| Next changeset 1:3b54b419b5cb (2021-11-09) |
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Commit message:
"planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101" |
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added:
instrain_compare.xml macros.xml test-data/N5_271_010G1.maxbin2.stb test-data/N5_271_010G1_scaffold_min1000.fa-vs-N5_271_010G1.IS.zip test-data/N5_271_010G1_scaffold_min1000.fa-vs-N5_271_010G2.IS.zip test-data/SmallScaffold.fa test-data/SmallScaffold.fa.sorted.bam |
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| diff -r 000000000000 -r dff92aac9f75 instrain_compare.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/instrain_compare.xml Wed Aug 11 21:11:53 2021 +0000 |
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| b'@@ -0,0 +1,212 @@\n+<tool id="instrain_compare" name="InStrain Compare" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>Compares multiple inStrain profiles (popANI, coverage_overlap, etc.) </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="edam_ontology"/>\n+ <expand macro="requirements"/>\n+ <version_command>inStrain compare --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+#if $stb\n+ ln -s \'$stb\' \'stb_file.stb\' &&\n+#end if\n+#if $other.genome\n+ ln -s \'$other.genome\' \'genome_file.stb\' &&\n+#end if\n+#for $i, $s in enumerate($input_is)\n+ #if $s\n+ input_count=$i \n+ mkdir -p $i-input.IS &&\n+ unzip \'$s\' -d \'$i-input.IS/\' &&\n+ #end if\n+#end for\n+inStrain compare\n+ --input\n+ #for $i, $s in enumerate($input_is)\n+ #if $s\n+ \'$i-input.IS\'\n+ #end if\n+ #end for \n+ --output \'output.IS.COMPARE\'\n+ --processes "\\${GALAXY_SLOTS:-6}"\n+#if $stb\n+ --stb \'stb_file.stb\'\n+#end if \n+ --min_cov $variant_calling.min_cov\n+ --min_freq $variant_calling.min_freq\n+ --fdr $variant_calling.fdr\n+ $database.database_mode\n+ --breadth $database.breadth\n+#if $other.scaffolds\n+ --scaffolds \'$other.scaffolds\'\n+#end if\n+#if $other.genome\n+ --genome \'genome_file.stb\'\n+#end if\n+ $other.store_coverage_overlap\n+ $other.store_mismatch_locations\n+ $other.include_self_comparisons\n+ $other.skip_plot_generation\n+ --group_length $other.group_length\n+ --ani_threshold $genome_clustering.ani_threshold\n+ --coverage_treshold $genome_clustering.coverage_treshold\n+ --clusterAlg \'$genome_clustering.clusterAlg\'\n+ ]]></command> \n+ <inputs>\n+ <param name="input_is" type="data" format="zip" multiple="true" label="inStrain Profile IS folder" help=" The Zip files for the IS profiles outputs you want to compare"/> \n+ <param argument="--stb" type="data" format="tabular" optional="true" label="Scaffold to bin" help="This can be a file with each line listing a scaffold and a bin name, tab-seperated. This can also be a space-seperated list of .fasta files, with one genome per .fasta file. If nothing is provided, all scaffolds will be treated as belonging to the same genome"/>\n+ <section name="variant_calling" title="Variant Calling Options" expanded="true">\n+ <param argument="--min_cov" type="integer" value="5" label=" Minimum coverage to call an variant"/>\n+ <param argument="--min_freq" type="float" value="0.05" label="Minimum SNP frequency to confirm a SNV" help="Both this AND the FDR snp count cutoff must be true to call a SNP."/>\n+ <param argument="--fdr" type="float" value="1e-06" min="0" max="1" help="SNP false discovery rate- based on simulation data with a 0.1 percent error rate (Q30)"/>\n+ </section>\n+ <section name="database" title="Database Mode Parameters" expanded="true">\n+ <param argument="--database_mode" type="boolean" truevalue="--debugdatabase_mode" falsevalue="" checked="false" label="Automatically determine which genomes are present in each Profile and only compare scaffolds from those genomes." help="All profiles must have run Profile with the same .stb"/>\n+ <param argument="--breadth" type="float" value="0.5" label="Minimum breadth_minCov required to count a genome present"/>\n+ </section>\n+ <section name="other" title="Other Options" expanded="true">\n+ <param argument="--scaffolds" type="data" format="fasta" optional="true" label="Location to a list of scaffolds to compare. You can also make this a .fasta file and it will load the scaffold names"/>\n+ <param argument="--genome" type="data" format="tabular" optional="true" label="Run scaffolds belonging to this single genome only. Must provide an .stb file"/>\n+ <param argument="--store_coverage_overlap" type="boolean" t'..b'e="false"/>\n+ <param name="skip_plot_generation" value="false"/>\n+ <param name="group_length" value="10000000"/>\n+ </section>\n+ <section name="genome_clustering">\n+ <param name="ani_threshold" value="0.99999"/>\n+ <param name="coverage_treshold" value="0.1"/>\n+ <param name="clusterAlg" value="average"/>\n+ </section>\n+ <output name="comparisonsTable">\n+ <assert_contents>\n+ <has_text text="N5_271_010G1_scaffold_73"/>\n+ <has_n_lines n="168"/>\n+ <has_n_columns n="11"/>\n+ </assert_contents>\n+ </output>\n+ <output name="pairwise_SNP_locations">\n+ <assert_contents>\n+ <has_n_lines n="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="genomeWide_compare">\n+ <assert_contents>\n+ <has_text text="name1"/>\n+ <has_n_lines n="3"/>\n+ <has_n_columns n="10"/>\n+ </assert_contents>\n+ </output>\n+ <output name="strain_clusters">\n+ <assert_contents>\n+ <has_text text="1_1"/>\n+ <has_n_lines n="5"/>\n+ <has_n_columns n="3"/>\n+ </assert_contents>\n+ </output>\n+ <output name="inStrainCompare_dendrograms">\n+ <assert_contents>\n+ <has_size value="384512" delta="10000" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+@HELP_HEADER@\n+\n+Compare\n+=======\n+\n+is part of the inStrain module that provides the ability to compare multiple inStrain profiles (created by running inStrain profile).\n+\n+Note\n+====\n+\n+inStrain can only compare inStrain profiles that have been mapped to the same .fasta file\n+\n+inStrain compare does pairwise comparisons between each input inStrain profile. For each pair, a series of steps are undertaken:\n+\n+1. All positions in which both IS_profile objects have at least min_cov coverage (5x by default) are identified. This information can be stored in the output by using the flag \xe2\x80\x93store_coverage_overlap, but due to it\xe2\x80\x99s size, it\xe2\x80\x99s not stored by default.