Repository 'hicup_hicup'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/hicup_hicup

Changeset 0:7e9e8da0522d (2017-03-09)
Next changeset 1:b191af7e2476 (2017-08-19)
Commit message:
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
added:
hicup_hicup.xml
hicup_macros.xml
test-data/HiCUP_summary_report.txt
test-data/chr1.fa
test-data/dataset.contiguous.filter.sam
test-data/dataset.filt.sam
test-data/dataset.hicup.sam
test-data/dataset.invalid.filter.sam
test-data/dataset.re_ligation.filter.sam
test-data/dataset.same_circularised.filter.sam
test-data/dataset.same_dangling_ends.filter.sam
test-data/dataset.same_internal.filter.sam
test-data/dataset1.fastq
test-data/dataset1.mapper_barchart.svg
test-data/dataset1.trunc.fastq
test-data/dataset1.truncation_barchart.svg
test-data/dataset2.fastq
test-data/dataset2.mapper_barchart.svg
test-data/dataset2.trunc.fastq
test-data/dataset2.truncation_barchart.svg
test-data/deduplicator_cis_trans_piechart.svg
test-data/deduplicator_uniques_barchart.svg
test-data/digester_file.txt
test-data/filter_piechart.svg
test-data/hicup_deduplicator_summary.txt
test-data/hicup_filter_summary.txt
test-data/hicup_mapper_summary.txt
test-data/hicup_truncater_summary.txt
test-data/result.pair.sam
test-data/results.html
tool-data/bowtie2_indices.loc.sample
tool_data_table_conf.xml.sample
b
diff -r 000000000000 -r 7e9e8da0522d hicup_hicup.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hicup_hicup.xml Thu Mar 09 09:31:57 2017 -0500
[
b'@@ -0,0 +1,179 @@\n+<tool id="hicup_hicup" name="Hicup Pipeline" version="0.1.0">\n+    <description>controls the other programs in the HiCUP pipeline.</description>\n+    <macros>\n+        <import>hicup_macros.xml</import>\n+    </macros>\n+    <expand macro="requirements_hicup" />\n+    <expand macro="stdio" />\n+\n+    <command><![CDATA[\n+        \n+        BOWTIE_PATH_BASH="\\$(which bowtie2)" &&\n+        #set index_path = \'\'\n+        #if str($reference_genome.source) == "history":\n+            bowtie2-build "$reference_genome.own_file" genome &&\n+            ln -s "$reference_genome.own_file" genome.fa &&\n+            #set index_path = \'genome\'\n+        #else:\n+            #set index_path = $reference_genome.index.fields.path\n+        #end if\n+        hicup_digester --re1 \'$re1\' --genome \'$genome\'\n+        #if $advanced_options.re2:\n+            --re2 \'$advanced_options.re2\'\n+        #end if\n+        #for $file in $input_files_digest:\n+            $file\n+        #end for\n+        && mv *Digest_* digest_file.txt\n+        && hicup \n+        --digest digest_file.txt\n+        --index \'$index_path\'\n+        --bowtie2 \\$BOWTIE_PATH_BASH\n+        $advanced_options.nofill --keep\n+        \n+        #if $advanced_options.longest:\n+            --longest \'$advanced_options.longest\'\n+        #end if\n+\n+        #if $advanced_options.shortest:\n+            --shortest \'$advanced_options.shortest\'\n+        #end if\n+        \n+        $input_first_sequence $input_second_sequence\n+       \n+        ## process truncater files\n+        && ls -la\n+       \n+        && mv hicup_truncater_summary_* hicup_truncater_summary.txt\n+        && trunc_result_1=\\$(echo \'$input_first_sequence\' | rev | cut -d\'/\' -f1 | rev)\n+        && mv \\$trunc_result_1.truncation_barchart.svg dataset1.truncation_barchart.svg\n+        && mv \\$trunc_result_1.trunc.fastq dataset1.trunc.fastq\n+        && trunc_result_2=\\$(echo \'$input_second_sequence\' | rev | cut -d\'/\' -f1 | rev)\n+        && mv \\$trunc_result_2.truncation_barchart.svg dataset2.truncation_barchart.svg\n+        && mv \\$trunc_result_2.trunc.fastq dataset2.trunc.fastq\n+\n+        && echo \\$trunc_result_1\n+        && echo \\$trunc_result_2\n+        \n+        ## process mapper\n+        && mv hicup_mapper_summary* hicup_mapper_summary.txt\n+        && mv *.pair.sam result.pair.sam\n+        \n+        && mv \\$trunc_result_1.trunc.fastq.mapper_barchart.svg dataset1.mapper_barchart.svg\n+        && mv \\$trunc_result_2.trunc.fastq.mapper_barchart.svg dataset2.mapper_barchart.svg\n+        \n+\n+        ## process filter\n+        && mv hicup_filter_ditag_rejects* hicup_filter_ditag_rejects\n+        && ls -la hicup_filter_ditag_rejects/\n+        && mv *filt.sam dataset.filt.sam\n+        && mv hicup_filter_summary* hicup_filter_summary.txt\n+        && mv hicup_filter_ditag_rejects/*contiguous.filter.sam hicup_filter_ditag_rejects/dataset.contiguous.filter.sam\n+        && mv hicup_filter_ditag_rejects/*re_ligation.filter.sam  hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam \n+        && mv hicup_filter_ditag_rejects/*same_dangling_ends.filter.sam hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam\n+        && mv hicup_filter_ditag_rejects/*invalid.filter.sam hicup_filter_ditag_rejects/dataset.invalid.filter.sam \n+        && mv hicup_filter_ditag_rejects/*same_circularised.filter.sam hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam\n+        && mv hicup_filter_ditag_rejects/*same_internal.filter.sam hicup_filter_ditag_rejects/dataset.same_internal.filter.sam\n+        #if $advanced_options.longest or $advanced_options.shortest: \n+            && mv hicup_filter_ditag_rejects/*wrong_size.filter.sam hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam\n+        #end if\n+        && mv *pair.sam.filter_piechart.svg filter_piechart.svg\n+\n+        ## deduplicator\n+        && mv *filt.sam.deduplicator_cis_trans_piechart.svg deduplicator_cis_trans_piechart.svg\n+        && mv *filt.sam.deduplicator_uniques_barchart.'..b'\n+            <expand macro="deduplicator_output" />\n+        </collection>\n+    </outputs>\n+    <tests>\n+         <test>\n+            <!-- inputs -->\n+            <param name="input_first_sequence" value="dataset1.fastq" ftype="fastq"/>\n+            <param name="input_second_sequence" value="dataset2.fastq" ftype="fastq"/>\n+            <param name="re1" value="A^AGCTT"/>\n+            <param name="input_files_digest" value="chr1.fa"/>\n+            <param name="genome" value="human"/>\n+            <conditional name="reference_genome">\n+                <param name="source" value="history" />\n+                <param name="own_file" value="chr1.fa"/>\n+            </conditional>\n+\n+            <!-- outputs -->\n+            <output name="hicup_results" file="results.html" ftype="html" lines_diff="10000"/>\n+            <output name="dataset_hicup" file="dataset.hicup.sam" lines_diff="5" />\n+            <output name="hicup_report" file="HiCUP_summary_report.txt" lines_diff="2"/>\n+            \n+            <output_collection name="intermediate_results">\n+                <!-- truncater step-->\n+                <element name="hicup_truncater_summary" file="hicup_truncater_summary.txt" lines_diff="8"/>\n+                <element name="dataset1_trunc" file="dataset1.trunc.fastq" lines_diff="8" />\n+                <element name="dataset2_trunc" file="dataset2.trunc.fastq" lines_diff="8"/>\n+                <element name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" lines_diff="1000" />\n+                <element name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" lines_diff="1000" />\n+                \n+                <!