-
+chrM	5403	5404	1	9.36364	-
+chrM	5404	5405	1	9.36364	-
+chrM	5405	5406	1	9.36364	-
+chrM	5425	5426	4	8.73239	-
+chrM	5426	5427	4	8.73239	-
+chrM	5427	5428	4	8.73239	-
+chrM	5428	5429	4	8.73239	-
+chrM	5429	5430	4	8.73239	-
+chrM	5430	5431	4	8.73239	-
+chrM	5492	5493	4	8.05634	+
+chrM	5493	5494	4	8.05634	+
+chrM	5494	5495	4	8.05634	+
+chrM	5495	5496	4	8.05634	+
+chrM	5496	5497	4	8.05634	+
+chrM	5497	5498	4	8.05634	+
+chrM	5510	5511	4	9.19718	-
+chrM	5511	5512	4	9.19718	-
+chrM	5512	5513	4	9.19718	-
+chrM	5513	5514	4	9.19718	-
+chrM	5514	5515	4	9.19718	-
+chrM	5515	5516	4	9.19718	-
+chrM	5573	5574	4	9.85915	+
+chrM	5574	5575	4	9.85915	+
+chrM	5575	5576	4	9.85915	+
+chrM	5576	5577	4	9.85915	+
+chrM	5577	5578	4	9.85915	+
+chrM	5578	5579	4	9.85915	+
+chrM	5594	5595	1	5.61818	-
+chrM	5595	5596	1	5.61818	-
+chrM	5596	5597	1	5.61818	-
+chrM	5597	5598	1	5.61818	-
+chrM	5598	5599	1	5.61818	-
+chrM	5599	5600	1	5.61818	-
+chrM	5678	5679	4	9.39437	-
+chrM	5679	5680	4	9.39437	-
+chrM	5680	5681	4	9.39437	-
+chrM	5681	5682	4	9.39437	-
+chrM	5682	5683	4	9.39437	-
+chrM	5683	5684	4	9.39437	-
+chrM	5744	5745	1	5.67273	-
+chrM	5745	5746	1	9.10909	-
+chrM	5746	5747	1	9.10909	-
+chrM	5747	5748	1	9.10909	-
+chrM	5748	5749	1	9.10909	-
+chrM	5749	5750	1	9.10909	-
+chrM	5750	5751	1	9.10909	-
+chrM	5807	5808	1	5.92727	-
+chrM	5808	5809	1	5.92727	-
+chrM	5809	5810	1	5.92727	-
+chrM	5810	5811	1	5.92727	-
+chrM	5811	5812	1	5.92727	-
+chrM	5812	5813	1	5.92727	-
+chrM	5827	5828	1	5.03636	-
+chrM	5828	5829	1	9.36364	-
+chrM	5829	5830	1	9.36364	-
+chrM	5830	5831	1	9.36364	-
+chrM	5831	5832	1	9.36364	-
+chrM	5832	5833	1	9.36364	-
+chrM	5833	5834	1	9.36364	-
+chrM	5884	5885	1	5.03636	+
+chrM	5885	5886	1	5.03636	+
+chrM	5886	5887	1	5.03636	+
+chrM	5887	5888	1	5.03636	+
+chrM	5888	5889	1	5.03636	+
+chrM	5889	5890	1	5.03636	+
+chrM	5929	5930	4	8.73239	-
+chrM	5930	5931	4	8.73239	-
+chrM	5931	5932	4	8.73239	-
+chrM	5932	5933	4	8.73239	-
+chrM	5933	5934	4	8.73239	-
+chrM	5934	5935	4	8.73239	-
+chrM	5936	5937	4	9.39437	-
+chrM	5937	5938	4	9.39437	-
+chrM	5938	5939	4	9.39437	-
+chrM	5939	5940	4	9.39437	-
+chrM	5940	5941	4	9.39437	-
+chrM	5941	5942	4	9.39437	-
+chrM	6068	6069	3	9.35714	+
+chrM	6069	6070	3	9.35714	+
+chrM	6070	6071	3	9.35714	+
+chrM	6071	6072	3	9.35714	+
+chrM	6072	6073	3	9.35714	+
+chrM	6073	6074	3	9.35714	+
+chrM	6089	6090	4	8.73239	+
+chrM	6090	6091	4	8.73239	+
+chrM	6091	6092	4	8.73239	+
+chrM	6092	6093	4	8.73239	+
+chrM	6093	6094	4	8.73239	+
+chrM	6094	6095	4	8.73239	+
+chrM	6190	6191	4	8.71831	-
+chrM	6191	6192	4	8.71831	-
+chrM	6192	6193	4	8.71831	-
+chrM	6193	6194	4	8.71831	-
+chrM	6194	6195	4	8.71831	-
+chrM	6195	6196	4	8.71831	-
+chrM	6392	6393	3	9.37143	+
+chrM	6393	6394	3	9.37143	+
+chrM	6394	6395	3	9.37143	+
+chrM	6395	6396	3	9.37143	+
+chrM	6396	6397	3	9.37143	+
+chrM	6397	6398	3	9.37143	+
+chrM	6404	6405	3	8.82857	+
+chrM	6405	6406	3	8.82857	+
+chrM	6406	6407	3	8.82857	+
+chrM	6407	6408	3	8.82857	+
+chrM	6408	6409	3	8.82857	+
+chrM	6409	6410	3	8.82857	+
+chrM	6412	6413	4	8.05634	-
+chrM	6413	6414	4	8.05634	-
+chrM	6414	6415	4	8.05634	-
+chrM	6415	6416	4	8.05634	-
+chrM	6416	6417	4	8.05634	-
+chrM	6417	6418	4	8.05634	-
+chrM	6611	6612	1	9.10909	+
+chrM	6612	6613	1	9.10909	+
+chrM	6613	6614	1	9.10909	+
+chrM	6614	6615	1	9.10909	+
+chrM	6615	6616	1	9.10909	+
+chrM	6616	6617	1	9.10909	+
+chrM	6617	6618	1	6.92727	+
+chrM	6630	6631	4	8.05634	+
+chrM	6631	6632	4	8.05634	+
+chrM	6632	6633	4	8.05634	+
+chrM	6633	6634	4	8.05634	+
+chrM	6634	6635	4	8.05634	+
+chrM	6635	6636	4	8.05634	+
+chrM	6689	6690	1	5.67273	-
+chrM	6690	6691	1	9.10909	-
+chrM	6691	6692	1	9.10909	-
+chrM	6692	6693	1	9.10909	-
+chrM	6693	6694	1	9.10909	-
+chrM	6694	6695	1	9.10909	-
+chrM	6695	6696	1	9.10909	-
+chrM	6755	6756	3	9.42857	+
+chrM	6756	6757	3	9.42857	+
+chrM	6757	6758	3	9.42857	+
+chrM	6758	6759	3	9.42857	+
+chrM	6759	6760	3	9.42857	+
+chrM	6760	6761	3	9.42857	+
+chrM	6833	6834	3	8.77143	+
+chrM	6834	6835	3	8.77143	+
+chrM	6835	6836	3	8.77143	+
+chrM	6836	6837	3	8.77143	+
+chrM	6837	6838	3	8.77143	+
+chrM	6838	6839	3	8.77143	+
+chrM	6932	6933	3	9.37143	+
+chrM	6933	6934	3	9.37143	+
+chrM	6934	6935	3	9.37143	+
+chrM	6935	6936	3	9.37143	+
+chrM	6936	6937	3	9.37143	+
+chrM	6937	6938	3	9.37143	+
+chrM	6942	6943	1	5.92727	+
+chrM	6943	6944	1	5.92727	+
+chrM	6944	6945	1	5.92727	+
+chrM	6945	6946	1	5.92727	+
+chrM	6946	6947	1	5.92727	+
+chrM	6947	6948	1	5.92727	+
+chrM	7090	7091	2	9	+
+chrM	7091	7092	2	9	+
+chrM	7092	7093	2	9	+
+chrM	7093	7094	2	9	+
+chrM	7094	7095	2	9	+
+chrM	7095	7096	2	9	+
+chrM	7131	7132	1	6.87273	-
+chrM	7132	7133	1	6.87273	-
+chrM	7133	7134	1	6.87273	-
+chrM	7134	7135	1	6.87273	-
+chrM	7135	7136	1	6.87273	-
+chrM	7136	7137	1	6.87273	-
+chrM	7154	7155	3	9.37143	+
+chrM	7155	7156	3	9.37143	+
+chrM	7156	7157	3	9.37143	+
+chrM	7157	7158	3	9.37143	+
+chrM	7158	7159	3	9.37143	+
+chrM	7159	7160	3	9.37143	+
+chrM	7261	7262	3	8.77143	+
+chrM	7262	7263	3	8.77143	+
+chrM	7263	7264	3	8.77143	+
+chrM	7264	7265	3	8.77143	+
+chrM	7265	7266	3	8.77143	+
+chrM	7266	7267	3	8.77143	+
+chrM	7308	7309	1	5.92727	+
+chrM	7309	7310	1	5.92727	+
+chrM	7310	7311	1	5.92727	+
