| Next changeset 1:fd1f57782683 (2018-05-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b |
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added:
pureclip.xml test-data/aligned.prepro.R2.chrM:4000-8300.bam test-data/chrM:4000-8300.binding_regions.bed test-data/chrM:4000-8300.binding_regions.cov_CLmotifs.bed test-data/chrM:4000-8300.binding_regions.cov_input_signal.bed test-data/chrM:4000-8300.binding_regions.test4.bed test-data/chrM:4000-8300.crosslink_sites.bed test-data/chrM:4000-8300.crosslink_sites.bed.stats test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats test-data/chrM:4000-8300.crosslink_sites.cov_input_signal.bed test-data/chrM:4000-8300.crosslink_sites.cov_input_signal.bed.stats test-data/chrM:4000-8300.crosslink_sites.test4.bed test-data/chrM:4000-8300.crosslink_sites.test4.bed.stats test-data/fimo_clmotif_occurences.chrM:4000-8300.bed test-data/hsa_chrM.fa test-data/input.aligned.prepro.R2.chrM:4000-8300.bam |
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| 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 |
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| b'@@ -0,0 +1,306 @@\n+<tool id="pureclip" name="PureCLIP" version="1.0.4">\n+ <description>- HMM based peak caller designed for eCLIP/iCLIP data</description>\n+ <requirements>\n+ <requirement type="package" version="1.0.4">pureclip</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ln -s \'${target_bam_file}\' target.bam && \n+ln -f -s \'${target_bam_file.metadata.bam_index}\' target.bam.bai && \n+ln -s \'${genome_fasta_file}\' genome.fa &&\n+#if $control_bam_file:\n+ ln -s \'${control_bam_file}\' control.bam && \n+ ln -f -s \'${control_bam_file.metadata.bam_index}\' control.bam.bai && \n+#end if\n+#if $motif_data.motif_data_selector == \'supply_CL_motifs\':\n+ ln -s \'${motif_data.cl_motif_bed_file}\' motif_hits.bed &&\n+#end if\n+\n+pureclip\n+ -o crosslink_sites.bed\n+ -or binding_regions.bed\n+ -i target.bam\n+ -bai target.bam.bai\n+ -g genome.fa\n+ #if $learn_params_contigs\n+ -iv \'$learn_params_contigs\'\n+ #end if\n+ #if $apply_hmm_contigs\n+ -iv \'$apply_hmm_contigs\'\n+ #end if\n+ -dm $merge_dist\n+ #if $control_bam_file:\n+ -ibam control.bam\n+ -ibai control.bam.bai\n+ #end if\n+ #if $motif_data.motif_data_selector == \'supply_CL_motifs\':\n+ -fis motif_hits.bed\n+ -nim $motif_data.max_motif_id\n+ #end if\n+ #if $bc_data.bc_data_selector == \'bc_0\':\n+ -bc 0\n+ #elif $bc_data.bc_data_selector == \'bc_1\':\n+ -bc 1\n+ #elif $bc_data.bc_data_selector == \'manual_setting\':\n+ -bw $bc_data.bandwidth\n+ -bwn $bc_data.bandwidthn\n+ -b1p $bc_data.b1p\n+ -b2p $bc_data.b2p\n+ #if $bc_data.antp_option.antp_option_selector == \'antp_select\':\n+ -antp\n+ #elif $bc_data.antp_option.antp_option_selector == \'manual_select\':\n+ -ntp $bc_data.antp_option.ntp\n+ -ntp2 $bc_data.antp_option.ntp2\n+ #end if\n+ #end if\n+ #if $advanced_params.advanced_params_selector == \'ap_specify\':\n+ $advanced_params.ld_precision\n+ $advanced_params.use_viterbi\n+ #if $advanced_params.max_iter_brent\n+ -m $advanced_params.max_iter_brent\n+ #end if\n+ #if $advanced_params.max_iter_bw\n+ -w $advanced_params.max_iter_bw\n+ #end if\n+ #if $advanced_params.g1kmin\n+ -g1kmin $advanced_params.g1kmin\n+ #end if\n+ #if $advanced_params.g1kmax\n+ -g1kmax $advanced_params.g1kmax\n+ #end if\n+ #if $advanced_params.g2kmin\n+ -g2kmin $advanced_params.g2kmin\n+ #end if\n+ #if $advanced_params.g2kmax\n+ -g2kmax $advanced_params.g2kmax\n+ #end if\n+ $advanced_params.fk\n+ -mkn $advanced_params.mkn\n+ -mtp $advanced_params.mtp\n+ #if $advanced_params.mk\n+ -mk $advanced_params.mk\n+ #end if\n+ #if $advanced_params.pa\n+ -pa $advanced_params.pa\n+ #end if\n+ $advanced_params.ea1\n+ $advanced_params.ea2\n+ $advanced_params.et1\n+ $advanced_params.et2\n+ #if $advanced_params.mrtf\n+ -mrtf $advanced_params.mrtf\n+ #end if\n+ -mtc $advanced_params.mtc\n+ -pet $advanced_params.pet\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <param name="target_bam_file" type="data" format="bam" label="Target BAM file" argument="-i"/>\n+ <param name="genome_fasta_file" type="data" format="fasta" label="Genome reference file" argument="-g"/>\n+ <!