\n+\n+\n+2. Each position identified in step 1 is compared to calculate both conANI and popANI. The way that it compares positions is by testing whether the consensus base in sample 1 is detected at all in sample 2 and vice-versa. Detection of an allele in a sample is based on that allele being above the set -min_freq and -fdr. All detected differences between each pair of samples can be reported if the flag \xe2\x80\x93store_mismatch_locations is set.\n+\n+\n+3. The coverage overlap and the average nucleotide identity for each scaffold is reported. For details on how this is done.\n+\n+\n+Inputs\n+======\n+\n+Multiple inStrain profiles IS outputs (zip files), all mapped to the same .fasta file\n+\n+\n+Outputs\n+=======\n+\n+1. comparisonsTable.tsv\n+ \n+ Summarizes the differences between two inStrain profiles on a scaffold by scaffold level\n+\n+2. pairwise_SNP_locations.tsv\n+\n+ Lists the locations of all differences between profiles. Because it\xe2\x80\x99s a big file, this will only be created is you include the flag --store_mismatch_locations in your inStrain compare command.\n+\n+3. genomeWide_compare.tsv\n+\n+ A genome-level summary of the differences detected by inStrain compare. Generated by running inStrain genome_wide on the results of inStrain compare\n+\n+4. strain_clusters.tsv\n+\n+ The result of clustering the pairwise comparison data provided in genomeWide_compare.tsv to generate strain-level clusters. Performed using hierarchical clustering in the same manner as the program dRep\n+\n+5. Compare dendrograms (PDF) figure/plot\n+ \n+ A dendrogram comparing all samples based on popANI and based on shared_bases.\n+\n+ ]]></help> \n+ <citations>\n+ <citation type="doi">10.1101/2020.01.22.915579</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r dff92aac9f75 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Aug 11 21:11:53 2021 +0000 |
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| @@ -0,0 +1,36 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">1.5.3</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.01</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0796</edam_topic> + <edam_topic>topic_3174</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0484</edam_operation> + <edam_operation>operation_3209</edam_operation> + <edam_operation>operation_3730</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">instrain</requirement> + <yield/> + </requirements> + </xml> + <token name="@HELP_HEADER@"> +What it does +============ + +inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification. + +Read more about the tool: https://instrain.readthedocs.io/en/latest/ + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/2020.01.22.915579</citation> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r dff92aac9f75 test-data/N5_271_010G1.maxbin2.stb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/N5_271_010G1.maxbin2.stb Wed Aug 11 21:11:53 2021 +0000 |
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| b'@@ -0,0 +1,167 @@\n+N5_271_010G1_scaffold_0 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_1 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_2 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_3 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_4 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_5 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_6 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_7 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_8 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_9 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_10 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_11 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_12 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_13 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_14 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_15 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_16 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_17 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_18 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_19 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_20 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_21 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_22 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_23 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_24 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_25 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_26 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_27 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_28 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_29 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_30 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_31 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_32 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_33 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_34 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_35 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_36 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_37 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_39 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_40 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_41 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_42 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_43 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_44 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_45 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_46 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_47 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_48 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_49 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_50 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_51 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_52 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_53 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_54 