-- mapper step -->\n+                <element name="hicup_mapper_summary" file="hicup_mapper_summary.txt" lines_diff="4"/>\n+                <element name="result_pair" file="result.pair.sam" lines_diff="8"/>\n+                <element name="dataset1_mapper_barchart" file="dataset1.mapper_barchart.svg" ftype="svg" lines_diff="1000"/>\n+                <element name="dataset2_mapper_barchart" file="dataset2.mapper_barchart.svg" ftype="svg" lines_diff="1000"/>\n+    \n+                <!-- filter step-->\n+                <element name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/>\n+                <element name="dataset_filt" file="dataset.filt.sam" lines_diff="8" />\n+                <element name="contiguous_filter" file="dataset.contiguous.filter.sam" lines_diff="8" />\n+                <element name="re_ligation_filter" file="dataset.re_ligation.filter.sam" lines_diff="8" />\n+                <element name="same_dangling_ends_filter" file="dataset.same_dangling_ends.filter.sam" lines_diff="8" />\n+                <element name="invalid_filter" file="dataset.invalid.filter.sam"  lines_diff="8" />\n+                <element name="same_circularised_filter" file="dataset.same_circularised.filter.sam" lines_diff="8" />\n+                <element name="same_internal_filter" file="dataset.same_internal.filter.sam" lines_diff="8" />\n+                <element name="filter_piechart" file="filter_piechart.svg" ftype="svg" lines_diff="1000" />\n+\n+                <!-- deduplicator step-->\n+                <element name="cis_trans_piechart" file="deduplicator_cis_trans_piechart.svg" ftype="svg" lines_diff="1000"/>\n+                <element name="uniques_barchart" file="deduplicator_uniques_barchart.svg" ftype="svg" lines_diff="1000"/>\n+                <element name="hicup_deduplicator_summary" file="hicup_deduplicator_summary.txt" lines_diff="2"/>\n+            </output_collection>\n+        </test>\n+    </tests>\n+    <help><![CDATA[\n+\n+    For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/\n+\n+    To get more information about the pipeline visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#HiCUP\n+    ]]></help>\n+    <expand macro="citation_hicup" />\n+</tool>\n'
b
diff -r 000000000000 -r 7e9e8da0522d hicup_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hicup_macros.xml Thu Mar 09 09:31:57 2017 -0500
b
@@ -0,0 +1,94 @@
+
+<macros>
+   <xml name="requirements_hicup">
+        <requirements>
+            <requirement type="package" version="0.5.9">hicup</requirement>
+            <requirement type="package" version="2.2.6">bowtie2</requirement>
+            <requirement type="package" version="1.2">samtools</requirement>
+            <requirement type="package" version="0.13.1">docutils</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" />
+        </stdio>
+    </xml>
+    <xml name="citation_hicup">
+       <citations>
+         <citation type="doi">10.12688/f1000research.7334.1</citation>
+     </citations>  
+    </xml>
+    <xml name="reference_genome_macro">
+        <conditional name="reference_genome">
+            <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
+                <option value="indexed">Use a built-in genome index</option>
+                <option value="history">Use a genome from the history and build index</option>
+            </param>
+            <when value="indexed">
+                <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+                <options from_data_table="bowtie2_indices">
+                    <filter type="sort_by" column="2"/>
+                    <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+                </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="own_file" type="data" format="fasta" label="Select reference genome" />
+                <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />-->
+            </when>
+        </conditional>
+    </xml>
+    <xml name="filter_output">
+        <data name="dataset_filt" format="sam" from_work_dir="dataset.filt.sam" label="filt.sam" />
+        <data name="hicup_filter_summary" format="txt" from_work_dir="hicup_filter_summary.txt" label="hicup_filter_summary.txt" />
+        <data name="contiguous_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.contiguous.filter.sam" label="contiguous.filter.sam" />
+        <data name="re_ligation_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam" label="re_ligation.filter.sam" />
+        <data name="same_dangling_ends_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam" label="same_dangling_ends.filter.sam" />
+        <data name="invalid_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.invalid.filter.sam" label="invalid.filter.sam" />
+        <data name="same_circularised_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam" label="same_circularised.filter.sam" />
+        <data name="same_internal_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_internal.filter.sam" label="same_internal.filter.sam" />
+        <data name="wrong_size_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam" label="wrong_size.filter.sam"/>
+        <data name="filter_piechart" format="svg" from_work_dir="filter_piechart.svg" label="Filter piechart.svg" />
+    </xml>
+    <xml name="mapper_output">
+        <data name="hicup_mapper_summary" format="txt" from_work_dir="hicup_mapper_summary.txt" label="hicup_mapper_summary.txt"/>
+        <data name="result_pair" format="sam" from_work_dir="result.pair.sam" label="pair.sam"/>
+        <data name="dataset1_mapper_barchart" format="svg" from_work_dir="dataset1.mapper_barchart.svg" label="Mapper Dataset1 Barchart.svg" />
+        <data name="dataset2_mapper_barchart" format="svg" from_work_dir="dataset2.mapper_barchart.svg" label="Mapper Dataset2 Barchart.svg" />
+    </xml>
+    <xml name="truncater_output">
+        <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary.txt" />
+        <data name="dataset1_trunc" format="fastq" label="Hicup Dataset1 Truncation" from_work_dir="dataset1.trunc.fastq" />
+        <data name="dataset2_trunc" format="fastq" label="Hicup Dataset2 Truncation" from_work_dir="dataset2.trunc.fastq" />
+        <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1.truncation_barchart.svg" />
+        <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2.truncation_barchart.svg" />
+        
+    </xml>
+    <xml name="input_files">
+        <param name="input_first_sequence" type="data" format="fastq" label="First input sequence" help="The first sequence:"/>
+        <param name="input_second_sequence" type="data" format="fastq" label="Second input sequence" help="The second sequence:"/>
+    </xml>
+    <xml name="re1">
+        <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme recognition sequence"/>
+    </xml>
+    <xml name="re2">
+        <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags." help="To specify a restriction enzyme instead of sonication to shorten di-tags. This restriction site does NOT form a Hi-C ligation junction. 2 .g. AG^CT,AluI. Typically the sonication protocol is followed."/>
+    </xml>
+    <xml name="digester_input">
+        <param name="input_files_digest" type="data" multiple="true" format="fa" label="Input DNA sequence files that should be digested"/>
+        <param argument="--genome" type="text" label="Genome" help="Name of the genome to be digested (not the path to the genome 
+        file or files, but the genome name to include in the output file)"/>