+chrM	7311	7312	1	5.92727	+
+chrM	7312	7313	1	5.92727	+
+chrM	7313	7314	1	5.92727	+
+chrM	7340	7341	1	6.92727	-
+chrM	7341	7342	1	6.92727	-
+chrM	7342	7343	1	6.92727	-
+chrM	7343	7344	1	6.92727	-
+chrM	7344	7345	1	6.92727	-
+chrM	7345	7346	1	6.92727	-
+chrM	7369	7370	4	8.71831	-
+chrM	7370	7371	4	8.71831	-
+chrM	7371	7372	4	8.71831	-
+chrM	7372	7373	4	8.71831	-
+chrM	7373	7374	4	8.71831	-
+chrM	7374	7375	4	8.71831	-
+chrM	7432	7433	4	8.71831	-
+chrM	7433	7434	4	8.71831	-
+chrM	7434	7435	4	8.71831	-
+chrM	7435	7436	4	8.71831	-
+chrM	7436	7437	4	8.71831	-
+chrM	7437	7438	4	8.71831	-
+chrM	7445	7446	1	10.3636	-
+chrM	7446	7447	1	10.3636	-
+chrM	7447	7448	1	10.3636	-
+chrM	7448	7449	1	10.3636	-
+chrM	7449	7450	1	10.3636	-
+chrM	7450	7451	1	10.3636	-
+chrM	7508	7509	1	9.10909	+
+chrM	7509	7510	1	9.10909	+
+chrM	7510	7511	1	9.10909	+
+chrM	7511	7512	1	9.10909	+
+chrM	7512	7513	1	9.10909	+
+chrM	7513	7514	1	10.3636	-
+chrM	7514	7515	1	10.3636	-
+chrM	7515	7516	1	10.3636	-
+chrM	7516	7517	1	10.3636	-
+chrM	7517	7518	1	10.3636	-
+chrM	7518	7519	1	10.3636	-
+chrM	7524	7525	4	9.19718	-
+chrM	7525	7526	4	9.19718	-
+chrM	7526	7527	4	9.19718	-
+chrM	7527	7528	4	9.19718	-
+chrM	7528	7529	4	9.19718	-
+chrM	7529	7530	4	9.19718	-
+chrM	7530	7531	1	9.10909	-
+chrM	7531	7532	1	9.10909	-
diff -r 000000000000 -r eb000bccef28 test-data/hsa_chrM.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hsa_chrM.fa	Thu May 17 14:11:39 2018 -0400
@@ -0,0 +1,238 @@
+>chrM
+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG
+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC
+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA
+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC
+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA
+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC
+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA
+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC
+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC
+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA
+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC
+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA
+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA
+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT
+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC
+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC
+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC
+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA
+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC
+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT
+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA
+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA
+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA
+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA
+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG
+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA
+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC
+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA
+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT
+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC
+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG
+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC
+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG
+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC
+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA
+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC
+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA
+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT
+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA
+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT
+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG
+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA
+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG
+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG
+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT
+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA
+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT
+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA
+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC
+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC
+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC
+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG
+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC
+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC
+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG
+CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTC
+CGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATAC
+ACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCC
+CTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAAC
+AGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA
+GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATAT
+GTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTAGGACTATGA
+GAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAAGTAAGGTC
+AGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCT
+GGCCCAACCCGTCATCTACTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT
+TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTC
+GTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTAT
+CCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTCATCATTAATA
+ATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAG
+GCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA
+AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGA
+GGTGGATTAAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAA
+TAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCCTAACTACTAC
+CGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACTATCTCGCACCTGAAACAAGCTA
+ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT
+TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCAC
+CATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATA
+TCTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCG
+CCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATTTAGGTTAAATAC
+AGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA
+CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGA
+CTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCC
+GCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGA
+AAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCA
+GCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG
+AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCC
+GAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCAT
+TTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAAT
+AATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTC
+CTACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG
+CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTC
+CTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATAC
+CAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAG
+CTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGG
+AGACCCCATTCTATACCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA
+GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTA
+TGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGG
+AATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAA
+GTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAG
+GATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT
+ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATC
+ATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCC
+ATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAAT
+GCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTC
+ATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC
+TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGA
+AGAACCCGTATACATAAAATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAA
+CCCCATGGCCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAAT
+TATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCT
+ATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC
+TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGA
+AACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTAC
+ATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACG
+AGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGA
+CCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA
+TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTC
+TAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGC
+AAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTT
+ACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTT
+AAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT
+AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTA
+CCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCT
+GTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCT
+CTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAAC
+TAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT
+AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTA
+TCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTA
+AAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGA
+AACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCAC
+CTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA
+TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCAC
+ACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAA
+AACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATT
+TCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGG
+CGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG
+GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAG
+CCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAA
+GTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAA
+TAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCT
+CCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT
+GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCC
+AACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGT
+AGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGT
+ACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTAA
+TAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT
+AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAA
+TTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAG
+CCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAG
+TCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAAT
+GATTTCGACTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG
+CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGA
+AGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAAT
+ATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAA
+TCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCA
+ACAATTATATTACTACCACTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA
+GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCC
+AACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATC
+ATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCT
+CCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAAC
+CACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA
+TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCC
+TAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTT
+AATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCT
+AAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCT
+ATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT
+ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCA
+TACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCG
+GCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTA
+CGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTT
+TGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG
+TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGC
+CCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAA
+CCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACC
+CCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAA
+CAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC
+AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCA
+ACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCC
+ATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCAT
+CCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAA
+CTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA
+TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACC
+CAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA
+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA
+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT
+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA
+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT
+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA
+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC
+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC
+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC
+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC
+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC
+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA
+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC
+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC
+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC
+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA
+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC
+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA
+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT
+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA
+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA
+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA
+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA
+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC
+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC
+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC
+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG
+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC
+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC
+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC
+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA
+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA
+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC
+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC
+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC
+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC
+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA
+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT
+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC
+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT
+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC
+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA
+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC
+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT
+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC
+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC
+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA
+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC
+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA
+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA
+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA
+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG
+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG
+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC
+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG
diff -r 000000000000 -r eb000bccef28 test-data/input.aligned.prepro.R2.chrM:4000-8300.bam
Binary file test-data/input.aligned.prepro.R2.chrM:4000-8300.bam has changed