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_55 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_56 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_57 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_58 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_59 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_60 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_61 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_63 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_64 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_65 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_66 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_67 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_68 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_69 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_70 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_71 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_73 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_74 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_75 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_76 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_77 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_sc'..b'in2.maxbin.001.fasta\n+N5_271_010G1_scaffold_97 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_98 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_99 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_100 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_101 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_102 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_103 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_104 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_105 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_106 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_107 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_108 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_109 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_111 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_112 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_113 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_114 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_116 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_117 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_118 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_119 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_120 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_121 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_122 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_123 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_125 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_126 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_127 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_128 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_129 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_130 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_131 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_132 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_133 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_134 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_135 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_136 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_137 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_138 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_139 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_141 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_142 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_143 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_144 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_145 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_147 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_148 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_149 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_150 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_151 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_152 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_153 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_154 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_155 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_156 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_157 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_158 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_159 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_160 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_161 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_162 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_163 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_185 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_197 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_341 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_350 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_362 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_376 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_419 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_443 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_484 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_618 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_836 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_963\tfobin.fasta\n' |
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| diff -r 000000000000 -r dff92aac9f75 test-data/SmallScaffold.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SmallScaffold.fa Wed Aug 11 21:11:53 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +>WeirdBoi +AAAAAAAAAAAAAAAAAAAAAAA +>N5_271_010G1_scaffold_963 read_length_150 read_count_3782 +TCTCCATTACATTCCATTCCATTCGGGTTGTTCCATTCCATTCCATTCCA +TTCCACTCCATTCCATTGCACTCGGGTTGATTCCATTCCATTCCATTCCG +GATGATTCCATTCCATTGCATTCCGT |
| b |
| diff -r 000000000000 -r dff92aac9f75 test-data/SmallScaffold.fa.sorted.bam |
| b |
| Binary file test-data/SmallScaffold.fa.sorted.bam has changed |