+    </xml>
+    <xml name="filter_longest_shortest">
+        <param argument="--longest" type="text" value="" label="Max insert size" help="Maximum allowable insert size (bps)"/>
+        <param argument="--shortest" type="text" value="" label="Min insert size" help="Minimum allowable insert size (bps)"/>
+    </xml>
+    <xml name="no_fill">
+        <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill" help="Hi-C protocol did NOT include a fill-in of sticky ends prior to re-ligation and therefore reads shall be truncated at the restriction site sequence"/>
+    </xml>
+    <xml name="deduplicator_output">
+        <data name="cis_trans_piechart" format="svg" from_work_dir="deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/>
+        <data name="uniques_barchart" format="svg" from_work_dir="deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" />
+        <data name="hicup_deduplicator_summary" format="txt" from_work_dir="hicup_deduplicator_summary.txt" label="Hicup Deduplicator Summary" />
+    </xml>
+</macros>
\ No newline at end of file
b
diff -r 000000000000 -r 7e9e8da0522d test-data/HiCUP_summary_report.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HiCUP_summary_report.txt Thu Mar 09 09:31:57 2017 -0500
b
@@ -0,0 +1,2 @@
+File Total_Reads_1 Total_Reads_2 Not_Truncated_Reads_1 Not_Truncated_Reads_2 Truncated_Read_1 Truncated_Read_2 Average_Length_Truncated_1 Average_Length_Truncated_2 Too_Short_To_Map_Read_1 Too_Short_To_Map_Read_2 Unique_Alignments_Read_1 Unique_Alignments_Read_2 Multiple_Alignments_Read_1 Multiple_Alignments_Read_2 Failed_To_Align_Read_1 Failed_To_Align_Read_2 Paired_Read_1 Paired_Read_2 Valid_Pairs Invalid_Pairs Same_Circularised Same_Dangling_Ends Same_Fragment_Internal Re_Ligation Contiguous_Sequence Wrong_Size Deduplication_Read_Pairs_Uniques Deduplication_Cis_Close_Uniques Deduplication_Cis_Far_Uniques Deduplication_Trans_Uniques Percentage_Mapped Percentage_Valid Percentage_Uniques Percentage_Unique_Trans Percentage_Ditags_Passed_Through_HiCUP
+dataset_1265_4.dat.hicup.sam 1000 1000 923 939 77 61 21.39 22.21 35 24 14 23 13 7 938 946 1 1 1 0 0 0 0 0 0 0 1 0 1 0 0.10 100.00 100.00 0.00 0.10
b
diff -r 000000000000 -r 7e9e8da0522d test-data/chr1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr1.fa Thu Mar 09 09:31:57 2017 -0500
b
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b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset.contiguous.filter.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset.contiguous.filter.sam Thu Mar 09 09:31:57 2017 -0500
b
@@ -0,0 +1,6 @@
+@HD VN:1.0 SO:unsorted
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+@PG ID:HiCUP Mapper VN:0.5.9
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b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset.filt.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset.filt.sam Thu Mar 09 09:31:57 2017 -0500
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@@ -0,0 +1,8 @@
+@HD VN:1.0 SO:unsorted
+@SQ SN:chr1 LN:199950
+@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough"
+@PG ID:HiCUP Mapper VN:0.5.9
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+@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt"
+SRR071233.43293 83 chr1 35433 3 40M = 75323 0 GAGTCCAGGAGTTCAAGACCAGCCTGGGTAACATAGTGAG CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-15 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:3G22A1C11 YT:Z:UU CT:Z:FAR
+SRR071233.43293 163 chr1 75323 23 40M = 35433 0 CTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCG CCBCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-10 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:20A18A0 YT:Z:UU CT:Z:FAR
b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset.hicup.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset.hicup.sam Thu Mar 09 09:31:57 2017 -0500
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@@ -0,0 +1,9 @@
+@HD VN:1.0 SO:unsorted
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+@PG ID:HiCUP Mapper VN:0.5.9
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+@PG HiCUP Deduplicator VN:0.5.9
+SRR071233.43293 83 chr1 35433 3 40M = 75323 0 GAGTCCAGGAGTTCAAGACCAGCCTGGGTAACATAGTGAG CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-15 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:3G22A1C11 YT:Z:UU CT:Z:FAR
+SRR071233.43293 163 chr1 75323 23 40M = 35433 0 CTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCG CCBCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-10 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:20A18A0 YT:Z:UU CT:Z:FAR
b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset.invalid.filter.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset.invalid.filter.sam Thu Mar 09 09:31:57 2017 -0500
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@@ -0,0 +1,6 @@
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b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset.re_ligation.filter.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset.re_ligation.filter.sam Thu Mar 09 09:31:57 2017 -0500
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@@ -0,0 +1,6 @@
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+@PG ID:HiCUP Mapper VN:0.5.9
+@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT"
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b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset.same_circularised.filter.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset.same_circularised.filter.sam Thu Mar 09 09:31:57 2017 -0500
b
@@ -0,0 +1,6 @@
+@HD VN:1.0 SO:unsorted
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+@PG ID:HiCUP Mapper VN:0.5.9
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b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset.same_dangling_ends.filter.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset.same_dangling_ends.filter.sam Thu Mar 09 09:31:57 2017 -0500
b
@@ -0,0 +1,6 @@
+@HD VN:1.0 SO:unsorted
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+@PG ID:HiCUP Mapper VN:0.5.9
+@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT"
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b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset.same_internal.filter.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset.same_internal.filter.sam Thu Mar 09 09:31:57 2017 -0500
b
@@ -0,0 +1,6 @@
+@HD VN:1.0 SO:unsorted
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+@PG ID:HiCUP Mapper VN:0.5.9
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b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset1.fastq Thu Mar 09 09:31:57 2017 -0500
b