-- Options -->\n+ <param name="learn_params_contigs" type="text" optional="True"\n+ label="Genomic chromosomes to learn HMM parameters" argument="-iv" \n+ 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).">\n+ <sanitiz'..b'ink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_input_signal.bed"/>\n+ <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_input_signal.bed"/>\n+ <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_input_signal.bed.stats"/>\n+ </test>\n+ <test>\n+ <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>\n+ <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>\n+ <param name="motif_data_selector" value="supply_CL_motifs"/>\n+ <param name="cl_motif_bed_file" value="fimo_clmotif_occurences.chrM:4000-8300.bed" ftype="bed"/>\n+ <param name="max_motif_id" value="4"/>\n+ <param name="crosslink_bed_stats" value="True"/>\n+ <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed"/>\n+ <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_CLmotifs.bed"/>\n+ <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats"/>\n+ </test>\n+ <test>\n+ <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>\n+ <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>\n+ <param name="control_bam_file" value="input.aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>\n+ <param name="bc_data_selector" value="manual_setting"/>\n+ <param name="bandwidthn" value="50"/>\n+ <param name="b1p" value="0.01"/>\n+ <param name="b2p" value="0.15"/>\n+ <param name="antp_option_selector" value="manual_select"/>\n+ <param name="ntp" value="10"/>\n+ <param name="ntp2" value="0"/>\n+ <param name="advanced_params_selector" value="ap_specify"/>\n+ <param name="fk" value="True"/>\n+ <param name="mkn" value="0.9"/>\n+ <param name="mtc" value="200"/>\n+ <param name="crosslink_bed_stats" value="True"/>\n+ <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.test4.bed"/>\n+ <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.test4.bed"/>\n+ <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.test4.bed.stats"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+ 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.\n+\n+ 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).\n+\n+ 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.\n+\n+ 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:\n+\n+ http://pureclip.readthedocs.io/en/latest/index.html\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1186/s13059-017-1364-2</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r eb000bccef28 test-data/aligned.prepro.R2.chrM:4000-8300.bam |
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| Binary file test-data/aligned.prepro.R2.chrM:4000-8300.bam has changed |
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| 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 |
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| @@ -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 - |
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| 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 |
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| @@ -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 - |
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| 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 |
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| @@ -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 - |
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| 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 |
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| @@ -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 - |
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| 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 |
| b |
| @@ -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 - |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 - |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 - |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 - |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| b'@@ -0,0 +1,310 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|
| b |
| 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 |
| b |
| b'@@ -0,0 +1,238 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'CAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n' |
| b |
| diff -r 000000000000 -r eb000bccef28 test-data/input.aligned.prepro.R2.chrM:4000-8300.bam |
| b |
| Binary file test-data/input.aligned.prepro.R2.chrM:4000-8300.bam has changed |