b'@@ -0,0 +1,4000 @@\n+@SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+NAAGATACCTTGACCGCTCATCCCCTGNNTTCATGAAAGA\n++SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+!##########################!!###########\n+@SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+AGCTTTCTCCTTCTTTTGTCTTTCCCTCCTTTCTGTTGGG\n++SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+:BBBBBA??BABBB@<:;A?@B@BBB?BB?6;9<9AA?:0\n+@SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+CATAGACAATACAATGGCAGCATTGAATAGTTGTGGCAGA\n++SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+C@CCB@CCCCCCCACC@BCAC?CC@?;:?BAAC@A=A<A5\n+@SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+AGATCAAGCTCAGGACAGTCTTGATCTCCTGACCTCATGA\n++SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+ACCAACCCACCCCCCCCCCCCBCCCCCCCCCCCCCBCCCC\n+@SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+ATACTGGCAAACTGAATCCAGCAGCACATCAAAAAGCTAG\n++SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCC@C@CBCACC\n+@SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+AGAAAACTGGAGAAGAAAGAGCCAGGGTAGTCAAAGGACT\n++SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+C?<CCCCCCCCCCCCCBCCCCCCCCCCC?CCCCC@CCCCC\n+@SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+AAAAAACCCTTCCTATTTGAAGAGCAAGCTACATAAGCAA\n++SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+CCCCBCCCCCCCCCBCCCCCCABCCC?BCCCCACCCBCC?\n+@SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+GGACTGAATGAAATAATATATGCATAAAGTACATAAAAAT\n++SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+CCCCCCCCCCCBACC<7<<:CCCCCCCCC@CCCCBCCC=>\n+@SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+GCTTTCATCAAATGCCTTTGTCTTGGCATCTGAATTCCAG\n++SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCACCACCCCCCBCCCC\n+@SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CTATGAAAAGAAAAGAAGAAAAGCTAGCTTGTTTACATTG\n++SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CCCCCCCCCCCBBBBCBBCCCBBCCCCCCCCCCCCCCCCC\n+@SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+AGAAGAGACACCTGCACACTTCCCTCCAAGAAGCTAGCTT\n++SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+CCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+CGCATCACAAAGCTAGCTTAAGATTCCTTGTTGTTTCATC\n++SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+CACCCCCCDCCCCCCCCCCCBCCCBCCCCCCCCCCCCCCC\n+@SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CATGCACACAATGGACAATCCCAGCAGAATTTGCTTTTCA\n++SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+AGTTTTTCCTTGCATATGTGAAGCTAGCTTTCTCATCATC\n++SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+GGCTTGGCTTAACCAATAACTTTTGTAGAAACCTTTATGA\n++SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+AGCTTGGGCAGGAAGATGACCTACATGAATGAGGTGAGGA\n++SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCC\n+@SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+TTGGTGTGTGGCCAGTGCTGACAACAGCATTTTGAACTAC\n++SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+CCCCCCCCCCCCCBCCCCCCACCCCCCCCCCCCCCCCCCC\n+@SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+ATAATTCTGCAAAAGGCCATAAGCTAGCTTGCACACTGCC\n++SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+TGTGTTCCATTTGATGTCAAACAATAGGTTGAAAAATTAG\n++SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+00///9;<;;BBBBBB@@B@BABBBBBB@BBBBBBBBBBB\n+@SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+TGTGGGACCAGTGCAGCATTTAGTCTAGGAATAAATTTGT\n++SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR07123'..b'GAGGGTTTTTTCCTCGCTTGGGTTCATTAAGCTAGC\n++SRR071233.154841 NRTG514-16_0001:3:2:1055:18658 length=40\n+CBCCCCCCACCCCCCBC@?CBB@BB@BBBBBB<B>B9BBB\n+@SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+AGCTTAGAATATACTATTATTGAAGAAGGAAAGCCTTAGA\n++SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+CCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+TCTGAGAGTTCCAGTAGCTTCACATGCTCCAGTAATTGGT\n++SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCC>\n+@SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CATGGAAGACAGCCCTGCAGAGCTAAATTTAGGCAGAGAC\n++SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CCCCCCBCCCCCCCCCCDCCCACCCCACCCCCCCDCDCCB\n+@SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+ATCCACCCACCTTGGCCTCCCAAAGTGCTAGAATTACAGG\n++SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCC?CCCACCCCCCCCCC\n+@SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+ACTCATCTTGGACCTTGTTCTTCTTCTAATTCCACCATCA\n++SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+AGCAGTGGTTCTCCCAGCACAGCATTTGAGCTCCAACAAC\n++SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+CCCCCCCBCCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCC\n+@SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+CCTCTGAGACAAAGCTAGCTTCCTTTCACAGCTTGCTCCA\n++SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+CCCCCCDCCCBCCCCCCCCCCCBCCCCCCCCCCCCCCCCC\n+@SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+TCTTTAAAGTTCGCACAGAGTTTGGGGTATTCATTTTCAG\n++SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCACCCBCCCB\n+@SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+TAGGTAGAGGGATTAGTTGAGGCCAAGGCCTTGATCTGGG\n++SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+CCCCBCCACCC@CCCCCCCCCCCCCCCCCCCBCC@CCC@=\n+@SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+TCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAG\n++SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+CCCCCBCCCCCCBACCCCCCC@BCCBCCCCCCCCCCCCCC\n+@SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+TTGGGGAGGTGGCTGGGGAAGACCAGGGGCTACCTAAAAA\n++SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+DCCCCCCCBBCCDCCCCBCCBCCCBABCCC@CCCBCC?CC\n+@SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+GGAGAGATGAAAGAGTCAGACAGCTCTACAAAGCCTCTTT\n++SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+CCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCBCC\n+@SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+TAAACACTATGACCATTTCCATCTTTCAGCCCTCTTGATT\n++SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CC\n+@SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+TTAAAGACTAAATGCTTACCATGTGTATGCTAGGTGTACA\n++SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+CC@CCBCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCDCCC\n+@SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+ACGTTACACAGTGCATGACTATGCATGGTTTTTGGATTAA\n++SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCC\n+@SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+AAAGTTTTCCCGTTTAATATTATAAAATGGAATCATGTAA\n++SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+00//0+AAAACCCCCCBCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+TTTGGTAAGATTCTGAATGATTTTTCTGGTTTTATTTTTT\n++SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+CCCCCCCCCCCCCCCCCCC@CCCCCCBBCCCCCCCBBBBB\n+@SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+TCATTAAATGTACTCTAATGGAATCATGGAATGGACTCGA\n++SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+ABCCBCC@CCCCCCCCCBCCCACCCCCCCC=B@B@CCCCC\n+@SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+TCATAAAATCATTTGTAGATTGAAGCTAGCTTCTCAGTTG\n++SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+CCCACCCCCCCCCCCCCCCCCCCCBCC?CCCCCCCCCCCC\n'
b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset1.mapper_barchart.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset1.mapper_barchart.svg Thu Mar 09 09:31:57 2017 -0500
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b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset1.trunc.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset1.trunc.fastq Thu Mar 09 09:31:57 2017 -0500
b
b'@@ -0,0 +1,4000 @@\n+@SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+NAAGATACCTTGACCGCTCATCCCCTGNNTTCATGAAAGA\n++SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+!##########################!!###########\n+@SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+AGCTTTCTCCTTCTTTTGTCTTTCCCTCCTTTCTGTTGGG\n++SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+:BBBBBA??BABBB@<:;A?@B@BBB?BB?6;9<9AA?:0\n+@SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+CATAGACAATACAATGGCAGCATTGAATAGTTGTGGCAGA\n++SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+C@CCB@CCCCCCCACC@BCAC?CC@?;:?BAAC@A=A<A5\n+@SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+AGATCAAGCTCAGGACAGTCTTGATCTCCTGACCTCATGA\n++SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+ACCAACCCACCCCCCCCCCCCBCCCCCCCCCCCCCBCCCC\n+@SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+ATACTGGCAAACTGAATCCAGCAGCACATCAAAAAGCTAG\n++SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCC@C@CBCACC\n+@SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+AGAAAACTGGAGAAGAAAGAGCCAGGGTAGTCAAAGGACT\n++SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+C?<CCCCCCCCCCCCCBCCCCCCCCCCC?CCCCC@CCCCC\n+@SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+AAAAAACCCTTCCTATTTGAAGAGCAAGCTACATAAGCAA\n++SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+CCCCBCCCCCCCCCBCCCCCCABCCC?BCCCCACCCBCC?\n+@SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+GGACTGAATGAAATAATATATGCATAAAGTACATAAAAAT\n++SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+CCCCCCCCCCCBACC<7<<:CCCCCCCCC@CCCCBCCC=>\n+@SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+GCTTTCATCAAATGCCTTTGTCTTGGCATCTGAATTCCAG\n++SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCACCACCCCCCBCCCC\n+@SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CTATGAAAAGAAAAGAAGAAAAGCTT\n++SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CCCCCCCCCCCBBBBCBBCCCBBCCC\n+@SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+AGAAGAGACACCTGCACACTTCCCTCCAAGAAGCTT\n++SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+CCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCC\n+@SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+CGCATCACAAAGCTT\n++SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+CACCCCCCDCCCCCC\n+@SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CATGCACACAATGGACAATCCCAGCAGAATTTGCTTTTCA\n++SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+AGTTTTTCCTTGCATATGTGAAGCTT\n++SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+GGCTTGGCTTAACCAATAACTTTTGTAGAAACCTTTATGA\n++SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+AGCTTGGGCAGGAAGATGACCTACATGAATGAGGTGAGGA\n++SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCC\n+@SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+TTGGTGTGTGGCCAGTGCTGACAACAGCATTTTGAACTAC\n++SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+CCCCCCCCCCCCCBCCCCCCACCCCCCCCCCCCCCCCCCC\n+@SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+ATAATTCTGCAAAAGGCCATAAGCTT\n++SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+TGTGTTCCATTTGATGTCAAACAATAGGTTGAAAAATTAG\n++SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+00///9;<;;BBBBBB@@B@BABBBBBB@BBBBBBBBBBB\n+@SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+TGTGGGACCAGTGCAGCATTTAGTCTAGGAATAAATTTGT\n++SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.3161 NRTG514-16_0001:3:1:1426:3923 length=40\n+TGAAAAAGCCAAACATAGAAAACGAAACTTTAAAACAGCA\n++SRR071233.3161 NRTG514-16_0001:3:1:1426:3923 length'..b'===:\n+@SRR071233.154841 NRTG514-16_0001:3:2:1055:18658 length=40\n+TGTGGAGGGTTTTTTCCTCGCTTGGGTTCATTAAGCTAGC\n++SRR071233.154841 NRTG514-16_0001:3:2:1055:18658 length=40\n+CBCCCCCCACCCCCCBC@?CBB@BB@BBBBBB<B>B9BBB\n+@SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+AGCTTAGAATATACTATTATTGAAGAAGGAAAGCCTTAGA\n++SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+CCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+TCTGAGAGTTCCAGTAGCTTCACATGCTCCAGTAATTGGT\n++SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCC>\n+@SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CATGGAAGACAGCCCTGCAGAGCTAAATTTAGGCAGAGAC\n++SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CCCCCCBCCCCCCCCCCDCCCACCCCACCCCCCCDCDCCB\n+@SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+ATCCACCCACCTTGGCCTCCCAAAGTGCTAGAATTACAGG\n++SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCC?CCCACCCCCCCCCC\n+@SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+ACTCATCTTGGACCTTGTTCTTCTTCTAATTCCACCATCA\n++SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+AGCAGTGGTTCTCCCAGCACAGCATTTGAGCTCCAACAAC\n++SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+CCCCCCCBCCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCC\n+@SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+CCTCTGAGACAAAGCTT\n++SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+CCCCCCDCCCBCCCCCC\n+@SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+TCTTTAAAGTTCGCACAGAGTTTGGGGTATTCATTTTCAG\n++SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCACCCBCCCB\n+@SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+TAGGTAGAGGGATTAGTTGAGGCCAAGGCCTTGATCTGGG\n++SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+CCCCBCCACCC@CCCCCCCCCCCCCCCCCCCBCC@CCC@=\n+@SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+TCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAG\n++SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+CCCCCBCCCCCCBACCCCCCC@BCCBCCCCCCCCCCCCCC\n+@SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+TTGGGGAGGTGGCTGGGGAAGACCAGGGGCTACCTAAAAA\n++SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+DCCCCCCCBBCCDCCCCBCCBCCCBABCCC@CCCBCC?CC\n+@SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+GGAGAGATGAAAGAGTCAGACAGCTCTACAAAGCCTCTTT\n++SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+CCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCBCC\n+@SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+TAAACACTATGACCATTTCCATCTTTCAGCCCTCTTGATT\n++SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CC\n+@SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+TTAAAGACTAAATGCTTACCATGTGTATGCTAGGTGTACA\n++SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+CC@CCBCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCDCCC\n+@SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+ACGTTACACAGTGCATGACTATGCATGGTTTTTGGATTAA\n++SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCC\n+@SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+AAAGTTTTCCCGTTTAATATTATAAAATGGAATCATGTAA\n++SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+00//0+AAAACCCCCCBCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+TTTGGTAAGATTCTGAATGATTTTTCTGGTTTTATTTTTT\n++SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+CCCCCCCCCCCCCCCCCCC@CCCCCCBBCCCCCCCBBBBB\n+@SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+TCATTAAATGTACTCTAATGGAATCATGGAATGGACTCGA\n++SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+ABCCBCC@CCCCCCCCCBCCCACCCCCCCC=B@B@CCCCC\n+@SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+TCATAAAATCATTTGTAGATTGAAGCTT\n++SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+CCCACCCCCCCCCCCCCCCCCCCCBCC?\n'
b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset1.truncation_barchart.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset1.truncation_barchart.svg Thu Mar 09 09:31:57 2017 -0500
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b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset2.fastq Thu Mar 09 09:31:57 2017 -0500
b
b'@@ -0,0 +1,4000 @@\n+@SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+AGAACCCATTCACACTCCCGCCAGCAGCAGGTTCGTGCCA\n++SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+@BABA@BBBBBBBB?BBBB@:?AAAB5<BAA92A=2:;77\n+@SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+GTTGGAAACGGGATAAACCGCACAGAACTAAACAGAAGCA\n++SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+?????<B???A:5>-794<4<7>>97?9?;BAB@@7895;\n+@SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+GATGCAGCTAGCAAGCAGGAGGGCCAGGTTTCCAACCGCG\n++SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+BCCCBCC@CCCCCCC=CBBACCAACCCCCBCCB;CCCCC?\n+@SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+GACCATGCTCCCTATTATTCTTGTTGAGTAACTGTAAGAC\n++SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+CCCCCCCB8CCCCCCCCCCCCCCCCBCCCCBBACCCBCCC\n+@SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CTAGTGGGAAAGTGAAATGGTGTTGCATGTATGCAAGCTT\n++SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CCCC>CCCCCCCBCC@CCCC@CCCCCCCCCCCCCCCCC@C\n+@SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+GCAAGAGGCCTAGCTTTAAGGCTATCTCAGTTTTTGACAT\n++SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+CCC@CCCCCCCCCB?CCCCC@CC?@@@@@?C@CC?C?CC@\n+@SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+GGTAGCCATCCCAACAGCCTTGGACCTCACTGCAGATCTA\n++SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+CCCCCCC>CCCCACCBCBACBCCCCCCCBCCCCCCCCC@B\n+@SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+GCTCCCAACTCAGAGGAGTTGGCCGGGTAAGCTGTTTTCA\n++SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+BCCCCC@CBBCC@?@C?C=@BBBB>CC;?CC@CC=CB>C@\n+@SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+GAATTTCATATCCAGCCAAACTAAGCTACCTTTGCTATCA\n++SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+CCCCCCCCDCCCCCCDCCCCCCCCCBACCCCC@CCCCCCC\n+@SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+GCCATGGTGAGCATTTACACCATGGACACTGGCAAACTCC\n++SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CCCCCCCCCBCC@CCCCCCCCCCCCACCCCCCC@CCDCCC\n+@SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+TAGTATTTTTATCATTTTATCTAAAGATCTTTACTTTTCG\n++SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+CCCCCCCCCBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+TAAAAGACTTGGGTGGCATGTGGTTTTTAGAAGAAATTTA\n++SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+@CCCCCCCCCCBCBCCCCCCCCCBCCCCCCC:CCC?BCCC\n+@SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+AACCCCAGGAAAGCTAGCTTTCGTGGATTTTCTGAGGTCA\n++SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCBCC\n+@SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+AGCTTTTCGGAGCTAAATCATGCCCCAACAAAGGATAGCA\n++SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC\n+@SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+TACTAACTGTTTTAGTTTACCTCTTAGTTTTCCGCATGTC\n++SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+CCCCCCCCCCCCCACCCCCCCCCCCDCCCCCCCCCCCCCC\n+@SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CGCATTTAAGCTTCTCAAAGATGGTCATGCCTCCCTCACC\n++SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CCCCCCCCCCCCCCCCC6CCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+GGTCAAATCTAAGCTAGCTTACTTAGAATTACAGCTCTTT\n++SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+AATAAATAAAGTATTTAGGAAACAGATCTTACCTCACTTG\n++SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+CCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+CAAGGCTCTGATTTATCTCTTGATTTTTATTCTTACTTTT\n++SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+BBBBBBBBBB>BBBBBAB@B?@3>@BBBB===BBBBBBAB\n+@SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+AATAGTTTGTGCCTCTAAAAACAGGCAGGCTAAATAAGCT\n++SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+CDCCCCCCCCCCCCCCCCCCCCBBCCCCCCCACCCCCCCC\n+@SRR07123'..b'AAGGGCAAGGAAGACTTTTACAGGTGCTGGATCCGG\n++SRR071233.154841 NRTG514-16_0001:3:2:1055:18658 length=40\n+>>6>>@<@?@B>BBBBBBBBBB>BBBBBBBBBBBB8@B@B\n+@SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+TCTCATATTTTTTGAAGTAAACATCAAAATCACCATCCAG\n++SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+CCCCCCCCCCC@@@CCCCCCCCCACCCCCCCCCCCCCCCC\n+@SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+AATGAGAGAAAACTTCAGTAATCACCTAACCCCAAAAAAT\n++SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+CCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCC@CCCCC\n+@SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CACACCACTGCCCTGCACACAAACCCTCCAGGAGGTTTAT\n++SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCB>CCBC\n+@SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+TGGATTTCTCATGAATGGTTGAGTACTATCCTTTTGCTAC\n++SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+CCCCCCBCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCC\n+@SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+GGTGACGGATGTCCCAGGAGGACGACCCAAGCCCACCCGC\n++SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+CCCCCCCCCBCCCCCBCCCCCCCCCCCCCCCCCB<CBB@?\n+@SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+GGCCTTGATAAATTGTAACTACCATGATTAGACTTTTGTA\n++SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+CCCCCBCCCCCACCCCCCCCCCCCCCCACCCCCCCCCCCC\n+@SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+AGTCTCCTTACTAGGGCAGTTCAACTTCATAGTGGTGCAG\n++SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+CCCCCCCCC;CBCCCCCCCCCCCCCCCDBCCCBCCCCCCC\n+@SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+CCTACAATGCTCCCATCCAAGCTAGGGTGAAGGCAGATCC\n++SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+CCCCCCCCCCCCCCCBCCCCCCCCCCA@CCCCC>@CACCC\n+@SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+ATGCTCCTTTCTCAGTACTTTCATAGCACCTTCTTCATAC\n++SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+CCACCCCCCCCCBCC@BCCCACBCCCCCCCACCCC@BCCC\n+@SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+AAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGG\n++SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+CCCCC?@@CBCCCCCCCBCCCCCCCCC@CCCC@CCCCCC?\n+@SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+ACAGAGCGCAGGACAGAAAGTAAGGCATTTCAAGCAGAGA\n++SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+CCCCCCCCCCCCCCCCCACB@CCCCCCCCCCCCC?A8AAA\n+@SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+AACACTTAAAAAAAAAAAAAAAAAACCAAACCCCAGGCTC\n++SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+BBCCCCCDCCCCC@BBBBBBBBBB################\n+@SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+CTAAAACTGGACTGAGAAAAGGTGATCCCATTTGGCTTCA\n++SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+CCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCC\n+@SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+TATAATTTCTGTTCTTTTACATTTGCTGAGGAGTGCTTTA\n++SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+CCCCCCCCCCCCCCCCC@@CCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+CTATCCTAAGGTTATGAATGTATTCTCCTATATTATATTC\n++SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+CCCCCCCCCCCCCCCCCACCDCCCCCCCCCCACCCCCCCC\n+@SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+TAAAATTCAAAATTTCTGCTCCCCTATCCAGACCACTGGC\n++SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+AGCTTTGCCCATCATGAGGAATGAACCTAGCTCCTATTGC\n++SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+CCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCDCADCCCC\n+@SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+ATTTGATTCCATTCAATGATGATTCCATTCTATTCCATTC\n++SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+@BABAACCCCCCCCCCCCBB@=@AACBCCCCCCBCCC?CC\n+@SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+AGGATGTATTGGCAAGAGGAACTATTAAGACCATTGTTAC\n++SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+CCCBCCCCCCCCCCCCCCC?CCBCCCCCCCCCCCCCCCCC\n'
b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset2.mapper_barchart.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset2.mapper_barchart.svg Thu Mar 09 09:31:57 2017 -0500
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b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset2.trunc.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset2.trunc.fastq Thu Mar 09 09:31:57 2017 -0500
b
b'@@ -0,0 +1,4000 @@\n+@SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+AGAACCCATTCACACTCCCGCCAGCAGCAGGTTCGTGCCA\n++SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+@BABA@BBBBBBBB?BBBB@:?AAAB5<BAA92A=2:;77\n+@SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+GTTGGAAACGGGATAAACCGCACAGAACTAAACAGAAGCA\n++SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+?????<B???A:5>-794<4<7>>97?9?;BAB@@7895;\n+@SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+GATGCAGCTAGCAAGCAGGAGGGCCAGGTTTCCAACCGCG\n++SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+BCCCBCC@CCCCCCC=CBBACCAACCCCCBCCB;CCCCC?\n+@SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+GACCATGCTCCCTATTATTCTTGTTGAGTAACTGTAAGAC\n++SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+CCCCCCCB8CCCCCCCCCCCCCCCCBCCCCBBACCCBCCC\n+@SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CTAGTGGGAAAGTGAAATGGTGTTGCATGTATGCAAGCTT\n++SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CCCC>CCCCCCCBCC@CCCC@CCCCCCCCCCCCCCCCC@C\n+@SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+GCAAGAGGCCTAGCTTTAAGGCTATCTCAGTTTTTGACAT\n++SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+CCC@CCCCCCCCCB?CCCCC@CC?@@@@@?C@CC?C?CC@\n+@SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+GGTAGCCATCCCAACAGCCTTGGACCTCACTGCAGATCTA\n++SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+CCCCCCC>CCCCACCBCBACBCCCCCCCBCCCCCCCCC@B\n+@SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+GCTCCCAACTCAGAGGAGTTGGCCGGGTAAGCTGTTTTCA\n++SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+BCCCCC@CBBCC@?@C?C=@BBBB>CC;?CC@CC=CB>C@\n+@SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+GAATTTCATATCCAGCCAAACTAAGCTACCTTTGCTATCA\n++SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+CCCCCCCCDCCCCCCDCCCCCCCCCBACCCCC@CCCCCCC\n+@SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+GCCATGGTGAGCATTTACACCATGGACACTGGCAAACTCC\n++SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CCCCCCCCCBCC@CCCCCCCCCCCCACCCCCCC@CCDCCC\n+@SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+TAGTATTTTTATCATTTTATCTAAAGATCTTTACTTTTCG\n++SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+CCCCCCCCCBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+TAAAAGACTTGGGTGGCATGTGGTTTTTAGAAGAAATTTA\n++SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+@CCCCCCCCCCBCBCCCCCCCCCBCCCCCCC:CCC?BCCC\n+@SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+AACCCCAGGAAAGCTT\n++SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CCCCCCCCCCCCCCCC\n+@SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+AGCTTTTCGGAGCTAAATCATGCCCCAACAAAGGATAGCA\n++SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC\n+@SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+TACTAACTGTTTTAGTTTACCTCTTAGTTTTCCGCATGTC\n++SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+CCCCCCCCCCCCCACCCCCCCCCCCDCCCCCCCCCCCCCC\n+@SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CGCATTTAAGCTTCTCAAAGATGGTCATGCCTCCCTCACC\n++SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CCCCCCCCCCCCCCCCC6CCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+GGTCAAATCTAAGCTT\n++SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+CCCCCCCCCCCCCCCC\n+@SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+AATAAATAAAGTATTTAGGAAACAGATCTTACCTCACTTG\n++SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+CCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+CAAGGCTCTGATTTATCTCTTGATTTTTATTCTTACTTTT\n++SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+BBBBBBBBBB>BBBBBAB@B?@3>@BBBB===BBBBBBAB\n+@SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+AATAGTTTGTGCCTCTAAAAACAGGCAGGCTAAATAAGCT\n++SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+CDCCCCCCCCCCCCCCCCCCCCBBCCCCCCCACCCCCCCC\n+@SRR071233.3161 NRTG514-16_0001:3:1:1426:3923 length=40\n+AACAAGGACTCCTGGGTTGATCTCCAGCCTCAAAAATCCT\n++SRR07'..b'AAGGGCAAGGAAGACTTTTACAGGTGCTGGATCCGG\n++SRR071233.154841 NRTG514-16_0001:3:2:1055:18658 length=40\n+>>6>>@<@?@B>BBBBBBBBBB>BBBBBBBBBBBB8@B@B\n+@SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+TCTCATATTTTTTGAAGTAAACATCAAAATCACCATCCAG\n++SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+CCCCCCCCCCC@@@CCCCCCCCCACCCCCCCCCCCCCCCC\n+@SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+AATGAGAGAAAACTTCAGTAATCACCTAACCCCAAAAAAT\n++SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+CCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCC@CCCCC\n+@SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CACACCACTGCCCTGCACACAAACCCTCCAGGAGGTTTAT\n++SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCB>CCBC\n+@SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+TGGATTTCTCATGAATGGTTGAGTACTATCCTTTTGCTAC\n++SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+CCCCCCBCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCC\n+@SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+GGTGACGGATGTCCCAGGAGGACGACCCAAGCCCACCCGC\n++SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+CCCCCCCCCBCCCCCBCCCCCCCCCCCCCCCCCB<CBB@?\n+@SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+GGCCTTGATAAATTGTAACTACCATGATTAGACTTTTGTA\n++SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+CCCCCBCCCCCACCCCCCCCCCCCCCCACCCCCCCCCCCC\n+@SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+AGTCTCCTTACTAGGGCAGTTCAACTTCATAGTGGTGCAG\n++SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+CCCCCCCCC;CBCCCCCCCCCCCCCCCDBCCCBCCCCCCC\n+@SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+CCTACAATGCTCCCATCCAAGCTAGGGTGAAGGCAGATCC\n++SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+CCCCCCCCCCCCCCCBCCCCCCCCCCA@CCCCC>@CACCC\n+@SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+ATGCTCCTTTCTCAGTACTTTCATAGCACCTTCTTCATAC\n++SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+CCACCCCCCCCCBCC@BCCCACBCCCCCCCACCCC@BCCC\n+@SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+AAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGG\n++SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+CCCCC?@@CBCCCCCCCBCCCCCCCCC@CCCC@CCCCCC?\n+@SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+ACAGAGCGCAGGACAGAAAGTAAGGCATTTCAAGCAGAGA\n++SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+CCCCCCCCCCCCCCCCCACB@CCCCCCCCCCCCC?A8AAA\n+@SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+AACACTTAAAAAAAAAAAAAAAAAACCAAACCCCAGGCTC\n++SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+BBCCCCCDCCCCC@BBBBBBBBBB################\n+@SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+CTAAAACTGGACTGAGAAAAGGTGATCCCATTTGGCTTCA\n++SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+CCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCC\n+@SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+TATAATTTCTGTTCTTTTACATTTGCTGAGGAGTGCTTTA\n++SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+CCCCCCCCCCCCCCCCC@@CCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+CTATCCTAAGGTTATGAATGTATTCTCCTATATTATATTC\n++SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+CCCCCCCCCCCCCCCCCACCDCCCCCCCCCCACCCCCCCC\n+@SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+TAAAATTCAAAATTTCTGCTCCCCTATCCAGACCACTGGC\n++SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+AGCTTTGCCCATCATGAGGAATGAACCTAGCTCCTATTGC\n++SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+CCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCDCADCCCC\n+@SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+ATTTGATTCCATTCAATGATGATTCCATTCTATTCCATTC\n++SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+@BABAACCCCCCCCCCCCBB@=@AACBCCCCCCBCCC?CC\n+@SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+AGGATGTATTGGCAAGAGGAACTATTAAGACCATTGTTAC\n++SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+CCCBCCCCCCCCCCCCCCC?CCBCCCCCCCCCCCCCCCCC\n'
b
diff -r 000000000000 -r 7e9e8da0522d test-data/dataset2.truncation_barchart.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset2.truncation_barchart.svg Thu Mar 09 09:31:57 2017 -0500
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diff -r 000000000000 -r 7e9e8da0522d test-data/deduplicator_cis_trans_piechart.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/deduplicator_cis_trans_piechart.svg Thu Mar 09 09:31:57 2017 -0500
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diff -r 000000000000 -r 7e9e8da0522d test-data/deduplicator_uniques_barchart.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/deduplicator_uniques_barchart.svg Thu Mar 09 09:31:57 2017 -0500
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b
diff -r 000000000000 -r 7e9e8da0522d test-data/digester_file.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/digester_file.txt Thu Mar 09 09:31:57 2017 -0500
[
@@ -0,0 +1,56 @@
+Genome:genome Restriction_Enzyme1:re1_unspecified [A^AGCTT] Restriction_Enzyme2:None Hicup digester version 0.5.9
+Chromosome Fragment_Start_Position Fragment_End_Position Fragment_Number RE1_Fragment_Number 5'_Restriction_Site 3'_Restriction_Site
+chr1 1 16007 1 1 None Re1
+chr1 16008 24571 2 2 Re1 Re1
+chr1 24572 27981 3 3 Re1 Re1
+chr1 27982 30429 4 4 Re1 Re1
+chr1 30430 32153 5 5 Re1 Re1
+chr1 32154 32774 6 6 Re1 Re1
+chr1 32775 37752 7 7 Re1 Re1
+chr1 37753 38369 8 8 Re1 Re1
+chr1 38370 38791 9 9 Re1 Re1
+chr1 38792 39255 10 10 Re1 Re1
+chr1 39256 43602 11 11 Re1 Re1
+chr1 43603 46455 12 12 Re1 Re1
+chr1 46456 52419 13 13 Re1 Re1
+chr1 52420 56815 14 14 Re1 Re1
+chr1 56816 58747 15 15 Re1 Re1
+chr1 58748 58954 16 16 Re1 Re1
+chr1 58955 59356 17 17 Re1 Re1
+chr1 59357 75365 18 18 Re1 Re1
+chr1 75366 83359 19 19 Re1 Re1
+chr1 83360 84049 20 20 Re1 Re1
+chr1 84050 90742 21 21 Re1 Re1
+chr1 90743 91319 22 22 Re1 Re1
+chr1 91320 91586 23 23 Re1 Re1
+chr1 91587 92457 24 24 Re1 Re1
+chr1 92458 97923 25 25 Re1 Re1
+chr1 97924 101016 26 26 Re1 Re1
+chr1 101017 102672 27 27 Re1 Re1
+chr1 102673 105557 28 28 Re1 Re1
+chr1 105558 106650 29 29 Re1 Re1
+chr1 106651 107958 30 30 Re1 Re1
+chr1 107959 108196 31 31 Re1 Re1
+chr1 108197 109517 32 32 Re1 Re1
+chr1 109518 114993 33 33 Re1 Re1
+chr1 114994 115427 34 34 Re1 Re1
+chr1 115428 116791 35 35 Re1 Re1
+chr1 116792 117059 36 36 Re1 Re1
+chr1 117060 118299 37 37 Re1 Re1
+chr1 118300 121955 38 38 Re1 Re1
+chr1 121956 124936 39 39 Re1 Re1
+chr1 124937 130392 40 40 Re1 Re1
+chr1 130393 130459 41 41 Re1 Re1
+chr1 130460 139816 42 42 Re1 Re1
+chr1 139817 140040 43 43 Re1 Re1
+chr1 140041 142850 44 44 Re1 Re1
+chr1 142851 155672 45 45 Re1 Re1
+chr1 155673 157485 46 46 Re1 Re1
+chr1 157486 157620 47 47 Re1 Re1
+chr1 157621 159124 48 48 Re1 Re1
+chr1 159125 159859 49 49 Re1 Re1
+chr1 159860 161088 50 50 Re1 Re1
+chr1 161089 173279 51 51 Re1 Re1
+chr1 173280 174257 52 52 Re1 Re1
+chr1 174258 175543 53 53 Re1 Re1
+chr1 175544 199950 54 54 Re1 None
b
diff -r 000000000000 -r 7e9e8da0522d test-data/filter_piechart.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_piechart.svg Thu Mar 09 09:31:57 2017 -0500
b
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diff -r 000000000000 -r 7e9e8da0522d test-data/hicup_deduplicator_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicup_deduplicator_summary.txt Thu Mar 09 09:31:57 2017 -0500
b
@@ -0,0 +1,2 @@
+File Read_pairs_processed Unique_di-tags Cis_<10kbp_of_uniques Cis_>10kbp_of_uniques Trans_of_uniques
+dataset_1265_4.dat.filt.sam 1 1 0 1 0
b
diff -r 000000000000 -r 7e9e8da0522d test-data/hicup_filter_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicup_filter_summary.txt Thu Mar 09 09:31:57 2017 -0500
b
@@ -0,0 +1,2 @@
+File Total_pairs Valid_pairs Cis_<10kbp Cis_>10kbp Trans Invalid_pairs Same_circularised Same_dangling_ends Same_internal Re-ligation Contiguous_sequence Wrong_size
+dataset_1265_4.dat.pair.sam 1 1 0 1 0 0 0 0 0 0 0 0
b
diff -r 000000000000 -r 7e9e8da0522d test-data/hicup_mapper_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicup_mapper_summary.txt Thu Mar 09 09:31:57 2017 -0500
b
@@ -0,0 +1,3 @@
+File Total_reads_processed Reads_too_short_to_map %Reads_too_short_to_map Unique_alignments %Unique_alignments Multiple_alignments %Multiple_alignments Failed_to_align %failed_to_align Paired %Paired
+dataset_1265.dat.trunc.fastq 1000 35 3.5 14 1.4 13 1.3 938 93.8 1 0.1
+dataset_1264.dat.trunc.fastq 1000 24 2.4 23 2.3 7 0.7 946 94.6 1 0.1
b
diff -r 000000000000 -r 7e9e8da0522d test-data/hicup_truncater_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicup_truncater_summary.txt Thu Mar 09 09:31:57 2017 -0500
b
@@ -0,0 +1,3 @@
+File Total_Reads_Processed Truncated %Truncated Not_truncated %Not_truncated Average_length_truncated_sequence
+dataset_1265.dat 1000 77 7.70 923 92.30 21.39
+dataset_1264.dat 1000 61 6.10 939 93.90 22.21
b
diff -r 000000000000 -r 7e9e8da0522d test-data/result.pair.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result.pair.sam Thu Mar 09 09:31:57 2017 -0500
b
@@ -0,0 +1,7 @@
+@HD VN:1.0 SO:unsorted
+@SQ SN:chr1 LN:199950
+@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough"
+@PG ID:HiCUP Mapper VN:0.5.9
+@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT"
+SRR071233.43293 83 chr1 35433 3 40M = 75323 0 GAGTCCAGGAGTTCAAGACCAGCCTGGGTAACATAGTGAG CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-15 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:3G22A1C11 YT:Z:UU
+SRR071233.43293 163 chr1 75323 23 40M = 35433 0 CTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCG CCBCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-10 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:20A18A0 YT:Z:UU
b
diff -r 000000000000 -r 7e9e8da0522d test-data/results.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/results.html Thu Mar 09 09:31:57 2017 -0500
[
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b
diff -r 000000000000 -r 7e9e8da0522d tool-data/bowtie2_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie2_indices.loc.sample Thu Mar 09 09:31:57 2017 -0500
b
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie2 indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie2_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
+#
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/bowtie2/hg18/,
+#then the bowtie2_indices.loc entry would look like this:
+#
+#hg18 hg18 hg18 /depot/data2/galaxy/bowtie2/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie2/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 hg18.3.ebwt
+#...etc...
+#
+#Your bowtie2_indices.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie2/hg18/hg18canon
+#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie2/hg18/hg18full
+#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
b
diff -r 000000000000 -r 7e9e8da0522d tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Mar 09 09:31:57 2017 -0500
b
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of indexes in the Bowtie2 mapper format -->
+    <table name="bowtie2_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bowtie2_indices.loc" />
+    </table>
+</tables>